Search

Abstract The KidGen Collaborative's Policy Implementation Workshop 2023 celebrated the 10th anniversary of Australia's first kidney genetics clinic in Brisbane. This event marked the establishment of a national network now comprising 19 kidney genetics clinics across Australia, all dedicated to providing equitable access to genomic testing for families affected by genetic kidney diseases. The workshop reflected on past progress and outlined future objectives for kidney genetics in Australia, recognising the collaborative efforts of clinical teams, researchers, and patients. Key insights from the workshop are documented in the proceedings.

Abstract Background Cognitive dysfunction caused by infection frequently emerges as a complication in sepsis survivor patients. However, a comprehensive understanding of its pathogenesis remains elusive. Methods In our in vivo experiments, an animal model of endotoxemia was employed, utilizing the Novel Object Recognition Test and Morris Water Maze Test to assess cognitive function. Various techniques, including immunofluorescent staining, Western blotting, blood‒brain barrier permeability assessment, Limulus Amebocyte Lysate (LAL) assay, and Proximity-ligation assay, were employed to identify brain pathological injury and neuroinflammation. To discern the role of Caspase-11 (Casp11) in hematopoietic or non-hematopoietic cells in endotoxemia-induced cognitive decline, bone marrow chimeras were generated through bone marrow transplantation (BMT) using wild-type (WT) and Casp11-deficient mice. In vitro studies involved treating BV2 cells with E. coli-derived outer membrane vesicles to mimic in vivo conditions. Results Our findings indicate that the deficiency of Casp11-GSDMD signaling pathways reverses infection-induced cognitive dysfunction. Moreover, cognitive dysfunction can be ameliorated by blocking the IL-1 effect. Mechanistically, the absence of Casp11 signaling significantly mitigated blood‒brain barrier leakage, microglial activation, and synaptic damage in the hippocampal CA3 region, ultimately leading to improved cognitive function. Conclusion This study unveils the crucial contribution of Casp11 and GSDMD to cognitive impairments and spatial memory loss in a murine sepsis model. Targeting Casp11 signaling emerges as a promising strategy for preventing or treating cognitive dysfunction in patients with severe infections.

Aiming at the key problems need to be solved, such as cascade channel sparse representation, time-varying channel parameter tracking and signal reconstruction, for time-varying cascade channels estimation of reconfigurable intelligent surface (RIS) assisted communication system, a Khatri-Rao and hierarchical Bayesian Kalman filter (KR-HBKF) algorithm was proposed.Firstly, the Khatri-Rao product and Kronecker product transformations were used to obtain the sparse representation of RIS cascaded channels based on the sparse characteristics of channels, thus the RIS cascaded channel estimation problem was transformed into a low-dimensional sparse signal recovery problem.Then, according to the state evolution model of RIS cascaded channel, the time correlation parameter was introduced into the prediction model of HBKF algorithm, and the improved HBKF was applied to solve the problem of time-varying channel parameter tracking and signal reconstruction for completing the time-varying cascaded channels estimation.The sparsity and time correlation of the channel were comprehensively considered in the KR-HBKF algorithm, thus better estimation accuracy could be obtained with small pilot overhead.Compared with the traditional compressed sensing algorithm, the simulation results show that the proposed algorithm has about 5 dB estimated performance improvement, and better robustness performance under different time-varying channel conditions.

Abstract Full activation of the NLRP3 inflammasome needs two sequential signals: a priming signal, followed by a second, assembly signal. Several studies have shown that the two signals trigger post-translational modification (PTM) of NLRP3, affecting activity of the inflammasome, however, the PTMs induced by the second signal are less well characterized. Here, we show that the assembly signal involves acetylation of NLRP3 at lysine 24, which is important for the oligomerization and the actual assembly of NLRP3 without affecting its recruitment to dispersed trans-Golgi network (dTGN). Accordingly, NLRP3 inflammasome activation is impaired in NLRP3-K24R knock-in mice. We identify KAT5 as an acetyltransferase able to acetylate NLRP3. KAT5 deficiency in myeloid cells and pharmacological inhibition of KAT5 enzymatic activity reduce activation of the NLRP3 inflammasome, both in vitro and in vivo. Thus, our study reveals a key mechanism for the oligomerization and full activation of NLRP3 and lays down the proof of principle for therapeutic targeting of the KAT5-NLRP3 axis.

Many insects selectively associate with specific microbes in long-term, symbiotic relationships. Maintaining these associations can be vital for the insect hosts’ development, but insects must also contend with potential coinfections from other microbes in the environment. Fending off microbial threats while maintaining mutualistic microbes has resulted in many insects developing specialized symbiotic organs to house beneficial microbes. Though locally concentrated in these organs, symbiont establishment can have global consequences for the insect, including influence over the success of coinfecting microbes in colonizing the insect host. We use a transcriptomic approach to examine how the mutualistic symbiosis between the agricultural pest Anasa tristis and bacteria in the genus Caballeronia affects insect gene expression locally within the symbiotic organs and in the insect host at large. We simultaneously determine whether Caballeronia colonization impacts insect host responses to infection with the plant pathogen Serratia marcescens, which it vectors to plants. We found that no significant differential gene expression was elicited by infection with S. marcescens. This was a surprising finding given previous work indicating that symbiotic A. tristis clear S. marcescens infection rapidly compared to aposymbiotic individuals. Our results indicate that symbiotic and nonsymbiotic tissues in A. tristis differ greatly in their gene expression, particularly following successful symbiont colonization. We found evidence for local downregulation of host immunity and upregulation of cell communication within the symbiotic organs, functions which can facilitate the success of the A. tristis-Caballeronia symbiosis.

