Miracle-dz/UniFAR-FTUs huggingface dataset:
Beyond serosurveys: Human biology and the measurement of SARS‐Cov‐2 antibodies

Coronavirus disease 2019 (COVID-19) has emerged as a deadly clinical disease. The virus that causes COVID-19, severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), is readily transmitted in the community, where it is having devastating social and economic impacts. Yet our understanding of SARS and COVID-19 is derived primarily from studying the most severe cases in clinical and hospital settings. A complementary, field-based approach is desperately needed, and human biologists are well-positioned to make important contributions to our understanding of which individuals, and communities, are most vulnerable and why. Much has been said about shortcomings in the roll out ofSARS-CoV-2 testing and how it has frustrated efforts to identify cases and isolate individuals who are shedding virus. Less has been said about the opportunities that testing provides for a wide range of research applications. In this commentary, we describe antibody testing and how human biologists can use it to inform our understanding of the pandemic, and to address questions of longstanding interest regarding the causes and consequences of human biological variation.
A Distracted Scientist: The Life and Contributions of John Senders

Objective To provide an evaluative and personal overview of the life and contributions of Professor John Senders and to introduce this Special Issue dedicated to his memory. Background John Senders made many profound contributions to HF/E. These various topics are exemplified by the range of papers which compose the Special Issue. Collectively, these works document and demonstrate the impact of his many valuable research works. Method The Special Issue serves to summarize Senders’ collective body of work as can be extracted from archival sources. This introductory paper recounts a series of remembrances derived from personal relationships, as well as the products of cooperative investigative research. Results This collective evaluative process documents Senders’ evident and deserved status in the highest pantheon of HF/E pioneers. It records his extraordinary life, replete with accounts of his insights and joie de vivre in exploring and explaining the world which surrounded him. Applications Senders’ record of critical contributions provides the example, par excellence, of the successful and fulfilling life in science. It encourages all, both researchers and practitioners alike, in their own individual search for excellence.
The global progress of soil-transmitted helminthiases control in 2020 and World Health Organization targets for 2030

Soil-transmitted helminth (STH) infections are the most widespread of the neglected tropical diseases, primarily affecting marginalized populations in low- and middle-income countries. More than one billion people are currently infected with STHs. For the control of these infections, the World Health Organization (WHO) recommends an integrated approach, which includes access to appropriate sanitation, hygiene education, and preventive chemotherapy (i.e., large-scale, periodic distribution of anthelmintic drugs). Since 2010, WHO has coordinated two large donations of benzimidazoles to endemic countries. Thus far, more than 3.3 billion benzimidazole tablets have been distributed in schools for the control of STH infections, resulting in an important reduction in STH-attributable morbidity in children, while additional tablets have been distributed for the control of lymphatic filariasis. This paper (i) summarizes the progress of global STH control between 2008 to 2018 (based on over 690 reports submitted by endemic countries to WHO); (ii) provides regional and country details on preventive chemotherapy coverage; and (iii) indicates the targets identified by WHO for the next decade and the tools that should be developed to attain these targets. The main message is that STH-attributable morbidity can be averted with evidence-informed program planning, implementation, and monitoring. Caution will still need to be exercised in stopping control programs to avoid any rebound of prevalence and loss of accrued morbidity gains. Over the next decade, with increased country leadership and multi-sector engagement, the goal of eliminating STH infections as a public health problem can be achieved.
Targeting MAPK Signaling in Hepatocellular Carcinoma - Implications for Cell Fate, Microenvironment and Immune Recognition

Hepatocellular carcinoma (HCC) is one of the most lethal tumors worldwide. So far, the only treatment option for unresectable HCC is the multikinase inhibitor sorafenib, an inhibitor of the Raf/MEK/ERK (MAPK) signaling pathway, which is one of the major pathways implicated in HCC. Although HCC cannot be cured by sorafenib treatment, targeting the MAPK pathway may be a promising strategy for HCC therapy. In order to improve HCC treatment, it is of particular importance to understand the action of sorafenib in more detail. Therefore, a comprehensive analysis of its effects was performed in HCC cells and tissue and compared to specific inhibitors of the MAPK pathway. In my thesis, the following aspects could be demonstrated: 1.Both, Sorafenib and MEK-specific inhibitors repressed the MAPK signaling pathway, but had partially opposite effects on other signaling pathways like Akt signaling. As a consequence, HCC cell numbers were reduced after sorafenib and MEK inhibitor treatment, but cell division was mainly inhibited by sorafenib and to a low extent by the MEK inhibitors. In contrast, apoptosis was stronger induced by the MEK inhibitors, but differences were observed between the cell lines. This suggests that in HCC besides the MAPK pathway other signaling pathways play an important role and need to be targeted in addition to the MAPK pathway. 2.HCC cell lines expressed a variety of surface molecules which are associated with tumor progression. In addition, they secreted several chemokines and growth factors which favor tumorigenesis and angiogenesis. Inhibition of the MAPK pathway modulated both surface molecule expression and secretion of several chemokines and growth factors, whereby, tumor progression is inhibited. 3.NK cells are supposed to be important for fighting against HCC, but in HCC tumor tissue, NK cells were almost absent. There, the microenvironment was altered with an increase of several chemokines and angiogenic factors. These alterations might account for the decreased numbers of NK cells. In vitro treatment of resected HCC tissue with sorafenib resulted in a substantial decrease in the concentration of these increased factors. This indicates that alterations of the microenvironment might be also induced by sorafenib in HCC patients and, thereby, affecting recruitment of immune cells, NK cells in particular, into the tumor tissue.
Gingival tissue autophagy pathway gene expression profiles in periodontitis and aging.

