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Generative-AI (GAI) models like ChatGPT are becoming widely discussed and utilized tools in medical education. For example, it can be used to assist with studying for exams, shown capable of passing the USMLE board exams. However, there have been concerns expressed regarding its fair and ethical use. We designed an electronic survey for students across North American medical colleges to gauge their views on and current use of ChatGPT and similar technologies in May, 2023. Overall, 415 students from at least 28 medical schools completed the questionnaire and 96% of respondents had heard of ChatGPT and 52% had used it for medical school coursework. The most common use in pre-clerkship and clerkship phase was asking for explanations of medical concepts and assisting with diagnosis/treatment plans, respectively. The most common use in academic research was for proof reading and grammar edits. Respondents recognized the potential limitations of ChatGPT, including inaccurate responses, patient privacy, and plagiarism. Students recognized the importance of regulations to ensure proper use of this novel technology. Understanding the views of students is essential to crafting workable instructional courses, guidelines, and regulations that ensure the safe, productive use of generative-AI in medical school.

CD8 T cells are the predominant effector cells of adaptive immunity in preventing cytomegalovirus (CMV) multiple-organ disease caused by cytopathogenic tissue infection. The mechanism by which CMV-specific, naïve CD8 T cells become primed and clonally expand is of fundamental importance for our understanding of CMV immune control. For CD8 T-cell priming, two pathways have been identified: direct antigen presentation by infected professional antigen-presenting cells (pAPCs) and antigen cross-presentation by uninfected pAPCs that take up antigenic material derived from infected tissue cells. Studies in mouse models using murine CMV (mCMV) and precluding either pathway genetically or experimentally have shown that, in principle, both pathways can congruently generate the mouse MHC/H-2 class-I-determined epitope-specificity repertoire of the CD8 T-cell response. Recent studies, however, have shown that direct antigen presentation is the canonical pathway when both are accessible. This raised the question of why antigen cross-presentation is ineffective even under conditions of high virus replication thought to provide high amounts of antigenic material for feeding cross-presenting pAPCs. As delivery of antigenic material for cross-presentation is associated with programmed cell death, and as CMVs encode inhibitors of different cell death pathways, we pursued the idea that these inhibitors restrict antigen delivery and thus CD8 T-cell priming by cross-presentation. To test this hypothesis, we compared the CD8 T-cell responses to recombinant mCMVs lacking expression of the apoptosis-inhibiting protein M36 or the necroptosis-inhibiting protein M45 with responses to wild-type mCMV and revertant viruses expressing the respective cell death inhibitors. The data reveal that increased programmed cell death improves CD8 T-cell priming in mice capable of antigen cross-presentation but not in a mutant mouse strain unable to cross-present. These findings strongly support the conclusion that CMV cell death inhibitors restrict the priming of CD8 T cells by antigen cross-presentation.

Enrichment analysis is frequently used in combination with differential expression data to investigate potential commonalities amongst lists of genes and generate hypotheses for further experiments. However, current enrichment analysis approaches on pathways ignore the functional relationships between genes in a pathway, particularly OR logic that occurs when a set of proteins can each individually perform the same step in a pathway. As a result, these approaches miss pathways with large or multiple sets because of an inflation of pathway size (when measured as the total gene count) relative to the number of steps. We address this problem by enriching on step-enabling entities in pathways. We treat sets of protein-coding genes as single entities, and we also weight sets to account for the number of genes in them using the multivariate Fisher's noncentral hypergeometric distribution. We then show three examples of pathways that are recovered with this method and find that the results have significant proportions of pathways not found in gene list enrichment analysis.

BackgroundGammaKnife (GK) and CyberKnife (CK) have been the mainstay stereotactic radiosurgery (SRS) solution for multiple brain metastases (MBM) for several years. Recent technological advancement has seen an increase in single-isocentre C-arm linac-based SRS. This systematic review focuses on dosimetric and geometric insights into contemporary MBM SRS and thereby establish if linac-based SRS has matured to match the mainstay SRS delivery systems.MethodsThe PubMed, Web of Science and Scopus databases were interrogated which yielded 891 relevant articles that narrowed to 20 articles after removing duplicates and applying the inclusion and exclusion criteria. Primary studies which reported the use of SRS for treatment of MBM SRS and reported the technical aspects including dosimetry were included. The review was limited to English language publications from January 2015 to August 2023. Only full-length papers were included in the final analysis. Opinion papers, commentary pieces, letters to the editor, abstracts, conference proceedings and editorials were excluded. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed. The reporting of conformity indices (CI) and gradient indices, V12Gy, monitor units and the impact of translational and rotational shifts were extracted and analysed.ResultsThe single-isocentre technique for MBM dominated recent SRS studies and the most studied delivery platforms were Varian. The C-arm linac-based SRS plan quality and normal brain tissue sparing was comparable to GK and CK and in some cases better. The most used nominal beam energy was 6FFF, and optimised couch and collimator angles could reduce mean normal brain dose by 11.3%. Reduction in volume of the healthy brain receiving a certain dose was dependent on the number and size of the metastases and the relative geometric location. GK and CK required 4.5-8.4 times treatment time compared with linac-based SRS. Rotational shifts caused larger changes in CI in C-arm linac-based single-isocentre SRS.ConclusionC-arm linac-based SRS produced comparable MBM plan quality and the delivery is notably shorter compared to GK and CK SRS.

In recent years, much of the emphasis for transformation of introductory STEM courses has focused on "active learning", and while this approach has been shown to produce more equitable outcomes for students, the construct of "active learning" is somewhat ill-defined and is often used as a "catch-all" that can encompass a wide range of pedagogical techniques. Here we present an alternative approach for how to think about the transformation of STEM courses that focuses instead on what students should know and what they can do with that knowledge. This approach, known as three-dimensional learning (3DL), emerged from the National Academy's "A Framework for K-12 Science Education", which describes a vision for science education that centers the role of constructing productive causal accounts for phenomena. Over the past 10 years, we have collected data from introductory biology, chemistry, and physics courses to assess the impact of such a transformation on higher education courses. Here we report on an analysis of video data of class sessions that allows us to characterize these sessions as active, 3D, neither, or both 3D and active. We find that 3D classes are likely to also involve student engagement (i.e. be active), but the reverse is not necessarily true. That is, focusing on transformations involving 3DL also tends to increase student engagement, whereas focusing solely on student engagement might result in courses where students are engaged in activities that do not involve meaningful engagement with core ideas of the discipline.

Specific interactions of host and parasite genotypes can lead to balancing selection, maintaining genetic diversity within populations. In order to understand the drivers of such specific coevolution, it is necessary to identify the molecular underpinnings of these genotypic interactions. Here, we investigate the genetic basis of resistance in the crustacean host, Daphnia magna, to attachment and subsequent infection by the bacterial parasite, Pasteuria ramosa. We discover a single locus with Mendelian segregation (3:1 ratio) with resistance being dominant, which we call the F locus. We use QTL analysis and fine mapping to localize the F locus to a 28.8-kb region in the host genome, adjacent to a known resistance supergene. We compare the 28.8-kb region in the two QTL parents to identify differences between host genotypes that are resistant versus susceptible to attachment and infection by the parasite. We identify 13 genes in the region, from which we highlight eight biological candidates for the F locus, based on presence/absence polymorphisms and differential gene expression. The top candidates include a fucosyltransferase gene that is only present in one of the two QTL parents, as well as several Cladoceran-specific genes belonging to a large family that is represented in multiple locations of the host genome. Fucosyltransferases have been linked to resistance in previous studies of Daphnia-Pasteuria and other host-parasite systems, suggesting that P. ramosa spore attachment could be mediated by changes in glycan structures on D. magna cuticle proteins. The Cladoceran-specific candidate genes suggest a resistance strategy that relies on gene duplication. Our results add a new locus to a growing genetic model of resistance in the D. magna-P. ramosa system. The identified candidate genes will be used in future functional genetic studies, with the ultimate aim to test for cycles of allele frequencies in natural populations.