Abstract The world's 1.4 million lakes (≥10 ha) provide many ecosystem services that are essential for human well‐being; however, only if their health status is good. Here, we reviewed common lake health issues and classified them using a simple human health‐based approach to outline that lakes are living systems that are in need of oxygen, clean water and a balanced energy and nutrient supply. The main reason for adopting some of the human health terminology for the lake health classification is to increase the awareness and understanding of global lake health issues. We show that lakes are exposed to various anthropogenic stressors which can result in many lake health issues, ranging from thermal, circulatory, respiratory, nutritional and metabolic issues to infections and poisoning. Of particular concern for human well‐being is the widespread lake drying, which is a severe circulatory issue with many cascading effects on lake health. We estimated that ∼115,000 lakes evaporate twice as much water as they gain from direct precipitation, making them vulnerable to potential drying if inflowing waters follow the drying trend, putting more than 153 million people at risk who live in close vicinity to those lakes. Where lake health issues remain untreated, essential ecosystem services will decline or even vanish, posing a threat to the well‐being of millions of people. We recommend coordinated multisectoral and multidisciplinary prevention and treatment strategies, which need to include a follow‐up of the progress and an assessment of the resilience of lakes to intensifying threats. Priority should be given to implementing sewage water treatment, mitigating climate change, counteracting introductions of non‐native species to lakes and decreasing uncontrolled anthropogenic releases of chemicals into the hydro‐, bio‐, and atmosphere.

BackgroundThere are different types of transcatheter mitral valve repair (TMVr) currently in clinical use, including leaflet approximation, annular cinching, and restoration of the chordal apparatus of the mitral valve (MV). While the concomitant combination (COMBO) therapy of mitral transcatheter edge-to-edge repair (M-TEER) with another TMVr concept has been proven feasible, potentially offering patient-tailored treatment for severe mitral regurgitation (MR), a comparison with M-TEER alone has not been made.AimsTo evaluate the procedural and clinical outcome of COMBO therapies compared with M-TEER alone.MethodsWe included consecutive patients undergoing COMBO and M-TEER between March 2015 and April 2018 at our Heart Valve Center, while excluding patients presenting a case of redo or with previous MV surgery. Procedural outcomes and all-cause mortality were compared between COMBO therapy vs. M-TEER alone.ResultsA total of 357 patients (mean age 78.9 ± 7.0 years, 53.2% male, M-TEER n = 322, COMBO n = 35; COMBO: MitraClip and the Carillon mitral contour system n = 26, MitraClip and Cardioband n = 5, and MitraClip and NeoChord n = 4) were analyzed. Patients with COMBO therapy had larger left chamber sizes, a lower left ventricular systolic ejection fraction (LVEF; COMBO: 37.4 ± 13.8%, M-TEER: 47.9 ± 14.3%, p

Purpose: To understand diversity, inclusion, and capacity of genetic counselors (GCs) in Australasia (Australia and New Zealand). Methods: Individuals with or working toward a GC qualification in Australasia were invited to complete an online survey, between November 2022 and March 2023. Quantitative data were analyzed using descriptive statistics, 1-sample proportion z-tests, 2-sample z-tests, and χ2 tests. Qualitative data were analyzed using inductive content analysis. Results: A total of 252 participants responded to the survey. A subset analysis of respondents residing in Australia demonstrated a lack of representation across various characteristics including sex, relationship status, caregiver status, location, country of birth, Aboriginal/Torres Strait Islander identity, language, and religion. Analysis of the full data set demonstrated that most respondents also perceived that the workforce was not representative across gender, sexual orientation, ethnicity, or disability. Respondents provided examples of existing inclusive practice. They also suggested workforce needs, such as promoting education and employment for minority communities, more visible diversity, accessible services for clients, and professional development for GCs. Using survey and reference data, we estimated approximately 346 full-time equivalent GCs working in clinical practice in Australasia. Conclusion: Our study provides a first step in illuminating GC workforce changes needed in Australasia regarding diversity, inclusion, and capacity. The survey may be of use internationally, enabling other countries to understand these issues within their jurisdiction, and supporting the international community in addressing these challenges.

Abstract Background Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown. Results We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in “plant hormone signal transduction” were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance. Conclusion This study identifies specific genes involved in Ca2+ signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.

Abstract Emerged evidence has indicated that immunosuppression is involved in the occurrence and development of sepsis. To provide clinical practice recommendations on the immune function in sepsis, an expert consensus focusing on the monitoring and treatment of sepsis-induced immunosuppression was developed. Literature related to the immune monitoring and treatment of sepsis were retrieved from PubMed, Web of Science, and Chinese National Knowledge Infrastructure to design items and expert opinions were collected through an online questionnaire. Then, the Delphi method was used to form consensus opinions, and RAND appropriateness method was developed to provide consistency evaluation and recommendation levels for consensus opinions. This consensus achieved satisfactory results through two rounds of questionnaire survey, with 2 statements rated as perfect consistency, 13 as very good consistency, and 9 as good consistency. After summarizing the results, a total of 14 strong recommended opinions, 8 weak recommended opinions and 2 non-recommended opinions were produced. Finally, a face-to-face discussion of the consensus opinions was performed through an online meeting, and all judges unanimously agreed on the content of this consensus. In summary, this expert consensus provides a preliminary guidance for the monitoring and treatment of immunosuppression in patients with sepsis.

