43 results on '"Nevo E"'
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2. Using Drawings and Explanations Based on Attentive Teaching as a Means for Understanding the Social-Ecological Systems Concept
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Gal, A., Schur, Y., Nevo, E., and Gan, D.
- Abstract
The concept of 'social-ecological systems', which explores the relationships between society and the environment, was at the center of this study. The study aims to describe Israeli environmental-education master students' level of understanding of the social-ecological systems concept. We used a designated rubric score to analyze drawings and explanations and to identify the levels of understanding asking: How can the analysis of drawings and explanations, using Attentive Teaching as an educational approach, enable the identification of conceptual changes in understanding the social-ecological systems concept? The 270 drawings and explanations of 49 participants were analyzed, and they indicated a general increase in the level of understanding of the social-ecological systems concept. Attentive Teaching, as an educational approach, was found to lead to conceptual change. Drawings and explanations, as an assessment methodology may lead to better understanding of the social-ecological systems concept and may encourage action in relation to the environmental crisis.
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- 2023
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3. Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
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Zhang, W, Tan, C, Hu, H, Pan, R, Xiao, Y, Ouyang, K, Zhou, G, Jia, Y, Zhang, X-Q, Hill, CB, Wang, P, Chapman, B, Han, Y, Xu, L, Xu, Y, Angessa, T, Luo, H, Westcott, S, Sharma, D, Nevo, E, Barrero, RA, Bellgard, M, He, T, Tian, X, Li, C, Zhang, W, Tan, C, Hu, H, Pan, R, Xiao, Y, Ouyang, K, Zhou, G, Jia, Y, Zhang, X-Q, Hill, CB, Wang, P, Chapman, B, Han, Y, Xu, L, Xu, Y, Angessa, T, Luo, H, Westcott, S, Sharma, D, Nevo, E, Barrero, RA, Bellgard, M, He, T, Tian, X, and Li, C
- Abstract
Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.
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- 2023
4. Using drawings and explanations based on attentive teaching as a means for understanding the social-ecological systems concept
- Author
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Gal, A., primary, Schur, Y., additional, Nevo, E., additional, and Gan, D., additional
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- 2022
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5. Correction: Mapping the World Health Organization Disability Assessment Schedule (WHODAS 2.0) onto SF-6D Using Swedish General Population Data.
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Philipson A, Hagberg L, Hermansson L, Karlsson J, Ohlsson-Nevo E, and Ryen L
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- 2025
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6. Patient reported fatigue after proton therapy for malignant brain tumours - Is there a relation between radiation dose and brain structures?
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Kristensen I, Langegård U, Björk-Eriksson T, Blomstrand M, Brodin P, Fransson P, Rosenschöld PMA, Nordström F, Olsson-Nevo E, Sjövall K, and Ahlberg K
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- Humans, Male, Female, Middle Aged, Adult, Aged, Patient Reported Outcome Measures, Brain radiation effects, Aged, 80 and over, Proton Therapy adverse effects, Proton Therapy methods, Fatigue etiology, Brain Neoplasms radiotherapy, Quality of Life, Radiotherapy Dosage
- Abstract
Background: Fatigue may significantly effect everyday- and working life for radiotherapy patients. Some studies indicate a correlation between radiation dose and irradiated volume of the brain and the presence of fatigue. Our hypothesis was that patient reported outcome measures (PROMs) can improve our understanding of the patients' symptoms following proton beam therapy (PBT) and optimize PBT for future patients., Methods: This study included 167 adult patients (>18 years) who received PBT for malignant brain tumours. Data on dose metrics to intra-cranial structures was obtained from PBT treatment plans. To explore fatigue and health related quality of life (HRQoL); Multidimensional Fatigue Inventory (MFI-20) and EORTC QLQ-C30 was used at 6-, 12-, 24- and 36 months post PBT. The correlation between fatigue and dosimetry was explored using Spearman's signed rank test., Results: No severe fatigue was recorded during the 36 months follow-up. Correlations between higher radiation dose and worsened fatigue scores were generally weak (rho < 0.3). At 12 months post PBT, higher mean dose to the brain, brainstem, hippocampi and pituitary was correlated to worsened MFI Physical Fatigue. Further, Reduced Motivation according to MFI was correlated to higher radiation dose to the brainstem and the pituitary gland. At 36 months follow-up post-PBT, both Reduced Activity and Reduced motivation according to MFI were correlated to higher radiation dose to the brain, brainstem and hippocampi., Conclusion: Proton beam therapy are well tolerated, with similar degree of fatigue pre- and post PBT. Achieving further reduction in mean brain dose appears beneficial., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)
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- 2025
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7. Validation of the Assessment of Rehabilitation Needs Checklist in a Swedish cancer population.
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Ohlsson-Nevo E, Fogelkvist M, Lundqvist LO, Ahlgren J, and Karlsson J
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- Humans, Sweden, Male, Female, Middle Aged, Reproducibility of Results, Aged, Adult, Needs Assessment, Surveys and Questionnaires, Quality of Life, Registries, Factor Analysis, Statistical, Neoplasms rehabilitation, Neoplasms psychology, Checklist, Psychometrics methods, Psychometrics instrumentation
- Abstract
Background: Assessment of Rehabilitation Needs Checklist (ARNC), has been developed to assess rehabilitation need in cancer patients and is recommended by the Confederation of Regional Cancer Centres in Sweden, known as Hälsoskattningen. The aim of the study was to test the reliability and validity of the ARNC, mainly by comparing it with the Distress thermometer and EORTC QLQ-C30., Methodology: A sample of 993 persons identified in the Swedish cancer register. The study participants were diagnosed with cancer in 2021 in the Mid Sweden region. The psychometric methods tested reliability and validity including factor analysis., Results: The response rate was 38%. The test-retest analysis showed that ICC was 0.80 or higher for 12 of the ARNC items. A strong or modarete correlation between ARNC and the other instruments was found in all functional scales and for most items. CFA of the 13-item two-factor model showed a RMSEA value of 0.04, CFI and TLI values of 0.97 and 0.96, and a SRMR value of 0.05, indicating a satisfactory model fit., Conclusion: The evaluation of the ARNC suggests that it is an acceptable and reliable screening instrument for detecting symptoms and signs indicating a possible need of rehabilitation. The medium to strong correlations between ARNC items and the EORTC QLQ- C30 items and scales suggest that ARNC could be an alternative also for research purposes when a shorter and less comprehensive instrument is needed. The simple design could be an advantage as it lowers the burden on cancer patients., Competing Interests: Declarations. Ethics approval and consent to participate: All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. The study was approved by the Regional Ethical Review Board in Lund, Sweden (Dnr 2021-05567-01). Consent for publication: Informed written consent was collected from all participants prior to entry into the study. We received several incomplete consent forms that we had to return for a signature. They were never returned, resulting in a lower response rate. Participants were assured that they had the right to withdraw from the study at any point throughout the study. To ensure confidentiality, personal data were coded. Participant and study-related data are stored in digital form and are password-protected. The final results of this study will be disseminated by the research team to health care professionals, and relevant public and political groups. Presentations will be given at community forums such as patient support groups, in the media and at relevant national and international scientific conferences. Competing interests: The authors declare that they have no financial or other competing interests to disclose., (© 2024. The Author(s).)
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- 2024
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8. Open or closed: Experience of head and neck radiotherapy masks - A mixed-methods study.