Pyrin is a cytosolic immune sensor that nucleates an inflammasome in response to inhibition of RhoA by bacterial virulence factors, triggering the release of inflammatory cytokines, including IL-1β. Gain-of-function mutations in the MEFV gene encoding Pyrin cause autoinflammatory disorders, such as familial Mediterranean fever (FMF) and Pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). To precisely define the role of Pyrin in pathogen detection in human immune cells, we compared initiation and regulation of the Pyrin inflammasome response in monocyte-derived macrophages (hMDM). Unlike human monocytes and murine macrophages, we determined that hMDM failed to activate Pyrin in response to known Pyrin activators Clostridioides difficile (C. difficile) toxins A or B (TcdA or TcdB), as well as the bile acid analogue BAA-473. The Pyrin inflammasome response was enabled in hMDM by prolonged priming with either LPS or type I or II interferons and required an increase in Pyrin expression. Notably, FMF mutations lifted the requirement for prolonged priming for Pyrin activation in hMDM, enabling Pyrin activation in the absence of additional inflammatory signals. Unexpectedly, in the absence of a Pyrin response, we found that TcdB activated the NLRP3 inflammasome in hMDM. These data demonstrate that regulation of Pyrin activation in hMDM diverges from monocytes and highlights its dysregulation in FMF.

Incomplete and absent doses in routine childhood vaccinations are of major concern. Health systems in low- and middle-income countries (LMIC), in particular, often struggle to enable full vaccination of children, which affects their immunity against communicable diseases. Data on child vaccination cards from a cross-sectional primary survey with 1,967 households were used to assess the vaccination status. The association of timely postnatal care (PNC) and the place of delivery with any-dose (at least one dose of each vaccine) and full vaccination of children between 10-20 months in Bihar, India, was investigated. Bivariate and multivariable logistic regression models were used. The vaccines included targeted tuberculosis, hepatitis B, polio, diphtheria/pertussis/tetanus (DPT) and measles. Moreover predictors for perinatal health care uptake were analysed by multivariable logistic regression. Of the 1,011 children with card verification, 47.9% were fully vaccinated. Timely PNC was positively associated with full vaccination (adjusted odds ratio (aOR) 1.48, 95% confidence interval (CI) 1.06-2.08) and with the administration of at least one dose (any-dose) of polio vaccine (aOR 3.37 95% CI 1.79-6.36), hepatitis B/pentavalent vaccine (aOR 2.11 95% CI 1.24-3.59), and DPT/pentavalent vaccine (aOR 2.29 95% CI 1.35-3.88). Additionally, delivery in a public health care facility was positively associated with at least one dose of hepatitis B/pentavalent vaccine administration (aOR 4.86 95% CI 2.97-7.95). Predictors for timely PNC were institutional delivery (public and private) (aOR 2.7 95% CI 1.96-3.72, aOR 2.38 95% CI 1.56-3.64), at least one ANC visit (aOR 1.59 95% CI 1.18-2.15), wealth quintile (Middle aOR 1.57 95% CI 1.02-2.41, Richer aOR 1.51 95% CI 1.01-2.25, Richest aOR 2.06 95% CI 1.28-3.31) and household size (aOR 0.95 95% CI 0.92-0.99). The findings indicate a correlation between childhood vaccination and timely postnatal care. Further, delivery in a public facility correlates with the administration of at least one dose of hepatitis B vaccine and thus impedes zero-dose vaccination. Increasing uptake of timely PNC, encouraging institutional delivery, and improving vaccination services before discharge of health facilities may lead to improved vaccination rates among children.

Incomplete and absent doses in routine childhood vaccinations are of major concern. Health systems in low- and middle-income countries (LMIC), in particular, often struggle to enable full vaccination of children, which affects their immunity against communicable diseases. Data on child vaccination cards from a cross-sectional primary survey with 1,967 households were used to assess the vaccination status. The association of timely postnatal care (PNC) and the place of delivery with any-dose (at least one dose of each vaccine) and full vaccination of children between 10-20 months in Bihar, India, was investigated. Bivariate and multivariable logistic regression models were used. The vaccines included targeted tuberculosis, hepatitis B, polio, diphtheria/pertussis/tetanus (DPT) and measles. Moreover predictors for perinatal health care uptake were analysed by multivariable logistic regression. Of the 1,011 children with card verification, 47.9% were fully vaccinated. Timely PNC was positively associated with full vaccination (adjusted odds ratio (aOR) 1.48, 95% confidence interval (CI) 1.06-2.08) and with the administration of at least one dose (any-dose) of polio vaccine (aOR 3.37 95% CI 1.79-6.36), hepatitis B/pentavalent vaccine (aOR 2.11 95% CI 1.24-3.59), and DPT/pentavalent vaccine (aOR 2.29 95% CI 1.35-3.88). Additionally, delivery in a public health care facility was positively associated with at least one dose of hepatitis B/pentavalent vaccine administration (aOR 4.86 95% CI 2.97-7.95). Predictors for timely PNC were institutional delivery (public and private) (aOR 2.7 95% CI 1.96-3.72, aOR 2.38 95% CI 1.56-3.64), at least one ANC visit (aOR 1.59 95% CI 1.18-2.15), wealth quintile (Middle aOR 1.57 95% CI 1.02-2.41, Richer aOR 1.51 95% CI 1.01-2.25, Richest aOR 2.06 95% CI 1.28-3.31) and household size (aOR 0.95 95% CI 0.92-0.99). The findings indicate a correlation between childhood vaccination and timely postnatal care. Further, delivery in a public facility correlates with the administration of at least one dose of hepatitis B vaccine and thus impedes zero-dose vaccination. Increasing uptake of timely PNC, encouraging institutional delivery, and improving vaccination services before discharge of health facilities may lead to improved vaccination rates among children.

Many humans live in large, complex political centers, composed of multi-scalar communities including neighborhoods and districts. Both today and in the past, neighborhoods form a fundamental part of cities and are defined by their spatial, architectural, and material elements. Neighborhoods existed in ancient centers of various scales, and multiple methods have been employed to identify ancient neighborhoods in archaeological contexts. However, the use of different methods for neighborhood identification within the same spatiotemporal setting results in challenges for comparisons within and between ancient societies. Here, we focus on using a single method—combining Average Nearest Neighbor (ANN) and Kernel Density (KD) analyses of household groups—to identify potential neighborhoods based on clusters of households at 23 ancient centers across the Maya Lowlands. While a one-size-fits all model does not work for neighborhood identification everywhere, the ANN/KD method provides quantifiable data on the clustering of ancient households, which can be linked to environmental zones and urban scale. We found that centers in river valleys exhibited greater household clustering compared to centers in upland and escarpment environments. Settlement patterns on flat plains were more dispersed, with little discrete spatial clustering of households. Furthermore, we categorized the ancient Maya centers into discrete urban scales, finding that larger centers had greater variation in household spacing compared to medium-sized and smaller centers. Many larger political centers possess heterogeneity in household clustering between their civic-ceremonial cores, immediate hinterlands, and far peripheries. Smaller centers exhibit greater household clustering compared to larger ones. This paper quantitatively assesses household clustering among nearly two dozen centers across the Maya Lowlands, linking environment and urban scale to settlement patterns. The findings are applicable to ancient societies and modern cities alike; understanding how humans form multi-scalar social groupings, such as neighborhoods, is fundamental to human experience and social organization.

The Lower Paleolithic Late Acheulian in the Levant marks a fascinating chapter in human cultural and biological evolution. Nevertheless, many aspects of the Late Acheulian are still undeciphered, hindered by the complex nature of each site on the one hand, a scarcity of wide, multidisciplinary studies on the other, and by difficulties in obtaining absolute chronology for this timeframe. Therefore, subjects such as human subsistence strategies and modes of adaptation, regional diversity, and the possible existence and nature of interactions between hominin groups are largely understudied. The discovery and study of Jaljulia, a large-scale Late Acheulian site at the central Coastal Plain, Israel, add valuable insights to the research of this chapter in human history. Considered to represent recurrent occupations at a favored, water and flint-rich setting, the site has provided extensive lithic assemblages obtained from several localities. Absolute chronology places the human activity on-site at roughly 500–300 ky (and possibly even later), which is suggested to be divided into several main occupation phases. Geomorphological and sedimentological analyses show a change in environmental conditions, from aeolian sand deposition and overlying Hamra soil during the Middle Pleistocene to high energy fluvial regime which transported large gravels in a north-south paleo-channel. Wetland environments, correlating to the human activity on site, developed later due to higher sea levels and a coastline shifts to the eastward, which caused a blockage of the Yarkon stream corridor to the sea by marine sand. In this paper we present results of the study of the site, including geomorphological formation and post-depositional processes, absolute chronology, lithic and faunal analyses. The site’s extensive lithic assemblages are currently under study and future investigations are expected to shed more light on the technological nature of Late Acheulian Jaljulia.