Several factors, including breed, lead to divergent performance of pigs for production and reproduction traits in different environments. A recent genomics study showed that Modern European (ME) pig breeds contribute to the ancestry of smallholder pigs in the Hoima and Kamuli districts, Uganda. These pigs were also involved in a longitudinal study with several traits recorded, including 540 body weights (WT) of 374 growing pigs, 195 records of total number of piglets born alive (TBA) of 157 sows, and 110 total number weaned (TNW) records of 94 sows. Linear mixed-effects models were used to test for the significance of environmental effects, including housing system, geographic location, and the season when the events occurred as well as animal-specific effects like age, sex, parity, and farrow-to-weaning interval. Stepwise model reduction starting from models with all main effects and pairwise interactions was applied. The final models were then expanded to include proportions of Modern European (ME) ancestry for the subset of animals genotyped, following genomic ancestry analysis based on a Porcine 50K SNP Chip. ME ancestry proportions ranged from 0.02 to 0.50 and were categorized into three classes (low/medium/high ME) based on 33.3% quantiles. The effects of ME classes on WT and TBA were not significant. ME showed a significant effect on TNW. Sows with a high proportion of ME weaned 2.4 piglets more than the low group, the medium ME group being intermediate. This study used genomic data to investigate the effects of genetic ancestry on the performance of smallholder pigs in Uganda. The proportion of Modern European ancestry did not exceed 0.50, therefore not allowing for the comparison of local versus pure “exotic” types of pigs. For the range of ancestries observed, which is the relevant one for current smallholder systems in Uganda, differences were small for the body weight of growing pigs and the number of piglets born alive, while higher proportions of ME ancestry resulted in significantly more piglets weaned. The availability of genotypes of a higher number of growing pigs would have been beneficial for drawing conclusions on the effect of ME ancestry on the growth rates of smallholder pigs in Uganda.

Abstract Introduction Symphonia globulifera and Allophylus abyssinicus are used in the management of skin rashes and sores, cough, malaria, digestive diseases, stomach ache, wounds and helminthic infections among others in Uganda, Kenya, Ethiopia, Cameroon. This study aimed at determining the phytochemical profile and antimicrobial activity of these two plants. Methods The stem bark and leaves of both plants were collected from Bwindi Impenetrable National Park and air-dried under shade at room temperature. Cold maceration, decoction and infusion with methanol, water and ethyl acetate as solvents were used in phytochemical extraction. Preliminary qualitative screening and thin layer chromatography were used for phytochemical profiling. Antimicrobial activity was analysed by agar well diffusion assay, broth macro-dilution assay and fractional inhibition concentration index (FICI). Results The leaves and stem bark of both plants have a diverse set of phytochemical compounds of variable polarity including, tannins, alkaloids, flavonoids, saponins, quinones and anthraquinones among others. Generally, methanol and water extracts of S. globulifera and A. abyssinicus had in-vitro bactericidal activity against Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa but weak fungistatic activity against Candida albicans. Allophylus abyssinicus leaf water and S. globulifera leaf methanol extract combination had a synergistic activity (ΣFICI = 0.37) against S. aureus. Similarly, A. abyssinicus stem bark water extract and A. abyssinicus leaf water extract combination had an additive effect (ΣFICI = 1) against P. aeruginosa. Conclusion The leaves and stem bark crude extracts of S. globulifera and A. abyssinicus possess a wide range of bioactive phytochemical compounds but have weak antimicrobial activity against S. aureus, E. coli, P. aeruginosa and C. albicans.

Alfalfa (Medicago sativa L.), an important perennial legume forage crop with high nutritional value and forage yield, is widely used in animal husbandry. However, it is very sensitive to aluminum, which severely limits its growth in acidic soils. In this study, we analyzed the genotype variation of each agronomic trait in 44 alfalfa varieties in two acidic soil environments. Then, analysis of variance (ANOVA) of the variance components was performed using the Residual Maximum Likelihood (REML). The best linear unbiased predictor analysis was used to obtain the mean trait of each variety, and the mean values were used to construct the mean matrix of varieties × traits and interaction analysis of varieties × years. The results showed that there was significant (P < 0.05) genotypic variation for each trait of the 44 varieties and the genetic diversity was abundant. The average repeatability (R value) of interannual plant height (PH), stem thickness (ST), number of branches (NS), fresh weight (FW), total fresh weight (TFW), and total dry weight (TDW) was high (0.21–0.34), whereas the genetics were relatively stable. PH, NS, FW, TFW, and dry weight (DW) were positively correlated (P < 0.01) with TDW. Six alfalfa varieties (Algonquin, Xinjiang daye, Trifecta, Vernal, WL354HQ, and Boja) with excellent TDW and TFW were identified in different years, environmental regions, and climatic altitudes. Our research results can provide suggestions and critical information regarding the future improvement and development of new alfalfa strains and varieties that are resistant to acidic soil conditions.

YAP is known to play a role both in organ size via the Hippo signalling pathway and in inflammation, though the precise mechanism are unclear. Here, the authors report that YAP promotes activation of the NLRP3 inflammosome through binding interactions.

Background and Aim: Since 2015, local newspapers reported that pig and poultry farmers in Uganda use antiretroviral drugs (ARVs) to promote growth in animals and control diseases. This study was conducted to assess farmers' knowledge, attitude and perceptions about the use of antiretroviral drugs as boosters in pigs and poultry and the possibility of detecting the antiretroviral drugs in meat using available laboratory methods. Materials and Methods: In 2019, a cross-sectional study was conducted in ten districts in Uganda. In 20 focus group discussions with 100 pig and poultry farmers and 70 animal health service providers, we assessed the use of ARV in livestock enterprises. Subsequently, samples of chicken, pigs, and animal feeds were collected from volunteer participants, and screened for residues of saquinavir, lopinavir, nevirapine, and efavirenz using liquid chromatography-tandem mass spectrophotometer. Results: Participants in all ten districts were predominantly smallholder farmers supplying the local markets. All groups reported the use of ARVs in pigs and broiler birds but not in layer hens. In the absence of good quality feeds, the motivation for feeding ARVs was rapid animal weight gain, as well as the control of animal diseases, for which farmers have no alternative solutions. ARVs were obtained within the community for free, against cash, or in-kind payment. Residues of lopinavir were detected in four, and saquinavir in seven districts, and all three sample matrices. Conclusion: Our study findings confirm anecdotal news reports on ARV use in livestock. While our findings are not generalizable to the whole country, they call for a representative follow-up. As the drugs were detected in tissues destined for human consumption, the potential risk to human health warrants further investigation.