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Lundin E, Axelsson S, and Ohlsson-Nevo E
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Introduction: In radiotherapy for head and neck cancer, a mask is used to immobilise the head and shoulders. An open mask that does not cover the face is expected to cause less anxiety, but there is need to further investigate the patients' experience of open versus closed masks. Therefore, the aim of this study is to evaluate patient preferences for open or closed masks and whether an open mask can reduce discomfort and anxiety for patients., Methods: Twenty participants were treated in alternating weeks using open and closed masks. Their distress was evaluated through semi-structured interviews and patient-reported outcome measures., Results: When using the open mask, it took longer to position the patient correctly. The closed mask felt more confining and could induce a sense of claustrophobia. Participants employed both internal and external strategies to cope with the stressful situation. The Hospital Anxiety and Depression Scale (HADS) showed a significant reduction in anxiety over time during the treatment period, but no significant difference between the masks. When participants chose which mask to use for the final treatments, 12 chose the open mask, while 8 chose the closed mask. In addition to the 20 analysed participants, two participants withdrew from the study because they could only tolerate the open mask, one due to anxiety and the other due to swelling., Conclusions: The open mask seems to provide a less confined experience but may lead to greater difficulties in achieving the correct treatment position. While both masks can be viable options for most patients, some cannot tolerate closed masks but do tolerate open masks., (© 2024 The Author(s). Journal of Medical Radiation Sciences published by John Wiley & Sons Australia, Ltd on behalf of Australian Society of Medical Imaging and Radiation Therapy and New Zealand Institute of Medical Radiation Technology.)
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- 2024
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9. Cost-effectiveness of proton beam therapy vs. conventional radiotherapy for patients with brain tumors in Sweden: results from a non-randomized prospective multicenter study.
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Sampaio F, Langegård U, de Alva PM, Flores S, Nystrand C, Fransson P, Ohlsson-Nevo E, Kristensen I, Sjövall K, Feldman I, and Ahlberg K
- Abstract
Background: This study assessed the cost-effectiveness of proton beam therapy (PBT) compared to conventional radiotherapy (CRT) for treating patients with brain tumors in Sweden., Methods: Data from a longitudinal non-randomized study performed between 2015 and 2020 was used, and included adult patients with brain tumors, followed during treatment and through a one-year follow-up. Clinical and demographic data were sourced from the longitudinal study and linked to Swedish national registers to get information on healthcare resource use. A cost-utility framework was used to evaluate the cost-effectiveness of PBT vs. CRT. Patients in PBT group (n = 310) were matched with patients in CRT group (n = 40) on relevant observables using propensity score matching with replacement. Costs were estimated from a healthcare perspective and included costs related to inpatient and specialized outpatient care, and prescribed medications. The health outcome was quality-adjusted life-years (QALYs), derived from the EORTC-QLQ-C30. Generalized linear models (GLM) and two-part models were used to estimate differences in costs and QALYs., Results: PBT yielded higher total costs, 14,639 US$, than CRT, 13,308 US$, with a difference of 1,372 US$ (95% CI, -4,914-7,659) over a 58 weeks' time horizon. Further, PBT resulted in non-significantly lower QALYs, 0.746 compared to CRT, 0.774, with a difference of -0.049 (95% CI, -0.195-0.097). The probability of PBT being cost-effective was < 30% at any willingness to pay., Conclusions: These results suggest that PBT cannot be considered a cost-effective treatment for brain tumours, compared to CRT., Trial Registration: Not applicable., (© 2024. The Author(s).)
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- 2024
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10. Symptom experience and symptom distress in patients with malignant brain tumor treated with proton therapy: A five-year follow-up study.
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Kunni K, Langegård U, Ohlsson-Nevo E, Kristensen I, Sjövall K, Fessé P, Åkeflo L, Ahlberg K, and Fransson P
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Background and Purpose: Since patients with primary brain tumor are expected to become long-term survivors, the prevention of long-term treatment-induced side effects is particularly important. This study aimed to explore whether symptom experience and symptom distress change over five years in adults with primary brain tumors treated with proton therapy. An additional aim was to explore whether symptom experience and symptom distress correlate., Materials and Methods: The study had a longitudinal observational design. Adult (≥18 years) patients (n = 170) with primary brain tumors treated with proton therapy were followed over five years. Symptom experience and symptom distress were evaluated using the patient-reported Radiotherapy-Related Symptom Assessment Scale. Data from baseline, 1, 12, and 60 months were analyzed using non-parametric tests., Results: Of the 170 patients, the levels of symptoms and symptom distress were low. Fatigue increased at 1 (p=0.005) and 12 months (p=0.025) and was the most frequent symptom from baseline to 60 months' follow-up. Cognitive impairment increased at 12 (p=0.027) and 60 months (p<0.001) and was the most distressing symptom at 60 months' follow-up. There were significant, moderate to strong, correlations at all time points between symptom experience and symptom distress of fatigue, insomnia, pain, dyspnea, cognitive impairment, worry, anxiety, nausea, sadness, constipation, and skin reactions., Conclusion: Symptom experience and symptom distress changed in intensity over time with cognitive impairment as the most distressing symptom at 60 months. Future research should focus on identifying effective interventions aimed at alleviating these symptoms and reducing symptom distress for this vulnerable group of patients., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Author(s).)
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- 2024
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11. Splice Variant of Spalax Heparanase Skipping Exon 12.
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Nasser NJ, Nevo E, and Avivi A
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- Animals, Heparitin Sulfate metabolism, Humans, Glucuronidase genetics, Glucuronidase metabolism, Exons genetics, Alternative Splicing, Spalax genetics
- Abstract
The subterranean blind mole rat, Spalax , has evolved significantly over 47 million years to thrive in its underground habitat. A key enzyme in this adaptation is heparanase, which degrades heparan sulfate (HS) in the extracellular matrix (ECM), facilitating angiogenesis and releasing growth factors for endothelial cells. Spalax heparanase has various splice variants influencing tumor growth and metastasis differently. We report a novel splice variant from a hypoxia-exposed kidney sample resulting from exon 12 skipping. This variant maintains the translation frame but lacks enzymatic activity, offering insights into Spalax 's unique adaptations.
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- 2024
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12. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep.
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Liang X, Duan Q, Li B, Wang Y, Bu Y, Zhang Y, Kuang Z, Mao L, An X, Wang H, Yang X, Wan N, Feng Z, Shen W, Miao W, Chen J, Liu S, Storz JF, Liu J, Nevo E, and Li K
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- Animals, Sheep genetics, Tibet, Genomic Structural Variation, Basic Helix-Loop-Helix Transcription Factors genetics, Gene Expression Regulation, Genome, Acclimatization genetics, Altitude
- Abstract
Tibetan sheep were introduced to the Qinghai Tibet plateau roughly 3,000 B.P., making this species a good model for investigating genetic mechanisms of high-altitude adaptation over a relatively short timescale. Here, we characterize genomic structural variants (SVs) that distinguish Tibetan sheep from closely related, low-altitude Hu sheep, and we examine associated changes in tissue-specific gene expression. We document differentiation between the two sheep breeds in frequencies of SVs associated with genes involved in cardiac function and circulation. In Tibetan sheep, we identified high-frequency SVs in a total of 462 genes, including EPAS1 , PAPSS2 , and PTPRD . Single-cell RNA-Seq data and luciferase reporter assays revealed that the SVs had cis -acting effects on the expression levels of these three genes in specific tissues and cell types. In Tibetan sheep, we identified a high-frequency chromosomal inversion that exhibited modified chromatin architectures relative to the noninverted allele that predominates in Hu sheep. The inversion harbors several genes with altered expression patterns related to heart protection, brown adipocyte proliferation, angiogenesis, and DNA repair. These findings indicate that SVs represent an important source of genetic variation in gene expression and may have contributed to high-altitude adaptation in Tibetan sheep., Competing Interests: Competing interests statement:The authors declare no competing interest.