The Lower Paleolithic Late Acheulian in the Levant marks a fascinating chapter in human cultural and biological evolution. Nevertheless, many aspects of the Late Acheulian are still undeciphered, hindered by the complex nature of each site on the one hand, a scarcity of wide, multidisciplinary studies on the other, and by difficulties in obtaining absolute chronology for this timeframe. Therefore, subjects such as human subsistence strategies and modes of adaptation, regional diversity, and the possible existence and nature of interactions between hominin groups are largely understudied. The discovery and study of Jaljulia, a large-scale Late Acheulian site at the central Coastal Plain, Israel, add valuable insights to the research of this chapter in human history. Considered to represent recurrent occupations at a favored, water and flint-rich setting, the site has provided extensive lithic assemblages obtained from several localities. Absolute chronology places the human activity on-site at roughly 500-300 ky (and possibly even later), which is suggested to be divided into several main occupation phases. Geomorphological and sedimentological analyses show a change in environmental conditions, from aeolian sand deposition and overlying Hamra soil during the Middle Pleistocene to high energy fluvial regime which transported large gravels in a north-south paleo-channel. Wetland environments, correlating to the human activity on site, developed later due to higher sea levels and a coastline shifts to the eastward, which caused a blockage of the Yarkon stream corridor to the sea by marine sand. In this paper we present results of the study of the site, including geomorphological formation and post-depositional processes, absolute chronology, lithic and faunal analyses. The site's extensive lithic assemblages are currently under study and future investigations are expected to shed more light on the technological nature of Late Acheulian Jaljulia.

Over the past 20 years, 3 highly pathogenic human coronaviruses (HCoVs) have emerged-Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and, most recently, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)-demonstrating that coronaviruses (CoVs) pose a serious threat to human health and highlighting the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycles. Herein, we conducted 2 independent genome-wide CRISPR/Cas-9 knockout (KO) screens to identify MERS-CoV and HCoV-229E host dependency factors (HDFs) required for HCoV replication in the human Huh7 cell line. Top scoring genes were further validated and assessed in the context of MERS-CoV and HCoV-229E infection as well as SARS-CoV and SARS-CoV-2 infection. Strikingly, we found that several autophagy-related genes, including TMEM41B, MINAR1, and the immunophilin FKBP8, were common host factors required for pan-CoV replication. Importantly, inhibition of the immunophilin protein family with the compounds cyclosporine A, and the nonimmunosuppressive derivative alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures, which recapitulate the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrated that these factors constitute potential targets for therapeutic intervention by clinically approved drugs.

Background As the prevalence of hypercholesterolemia is increasing in low- and middle-income countries (LMICs), detailed evidence is urgently needed to guide the response of health systems to this epidemic. This study sought to quantify unmet need for hypercholesterolemia care among adults in 35 LMICs. Methods and findings We pooled individual-level data from 129,040 respondents aged 15 years and older from 35 nationally representative surveys conducted between 2009 and 2018. Hypercholesterolemia care was quantified using cascade of care analyses in the pooled sample and by region, country income group, and country. Hypercholesterolemia was defined as (i) total cholesterol (TC) ≥240 mg/dL or self-reported lipid-lowering medication use and, alternatively, as (ii) low-density lipoprotein cholesterol (LDL-C) ≥160 mg/dL or self-reported lipid-lowering medication use. Stages of the care cascade for hypercholesterolemia were defined as follows: screened (prior to the survey), aware of diagnosis, treated (lifestyle advice and/or medication), and controlled (TC Conclusions Cascade performance was poor across all stages, indicating large unmet need for hypercholesterolemia care in this sample of LMICs—calling for greater policy and research attention toward this cardiovascular disease (CVD) risk factor and highlighting opportunities for improved prevention of CVD. Maja Marcus and colleagues use nationally-representative surveys conducted between 2009 and 2018 to investigate the unmet need for hypercholesterolemia care in 35 low- and middle-income countries. Author summary Why was this study done? The prevalence of hypercholesterolemia is increasing in low- and middle-income countries (LMICs). Evidence on how well health systems address this rising hypercholesterolemia burden is limited. Nationally representative studies analyzing care at the individual level across a larger number of LMICs are largely missing. What did the researchers do and find? We analyzed access to hypercholesterolemia care using pooled data from 35 nationally representative, individual-level surveys from LMICs. We found a prevalence of high total cholesterol (TC) of 7.1% (95% CI: 6.8% to 7.4%) and a high low-density lipoprotein cholesterol (LDL-C) prevalence of 7.5% (95% CI: 7.1% to 7.9%) in this set of countries. Using a cascade of care approach, we found that 43% (95% CI: 40% to 45%) of individuals with high TC and 47% (95% CI: 44% to 50%) with high LDL-C ever had their cholesterol measured prior to the survey. About 31% (95% CI: 29% to 33%) and 36% (95% CI: 33% to 38%) were aware of their diagnosis; 29% (95% CI: 28% to 31%) and 33% (95% CI: 31% to 36%) were treated; 7% (95% CI: 6% to 9%) and 19% (95% CI: 18% to 21%) were controlled. Using modified Poisson regression models, we found that access to care was significantly associated with a range of sociodemographic characteristics, such as high education and old age, as well as with the presentation of other cardiovascular disease (CVD) risk factors, such as comorbid diabetes or hypertension and a high body mass index. What do these findings mean? We found large unmet need for hypercholesterolemia care in this sample of LMICs. This calls for greater policy and research attention toward this CVD risk factor. High-performing countries, such as Sri Lanka, Costa Rica, Iran, and Morocco, may highlight policy opportunities for improved prevention of CVD. The main limitations of this study are a potential recall bias in self-reported information on received health services as well as diminished comparability due to varying survey years and varying lipid guideline application across country and clinical settings.

BackgroundAs the prevalence of hypercholesterolemia is increasing in low- and middle-income countries (LMICs), detailed evidence is urgently needed to guide the response of health systems to this epidemic. This study sought to quantify unmet need for hypercholesterolemia care among adults in 35 LMICs.Methods and findingsWe pooled individual-level data from 129,040 respondents aged 15 years and older from 35 nationally representative surveys conducted between 2009 and 2018. Hypercholesterolemia care was quantified using cascade of care analyses in the pooled sample and by region, country income group, and country. Hypercholesterolemia was defined as (i) total cholesterol (TC) ≥240 mg/dL or self-reported lipid-lowering medication use and, alternatively, as (ii) low-density lipoprotein cholesterol (LDL-C) ≥160 mg/dL or self-reported lipid-lowering medication use. Stages of the care cascade for hypercholesterolemia were defined as follows: screened (prior to the survey), aware of diagnosis, treated (lifestyle advice and/or medication), and controlled (TC ConclusionsCascade performance was poor across all stages, indicating large unmet need for hypercholesterolemia care in this sample of LMICs-calling for greater policy and research attention toward this cardiovascular disease (CVD) risk factor and highlighting opportunities for improved prevention of CVD.

Oxytocin/vasopressin-related neuropeptides are highly conserved and play major roles in regulating social behavior across vertebrates. However, whether their insect orthologue, inotocin, regulates the behavior of social groups remains unknown. Here, we show that in the clonal raider ant Ooceraea biroi, individuals that perform tasks outside the nest have higher levels of inotocin in their brains than individuals of the same age that remain inside the nest. We also show that older ants, which spend more time outside the nest, have higher inotocin levels than younger ants. Inotocin thus correlates with the propensity to perform tasks outside the nest. Additionally, increasing inotocin pharmacologically increases the tendency of ants to leave the nest. However, this effect is contingent on age and social context. Pharmacologically treated older ants have a higher propensity to leave the nest only in the presence of larvae, whereas younger ants seem to do so only in the presence of pupae. Our results suggest that inotocin signaling plays an important role in modulating behaviors that correlate with age, such as social foraging, possibly by modulating behavioral response thresholds to specific social cues. Inotocin signaling thereby likely contributes to behavioral individuality and division of labor in ant societies.