Abstract Caspase-11, a cytosolic lipopolysaccharide (LPS) receptor, mediates lethal immune responses and coagulopathy in sepsis, a leading cause of death worldwide with limited therapeutic options. We previously showed that over-activation of caspase-11 is driven by hepatocyte-released high mobility group box 1 (HMGB1), which delivers extracellular LPS into the cytosol of host cells during sepsis. Using a phenotypic screening strategy with recombinant HMGB1 and peritoneal macrophages, we discovered that FeTPPS, a small molecule selectively inhibits HMGB1-mediated caspase-11 activation. The physical interaction between FeTPPS and HMGB1 disrupts the HMGB1-LPS binding and decreases the capacity of HMGB1 to induce lysosomal rupture, leading to the diminished cytosolic delivery of LPS. Treatment of FeTPPS significantly attenuates HMGB1- and caspase-11-mediated immune responses, organ damage, and lethality in endotoxemia and bacterial sepsis. These findings shed light on the development of HMGB1-targeting therapeutics for lethal immune disorders and might open a new avenue to treat sepsis.

Summary: Silicosis is caused by inhalation of crystalline silica dust particles and known as one of the most serious occupational diseases worldwide. However, little is known about intrinsic factors leading to disease susceptibility. Single-cell sequencing of bronchoalveolar lavage fluid cells of mine workers with silicosis and their co-workers who did not develop silicosis revealed that the impaired interferon (IFN)-γ signaling in myeloid cells was strongly associated with the occurrence of silicosis. Global or myeloid cell-specific deletion of interferon γ receptor (IFN-γR) markedly enhanced the crystalline silica-induced pulmonary injury in wild-type but not in NLRP3 deficient mice. In vitro, IFN-γ priming of macrophages suppressed the crystalline silica-induced NLRP3 inflammasome activation partly by inducing the formation of spacious phagosomes with relatively reduced ratio of crystalline silica/phagosomal areas volumes to resistant crystalline silica-induced lysosomal membrane damage. Thus, these findings provide molecular insights into the intricate mechanisms underlying innate immunity-mediated host responses to environmental irritants.

Abstract Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV, a WGS based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs > 10 kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5–4.5%) and reproducibility high (95–99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35–63% were not detectable by current clinical microarray designs. ClinSV is available at https://github.com/KCCG/ClinSV .

Abstract Aims Mitral annuloplasty using the Carillon Mitral Contour System (CMCS) reduces secondary mitral regurgitation (SMR) and leads to reverse left ventricular remodelling. The aim of this study was to evaluate the effect of the CMCS on the mitral valve annulus (MA) and left atrial volume (LAV). Methods and results We retrospectively evaluated the data of all patients treated with the CMCS at our centre. Using transthoracic echocardiography, MA diameters were assessed by measuring the anterolateral to posteromedial extend (ALPM) and the anterior to posterior (AP) dimensions, respectively. Also, LAV and left ventricular end‐diastolic volume (LVEDV) were assessed. Patients were examined at three time points: baseline, at 20–60 days (30dFUP), and at 9–15 months (1yFUP), using paired analysis. From July 2014 until March 2019, 75 cases of severe SMR were treated using CMCS. Cases in which other devices were used in combination (COMBO therapy, n = 35) or in which the device could not be implanted (implant failure, n = 3) were excluded, leaving 37 patients in the present analysis. Analysis at 30dFUP showed a significant reduction of 16% in the mean ALPM diameter (7.27 ± 5.40 mm) and 15% in the AP diameter (6.57 ± 5.33 mm). Analysis of LAV also showed a significant reduction of 21% (36.61 ± 82.67 mL), with no significant change in LVEDV. At 1yFUP, the reduction of both the mean ALPM diameter of 14% (6.24 ± 5.70 mm) and the mean AP diameter of 12% (5.46 ± 4.99 mm) remained significant and stable. The reduction in LAV was also maintained at 23% (37.03 ± 56.91 mL). LAV index was significantly reduced by 17% at 30dFUP (15.44 ± 40.98 mL/m2) and by 13% at 1yFUP (11.56 ± 31.87 mL/m2), respectively. LVEDV index showed no significant change at 30dFUP and a non‐significant 10% reduction at 1yFUP (17.75 ± 58.79 mL/m2). Conclusions The CMCS successfully treats symptomatic SMR with a stable reduction of not only the AP diameter of the MA, but the current study also demonstrates an additional reduction of the ALPM dimension at both 30dFUP and 1yFUP. We have also shown for the first time that LAV and LAV index are significantly reduced at both 30dFUP and 1yFUP and a non‐significant positive remodelling of the LVEDV. This positive left atrial remodelling has not been looked for and demonstrated in earlier randomized studies of CMCS.

The COVID-19 outbreak triggered a massive spread of unverified news on social media and has become a source of rumors. This paper studies the impact of a virtual rumor control center (RCC) on Weibo user behavior. The collected COVID-19 breaking news stories were divided into positive, negative, and neutral categories, while the moderating effect model was used to analyze the influence of anti-rumor on user behavior (forwarding, liking, and commenting). Our research found that rumor refuting does not directly affect user behavior but does have an indirect moderating effect. Rumor refuting has a profound impact on user forwarding behavior in cases of positive and negative news. Specifically, when the epidemic becomes more serious, the role of rumor refuting becomes critical, and vice versa. Refuting rumors reduces user willingness to forward positive or negative news, with more impact on negative news. Time lag analysis shows a significant moderation of unverified news within 72 h of refuting rumors but indicated an apparent weakening trend over time. Furthermore, we discovered non-linear feature and counter-cyclical phenomena in the moderating effect of rumor refutation.