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- 2024
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13. The effect of internet-administered support (carer eSupport) on preparedness for caregiving in informal caregivers of patients with head and neck cancer compared with support as usual: a study protocol for a randomized controlled trial.
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Johansson B, Cajander Å, Ahmad A, Ohlsson-Nevo E, Fransson P, Granström B, von Essen L, Langegård U, Pettersson M, Henriksson A, and Ehrsson YT
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- Humans, Quality of Life, Caregiver Burden, Internet, Randomized Controlled Trials as Topic, Caregivers, Head and Neck Neoplasms therapy
- Abstract
Background: Informal caregivers (ICs) of patients with cancer provide essential and mainly uncompensated care. A self-perceived preparedness to care for the patient is associated with a lower caregiver burden, described as the extent to which caregiving is perceived as having adverse effects on IC functioning and well-being. ICs' well-being is associated with patient-perceived quality of care, suggesting that interventions to optimize ICs' health are essential in order to improve patient care. Head and neck cancer (HNC) is the seventh most common malignant disease in the world. The disease and its treatment have a significant negative impact on the patient's health and quality of life. Symptoms usually interfere with swallowing, food and fluid intake, breathing, speaking, and communication. ICs frequently manage patients' symptoms and side effects, especially problems related to nutrition and oral pain, without being properly prepared. Carer eSupport is an Internet-administered intervention, based on focus group discussions with ICs, developed in collaboration with ICs and healthcare professionals, tested for feasibility, and deemed feasible. This study protocol outlines the methods of investigating the effects of Carer eSupport plus support as usual (SAU) on self-reported preparedness for caregiving, caregiver burden, and well-being in the ICs of patients with HNC, compared with ICs receiving SAU only., Methods and Analysis: In this randomized controlled trial, 110 ICs of patients with HNC, undergoing radiotherapy combined with surgery and/or medical oncological treatment, will be randomized (1:1) to Carer eSupport plus SAU or SAU only. Data will be collected at baseline (before randomization), post-intervention (after 18 weeks), and 3 months after post-intervention. The primary outcome is self-reported preparedness for caregiving. Secondary outcomes are self-reported caregiver burden, anxiety, depression, and health-related quality of life. The effect of Carer eSupport plus SAU on preparedness for caregiving and secondary outcomes, compared with SAU only, will be evaluated by intention to treat analyses using linear regression models, mixed-model regression, or analysis of covariance., Discussion: If proven effective, Carer eSupport has the potential to significantly improve ICs' preparedness for caregiving and their wellbeing, thereby improving patient-perceived quality of care and patient wellbeing., Trial Registration: ClinicalTrials.gov; NCT06307418, registered 12.03.2024 (https://clinicaltrials.gov/search? term=NCT06307418)., (© 2024. The Author(s).)
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- 2024
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14. The Impact of Morphological Intervention on Literacy Knowledge and Reading Motivation: A Cluster-Randomized Comparison Trial in Diverse Socioeconomic Status Kindergartens.
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Vaknin-Nusbaum V and Nevo E
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- Child, Humans, Language, Social Class, Educational Status, Vocabulary, Literacy, Reading
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Purpose: This study investigated the effectiveness of a storytelling-based morphological intervention program on the language and literacy knowledge and reading motivation of kindergarten children from low and mid socioeconomic status (SES) backgrounds. It also explored how these groups compared in change scores against a non-intervened high SES group., Method: Employing a cluster randomization approach, this study included 158 kindergarten children, comprising intervention and comparison groups from low and mid SES backgrounds, as well as a non-intervened high SES group. Assessments were conducted on morphological awareness (MA), print concepts, vocabulary, and reading motivation., Results: Children in the intervention groups showed better performance in MA and print concept scores than those in their respective comparison groups. The mid SES intervention group also displayed significant improvement in vocabulary and motivation scores compared to its counterpart. When examining the effects of SES on change scores, the low SES intervention group achieved superior results in vocabulary and print concept scores compared to both the mid SES intervention and the non-intervened high SES groups. For reading motivation, the mid SES group outperformed the low SES group., Conclusions: The morphological intervention program using storytelling positively impacts both the literacy skills and reading motivation of kindergarten children, especially those from low and mid SES backgrounds. This study emphasizes the significance of designing interventions that cater to the distinct educational needs of children from different SES backgrounds.
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- 2024
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15. A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew.
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Li M, Zhang H, Xiao H, Zhu K, Shi W, Zhang D, Wang Y, Yang L, Wu Q, Xie J, Chen Y, Qiu D, Guo G, Lu P, Li B, Dong L, Li W, Cui X, Li L, Tian X, Yuan C, Li Y, Yu D, Nevo E, Fahima T, Li H, Dong L, Zhao Y, and Liu Z
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- Plant Breeding, Genes, Plant, Chromosome Mapping, Disease Resistance genetics, Plant Diseases genetics, Triticum genetics, Ascomycota genetics
- Abstract
Crop wild relatives offer natural variations of disease resistance for crop improvement. Here, we report the isolation of broad-spectrum powdery mildew resistance gene Pm36, originated from wild emmer wheat, that encodes a tandem kinase with a transmembrane domain (WTK7-TM) through the combination of map-based cloning, PacBio SMRT long-read genome sequencing, mutagenesis, and transformation. Mutagenesis assay reveals that the two kinase domains and the transmembrane domain of WTK7-TM are critical for the powdery mildew resistance function. Consistently, in vitro phosphorylation assay shows that two kinase domains are indispensable for the kinase activity of WTK7-TM. Haplotype analysis uncovers that Pm36 is an orphan gene only present in a few wild emmer wheat, indicating its single ancient origin and potential contribution to the current wheat gene pool. Overall, our findings not only provide a powdery mildew resistance gene with great potential in wheat breeding but also sheds light into the mechanism underlying broad-spectrum resistance., (© 2024. The Author(s).)
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- 2024
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16. Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming.
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Zhou Y, Song R, Nevo E, Fu X, Wang X, Wang Y, Wang C, Chen J, Sun G, Sun D, and Ren X
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- Climate, Genomics, Temperature, Genes, Plant, Genetic Variation, Hordeum genetics
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The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)
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- 2024
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17. Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors.
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An X, Mao L, Wang Y, Xu Q, Liu X, Zhang S, Qiao Z, Li B, Li F, Kuang Z, Wan N, Liang X, Duan Q, Feng Z, Yang X, Liu S, Nevo E, Liu J, Storz JF, and Li K
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- Animals, Phylogeny, Hypoxia genetics, Genomic Structural Variation, Altitude, Rodentia genetics
- Abstract
Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO
2 ). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)- Published
- 2024
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18. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle.
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Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, and Gorbunova V
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- Animals, Longevity genetics, Mammals, Mole Rats genetics, Mutation, Hyaluronic Acid, Neoplasms
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Hyaluronic acid is a major component of extracellular matrix which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (Heterocephalus glaber) contains abundant high-molecular-mass hyaluronic acid in its tissues, which contributes to this species' cancer resistance and possibly to its longevity. Here we report that abundant high-molecular-mass hyaluronic acid is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These subterranean mammalian species accumulate abundant high-molecular-mass hyaluronic acid by regulating the expression of genes involved in hyaluronic acid degradation and synthesis and contain unique mutations in these genes. The abundant high-molecular-mass hyaluronic acid may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic conditions. Our work suggests that high-molecular-mass hyaluronic acid has evolved with subterranean lifestyle., (© 2023. The Author(s).)