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (33°C and 37°C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host innate immune response dynamics, we investigated the impact of temperature on SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33°C rather than 37°C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses induced by SARS-CoV-2 that were inversely proportional to its replication efficiency at 33°C or 37°C. These data provide crucial insight on pivotal virus-host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies.

The world's most severe thunderstorm asthma event occurred in Melbourne, Australia on 21 November 2016, coinciding with the peak of the grass pollen season. The aetiological role of thunderstorms in these events is thought to cause pollen to rupture in high humidity conditions, releasing large numbers of sub-pollen particles (SPPs) with sizes very easily inhaled deep into the lungs. The humidity hypothesis was implemented into a three-dimensional atmospheric model and driven by inputs from three meteorological models. However, the mechanism could not explain how the Melbourne event occurred as relative humidity was very low throughout the atmosphere, and most available grass pollen remained within 40 m of the surface. Our tests showed humidity induced rupturing occurred frequently at other times and would likely lead to recurrent false alarms if used in a predictive capacity. We used the model to investigate a range of other possible pollen rupturing mechanisms which could have produced high concentrations of SPPs in the atmosphere during the storm. The mechanisms studied involve mechanical friction from wind gusts, electrical build up and discharge incurred during conditions of low relative humidity, and lightning strikes. Our results suggest that these mechanisms likely operated in tandem with one another, but the lightning method was the only mechanism to generate a pattern in SPPs following the path of the storm. If humidity induced rupturing cannot explain the 2016 Melbourne event, then new targeted laboratory studies of alternative pollen rupture mechanisms would be of considerable value to help constrain the parameterisation of the pollen rupturing process.

Research-based teaching practices can improve student learning outcomes in a variety of complex educational environments. The implementation of learner-centered teaching practices in STEM can both benefit from or be constrained by different factors related to individual instructors and the teaching environment. Additionally, we know little of how the instructional climate varies across institutions and how this climate affects teaching practices. Our study sought to examine the relative importance of environmental influences and individual characteristics on learner-centered teaching practices across institutions. We also assessed differences in our study population and departmental climate for 35 US higher education institutions across the country. We found that self-efficacy in teaching and professional development exert a strong influence on faculty teaching practices in biology. While departmental climate did not emerge as a significant predictor of teaching practices, there was consistently low support for teaching, and institution size was negatively correlated with leadership and evaluation of effective teaching. We also found that intensive professional development programs, such as the Faculty Institutes for Reforming Science Teaching IV program, may prepare instructors to teach learner-centered courses in different collegial teaching climates. Our results suggest that through cultivating self-efficacy and participating in iterative professional development, instructors can implement effective teaching practices in a variety of institutional environments.

Electronic mental health services (eMHSs) offer additional options for the dissemination of psychological interventions for university students. Still, many university students are reluctant to use eMHSs. Narrative messages may help increase the awareness and acceptance of quality-approved programs. However, little is known about the usefulness of narrative messages to improve attitudes towards eMHSs. In this experiment, we thus aimed to explore in how far different ways of targeting information to students affect their attitudes towards eMHSs for stress prevention and therapy, and to identify potential determinants of attitude change. N = 451 students (Mean = 32.6 years, SD = 10.2, 75% female, 7% with eMHS experience) were randomly assigned to one of four study arms involving information designed to induce different levels of perceived similarity. While the active control condition only received general information (arm 1, "information only", n = 116), the other experimental arms were additionally exposed to testimonials on specific eMHSs either addressing an unspecified audience (arm 2, n = 112), employees (arm 3, n = 115) or working university students (arm 4, n = 108). Two-way ANOVA revealed no impact of information on the alteration of attitudes towards eMHSs for stress coping (d = 0.20). Only a small effect of target-group specific testimonials on attitudes towards online therapies was identified at post-intervention (d = 0.29). Regression analyses demonstrated significant influences of source credibility and perceived similarity on attitudes for preventative eMHSs (ps

Maya archaeologists have long been interested in understanding ancient diets because they provide information about broad-scale economic and societal transformations. Though paleodietary studies have primarily relied on stable carbon (δ13C) and nitrogen (δ15N) isotopic analyses of human bone collagen to document the types of food people consumed, stable sulfur (δ34S) isotope analysis can potentially provide valuable data to identify terrestrial, freshwater, or marine/coastal food sources, as well as determine human mobility and migration patterns. Here we assess applications of δ34S for investigating Maya diet and migration through stable isotope analyses of human bone collagen (δ13C, δ15N, and δ34S) from 114 individuals from 12 sites in the Eastern Maya lowlands, temporally spanning from the Late Preclassic (300 BCE-300 CE) through Colonial periods (1520-1800 CE). Results document a diet dominated by maize and other terrestrial resources, consistent with expectations for this inland region. Because δ34S values reflect local geology, our analyses also identified recent migrants to the Eastern lowlands who had non-local δ34S signatures. When combined with other indicators of mobility (e.g., strontium isotopes), sulfur isotopic data provide a powerful tool to investigate movement across a person's lifespan. This study represents the largest examination of archaeological human δ34S isotope values for the Maya lowlands and provides a foundation for novel insights into both subsistence practices and migration.

BackgroundCardiovascular diseases are leading causes of death, globally, and health systems that deliver quality clinical care are needed to manage an increasing number of people with risk factors for these diseases. Indicators of preparedness of countries to manage cardiovascular disease risk factors (CVDRFs) are regularly collected by ministries of health and global health agencies. We aimed to assess whether these indicators are associated with patient receipt of quality clinical care.Methods and findingsWe did a secondary analysis of cross-sectional, nationally representative, individual-patient data from 187,552 people with hypertension (mean age 48.1 years, 53.5% female) living in 43 low- and middle-income countries (LMICs) and 40,795 people with diabetes (mean age 52.2 years, 57.7% female) living in 28 LMICs on progress through cascades of care (condition diagnosed, treated, or controlled) for diabetes or hypertension, to indicate outcomes of provision of quality clinical care. Data were extracted from national-level World Health Organization (WHO) Stepwise Approach to Surveillance (STEPS), or other similar household surveys, conducted between July 2005 and November 2016. We used mixed-effects logistic regression to estimate associations between each quality clinical care outcome and indicators of country development (gross domestic product [GDP] per capita or Human Development Index [HDI]); national capacity for the prevention and control of noncommunicable diseases ('NCD readiness indicators' from surveys done by WHO); health system finance (domestic government expenditure on health [as percentage of GDP], private, and out-of-pocket expenditure on health [both as percentage of current]); and health service readiness (number of physicians, nurses, or hospital beds per 1,000 people) and performance (neonatal mortality rate). All models were adjusted for individual-level predictors including age, sex, and education. In an exploratory analysis, we tested whether national-level data on facility preparedness for diabetes were positively associated with outcomes. Associations were inconsistent between indicators and quality clinical care outcomes. For hypertension, GDP and HDI were both positively associated with each outcome. Of the 33 relationships tested between NCD readiness indicators and outcomes, only two showed a significant positive association: presence of guidelines with being diagnosed (odds ratio [OR], 1.86 [95% CI 1.08-3.21], p = 0.03) and availability of funding with being controlled (OR, 2.26 [95% CI 1.09-4.69], p = 0.03). Hospital beds (OR, 1.14 [95% CI 1.02-1.27], p = 0.02), nurses/midwives (OR, 1.24 [95% CI 1.06-1.44], p = 0.006), and physicians (OR, 1.21 [95% CI 1.11-1.32], p < 0.001) per 1,000 people were positively associated with being diagnosed and, similarly, with being treated; and the number of physicians was additionally associated with being controlled (OR, 1.12 [95% CI 1.01-1.23], p = 0.03). For diabetes, no positive associations were seen between NCD readiness indicators and outcomes. There was no association between country development, health service finance, or health service performance and readiness indicators and any outcome, apart from GDP (OR, 1.70 [95% CI 1.12-2.59], p = 0.01), HDI (OR, 1.21 [95% CI 1.01-1.44], p = 0.04), and number of physicians per 1,000 people (OR, 1.28 [95% CI 1.09-1.51], p = 0.003), which were associated with being diagnosed. Six countries had data on cascades of care and nationwide-level data on facility preparedness. Of the 27 associations tested between facility preparedness indicators and outcomes, the only association that was significant was having metformin available, which was positively associated with treatment (OR, 1.35 [95% CI 1.01-1.81], p = 0.04). The main limitation was use of blood pressure measurement on a single occasion to diagnose hypertension and a single blood glucose measurement to diagnose diabetes.ConclusionIn this study, we observed that indicators of country preparedness to deal with CVDRFs are poor proxies for quality clinical care received by patients for hypertension and diabetes. The major implication is that assessments of countries' preparedness to manage CVDRFs should not rely on proxies; rather, it should involve direct assessment of quality clinical care.