Background: Viruses cause various human diseases, some of which become pandemic outbreaks. This study synthesized evidence on antiviral medicinal plants in Africa which could potentially be further studied for viral infections including Coronavirus disease 2019 (COVID-19) treatment.Methods: PUBMED, CINAHIL, Scopus, Google Scholar, and Google databases were searched through keywords; antiviral, plant, herb, and Africa were combined using “AND” and “OR”. In-vitro studies, in-vivo studies, or clinical trials on botanical medicine used for the treatment of viruses in Africa were included.Results: Thirty-six studies were included in the evidence synthesis. Three hundred and twenty-eight plants were screened for antiviral activities of which 127 showed noteworthy activities against 25 viral species. These, were Poliovirus (42 plants), HSV (34 plants), Coxsackievirus (16 plants), Rhinovirus (14plants), Influenza (12 plants), Astrovirus (11 plants), SARS-CoV-2 (10 plants), HIV (10 plants), Echovirus (8 plants), Parvovirus (6 plants), Semiliki forest virus (5 plants), Measles virus (5 plants), Hepatitis virus (3 plants), Canine distemper virus (3 plants), Zika virus (2 plants), Vesicular stomatitis virus T2 (2 plants). Feline herpesvirus (FHV-1), Enterovirus, Dengue virus, Ebola virus, Chikungunya virus, Yellow fever virus, Respiratory syncytial virus, Rift Valley fever virus, Human cytomegalovirus each showed sensitivities to one plant.Conclusion: The current study provided a list of African medicinal plants which demonstrated antiviral activities and could potentially be candidates for COVID-19 treatment. However, all studies were preliminary and in vitro screening. Further in vivo studies are required for plant-based management of viral diseases.

In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2 or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2 or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2 signaling, and pyrenoid morphologies.

Background Deliberate practice (DP) was proposed for effective clinical skill training, which highlights focused, repetitive practice and feedback as the key points for practice. Although previous studies have investigated the effect of feedback in DP, little is known about the proper repetitive cycles of clinical skills training especially in physical examination (PE) training. Methods We drew learning curves and designed a comparative study to find out the optimal number of hands-on practice cycles, an important aspect of DP, in abdominal PE training for medical students. A comparative study was conducted to validate the optimal number of hands-on practice by dividing students into two cohorts including Cohort A (high-frequency hand-on training) and B (low-frequency hand-on training). Results The learning curve study of 16 students exhibited a threshold of four repetitive practices when 81.25% students reached the competence score. A total of 74 students’ final exam scores were collected for analysis. Students in Cohort A (4–5 PEs) scored significantly higher than those in Cohort B (≤3 PEs) (84.41 ± 11.78 vs 76.83 ± 17.51] in the final exam (P = 0.030)). Conclusion High-frequency practice can improve students’ competence of abdominal PE skill. We recommend four cycles of hands-on practice for each student in a training course like PE training.

An increasing number of inflammatory pathologies is associated with IL-1 production downstream of caspases 1 and 11. Here the authors show that graft-versus-host-disease (GvHD) is diminished in mice with genetic or pharmacological ablation of caspase-11, and provide mechanistic insights into the signals leading to caspase-11 activation in GvHD.

Learning assistants (LAs) are peer educators who work alongside faculty to facilitate active learning activities and help students develop conceptual understanding. LAs and LA training programs are becoming increasingly prevalent in science, technology, engineering, and mathematics (STEM) gateway courses in the United States, and research continues to document the positive impacts on students and LAs in LA-facilitated classrooms. While evidence accumulates regarding positive student impact, relatively less work has investigated the ways LAs themselves might also be impacted by their participation in these programs. To improve LA training and student learning in STEM, it is vital that educators better understand the ways the experiences of LAs can promote personal and professional growth as members of the STEM community. To address this gap, we explored the epistemological development of LAs who participated in an LA program (i.e., pedagogy training and classroom practice) at a large, public, teaching-focused university. LAs participated in semi-structured interviews at the beginning and end of the academic term and completed bi-weekly reflections where they described impactful events and challenges. Using qualitative coding, we operationalized Baxter Magolda’s epistemological reflection model to identify the impactful experiences that provoke epistemological development or reorientation. Our findings highlight three impactful experiences that help promote epistemological development for LAs: (i) recognizing the importance of language and listening; (ii) observing more knowledgeable others struggle with content; and (iii) providing students with the “wrong” answer to a question. We argue that these experiences can promote epistemological development in ways that help LAs become more effective in facilitating student learning and, ultimately, more thoughtful members of STEM disciplines. By working to create spaces for LAs to have these impactful experiences in training and preparation, educators can promote epistemological growth in ways that benefit both LAs and the students they serve.

High-mobility group box-1 (HMGB1), a ubiquitous nuclear protein, acts as a late mediator of lethality when released extracellularly during sepsis. The major source of circulating HMGB1 in sepsis is hepatocytes. However, the mechanism of HMGB1 release of hepatocytes during sepsis is not very clear. We have previously shown that bacterial endotoxin [lipopolysaccharide (LPS)] sensing pathways, including Toll-like receptor (TLR)4 and caspase-11, regulate hepatocyte HMGB1 release in response to LPS. Here, we report the novel function of caspase-11 and gasdermin D (GsdmD) in LPS-induced active HMGB1 released from hepatocytes. HMGB1 release during endotoxemia was caspase-11/GsdmD dependent via an active way in vivo and in vitro. Caspase-11/GsdmD was responsible for HMGB1 translocation from nucleus to the cytoplasm via calcium changing-induced phosphorylation of calcium-calmodulin kinase kinase (camkk)β during endotoxemia. Cleaved GsdmD accumulated on the endoplasmic reticulum, suggesting this may lead to calcium leak and intracellular calcium increase. Furthermore, we investigated that exosome was an important pathway for HMGB1 release from hepatocytes; this process was dependent on TLR4, independent of caspase-11 and GsdmD in vivo and in vitro. These findings provide a novel mechanism that TLR4 signaling results in an increase in caspase-11 expression, as well as increased exosome release, while caspase-11/GsdmD activation/cleavage leads to accumulation of HMGB1 in the cytoplasm through a process associated with the release of calcium from the endoplasmic reticulum and camkkβ activation.