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- 2023
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19. Levels of Physical Activity, Enjoyment, Self-Efficacy for Exercise, and Social Support Before and After Metabolic and Bariatric Surgery: a Longitudinal Prospective Observational Study.
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Imhagen A, Karlsson J, Ohlsson-Nevo E, Stenberg E, Jansson S, and Hagberg L
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- Adult, Humans, Pleasure, Self Efficacy, Quality of Life, Exercise, Social Support, Obesity, Morbid surgery, Bariatric Surgery
- Abstract
Introduction: Physical activity (PA) after metabolic and bariatric surgery (MBS) can influence weight loss, health status, and quality of life. Known mediators to participate in PA are enjoyment, self-efficacy, and social support. Little is known about PA behavior in MBS individuals. The aim of this study was to explore levels of PA and the PA mediators enjoyment, self-efficacy, and social support before and after MBS and to investigate changes over time., Methods: Adults scheduled to undergo MBS were recruited from a Swedish university hospital. Accelerometer-measured and self-reported PA, body weight, and PA mediators were collected at baseline and at 12 to 18 months post-surgery., Results: Among 90 individuals included, 50 completed the follow-up assessment and had valid accelerometer data. Sedentary time (minutes/day) was unchanged, but sedentary time as percentage of wear time decreased significantly from 67.2% to 64.5% (p<0.05). Time spent in light PA and total PA increased significantly from 259.3 to 288.7 min/day (p < 0.05) and from 270.5 to 303.5 min/day (p < 0.01), respectively. Step counts increased significantly from 6013 to 7460 steps/day (p < 0.01). There was a significant increase in self-reported PA, enjoyment, self-efficacy for exercise, and positive social support from family. The increase in PA mediators did not lead to a significant change in time spent in moderate to vigorous PA., Conclusion: The increase in PA-mediators was not associated with an increase in moderate to vigorous PA, but the strengthened PA mediators suggest potential for an increase in moderate to vigorous PA in patients undergoing MBS., (© 2023. The Author(s).)
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- 2023
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20. Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum.
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Mu W, Li K, Yang Y, Breiman A, Yang J, Wu Y, Zhu M, Wang S, Catalan P, Nevo E, and Liu J
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- Genome, Plant, Polyploidy, Brachypodium genetics
- Abstract
Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes., Competing Interests: Conflict of interest statement. The authors declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2023
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21. Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei .
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Mu W, Li K, Yang Y, Breiman A, Lou S, Yang J, Wu Y, Wu S, Liu J, Nevo E, and Catalan P
- Subjects
- Diploidy, Reproductive Isolation, Ecosystem, Genome, Plant genetics, Genetic Speciation, Brachypodium genetics
- Abstract
Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains a captivating topic in evolutionary biology. However, the pattern of genetic divergence underlying this process across the genome may vary between species and mating systems. Here, we present evidence that Brachypodium stacei, an annual and highly selfing grass model species, has undergone sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses together with lab experiments mimicking the two opposite environmental conditions suggest that diploid B. stacei populations have diverged sympatrically in two slopes characterized by distinct biomes at Evolution Canyon I (ECI), Mount Carmel, Israel. Despite ongoing gene flow, primarily facilitated by seed dispersal, the level of gene flow has progressively decreased over time. This local adaptation involves the scattered divergence of many unlinked loci across the total genome that include both coding genes and noncoding regions. Additionally, we have identified significant differential expressions of genes related to the ABA signaling pathway and contrasting metabolome composition between the arid- vs. forest-adapted B. stacei populations in ECI. These results suggest that multiple small loci involved in environmental responses act additively to account for ecological adaptations by this selfing species in contrasting environments.
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- 2023
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22. Species Diversity of Lycoperdaceae (Agaricales) in Israel, with Some Insights into the Phylogenetic Structure of the Family.
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Krakhmalnyi M, Isikhuemhen OS, Jeppson M, Wasser SP, and Nevo E
- Abstract
The diversity of Lycoperdaceae in Israel was studied. Molecular phylogenetic relationships within the family, and genus Lycoperdon in particular, were inferred using original ITS rDNA sequences of 58 samples belonging to 25 species from Israel and six other countries, together with 66 sequences stored in the GenBank database. The current molecular phylogenetic study recovered the family Lycoperdaceae as a monophyletic group, which was supported in both maximum likelihood and Bayesian analyses. The clades corresponding to the genera Apioperdon , Bovista , Calvatia , Disciseda , and Lycoperdon were revealed. The taxonomic structure of the named genera was partially resolved. Within the genus Lycoperdon , some species received significant statistical support; however, their relationships, as well as the problem of the genus monophyly, mostly remained questionable. As a result of a thorough literature survey, extensive sample collection, and studies of the material stored in the Herbarium of the Institute of Evolution, University of Haifa (HAI, Israel), fifteen species representing five genera were found in the territory of Israel. Six species, namely Apioperdon pyriforme , Bovista aestivalis , Calvatia candida , Lycoperdon decipiens , L. niveum , and L. perlatum , are new additions to the diversity of Lycoperdaceae in Israel. Detailed macro- and micromorphological descriptions, ecology, geography, and critical notes, together with light microscopy photos and SEM micrographs, are provided. In-depth discussion on some taxonomically challenging species is presented.
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- 2023
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23. Mapping the World Health Organization Disability Assessment Schedule (WHODAS 2.0) onto SF-6D Using Swedish General Population Data.
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Philipson A, Hagberg L, Hermansson L, Karlsson J, Ohlsson-Nevo E, and Ryen L
- Abstract
Background and Objective: Mapping algorithms can be used for estimating quality-adjusted life years (QALYs) when studies apply non-preference-based instruments. In this study, we estimate a regression-based algorithm for mapping between the World Health Organization Disability Assessment Schedule (WHODAS 2.0) and the preference-based instrument SF-6D to obtain preference estimates usable in health economic evaluations. This was done separately for the working and non-working populations, as WHODAS 2.0 discriminates between these groups when estimating scores., Methods: Using a dataset including 2258 participants from the general Swedish population, we estimated the statistical relationship between SF-6D and WHODAS 2.0. We applied three regression methods, i.e., ordinary least squares (OLS), generalized linear models (GLM), and Tobit, in mapping onto SF-6D from WHODAS 2.0 at the overall-score and domain levels. Root mean squared error (RMSE) and mean absolute error (MAE) were used for validation of the models; R
2 was used to assess model fit., Results: The best-performing models for both the working and non-working populations were GLM models with RMSE ranging from 0.084 to 0.088, MAE ranging from 0.068 to 0.071, and R2 ranging from 0.503 to 0.608. When mapping from the WHODAS 2.0 overall score, the preferred model also included sex for both the working and non-working populations. When mapping from the WHODAS 2.0 domain level, the preferred model for the working population included the domains mobility, household activities, work/study activities, and sex. For the non-working population, the domain-level model included the domains mobility, household activities, participation, and education., Conclusions: It is possible to apply the derived mapping algorithms for health economic evaluations in studies using WHODAS 2.0. As conceptual overlap is incomplete, we recommend using the domain-based algorithms over the overall score. Different algorithms must be applied depending on whether the population is working or non-working, due to the characteristics of WHODAS 2.0., (© 2023. The Author(s).)- Published
- 2023
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24. Thermal biology in the Upper Galili Mountain blind mole rat (Nannospalax galili) and an overview of spalacine energetics.