Targeted cancer therapies are powerful alternatives to chemotherapies or can be used complementary to these. Yet, the response to targeted treatments depends on a variety of factors, including mutations and expression levels, and therefore their outcome is difficult to predict. Here, we develop a mechanistic model of gastric cancer to study response and resistance factors for cetuximab treatment. The model captures the EGFR, ERK and AKT signaling pathways in two gastric cancer cell lines with different mutation patterns. We train the model using a comprehensive selection of time and dose response measurements, and provide an assessment of parameter and prediction uncertainties. We demonstrate that the proposed model facilitates the identification of causal differences between the cell lines. Furthermore, our study shows that the model provides predictions for the responses to different perturbations, such as knockdown and knockout experiments. Among other results, the model predicted the effect of MET mutations on cetuximab sensitivity. These predictive capabilities render the model a basis for the assessment of gastric cancer signaling and possibly for the development and discovery of predictive biomarkers.

BACKGROUND:European guidelines recommend the use of the Systematic COronary Risk Evaluation (SCORE) to assess 10-year risk of fatal cardiovascular events in people aged 40 to 65. The SCORE Older Persons (SCORE OP, 5-year and 10-year versions) was recently developed for people aged 65 or older. We assessed the performance of these risk scores in predicting fatal cardiovascular events in older persons in Berlin. METHODS AND FINDINGS:Data from the Berlin Initiative Study (BIS), a prospective, population-based study of older persons recruited from a German public health insurance company database were used. 1,657 participants aged 70 or older without reported previous myocardial infarction were included. We assessed calibration by comparing predicted risks to observed (for 5-year versions, 5y) or projected (for 10-year versions) probabilities. During follow-up (median: 4.8 years), 118 cardiovascular deaths occurred. The calibration assessment of the SCORE OP-H 5y and SCORE OP-L 5y equations revealed 2.1- and 1.5-fold overestimation. Comparing 10-year versions, the SCORE OP showed better discrimination ability compared to the SCORE (C-indices of around 0.80 compared to 0.72) and the SCORE for high-risk regions showed the best calibration (chi-square = 29.68). The SCORE OP overestimated the true risk; 519 and 677 events were predicted using the low-risk and high-risk region SCORE OP equations compared to 397 to 399 events projected based on BIS follow-up data (predicted/actual ratios of 1.3 and 1.7). CONCLUSIONS:Given the low transportability of the SCORE OP observed in our population, we caution against its use in routine clinical practice until further information is available to avoid possible overtreatment among older persons in Berlin.

[This corrects the article DOI: 10.1371/journal.pone.0231097.].

The importance of improving STEM education is of perennial interest, and to this end, the education community needs ways to characterize transformation efforts. Three-dimensional learning (3DL) is one such approach to transformation, in which core ideas of the discipline, scientific practices, and crosscutting concepts are combined to support student development of disciplinary expertise. We have previously reported on an approach to the characterization of assessments, the Three-Dimensional Learning Assessment Protocol (3D-LAP), that can be used to identify whether assessments have the potential to engage students in 3DL. Here we present the development of a companion, the Three-Dimensional Learning Observation Protocol (3D-LOP), an observation protocol that can reliably distinguish between instruction that has potential for engagement with 3DL and instruction that does not. The 3D-LOP goes beyond other observation protocols, because it is intended not only to characterize the pedagogical approaches being used in the instructional environment, but also to identify whether students are being asked to engage with scientific practices, core ideas, and crosscutting concepts. We demonstrate herein that the 3D-LOP can be used reliably to code for the presence of 3DL; further, we present data that show the utility of the 3D-LOP in differentiating between instruction that has the potential to promote 3DL from instruction that does not. Our team plans to continue using this protocol to evaluate outcomes of instructional transformation projects. We also propose that the 3D-LOP can be used to support practitioners in developing curricular materials and selecting instructional strategies to promote engagement in three-dimensional instruction.

Blended therapy is a new approach combining advantages of face-to-face psychotherapy and Internet- and mobile-based interventions. Acceptance is a fundamental precondition for its implementation. The aim of this study was to assess 1) the acceptance of psychotherapists towards blended therapy, 2) the effectiveness of an acceptance facilitating intervention (AFI) on psychotherapists' acceptance towards blended therapy and 3) to identify potential effect moderators. Psychotherapists (N = 284) were randomly assigned to a control (CG) or an intervention group (IG). The IG received a short video showing an example of blended therapy, the CG an attention placebo video. Both groups received a reliable online questionnaire assessing acceptance, effort expectancy, performance expectancy, facilitating conditions, social influence and internet anxiety. Between group differences were examined using t-tests and Mann-Whitney tests. Exploratory analysis was conducted to identify moderators. Psychotherapists in CG showed mixed baseline acceptance towards blended therapy (low = 40%, moderate = 33%, high = 27%). IG showed significantly higher acceptance compared to CG (d = .27, pone-sided = .029; low = 24%, moderate = 47%, high = 30%). Bootstrapped confidence intervals were overlapping. Performance expectancy (d = .35), effort expectancy (d = .44) and facilitating conditions (d = .28) were significantly increased (p < .05). No effects on social influence and internet anxiety were found (p>.05). Exploratory analysis indicated psychodynamic oriented psychotherapists profiting particularly from the AFI. Blended therapy is a promising approach to improve healthcare. Psychotherapists show mixed acceptance, which might be improvable by AFIs, particularly in subpopulations of initially rather skeptical psychotherapists. Forthcoming studies should extend the present study by shifting focus from attitudes to the impact of different forms of AFIs on uptake.

Enhancers are powerful and versatile agents of cell-type specific gene regulation, which are thought to play key roles in human disease. Enhancers are short DNA elements that function primarily as clusters of transcription factor binding sites that are spatially coordinated to regulate expression of one or more specific target genes. These regulatory connections between enhancers and target genes can therefore be characterized as enhancer-gene links that can affect development, disease, and homeostatic cellular processes. Despite their implication in disease and the establishment of cell identity during development, most enhancer-gene links remain unknown. Here we introduce a new, publicly accessible database of predicted enhancer-gene links, PEREGRINE. The PEREGRINE human enhancer-gene links interactive web interface incorporates publicly available experimental data from ChIA-PET, eQTL, and Hi-C assays across 78 cell and tissue types to link 449,627 enhancers to 17,643 protein-coding genes. These enhancer-gene links are made available through the new Enhancer module of the PANTHER database and website where the user may easily access the evidence for each enhancer-gene link, as well as query by target gene and enhancer location.

BACKGROUND:The prevalence of diabetes is increasing rapidly in low- and middle-income countries (LMICs), urgently requiring detailed evidence to guide the response of health systems to this epidemic. In an effort to understand at what step in the diabetes care continuum individuals are lost to care, and how this varies between countries and population groups, this study examined health system performance for diabetes among adults in 28 LMICs using a cascade of care approach. METHODS AND FINDINGS:We pooled individual participant data from nationally representative surveys done between 2008 and 2016 in 28 LMICs. Diabetes was defined as fasting plasma glucose ≥ 7.0 mmol/l (126 mg/dl), random plasma glucose ≥ 11.1 mmol/l (200 mg/dl), HbA1c ≥ 6.5%, or reporting to be taking medication for diabetes. Stages of the care cascade were as follows: tested, diagnosed, lifestyle advice and/or medication given ("treated"), and controlled (HbA1c < 8.0% or equivalent). We stratified cascades of care by country, geographic region, World Bank income group, and individual-level characteristics (age, sex, educational attainment, household wealth quintile, and body mass index [BMI]). We then used logistic regression models with country-level fixed effects to evaluate predictors of (1) testing, (2) treatment, and (3) control. The final sample included 847,413 adults in 28 LMICs (8 low income, 9 lower-middle income, 11 upper-middle income). Survey sample size ranged from 824 in Guyana to 750,451 in India. The prevalence of diabetes was 8.8% (95% CI: 8.2%-9.5%), and the prevalence of undiagnosed diabetes was 4.8% (95% CI: 4.5%-5.2%). Health system performance for management of diabetes showed large losses to care at the stage of being tested, and low rates of diabetes control. Total unmet need for diabetes care (defined as the sum of those not tested, tested but undiagnosed, diagnosed but untreated, and treated but with diabetes not controlled) was 77.0% (95% CI: 74.9%-78.9%). Performance along the care cascade was significantly better in upper-middle income countries, but across all World Bank income groups, only half of participants with diabetes who were tested achieved diabetes control. Greater age, educational attainment, and BMI were associated with higher odds of being tested, being treated, and achieving control. The limitations of this study included the use of a single glucose measurement to assess diabetes, differences in the approach to wealth measurement across surveys, and variation in the date of the surveys. CONCLUSIONS:The study uncovered poor management of diabetes along the care cascade, indicating large unmet need for diabetes care across 28 LMICs. Performance across the care cascade varied by World Bank income group and individual-level characteristics, particularly age, educational attainment, and BMI. This policy-relevant analysis can inform country-specific interventions and offers a baseline by which future progress can be measured.