Smallholder pig farmers in East Africa report that lack of feed, seasonal feed shortages, quality and cost are key constraints to pig rearing. Commercially prepared pig diets are too expensive and people and pigs compete for food. Smallholder farmers typically feed nutritionally unbalanced diets, resulting in low average daily gain (ADG) and poor farmer profits. Our objective was to compare the ADG of Ugandan pigs fed forage- or silage-based or commercial diets. Ugandan weaner-grower pigs were randomly assigned to forage- or silage-based diets or commercial diet. Pigs were weighed every 3 weeks from 9 to 32 weeks of age. Pen-level ADG and feed conversion were compared across diets using multiple linear regression. The ADG of pigs fed forage- or silage-based diets was lower than those fed commercial diets between 9 and 24 weeks of age (p

Abstract Background Caspase-11, a cytosolic receptor of bacterial endotoxin (lipopolysaccharide: LPS), mediates immune responses and lethality in endotoxemia and experimental sepsis. However, the upstream pathways that regulate caspase-11 activation in endotoxemia and sepsis are not fully understood. The aim of this study is to test whether TIR-domain-containing adapter-inducing interferon-β (TRIF) signaling is critical for caspase-11-dependent immune responses and lethality in endotoxemia. Methods Mice of indicated genotypes were subjected to endotoxemia or cecum ligation and puncture (CLP) and monitored daily by signs of a moribund state for lethality. Serum interleukin (IL)-1α, IL-1β, IL-6 and tumor necrosis factor (TNF) were measured by ELISA. Data were analyzed by using student’s t-test or one-way ANOVA followed by post-hoc Bonferroni test. Survival data were analyzed by using the log-rank test. Results Blockade of type 1 interferon signaling or genetic deletion of TRIF or guanylate-binding proteins (GBPs) prevented caspase-11-dependent immune responses, organ injury and lethality in endotoxemia and experimental sepsis. In vitro, deletion of GBPs blocked cytosolic LPS-induced caspase-11 activation in mouse macrophages. Conclusions These findings demonstrate that TRIF signaling is required for caspase-11-dependent immune responses and lethality in endotoxemia and sepsis, and provide novel mechanistic insights into how LPS induces caspase-11 activation during bacterial infection.

Abstract Background The NLRP3 inflammasome, a cytosolic complex that mediates the maturation of IL-1β and IL-18 as well as the release of high mobility group box 1 (HMGB1), contributes to the lethality of endotoxic shock. Ethyl pyruvate (EP) was previously shown to inhibit HMGB1 release and promote survival during endotoxemia and experimental sepsis. However, the underlying protective mechanism remains elusive. Result EP dose-dependently inhibited the ATP-, nigericin-, alum-, and silica-induced caspase-1 activation and HMGB1 release in mouse macrophages. EP failed to inhibit DNA transfection- or Salmonella Typhimurium-induced caspase-1 activation and HMGB1 release. Mechanistically, EP significantly attenuated mitochondrial damage and cytoplasmic translocation of mitochondrial DNA, a known NLRP3 ligand, without influencing the potassium efflux, the lysosomal rupture or the production of mitochondrial reactive oxygen species (mtROS). Conclusion Ethyl pyruvate acts as a novel NLRP3 inflammasome inhibitor that preserves the integrity of mitochondria during inflammation.

The design of bottom-overhead (or lift-up) buildings is advantageous in improving the thermal environment of high-density cities and enhancing the comfort level of occupants’ activity space on the ground floor. This study aims to investigate the impact of multiple architectural design variables on the ground floor overhead area of slab-like and tower high-rise residential buildings from the perspective of pedestrian-level thermal comfort with ENVI-met simulations and Standard Effective Temperature (SET*) evaluation. The design variables of the 25 tested models include the number of continuously arranged buildings, aspect ratio, overhead form, overhead space height, positions of overhead space enclosures, and openness degree, derived from existing overhead buildings in Chongqing. The results demonstrate that when the number of continuously arranged buildings and the aspect ratio increase, the overhead area has a more comfortable environmental state, while the overhead height is negatively correlated. In addition, when the enclosures are on opposite sides and their openness degree is 0.75–0.5, the area tends to be more comfortable. For slab-like buildings, the thermal comfort of the partial-overhead form is the worst while the semi-overhead form is relatively better. However, the overhead form has no significant impact on the thermal comfort of tower buildings. These findings can provide some suggestions and inspiration for the design of overhead buildings to create a more sustainable and livable microenvironment.

Background/Aims: Renal biopsy is the gold standard to determine the pathologic type of primary nephrotic syndrome, which is critical for diagnosis, choice of treatment and evaluation of prognosis. However, in some cases, renal biopsy cannot be performed. Methods: To explore the possibility of predicting the histology type of primary nephrotic syndrome without the need for biopsy, we trained and validated a machine learning algorithm using data from 222 patients with biopsy-confirmed primary nephrotic syndrome treated at our hospital between May 2008 and January 2016. The model was then tested prospectively on another sample of 63 patients with biopsy-confirmed primary nephrotic syndrome. Results: Overall accuracy of prediction from the retrospective set of 222 patients was 62.2% across all types of nephrotic syndrome. The accuracy of model prediction for the prospectively collected dataset of 63 patients was 61.9%. The algorithm identified 17 of 33 variables as contributing strongly to type of renal pathology. Conclusion: To our knowledge, this is the first such application of machine learning to predict the pathologic type of primary nephrotic syndrome, which may be clinically useful by itself as well as helpful for guiding future efforts at machine learning-based prediction in other disease contexts.