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Šumbera R, Lövy M, Nevo E, and Okrouhlík J
- Subjects
- Animals, Biology, Body Temperature, Muridae, Body Temperature Regulation, Mole Rats
- Abstract
Several hundred mammalian species thrive in complex burrow systems, which protect them from climatic extremes and predation. At the same time, it is also a stressful environment due to low food supply, high humidity, and, in some cases, a hypoxic and hypercapnic atmosphere. To face such conditions, subterranean rodents have convergently evolved low basal metabolic rate, high minimal thermal conductance and low body temperature. Although these parameters have been intensively studied in the last decades, such information is far from being well-known in one of the most studied groups of subterranean rodents, the blind mole rats of the genus Nannospalax. The lack of information is particularly noticeable for parameters such as the upper critical temperature and the width of the thermoneutral zone. In our study, we analysed the energetics of the Upper Galilee Mountain blind mole rat Nannospalax galili and found its basal metabolic rate of 0.84 ± 0.10 mL O
2 ×g-1 × h-1 , thermoneutral zone between 28 and 35 °C, mean Tb within the zone of 36.3 ± 0.6 °C, and minimal thermal conductance equal to 0.082 mL O2 ×g-1 × h-1 × C-1 . Nannospalax galili is a truly homeothermic rodent well adapted to face lower ambient temperatures, because its Tb was stable down to the lowest temperature measured (10 °C). At the same time, a relatively high basal metabolic rate and relatively low minimal thermal conductance for a subterranean rodent of such body mass, and the difficulty of surviving ambient temperatures slightly above upper critical temperature, indicates problems with sufficient heat dissipation at higher temperatures. This can easily lead to overheating, that is relevant mainly during the hot-dry season. These findings suggest that N. galili can be threatened by ongoing global climate change., Competing Interests: Declaration of competing interest Authors declare no potential conflict of interest., (Copyright © 2023 Elsevier Ltd. All rights reserved.)- Published
- 2023
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25. Quality of care in the oncological outpatient setting: Individual interviews with people receiving cancer treatment.
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Kittang J, Ohlsson-Nevo E, and Schröder A
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- Adult, Humans, Emotions, Hospitals, Quality of Health Care, Outpatients, Neoplasms therapy
- Abstract
Purpose: To describe how patients receiving cancer treatment perceive quality of care in the oncological outpatient settings., Method: A strategic sample of 20 adult patients with cancer treated in four oncological outpatient settings in four hospitals in Sweden participated in the study. Participants were interviewed using a semi-structured interview guide with open-ended questions. The interviews were audio-recorded, and the transcripts were analysed using a phenomenographic approach., Results: Three descriptive categories emerged from the data: The patient's care is designed to meet individual needs, The patient's dignity is respected, and The patient feels safe and secure with the care. Overall, quality of care in the oncological outpatient setting is perceived as something positive and described in normative terms by the participants., Conclusion: The results emphasises that in order to achieve quality of care it is important to the patients that they are able to meet with the same well-educated, professional, caring and sensible health care professionals every time., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)
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- 2023
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26. The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.
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Timmusk S, Pall T, Raz S, Fetsiukh A, and Nevo E
- Abstract
Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Timmusk, Pall, Raz, Fetsiukh and Nevo.)
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- 2023
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27. The Influence of Edaphic Factors on DNA Damage and Repair in Wild Wheat Triticum dicoccoides Körn. ( Poaceae , Triticeae).
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Raskina O, Shklyar B, and Nevo E
- Subjects
- DNA Damage, DNA Repair, DNA metabolism, Rad51 Recombinase genetics, DNA End-Joining Repair, Triticum genetics, Triticum metabolism, Poaceae genetics
- Abstract
A complex DNA repair network maintains genome integrity and genetic stability. In this study, the influence of edaphic factors on DNA damage and repair in wild wheat Triticum dicoccoides was addressed. Plants inhabiting two abutting microsites with dry terra rossa and humid basalt soils were studied. The relative expression level of seven genes involved in DNA repair pathways- RAD51 , BRCA1 , LigIV , KU70 , MLH1 , MSH2 , and MRE11 -was assessed using quantitative real-time PCR (qPCR). Immunolocalization of RAD51, LigIV, γH2AX, RNA Polymerase II, and DNA-RNA hybrid [S9.6] (R-loops) in somatic interphase nuclei and metaphase chromosomes was carried out in parallel. The results showed a lower expression level of genes involved in DNA repair and a higher number of DNA double-strand breaks (DSBs) in interphase nuclei in plants growing in terra rossa soil compared with plants in basalt soil. Further, the number of DSBs and R-loops in metaphase chromosomes was also greater in plants growing on terra rossa soil. Finally, RAD51 and LigIV foci on chromosomes indicate ongoing DSB repair during the M-phase via the Homologous Recombination and Non-Homologous End Joining pathways. Together, these results show the impact of edaphic factors on DNA damage and repair in the wheat genome adapted to contrasting environments.
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- 2023
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28. Psychometric evaluation of the WHODAS 2.0 and prevalence of disability in a Swedish general population.
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Norén P, Karlsson J, Ohlsson-Nevo E, Möller M, and Hermansson L
- Subjects
- Adult, Humans, Psychometrics, Reproducibility of Results, Cross-Sectional Studies, Prevalence, Sweden epidemiology, World Health Organization, Disability Evaluation, Language
- Abstract
Background: The World Health Organization Disability Assessment Schedule (WHODAS 2.0) is a generic questionnaire that captures health and disability-related functioning information corresponding to six major life domains: Cognition, Mobility, Self-care, Getting along, Life activities, and Participation. The WHODAS 2.0 is used in a wide range of international clinical and research settings. A psychometric evaluation of WHODAS 2.0, Swedish version, in the general population is lacking, together with national reference data to enable interpretation and comparison. This study aims to evaluate the psychometric properties of the Swedish 36-item version of WHODAS 2.0 and describe the prevalence of disability in a Swedish general population., Methods: A cross-sectional survey was performed. Internal consistency reliability was assessed with Cronbach's alpha. The construct validity was evaluated with item-total correlation, Pearson's correlation between the WHODAS 2.0 domains and the RAND-36 subscales, analysis of known groups by one-way ANOVA, and analysis of the factor structure by confirmatory factor analysis., Results: Three thousand four hundred and eighty two adults aged 19-103 years (response rate 43%) participated. Significantly higher degrees of disability were reported by the oldest age group (≥ 80 years), adults with a low level of education, and those on sick leave. Cronbach's alpha was from 0.84 to 0.95 for the domain scores and 0.97 for the total score. The item-scale convergent validity was satisfactory, and the item-scale discriminant validity was acceptable except for the item about sexual activity. The data partially supported the factor structure, with borderline fit indices., Conclusion: The psychometric properties of the self-administered Swedish 36-item version of the WHODAS 2.0 are comparable to those of other language versions of the instrument. Data of the prevalence of disability in Swedish general population enables normative comparisons of WHODAS 2.0 scores of individuals and groups within clinical practice. The instrument has certain limitations that could be improved on in a future revision. The test-retest reliability and responsiveness of the Swedish version of WHODAS 2.0 for different somatic patient populations remain to be evaluated., (© 2023. The Author(s).)
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- 2023
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29. The Effect of the COVID-19 Pandemic on Low SES Kindergarteners' Language Abilities.