Urothelial cancer (UC) is one of the most common cancers in Europe and is also one of the costliest to treat. When first line therapies show initial success, around 50% of cancers relapse and proceed to metastasis. In this study we assessed the Protein inhibitor of activated signal transducers and activators of transcription (PIAS)1 as a potential therapeutic target in urothelial cancer. PIAS1 is a key regulator of STAT1 signalling and may be implicated in carcinogenesis. In contrast to other cancer types PIAS1 protein expression is not significantly different in malignant areas of UC specimens compared to non-malignant tissue. In addition, we found that down-regulation and overexpression of PIAS1 had no effect on the viability or colony forming ability of tested cell lines. Whilst other studies of PIAS1 suggest an important biological role in cancer, this study shows that PIAS1 has no influence on reducing the cytotoxic effects of Cisplatin or cell recovery after DNA damage induced by irradiation. Taken together, these in vitro data demonstrate that PIAS1 is not a promising therapeutic target in UC cancer as previously shown in different entities such as prostate cancer (PCa).

The therapeutic options for advanced gastric cancer are still limited. Several drugs targeting the epidermal growth factor receptor family have been developed. So far, the HER2 antibody trastuzumab is the only drug targeting the HER-family that is available to gastric cancer patients. The pan-HER inhibitor afatinib is currently investigated in clinical trials and shows promising results in cell culture experiments and patient-derived xenograft (PDX) models. However, some cell lines do not respond to afatinib treatment. The determination of resistance factors in these cell lines can help to find the best treatment option for gastric cancer patients. In this study, we analyzed the role of MET as a resistance factor for afatinib therapy in a gastric cancer cell line. MET expression in afatinib-resistant MET-amplified Hs746T cells was reduced by means of siRNA transfection. The effects of MET knockdown on signal transduction, cell proliferation and motility were examined. In addition to the manual assessment of cell motility, a computational motility analysis involving parameters such as (approximate) average speed, displacement entropy or radial effectiveness was realized. Moreover, the impact of afatinib was compared between MET knockdown cells and control cells. MET knockdown in Hs746T cells resulted in impaired signal transduction and reduced cell proliferation and motility. Moreover, the afatinib resistance of Hs746T cells was reversed after MET knockdown. Therefore, the amplification of MET is confirmed as a resistance factor in gastric cancer cells. Whether MET is a useful resistance marker for afatinib therapy or other HER-targeting drugs in patients should be investigated in clinical trials.

BACKGROUND:Face-to-face brief interventions for problem drinking are effective, but they have found limited implementation in routine care and the community. Internet-based interventions could overcome this treatment gap. We investigated effectiveness and moderators of treatment outcomes in internet-based interventions for adult problem drinking (iAIs). METHODS AND FINDINGS:Systematic searches were performed in medical and psychological databases to 31 December 2016. A one-stage individual patient data meta-analysis (IPDMA) was conducted with a linear mixed model complete-case approach, using baseline and first follow-up data. The primary outcome measure was mean weekly alcohol consumption in standard units (SUs, 10 grams of ethanol). Secondary outcome was treatment response (TR), defined as less than 14/21 SUs for women/men weekly. Putative participant, intervention, and study moderators were included. Robustness was verified in three sensitivity analyses: a two-stage IPDMA, a one-stage IPDMA using multiple imputation, and a missing-not-at-random (MNAR) analysis. We obtained baseline data for 14,198 adult participants (19 randomised controlled trials [RCTs], mean age 40.7 [SD = 13.2], 47.6% women). Their baseline mean weekly alcohol consumption was 38.1 SUs (SD = 26.9). Most were regular problem drinkers (80.1%, SUs 44.7, SD = 26.4) and 19.9% (SUs 11.9, SD = 4.1) were binge-only drinkers. About one third were heavy drinkers, meaning that women/men consumed, respectively, more than 35/50 SUs of alcohol at baseline (34.2%, SUs 65.9, SD = 27.1). Post-intervention data were available for 8,095 participants. Compared with controls, iAI participants showed a greater mean weekly decrease at follow-up of 5.02 SUs (95% CI -7.57 to -2.48, p < 0.001) and a higher rate of TR (odds ratio [OR] 2.20, 95% CI 1.63-2.95, p < 0.001, number needed to treat [NNT] = 4.15, 95% CI 3.06-6.62). Persons above age 55 showed higher TR than their younger counterparts (OR = 1.66, 95% CI 1.21-2.27, p = 0.002). Drinking profiles were not significantly associated with treatment outcomes. Human-supported interventions were superior to fully automated ones on both outcome measures (comparative reduction: -6.78 SUs, 95% CI -12.11 to -1.45, p = 0.013; TR: OR = 2.23, 95% CI 1.22-4.08, p = 0.009). Participants treated in iAIs based on personalised normative feedback (PNF) alone were significantly less likely to sustain low-risk drinking at follow-up than those in iAIs based on integrated therapeutic principles (OR = 0.52, 95% CI 0.29-0.93, p = 0.029). The use of waitlist control in RCTs was associated with significantly better treatment outcomes than the use of other types of control (comparative reduction: -9.27 SUs, 95% CI -13.97 to -4.57, p < 0.001; TR: OR = 3.74, 95% CI 2.13-6.53, p < 0.001). The overall quality of the RCTs was high; a major limitation included high study dropout (43%). Sensitivity analyses confirmed the robustness of our primary analyses. CONCLUSION:To our knowledge, this is the first IPDMA on internet-based interventions that has shown them to be effective in curbing various patterns of adult problem drinking in both community and healthcare settings. Waitlist control may be conducive to inflation of treatment outcomes.

Phosphine is the only general use fumigant for the protection of stored grain, though its long-term utility is threatened by the emergence of highly phosphine-resistant pests. Given this precarious situation, it is essential to identify factors, such as stress preconditioning, that interfere with the efficacy of phosphine fumigation. We used Caenorhabditis elegans as a model organism to test the effect of pre-exposure to heat and cold shock, UV and gamma irradiation on phosphine potency. Heat shock significantly increased tolerance to phosphine by 3-fold in wild-type nematodes, a process that was dependent on the master regulator of the heat shock response, HSF-1. Heat shock did not, however, increase the resistance of a strain carrying the phosphine resistance mutation, dld-1(wr4), and cold shock did not alter the response to phosphine of either strain. Pretreatment with the LD50 of UV (18 J cm-2) did not alter phosphine tolerance in wild-type nematodes, but the LD50 (33 J cm-2) of the phosphine resistant strain (dld-1(wr4)) doubled the level of resistance. In addition, exposure to a mild dose of gamma radiation (200 Gy) elevated the phosphine tolerance by ~2-fold in both strains.