Abstract Background In recent years, predictive models based on machine learning techniques have proven to be feasible and effective in drug discovery. However, to develop such a model, researchers usually have to combine multiple tools and undergo several different steps (e.g., RDKit or ChemoPy package for molecular descriptor calculation, ChemAxon Standardizer for structure preprocessing, scikit-learn package for model building, and ggplot2 package for statistical analysis and visualization, etc.). In addition, it may require strong programming skills to accomplish these jobs, which poses severe challenges for users without advanced training in computer programming. Therefore, an online pipelining platform that integrates a number of selected tools is a valuable and efficient solution that can meet the needs of related researchers. Results This work presents a web-based pipelining platform, called ChemSAR, for generating SAR classification models of small molecules. The capabilities of ChemSAR include the validation and standardization of chemical structure representation, the computation of 783 1D/2D molecular descriptors and ten types of widely-used fingerprints for small molecules, the filtering methods for feature selection, the generation of predictive models via a step-by-step job submission process, model interpretation in terms of feature importance and tree visualization, as well as a helpful report generation system. The results can be visualized as high-quality plots and downloaded as local files. Conclusion ChemSAR provides an integrated web-based platform for generating SAR classification models that will benefit cheminformatics and other biomedical users. It is freely available at: http://chemsar.scbdd.com . Graphical abstract .

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The migration of Pacific salmon is an important part of functioning freshwater ecosystems, but as populations have decreased and ecological conditions have changed, so have migration patterns. Understanding how the environment, and human impacts, change salmon migration behavior requires observing migration at small temporal and spatial scales across large geographic areas. Studying these detailed fish movements is particularly important for one threatened population of Chinook salmon in the Snake River of Idaho whose juvenile behavior may be rapidly evolving in response to dams and anthropogenic impacts. However, exploring movement data sets of large numbers of salmon can present challenges due to the difficulty of visualizing the multivariate, time-series datasets. Previous research indicates that sonification, representing data using sound, has the potential to enhance exploration of multivariate, time-series datasets. We developed sonifications of individual fish movements using a large dataset of salmon otolith microchemistry from Snake River Fall Chinook salmon. Otoliths, a balance and hearing organ in fish, provide a detailed chemical record of fish movements recorded in the tree-like rings they deposit each day the fish is alive. This data represents a scalable, multivariate dataset of salmon movement ideal for sonification. We tested independent listener responses to validate the effectiveness of the sonification tool and mapping methods. The sonifications were presented in a survey to untrained listeners to identify salmon movements with increasingly more fish, with and without visualizations. Our results showed that untrained listeners were most sensitive to transitions mapped to pitch and timbre. Accuracy results were non-intuitive; in aggregate, respondents clearly identified important transitions, but individual accuracy was low. This aggregate effect has potential implications for the use of sonification in the context of crowd-sourced data exploration. The addition of more fish, and visuals, to the sonification increased response time in identifying transitions.

Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables.

The research on complex networks is a hot topic in many fields, among which community detection is a complex and meaningful process, which plays an important role in researching the characteristics of complex networks. Community structure is a common feature in the network. Given a graph, the process of uncovering its community structure is called community detection. Many community detection algorithms from different perspectives have been proposed. Achieving stable and accurate community division is still a non-trivial task due to the difficulty of setting specific parameters, high randomness and lack of ground-truth information. In this paper, we explore a new decision-making method through real-life communication and propose a preferential decision model based on dynamic relationships applied to dynamic systems. We apply this model to the label propagation algorithm and present a Community Detection based on Preferential Decision Model, called CDPD. This model intuitively aims to reveal the topological structure and the hierarchical structure between networks. By analyzing the structural characteristics of complex networks and mining the tightness between nodes, the priority of neighbor nodes is chosen to perform the required preferential decision, and finally the information in the system reaches a stable state. In the experiments, through the comparison of eight comparison algorithms, we verified the performance of CDPD in real-world networks and synthetic networks. The results show that CDPD not only has better performance than most recent algorithms on most datasets, but it is also more suitable for many community networks with ambiguous structure, especially sparse networks.

Using matching and regression analyses, we measure the difference in citations between articles posted to Academia.edu and other articles from similar journals, controlling for field, impact factor, and other variables. Based on a sample size of 31,216 papers, we find that a paper in a median impact factor journal uploaded to Academia.edu receives 16% more citations after one year than a similar article not available online, 51% more citations after three years, and 69% after five years. We also found that articles also posted to Academia.edu had 58% more citations than articles only posted to other online venues, such as personal and departmental home pages, after five years.

The effects of the pathogenic fungus Fusarium oxysporum f. sp. radicis-lycopersici and of the bacterial biocontrol strain Pseudomonas fluorescens WCS365, and of both microbes, on the amounts and composition of root exudate components of tomato plants grown in a gnotobiotic stonewool substrate system were studied. Conditions were selected under which introduction of F. oxysporum f. sp. radicis-lycopersici caused severe foot and root rot, whereas inoculation of the seed with P. fluorescens WCS365 decreased the percentage of diseased plants from 96 to 7%. This is a much better disease control level than was observed in potting soil. Analysis of root exudate revealed that the presence of F. oxysporum f. sp. radicis-lycopersici did not alter the total amount of organic acids, but that the amount of citric acid decreased and that of succinic acid increased compared with the nontreated control. In contrast, in the presence of the P. fluorescens biocontrol strain WCS365, the total amount of organic acid increased, mainly due to a strong increase of the amount of citric acid, whereas the amount of succinic acid decreased dramatically. Under biocontrol conditions, when both microbes are present, the content of succinic acid decreased and the level of citric acid was similar to that in the nontreated control. The amount of sugar was approximately half that of the control sample when either one of the microbes was present alone or when both were present. Analysis of the interactions between the two microbes grown together in sterile tomato root exudate showed that WCS365 inhibited multiplication of F. oxysporum f. sp. radicis-lycopersici, whereas the fungus did not affect the number of CFU of the bacterium.