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Nevo E
- Abstract
Young children's language skills have a significant positive impact on their academic success throughout school, especially on reading and writing performance. The spread of COVID-19, which has resulted in lockdowns, fewer learning hours in kindergarten, and distance learning, might have affected children's exposure to learning opportunities. The aim of the current study was to compare language abilities (vocabulary and morphological awareness) of two groups of low SES kindergarteners, 110 children who attended seven kindergartens before the COVID-19 pandemic, and 54 children who attended eight kindergartens during the COVID-19 pandemic. While both groups followed the same educational program with the same teachers, the pre-COVID-19 group studied in kindergarten before the first wave of COVID-19 restrictions, in 2018-2019, and the mid-COVID-19 group, during the pandemic, in 2020. The results showed that the mid-COVID-19 group of children achieved lower scores on morphological awareness ( d = 0.46 to d = 1.19, p = .006 to p < .001), pointing to a negative developmental effect of COVID-19 on young children's language abilities. Educational implications of the results are discussed., (© The Author(s), under exclusive licence to Springer Nature B.V. 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)
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- 2023
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30. Molecular evidence for adaptive evolution of drought tolerance in wild cereals.
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Wang Y, Chen G, Zeng F, Han Z, Qiu CW, Zeng M, Yang Z, Xu F, Wu D, Deng F, Xu S, Chater C, Korol A, Shabala S, Wu F, Franks P, Nevo E, and Chen ZH
- Subjects
- Drought Resistance, Plant Breeding, Crops, Agricultural genetics, Droughts, Edible Grain, Hordeum genetics
- Abstract
The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight. Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium species collected from dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. We present the genomic and transcriptomic evidence accounting for differences, including co-expression gene modules, correlated with physiological traits, and selective sweeps, driven by the xeric site conditions on the African Slope (AS) at ECI. Co-expression gene module 'circadian rhythm' was linked to significant drought-induced delay in flowering time in Brachypodium stacei genotypes. African Slope-specific differentially expressed genes are important in barley drought tolerance, verified by silencing Disease-Related Nonspecific Lipid Transfer 1 (DRN1), Nonphotochemical Quenching 4 (NPQ4), and Brassinosteroid-Responsive Ring-H1 (BRH1). Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate with increasingly frequent drought events., (© 2022 The Authors New Phytologist © 2022 New Phytologist Foundation.)
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- 2023
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31. Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.
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Zhang W, Tan C, Hu H, Pan R, Xiao Y, Ouyang K, Zhou G, Jia Y, Zhang XQ, Hill CB, Wang P, Chapman B, Han Y, Xu L, Xu Y, Angessa T, Luo H, Westcott S, Sharma D, Nevo E, Barrero RA, Bellgard MI, He T, Tian X, and Li C
- Subjects
- Genomics, Adaptation, Physiological genetics, Genes, Plant, Hordeum genetics
- Abstract
Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley., (© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)
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- 2023
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32. The CC-NB-LRR protein BSR1 from Brachypodium confers resistance to Barley stripe mosaic virus in gramineous plants by recognising TGB1 movement protein.
- Author
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Wu Q, Cui Y, Jin X, Wang G, Yan L, Zhong C, Yu M, Li W, Wang Y, Wang L, Wang H, Dang C, Zhang X, Chen Y, Zhang P, Zhao X, Wu J, Fu D, Xia L, Nevo E, Vogel J, Huo N, Li D, Gu YQ, Jackson AO, Zhang Y, and Liu Z
- Subjects
- Leucine-Rich Repeat Proteins, Protein Domains, Hordeum genetics, Brachypodium genetics
- Abstract
Although some nucleotide binding, leucine-rich repeat immune receptor (NLR) proteins conferring resistance to specific viruses have been identified in dicot plants, NLR proteins involved in viral resistance have not been described in monocots. We have used map-based cloning to isolate the CC-NB-LRR (CNL) Barley stripe mosaic virus (BSMV) resistance gene barley stripe resistance 1 (BSR1) from Brachypodium distachyon Bd3-1 inbred line. Stable BSR1 transgenic Brachypodium line Bd21-3, barley (Golden Promise) and wheat (Kenong 199) plants developed resistance against BSMV ND18 strain. Allelic variation analyses indicated that BSR1 is present in several Brachypodium accessions collected from countries in the Middle East. Protein domain swaps revealed that the intact LRR domain and the C-terminus of BSR1 are required for resistance. BSR1 interacts with the BSMV ND18 TGB1 protein in planta and shows temperature-sensitive antiviral resistance. The R
390 and T392 residues of TGB1ND (ND18 strain) and the G196 and K197 residues within the BSR1 P-loop motif are key amino acids required for immune activation. BSR1 is the first cloned virus resistance gene encoding a typical CNL protein in monocots, highlighting the utility of the Brachypodium model for isolation and analysis of agronomically important genes for crop improvement., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation. This article has been contributed to by US Government employees and their work is in the public domain in the USA.)- Published
- 2022
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33. New insights into the evolution of CAF1 family and utilization of TaCAF1Ia1 specificity to reveal the origin of the maternal progenitor for common wheat.
- Author
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Sun L, Song R, Wang Y, Wang X, Peng J, Nevo E, Ren X, and Sun D
- Subjects
- Phylogeny, Tetraploidy, Domestication, Triticum genetics, Evolution, Molecular
- Abstract
Introduction: Until now, the most likely direct maternal progenitor (AABB) for common wheat (AABBDD) has yet to be identified. Here, we try to solve this particular problem with the specificity of a novel gene family in wheat and by using large population of rare germplasm resources., Objectives: Dissect the novelty of TaCAF1Ia subfamily in wheat. Exploit the conservative and specific characteristics of TaCAF1Ia1 to reveal the origin of the maternal progenitor for common wheat., Methods: Phylogenetic and collinear analysis of TaCAF1 genes were performed to identify the evolutionary specificity of TaCAF1Ia subfamily. The large-scale expression patterns and interaction patterns analysis of CCR4-NOT complex were used to clarify the expressed and structural specificity of TaCAF1Ia subfamily in wheat. The population resequencing and phylogeny analysis of the TaCAF1Ia1 were utilized for the traceability analysis to understand gene-pool exchanges during the transferring and subsequent development from tetraploid to hexaploidy wheat., Results: TaCAF1Ia is a novel non-typical CAF1 subfamily without DEDD (Asp-Glu-Asp-Asp) domain, whose members were extensively duplicated in wheat genome. The replication events had started and constantly evolved from ancestor species. Specifically, it was found that a key member CAF1Ia1 was highly specialized and only existed in the subB genome and S genome. Unlike CAF1s reported in other plants, TaCAF1Ia genes may be new factors for anther development. These atypical TaCAF1s could also form CCR4-NOT complex in wheat but with new interaction sites. Utilizing the particular but conserved characteristics of the TaCAF1Ia1 gene, the comparative analysis of haplotypes composition for TaCAF1Ia1 were identified among wheat populations with different ploidy levels. Based on this, the dual-lineages origin model of maternal progenitor for common wheat and potential three-lineages domestication model for cultivated tetraploid wheat were proposed., Conclusion: This study brings fresh insights for revealing the origin of wheat and the function of CAF1 in plants., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Production and hosting by Elsevier B.V.)
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- 2022
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34. Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind mole rats in Upper Galilee, Israel.
- Author
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Kuang Z, Li F, Duan Q, Tian C, Nevo E, and Li K
- Abstract
The gut microbiome is important for host nutrient metabolism and ecological adaptation. However, how the gut microbiome is affected by host phylogeny, ecology and diet during sympatric speciation remain unclear. Here, we compare and contrast the gut microbiome of two sympatric blind mole rat species and correlate them with their corresponding host phylogeny, ecology soil metagenomes, and diet to determine how these factors may influence their gut microbiome. Our results indicate that within the host microbiome there is no significant difference in community composition, but the functions between the two sympatric species populations vary significantly. No significant correlations were found between the gut microbiome differentiation and their corresponding ecological soil metagenomes and host phylogeny. Functional enrichment analysis suggests that the host diets may account for the functional divergence of the gut microbiome. Our results will help us understand how the gut microbiome changes with corresponding ecological dietary factors in sympatric speciation of blind subterranean mole rats., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kuang, Li, Duan, Tian, Nevo and Li.)