BACKGROUND:Improving the accuracy and precision of predictive analytics for temporal trends in crime necessitates a good understanding of the how exogenous variables, such as weather and holidays, impact crime. METHODS:We examine 5.7 million reported incidents of crime that occurred in the City of Chicago between 2001 to 2014. Using linear regression methods, we examine the temporal relationship of the crime incidents to weather, holidays, school vacations, day-of-week, and paydays. We correct the data for dominant sources of auto-correlation, and we then employ bootstrap methods for model selection. Importantly for the aspect of predictive analytics, we validate the predictive capabilities of our model on an independent data set; model validation has been almost universally overlooked in the literature on this subject. RESULTS:We find significant dependence of crime on time of year, holidays, and weekdays. We find that dependence of aggressive crime on temperature depends on the hour of the day, and whether it takes place outside or inside. In addition, unusually hot/cold days are associated with unusual fluctuations upwards/downwards in crimes of aggression, respectively, regardless of the time of year. CONCLUSIONS:Including holidays, festivals, and school holiday periods in crime predictive analytics software can improve the accuracy and precision of temporal predictions. We also find that including forecasts for temperature may significantly improve short term crime forecasts for the temporal trends in many types of crime, particularly aggressive crime.

Electroporation of zygotes represents a rapid alternative to the elaborate pronuclear injection procedure for CRISPR/Cas9-mediated genome editing in mice. However, current protocols for electroporation either require the investment in specialized electroporators or corrosive pre-treatment of zygotes which compromises embryo viability. Here, we describe an easily adaptable approach for the introduction of specific mutations in C57BL/6 mice by electroporation of intact zygotes using a common electroporator with synthetic CRISPR/Cas9 components and minimal technical requirement. Direct comparison to conventional pronuclear injection demonstrates significantly reduced physical damage and thus improved embryo development with successful genome editing in up to 100% of living offspring. Hence, our novel approach for Easy Electroporation of Zygotes (EEZy) allows highly efficient generation of CRISPR/Cas9 transgenic mice while reducing the numbers of animals required.

[This corrects the article DOI: 10.1371/journal.pone.0185317.].

Patients suffering from Epidermodysplasia verruciformis (EV), a rare inherited skin disease, display a particular susceptibility to persistent infection with cutaneous genus beta-human papillomavirus (beta-HPV), such as HPV type 8. They have a high risk to develop non-melanoma skin cancer at sun-exposed sites. In various models evidence is emerging that cutaneous HPV E6 proteins disturb epidermal homeostasis and support carcinogenesis, however, the underlying mechanisms are not fully understood as yet. In this study we demonstrate that microRNA-203 (miR-203), a key regulator of epidermal proliferation and differentiation, is strongly down-regulated in HPV8-positive EV-lesions. We provide evidence that CCAAT/enhancer-binding protein α (C/EBPα), a differentiation-regulating transcription factor and suppressor of UV-induced skin carcinogenesis, directly binds the miR-203 gene within its hairpin region and thereby induces miR-203 transcription. Our data further demonstrate that the HPV8 E6 protein significantly suppresses this novel C/EBPα/mir-203-pathway. As a consequence, the miR-203 target ΔNp63α, a proliferation-inducing transcription factor, is up-regulated, while the differentiation factor involucrin is suppressed. HPV8 E6 specifically down-regulates C/EBPα but not C/EBPβ expression at the transcriptional level. As shown in knock-down experiments, C/EBPα is regulated by the acetyltransferase p300, a well-described target of cutaneous E6 proteins. Notably, p300 bound significantly less to the C/EBPα regulatory region in HPV8 E6 expressing keratinocytes than in control cells as demonstrated by chromatin immunoprecipitation. In situ analysis confirmed congruent suprabasal expression patterns of C/EBPα and miR-203 in non-lesional skin of EV-patients. In HPV8-positive EV-lesions both factors are potently down-regulated in vivo further supporting our in vitro data. In conclusion our study has unraveled a novel p300/C/EBPα/mir-203-dependent mechanism, by which the cutaneous HPV8 E6 protein may expand p63-positive cells in the epidermis of EV-patients and disturbs fundamental keratinocyte functions. This may drive HPV-mediated pathogenesis and may potentially also pave the way for skin carcinogenesis in EV-patients.

Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. We fine-map one locus associated with D. magna resistance to P. ramosa and genetically characterize two haplotypes of the Pasteuria resistance (PR-) locus using de novo genome and transcriptome sequencing. Sequence comparison of PR-locus haplotypes finds dramatic structural polymorphisms between PR-locus haplotypes including a large portion of each haplotype being composed of non-homologous sequences resulting in haplotypes differing in size by 66 kb. The high divergence of PR-locus haplotypes suggest a history of multiple, diverse and repeated instances of structural mutation events and restricted recombination. Annotation of the haplotypes reveals striking differences in gene content. In particular, a group of glycosyltransferase genes that is present in the susceptible but absent in the resistant haplotype. Moreover, in natural populations, we find that the PR-locus polymorphism is associated with variation in resistance to different P. ramosa genotypes, pointing to the PR-locus polymorphism as being responsible for the matching-allele interactions that have been previously described for this system. Our results conclusively identify a genetic basis for the matching-allele interaction observed in a coevolving host-parasite system and provide a first insight into its molecular basis.

The newly recognized Konservat-Lagerstätte of Ettling (Bavaria), field site of the Jura-Museum Eichstätt (JME), is unique among Late Jurassic plattenkalk basins (Solnhofen region) in its abundant, extremely well preserved fossil vertebrates, almost exclusively fishes. We report actinopterygians (ginglymodins, pycnodontiforms, halecomorphs, aspidorynchiforms, "pholidophoriforms," teleosts); turtles; and non-vertebrates (echinoderms, arthropods, brachiopods, mollusks, jellyfish, sponges, biomats, plants) in a current faunal list. Ettling has yielded several new fish species (Bavarichthys incognitus; Orthogonikleithrus hoelli; Aspidorhynchus sanzenbacheri; Macrosemimimus fegerti). Upper and lower Ettling strata differ in faunal content, with the lower dominated by the small teleost Orthogonikleithrus hoelli (absent from the upper layers, where other prey fishes, Leptolepides sp. and Tharsis sp., occur instead). Pharyngeal and stomach contents of Ettling fishes provide direct evidence that Orthogonikleithrus hoelli was a primary food source during early Ettling times. Scarcity of ammonites and absence of vampyromorph coleoids at Ettling differ markedly from the situation at other nearby localities in the region (e.g., Eichstätt, Painten, Schamhaupten, the Mörnsheim beds), where they are more common. Although the exact biochronological age of Ettling remains uncertain (lack of suitable index fossils), many Ettling fishes occur in other plattenkalk basins of Germany (e.g., Kelheim) and France (Cerin) dated as Late Kimmeridgian to Early Tithonian (eigeltingense horizon), suggesting a comparable geologic age. The Ettling deposits represent an independent basin within the larger Upper Jurassic "Solnhofen Archipelago", a shallow subtropical sea containing scattered islands, sponge-microbial and coral reefs, sandbars, and deeper basins on a vast carbonate platform along the northern margin of the Tethys Ocean.

Chemokines and their receptors are pivotal for the trafficking of leukocytes during immune responses, and host defense. However, immune cell migration also contributes to a wide variety of autoimmune and chronic inflammatory diseases. Compelling evidence suggests that both CXCR3 and CCR6 chemokine receptors play crucial roles in the migration of pathological Th1 and Th17 cells during the course of certain inflammatory diseases. The use of two or more receptors by pathogenic cells may explain why targeting of individual receptors has proven disappointing in the clinic. We therefore hypothesized that simultaneous targeting of both CXCR3 and CCR6 with a bispecific antibody (BsAb) might result in decreased chemotaxis and/or specific depletion of pro-inflammatory T cell subsets. In this study, we designed and characterized a fully humanized BsAb. We show that the BsAb binds to both chemokine receptors, as demonstrated by Flow Cytometry and Surface Plasmon Resonance analysis. Furthermore, we demonstrate that the BsAb effectively blocks cell chemotaxis and induces specific antibody-dependent cell-mediated cytotoxicity (ADCC) in vitro. Therefore, we propose that dual targeting of CXCR3 and CCR6 with a fully humanized BsAb may display a potent interventional approach for the treatment of inflammatory and autoimmune diseases.