The influence of stonewool substrate on the exudation of the major soluble carbon nutrients and of the auxin precursor tryptophane for Pseudomonas biocontrol agents was studied. To this end, the composition of the organic acids and sugars, as well that of tryptophane, of axenically collected exudates of seed, seedlings, and roots of tomato, cucumber, and sweet pepper was determined. The major results were as follows. i) The total amount of organic acid is much higher than that of total sugar. ii) Exudation of both organic acids and sugars increases during plant growth. iii) Citric, succinic, and malic acids represent the major organic acids, whereas fructose and glucose are the major sugars. iv) Compared with glass beads as a neutral substrate, stonewool substantially stimulates exudation of organic acids and sugars. v) It appeared that enhanced root-tip-colonizing bacteria isolated previously from the rhizosphere of tomato and cucumber grow much better in minimal medium with citrate as the sole carbon source than other, randomly selected rhizobacteria do. This indicates that the procedure which selects for excellent root-tip colonizers enriches for strains which utilize the major exudate carbon source citrate. vi) The content of L-tryp-tophane, the direct precursor of auxin, is approximately 60-fold higher in seedling exudates of tomato and sweet pepper than in cucumber seedling exudates, indicating a higher possibility of plant growth stimulation after inoculation with auxin-producing rhizobacteria for tomato and sweet pepper crops than for cucumber. However, the biocontrol strain Pseudomonas fluorescens WCS365, which is able to convert tryptophane into auxin, did not stimulate growth of these three crops. In contrast, this strain did stimulate growth of roots of radish, a plant which exudes nine times more tryptophane than tomato does.

Pseudomonas fluorescens PCL1751 is a rod-shaped Gram-negative bacterium isolated from the rhizosphere of a greenhouse-grown tomato plant in Uzbekistan. It controls several plant root diseases caused by Fusarium fungi through the mechanism of competition for nutrients and niches (CNN). This mechanism does not rely on the production of antibiotics, so it avoids the concerns of resistance development and is environmentally safe. Additionally, this bacterium promotes plant growth by alleviating salt stress for its plant host. To investigate the genetic mechanisms that may explain these observations, we determined the complete genome sequence of this bacterium, examined its gene content, and performed comparative genomics analysis with other Pseudomonas strains. The genome of P. fluorescens PCL1751 consisted of one circular chromosome that is 6,143,950 base-pairs (bp) in size; no plasmid was found. The annotation included 19 rRNA, 70 tRNA, and 5,534 protein-coding genes. The gene content analysis identified a large number of genes involved in chemotaxis and motility, colonization of the rhizosphere, siderophore biosynthesis, and osmoprotectant production. In contrast, the pathways involved in the biosynthesis of phytohormones or antibiotics were not found. Comparison with other Pseudomonas genomes revealed extensive variations in their genome size and gene content. The presence and absence of secretion system genes were highly variable. As expected, the synteny conservation among strains decreased as a function of phylogenetic divergence. The integration of prophages appeared to be an important driver for genome rearrangements. The whole-genome gene content analysis of this plant growth-promoting rhizobacterium (PGPR) provided some genetic explanations to its phenotypic characteristics. The extensive and versatile substrate utilization pathways, together with the presence of many genes involved in competitive root colonization, provided further support for the finding that this strain achieves biological control of pathogens through effective competition for nutrients and niches.

Inflammatory bowel disease (IBD) is chronic inflammation of the gastrointestinal tract that affects millions of people worldwide. Although the etiology of IBD is not clear, it is known that products from stressed cells and enteric microbes promote intestinal inflammation. High mobility group box 1 (HMGB1), originally identified as a nuclear DNA binding protein, is a cytokine-like protein mediator implicated in infection, sterile injury, autoimmune disease, and IBD. Elevated levels of HMGB1 have been detected in inflamed human intestinal tissues and in feces of IBD patients and mouse models of colitis. Neutralizing HMGB1 activity by administration of anti-HMGB1 antibodies or HMGB1-specific antagonist improves clinical outcomes in animal models of colitis. Since HMGB1 binds to DNA with high affinity, here we developed a novel strategy to sequester HMGB1 using DNA immobilized on sepharose beads. Screening of DNA-bead constructs revealed that B2 beads, one linear form of DNA conjugated beads, bind HMGB1 with high affinity, capture HMGB1 ex vivo from endotoxin-stimulated RAW 264.7 cell supernatant and from feces of mice with colitis. Oral administration of B2 DNA beads significantly improved body weight, reduced colon injury, and suppressed colonic and circulating cytokine levels in mice with spontaneous colitis (IL-10 knockout) and with dextran sulfate sodium-induced colitis. Thus, DNA beads reduce inflammation by sequestering HMGB1 and may have therapeutic potential for the treatment of IBD.

Previous observations have demonstrated that embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes transgenerational adult onset disease such as male infertility, kidney disease, prostate disease, immune abnormalities and tumor development. The current study investigates genome-wide promoter DNA methylation alterations in the sperm of F3 generation rats whose F0 generation mother was exposed to vinclozolin. A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip) procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. Mass spectrometry bisulfite analysis was used to map the CpG DNA methylation and 16 differential DNA methylation regions were confirmed, while the remainder could not be analyzed due to bisulfite technical limitations. Analysis of these validated regions identified a consensus DNA sequence (motif) that associated with 75% of the promoters. Interestingly, only 16.8% of a random set of 125 promoters contained this motif. One candidate promoter (Fam111a) was found to be due to a copy number variation (CNV) and not a methylation change, suggesting initial alterations in the germline epigenome may promote genetic abnormalities such as induced CNV in later generations. This study identifies differential DNA methylation sites in promoter regions three generations after the initial exposure and identifies common genome features present in these regions. In addition to primary epimutations, a potential indirect genetic abnormality was identified, and both are postulated to be involved in the epigenetic transgenerational inheritance observed. This study confirms that an environmental agent has the ability to induce epigenetic transgenerational changes in the sperm epigenome.