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- 2022
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35. Digitally distributed Yoga Intervention in Breast Cancer Rehabilitation (DigiYoga CaRe): protocol for a randomised controlled trial.
- Author
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Ohlsson Nevo E, Arvidsson-Lindvall M, Hellerstedt Börjeson S, Hagberg L, Hultgren Hörnqvist E, Valachis A, Wickberg Å, and Duberg A
- Subjects
- Humans, Female, Quality of Life, Fatigue, Breast, Randomized Controlled Trials as Topic, Multicenter Studies as Topic, Yoga, Breast Neoplasms
- Abstract
Introduction: Breast cancer is the most prevalent cancer among women. The treatment is extensive; in addition to surgery, various combinations of radiation therapy, chemotherapy and antibody and endocrine treatment can be applied. Cancer-related fatigue (CRF) is high in patients with breast cancer, peaking during chemotherapy, but may persist for several years. Physical activity has proven to be effective in reducing CRF in breast cancer rehabilitation, but many patients tend to be less active after the diagnosis. Yoga has a previously demonstrated effect on energy levels and digitally distributed yoga intervention can potentially increase accessibility in pandemic times and facilitate participation for patients susceptible to infection and those living far from organised rehabilitation opportunities. The purpose of this study, Digital Yoga Intervention in Cancer Rehabilitation (DigiYoga CaRe) is to investigate whether a 12-week digitally distributed yoga intervention can reduce CRF and stress, improve health-related quality of life (HRQL) and affect pro-inflammatory and metabolic markers in patients with breast cancer., Methods and Analysis: This multicentre study will adopt a randomised controlled design including 240 persons after their breast cancer surgery. They will be randomised to a 12-week digitally distributed yoga intervention or to a control group. The intervention group practice yoga two times a week, one yoga class live-streamed to the patient's computer or mobile device and one prerecorded video class for self-training. The controls receive standardised care, gift cards for flowers and access to yoga video links after the data collection has ended. The primary analysis will be performed following the principle of intention to treat. Data will be collected by questionnaires, blood samples, accelerometers and interviews., Ethics and Dissemination: The DigiYoga CaRe study was approved by the Regional Ethical Review Board in Lund. The final results of this study will be disseminated to conference, patient and public involvements and peer-reviewed publications., Trial Registration Number: NCT04812652., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2022
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36. Sympatric Speciation in Mole Rats and Wild Barley and Their Genome Repeatome Evolution: A Commentary.
- Author
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Nevo E and Li K
- Abstract
The theories of sympatric speciation (SS) and coding and noncoding (cd and ncd =repeatome) genome function are still contentious. Studies on SS in our two new models, "Evolution Canyon" and "Evolution Plateau", in Israel, divergent microclimatically and geologically-edaphically, respectively, indicated that in ecologically divergent microsites SS is a common speciation model across life from bacteria to mammals. Genomically, the intergenic ncd repeatome was and is still regarded by many biologists as "selfish," "junk," and non-functional. In contrast, it is considered by the encyclopedia of DNA elements discovery as biochemically functional and regulatory, and the transposable elements were considered earlier by Barbara McClintock as "controlling elements" of genes. Remarkably, it is found that repeated elements can statistically identify significantly, the five species of subterranean mole rats of Spalax ehrenbergi superspecies adapted to increasingly arid climatic trend southward in Israel. Moreover, it is first discovered in the SS studies in two distant taxa, subterranean mole rats and wild barley, and later also in spiny mice in Israel and subterranean zokors in China, that the noncoding repeatome is genomically mirroring the image of the protein-coding genome in divergent ecologies. It is shown that this mirroring image is statistically significant both within and between the ecologically divergent taxa supporting the hypothesis that much of the repeatome might be regulatory and selected as the protein-coding genome by the same ecological stresses., Competing Interests: The authors declare no conflict of interest., (© 2022 The Authors. Advanced Genetics published by Wiley Periodicals LLC.)
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- 2022
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37. Functional characterization of powdery mildew resistance gene MlIW172, a new Pm60 allele and its allelic variation in wild emmer wheat.
- Author
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Wu Q, Chen Y, Li B, Li J, Zhang P, Xie J, Zhang H, Guo G, Lu P, Li M, Zhu K, Li W, Fahima T, Nevo E, Li H, Dong L, and Liu Z
- Subjects
- Alleles, Chromosome Mapping, Disease Resistance, Genes, Plant, Plant Breeding, Plant Diseases, Triticum
- Abstract
Wild emmer wheat (Triticum dicoccoides, WEW) is an immediate progenitor of both the cultivated tetraploid and hexaploid wheats and it harbors rich genetic diversity against powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt). A powdery mildew resistance gene MlIW172 originated from WEW accession IW172 (G-797-M) is fine mapped in a 0.048 centimorgan (cM) genetic interval on 7AL, corresponding to a genomic region spanning 233 kb, 1 Mb and 800 kb in Chinese Spring, WEW Zavitan, and T. urartu G1812, respectively. MlIW172 encodes a typical NLR protein NLR
IW172 and physically locates in an NBS-LRR gene cluster. NLRIW172 is subsequently identified as a new allele of Pm60, and its function is validated by EMS mutagenesis and transgenic complementation. Haplotype analysis of the Pm60 alleles reveals diversifications in sequence variation in the locus and presence and absence variations (PAV) in WEW populations. Four common single nucleotide variations (SNV) are detected between the Pm60 alleles from WEW and T. urartu, indicative of speciation divergence between the two different wheat progenitors. The newly identified Pm60 alleles and haplotypes in WEW are anticipated to be valuable for breeding powdery mildew resistance wheat cultivars via marker-assisted selection., Competing Interests: Conflict of interest The authors declare no conflicts of interest., (Copyright © 2022 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.)- Published
- 2022
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38. Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis.
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Mukherjee S, Kuang Z, Ghosh S, Detroja R, Carmi G, Tripathy S, Barash D, Frenkel-Morgenstern M, Nevo E, and Li K
- Abstract
Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.
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- 2022
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39. Outcomes in patients not conveyed by emergency medical services (EMS): a one-year prospective study.
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Höglund E, Schröder A, Andersson-Hagiwara M, Möller M, and Ohlsson-Nevo E
- Subjects
- Ambulances, Emergency Service, Hospital, Follow-Up Studies, Humans, Prospective Studies, Triage, Emergency Medical Services
- Abstract
Background: The decision to not convey patients has become common in emergency medical services worldwide. A substantial proportion (12-51%) of the patients seen by emergency medical services are not conveyed by those services. The practice of non-conveyance is a result of the increasing and changing demands on the acute care system. Research focusing on the outcomes of the decision by emergency medical services to not convey patients is needed., Aim: The aim was to describe outcomes (emergency department visits, admission to in-hospital intensive care units and mortality, all within seven days) and their association with the variables (sex, age, day of week, time of day, emergency signs and symptoms codes, triage level colour, and destination) for non-conveyed patients., Methods: This was a prospective analytical study with consecutive inclusion of all patients not conveyed by emergency medical services. Patients were included between February 2016 and January 2017. The study was conducted in Region Örebro county, Sweden. The region consists of both rural and urban areas and has a population of approximately 295,000. The region had three ambulance departments that received approximately 30,000 assignments per year., Results: The result showed that no patient received intensive care, and 18 (0.7%) patients died within seven days after the non-conveyance decision. Older age was associated with a higher risk of hospitalisation and death within seven days after a non-conveyance decision., Conclusions: Based on the results of this one-year follow-up study, few patients compared to previous studies were admitted to the hospital, received intensive care or died within seven days. This study contributes insights that can be used to improve non-conveyance guidelines and minimise the risk of patient harm., (© 2022. The Author(s).)