Sex differences in the development of the normal heart and the prevalence of cardiomyopathies have been reported. The molecular basis of these differences remains unclear. Sex differences in the human heart might be related to patterns of gene expression. Recent studies have shown that sex specific differences in gene expression in tissues including the brain, kidney, skeletal muscle, and liver. Similar data is limited for the heart. Herein we address this issue by analyzing donor and post-mortem adult human heart samples originating from 46 control individuals to study whole-genome gene expression in the human left ventricle. Using data from the genotype tissue expression (GTEx) project, we compared the transcriptome expression profiles of male and female hearts. We found that genes located on sex chromosomes were the most abundant ones among the sexually dimorphic genes. The majority of differentially expressed autosomal genes were those involved in the regulation of inflammation, which has been found to be an important contributor to left ventricular remodeling. Specifically, genes on autosomal chromosomes encoding chemokines with inflammatory functions (e.g. CCL4, CX3CL1, TNFAIP3) and a gene that regulates adhesion of immune cells to the endothelium (e.g., VCAM1) were identified with sex-specific expression levels. This study underlines the relevance of sex as an important modifier of cardiac gene expression. These results have important implications in the understanding of the differences in the physiology of the male and female heart transcriptome and how they may lead to different sex specific difference in human cardiac health and its control.

Histidyl tRNA Synthetase (HARS) is a member of the aminoacyl tRNA synthetase (ARS) family of enzymes. This family of 20 enzymes is responsible for attaching specific amino acids to their cognate tRNA molecules, a critical step in protein synthesis. However, recent work highlighting a growing number of associations between ARS genes and diverse human diseases raises the possibility of new and unexpected functions in this ancient enzyme family. For example, mutations in HARS have been linked to two different neurological disorders, Usher Syndrome Type IIIB and Charcot Marie Tooth peripheral neuropathy. These connections raise the possibility of previously undiscovered roles for HARS in metazoan development, with alterations in these functions leading to complex diseases. In an attempt to establish Danio rerio as a model for studying HARS functions in human disease, we characterized the Danio rerio hars gene and compared it to that of human HARS. Using a combination of bioinformatics, molecular biology, and cellular approaches, we found that while the human genome encodes separate genes for cytoplasmic and mitochondrial HARS protein, the Danio rerio genome encodes a single hars gene which undergoes alternative splicing to produce the respective cytoplasmic and mitochondrial versions of Hars. Nevertheless, while the HARS genes of humans and Danio differ significantly at the genomic level, we found that they are still highly conserved at the amino acid level, underscoring the potential utility of Danio rerio as a model organism for investigating HARS function and its link to human diseases in vivo.

Genetic manipulation of the deadly malaria parasite Plasmodium falciparum remains challenging, but the rise of CRISPR/Cas9-based genome editing tools is increasing the feasibility of altering this parasite's genome in order to study its biology. Of particular interest is the investigation of drug targets and drug resistance mechanisms, which have major implications for fighting malaria. We present a new method for introducing drug resistance mutations in P. falciparum without the use of plasmids or the need for cloning homologous recombination templates. We demonstrate this method by introducing edits into the sodium efflux channel PfATP4 by transfection of a purified CRISPR/Cas9-guide RNA ribonucleoprotein complex and a 200-nucleotide single-stranded oligodeoxynucleotide (ssODN) repair template. Analysis of whole genome sequencing data with the variant-finding program MinorityReport confirmed that only the intended edits were made, and growth inhibition assays confirmed that these mutations confer resistance to the antimalarial SJ733. The method described here is ideally suited for the introduction of mutations that confer a fitness advantage under selection conditions, and the novel finding that an ssODN can function as a repair template in P. falciparum could greatly simplify future editing attempts regardless of the nuclease used or the delivery method.

Parent report is commonly used to assess language and attention in children for research and clinical purposes. It is therefore important to understand the convergent validity of parent-report tools in comparison to direct assessments of language and attention. In particular, cultural and linguistic background may influence this convergence. In this study a group of six- to eight-year old children (N = 110) completed direct assessments of language and attention and their parents reported on the same areas. Convergence between assessment types was explored using correlations. Possible influences of ethnicity (Hispanic or non-Hispanic) and of parent report language (English or Spanish) were explored using hierarchical linear regression. Correlations between parent report and direct child assessments were significant for both language and attention, suggesting convergence between assessment types. Ethnicity and parent report language did not moderate the relationships between direct child assessments and parent report tools for either attention or language.

The Golden Gate strategy entails the use of type IIS restriction enzymes, which cut outside of their recognition sequence. It enables unrestricted design of unique DNA fragments that can be readily and seamlessly recombined. Successfully employed in other synthetic biology applications, we demonstrate its advantageous use to engineer a biocatalyst. Hot-spots for mutations were individuated in three distinct regions of Candida antarctica lipase A (Cal-A), the biocatalyst chosen as a target to demonstrate the versatility of this recombination method. The three corresponding gene segments were subjected to the most appropriate method of mutagenesis (targeted or random). Their straightforward reassembly allowed combining products of different mutagenesis methods in a single round for rapid production of a series of diverse libraries, thus facilitating directed evolution. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by development of a general, automated method for visual discrimination of the hydrolysis of varied substrates by whole cells.

INTRODUCTION:One of the main obstacles in the widespread application of gene therapeutic approaches is the necessity for efficient and safe transfection methods. For the introduction of small oligonucleotide gene therapeutics into a target cell, nanoparticle-based methods have been shown to be highly effective and safe. While immune cells are a most interesting target for gene therapy, transfection might influence basic immune functions such as cytokine expression and proliferation, and thus positively or negatively affect therapeutic intervention. Therefore, we investigated the effects of nanoparticle-mediated transfection such as polyethylenimine (PEI) or magnetic beads on immune cell proliferation. METHODS:Human adherent and non-adherent PBMCs were transfected by various methods (e.g. PEI, Lipofectamine® 2000, magnetofection) and stimulated. Proliferation was measured by lymphocyte transformation test (LTT). Cell cycle stages as well as expression of proliferation relevant genes were analyzed. Additionally, the impact of nanoparticles was investigated in vivo in a murine model of the severe systemic immune disease GvHD (graft versus host disease). RESULTS:The proliferation of primary immune cells was influenced by nanoparticle-mediated transfection. In particular in the case of magnetic beads, proliferation inhibition coincided with short-term cell cycle arrest and reduced expression of genes relevant for immune cell proliferation. Notably, proliferation inhibition translated into beneficial effects in a murine GvHD model with animals treated with PEI-nanoparticles showing increased survival (pPEI = 0.002) most likely due to reduced inflammation. CONCLUSION:This study shows for the first time that nanoparticles utilized for gene therapeutic transfection are able to alter proliferation of immune cells and that this effect depends on the type of nanoparticle. For magnetic beads, this was accompanied by temporary cell cycle arrest. Notably, in GvHD this nonspecific anti-proliferative effect might contribute to reduced inflammation and increased survival.

Alterations of brain morphology in Crohn's disease have been reported, but data is scarce and heterogenous and the possible impact of disease predisposition on brain development is unknown. Assuming a systemic course of the disease, brain involvement seems more probable in presence of extraintestinal manifestations, but this question has not yet been addressed. The present study examined the relationship between Crohn's disease and brain structure and focused on the connection with extraintestinal manifestations and markers of brain development.In a pilot study, brains of 15 patients with Crohn's disease (of which 9 had a history of extraintestinal manifestations, i.e. arthritis, erythema nodosum and primary sclerosing cholangitis) were compared to matched healthy controls using high resolution magnetic resonance imaging. Patients and controls were tested for depression, fatigue and global cognitive function. Cortical thickness, surface area and folding were determined via cortical surface modeling.The overall group comparison (i.e. all patients vs. controls) yielded no significant results. In the patient subgroup with extraintestinal manifestations, changes in cortical area and folding, but not thickness, were identified: Patients showed elevated cortical surface area in the left middle frontal lobe (p

Many calls to improve science education in college and university settings have focused on improving instructor pedagogy. Meanwhile, science education at the K-12 level is undergoing significant changes as a result of the emphasis on scientific and engineering practices, crosscutting concepts, and disciplinary core ideas. This framework of "three-dimensional learning" is based on the literature about how people learn science and how we can help students put their knowledge to use. Recently, similar changes are underway in higher education by incorporating three-dimensional learning into college science courses. As these transformations move forward, it will become important to assess three-dimensional learning both to align assessments with the learning environment, and to assess the extent of the transformations. In this paper we introduce the Three-Dimensional Learning Assessment Protocol (3D-LAP), which is designed to characterize and support the development of assessment tasks in biology, chemistry, and physics that align with transformation efforts. We describe the development process used by our interdisciplinary team, discuss the validity and reliability of the protocol, and provide evidence that the protocol can distinguish between assessments that have the potential to elicit evidence of three-dimensional learning and those that do not.