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- 2022
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40. Genomic insights into zokors' phylogeny and speciation in China.
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Liu X, Zhang S, Cai Z, Kuang Z, Wan N, Wang Y, Mao L, An X, Li F, Feng T, Liang X, Qiao Z, Nevo E, and Li K
- Subjects
- Animals, China, Genomics, Phylogeny, Tibet, Genome, Rodentia genetics
- Abstract
The phylogeny and speciation of subterranean zokors in China are unclear, as previous studies on morphology and limited molecular markers have generated conflicting results. This study unraveled the complex evolutionary history of eight zokor species in China based on de novo assembly at chromosome level and whole-genome sequencing of 23 populations. We found extensive phylogenetic discordances between nuclear and mitochondrial phylogenies, and different coalescent phylogenies, which could be explained by introgression and incomplete lineage sorting (ILS). The recent Qinghai-Tibet Plateau uplift (∼3.60 million y ago; Mya) drove Eospalax to speciate into clade A and clade B (∼3.22 Mya), and discordant phylogenies in this node were mainly attributed to introgression rather than ILS. Clade A rapidly diverged into three lineages due to geographical isolation and glaciation, while glaciation and C4 plant expansion contributed to the speciation of clade B. ILS contributed to the discordances of two rapidly radiated nodes rather than introgression. The effective population sizes (Ne’s) of all the species of Eospalax were affected by three glaciations. Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of all the species pairs. Positively selected genes putatively related to specific inhabitation adaptations were identified, such as heart development, neurogenesis, DNA repair, and immune response. Climate, geological tectonism, and C4 vegetation shaped the adaptation and speciation of zokors in China.
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- 2022
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41. Sympatric speciation of the spiny mouse from Evolution Canyon in Israel substantiated genomically and methylomically.
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Wang Y, Qiao Z, Mao L, Li F, Liang X, An X, Zhang S, Liu X, Kuang Z, Wan N, Nevo E, and Li K
- Subjects
- Animals, Genetic Speciation, Genome, Israel, Murinae genetics, Reproductive Isolation, Sympatry genetics
- Abstract
SignificanceWhether sympatric speciation (SS) is rare or common is still debated. Two populations of the spiny mouse, Acomys cahirinus , from Evolution Canyon I (EC I) in Israel have been depicted earlier as speciating sympatrically by molecular markers and transcriptome. Here, we investigated SS both genomically and methylomically, demonstrating that the opposite populations of spiny mice are sister taxa and split from the common ancestor around 20,000 years ago without an allopatric history. Mate choice, olfactory receptors, and speciation genes contributed to prezygotic/postzygotic reproductive isolation. The two populations showed different methylation patterns, facilitating adaptation to their local environment. They cope with abiotic and biotic stresses, due to high solar interslope radiation differences. We conclude that our new genomic and methylomic data substantiated SS.
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- 2022
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42. PET/MRI, Part 3: Protocols and Procedures.
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Nevo E, Kamvosoulis P, and Currie G
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- Child, Humans, Molecular Imaging, Positron-Emission Tomography, Magnetic Resonance Imaging, Nuclear Medicine
- Abstract
CE credit : For CE credit, you can access the test for this article, as well as additional JNMT CE tests, online at https://www.snmmilearningcenter.org Complete the test online no later than March 2025. Your online test will be scored immediately. You may make 3 attempts to pass the test and must answer 75% of the questions correctly to receive Continuing Education Hour (CEH) credit. Credit amounts can be found in the SNMMI Learning Center Activity. SNMMI members will have their CEH credit added to their VOICE transcript automatically; nonmembers will be able to print out a CE certificate upon successfully completing the test. The online test is free to SNMMI members; nonmembers must pay $15.00 by credit card when logging onto the website to take the test.The emergence of PET and MRI as a hybrid modality has demanded new approaches to protocols and procedures. Although protocols for MRI and PET individually lend themselves to synergistic and simultaneous approaches, there are a number of unique challenges and patient preparations that require consideration. This article provides insight into the protocols, procedures, and challenges associated with simultaneous PET/MRI in both adult and pediatric populations. Although protocols may be specific to applications or pathologies of interest, a richer discussion of the clinical applications of PET/MRI is beyond the scope of this article and will be detailed in part 4 of the series. The foundation of PET/MRI protocols is an understanding of the various MRI sequences, which are outlined succinctly. The principles outlined for protocols and procedures are general, and specific application will vary among departments. Given that the procedures for PET are well established among the readership of this journal, this article emphasizes MRI factors unless specific variations in standard PET protocols or procedures are driven by the simultaneous MRI. This article is the third in a 4-part integrated series sponsored by the PET/MR and Publication Committees of the Society of Nuclear Medicine and Molecular Imaging-Technologist Section., (© 2022 by the Society of Nuclear Medicine and Molecular Imaging.)
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- 2022
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43. Reappraisal of the Genus Exsudoporus ( Boletaceae ) Worldwide Based on Multi-Gene Phylogeny, Morphology and Biogeography, and Insights on Amoenoboletus .
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Biketova AY, Gelardi M, Smith ME, Simonini G, Healy RA, Taneyama Y, Vasquez G, Kovács Á, Nagy LG, Wasser SP, Peintner U, Nevo E, Bunyard BA, and Vizzini A
- Abstract
The boletoid genera Butyriboletus and Exsudoporus have recently been suggested by some researchers to constitute a single genus, and Exsudoporus was merged into Butyriboletus as a later synonym. However, no convincing arguments have yet provided significant evidence for this congeneric placement. In this study, we analyze material from Exsudoporus species and closely related taxa to assess taxonomic and phylogenetic boundaries between these genera and to clarify species delimitation within Exsudoporus . Outcomes from a multilocus phylogenetic analysis (ITS, nrLSU, tef1-α and rpb2 ) clearly resolve Exsudoporus as a monophyletic, homogenous and independent genus that is sister to Butyriboletus . An accurate morphological description, comprehensive sampling, type studies, line drawings and a historical overview on the nomenclatural issues of the type species E. permagnificus are provided. Furthermore, this species is documented for the first time from Israel in association with Quercus calliprinos . The previously described North American species Exsudoporus frostii and E. floridanus are molecularly confirmed as representatives of Exsudoporus , and E. floridanus is epitypified. The eastern Asian species Leccinum rubrum is assigned here to Exsudoporus based on molecular evidence, and a new combination is proposed. Sequence data from the original material of the Japanese Boletus kermesinus were generated, and its conspecificity with L. rubrum is inferred as formerly presumed based on morphology. Four additional cryptic species from North and Central America previously misdetermined as either B. frostii or B. floridanus are phylogenetically placed but remain undescribed due to the paucity of available material. Boletus weberi (syn. B. pseudofrostii ) and Xerocomus cf. mcrobbii cluster outside of Exsudoporus and are herein assigned to the recently described genus Amoenoboletus . Biogeographic distribution patterns are elucidated, and a dichotomous key to all known species of Exsudoporus worldwide is presented.
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- 2022
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