OBJECTIVE We hypothesized that autophagy-related genes will be differentially expressed in periodontitis, suggesting an impaired gingival autophagic response associated with disease. BACKGROUND Autophagy is a cellular physiologic mechanism to maintain tissue homeostasis, while deficient autophagic responses increase inflammation and susceptibility to infection. METHODS Rhesus monkeys [<3 years to 23 years of age (n = 34)] were examined for periodontal health and naturally occurring periodontitis. Gingival tissues samples were obtained from healthy or diseased sites, total RNA was isolated, and the Rhesus Gene Chip 1.0 ST (Affymetrix) was used for gene expression analysis of 150 autophagy-related genes. RESULTS Comparison of expression levels with adult healthy tissues demonstrated a rather limited number of individual genes that were significantly different across the age-groups. In contrast, with periodontitis in the adults and aged animals, about 15% of the genes were significantly increased or decreased. The differences were reflected in the mTOR complex (5/12), ULK1/ATG1 complex (5/9), PI3K complex (5/21), ATG9 complex (2/7), ATG12 conjugation/LC3 lipidation (7/22), and lysosome fusion/vesicle degradation [LF/VD (5/10)] activities within the broader autophagic pathway. The genes most greatly altered in gingival tissues of naturally occurring periodontitis were identified in the ATG12 and LF/VD pathways that approximated 50% of the genes in each of those categories. While healthy gingival aging did not appear to reflect altered autophagy gene expression, substantial differences were noted with periodontitis irrespective of the age of the animals. Future studies into the role of autophagy in periodontitis and could offer potential new therapeutic strategies to prevent and/or treat periodontal disease.
Online Crowdsourcing as a Quasi-Experimental Method for Collecting Data on the Perpetration of Alcohol-Related Partner Aggression

Cross-sectional survey, prospective, and experimental data have been evaluated to better understand the role of alcohol as a contributing cause of intimate partner aggression. Laboratory-based alcohol administration studies provide controlled data regarding causality, but the use of this methodology lacks ecological validity and has been hampered by rigorous procedural and financial demands. Online crowdsourcing is an emerging pseudoexperimental methodology with low costs, rapid data collection, access to diverse populations, greater ecological validity, and the potential to facilitate prolific research to supplement the chronic scarcity of experimental data. The current rapid review first summarizes prior methodological approaches to investigating the proximal influence of alcohol on partner aggression, then reviews prior crowdsourcing research in the disparate areas of alcohol and partner aggression, then describes aggression paradigms that may be readily adapted to online administration. We conclude by introducing recommendations for future quasi-experimental research investigating alcohol-related partner aggression research using the online crowdsourcing methodology. Initial evidence suggests that online crowdsourcing may yield appropriate samples and that existing paradigms may be adapted to rapidly, efficiently, and ethically supplement experimental alcohol-related partner aggression research.
Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis

The study of differential gene expression patterns through RNA-Seq comprises a routine task in the daily lives of molecular bioscientists, who produce vast amounts of data requiring proper management and analysis. Despite widespread use, there are still no widely accepted golden standards for the normalization and statistical analysis of RNA-Seq data, and critical biases, such as gene lengths and problems in the detection of certain types of molecules, remain largely unaddressed. Stimulated by these unmet needs and the lack of in-depth research into the potential of combinatorial methods to enhance the analysis of differential gene expression, we had previously introduced the PANDORA P-value combination algorithm while presenting evidence for PANDORA's superior performance in optimizing the tradeoff between precision and sensitivity. In this article, we present the next generation of the algorithm along with a more in-depth investigation of its capabilities to effectively analyze RNA-Seq data. In particular, we show that PANDORA-reported lists of differentially expressed genes are unaffected by biases introduced by different normalization methods, while, at the same time, they comprise a reliable input option for downstream pathway analysis. Additionally, PANDORA outperforms other methods in detecting differential expression patterns in certain transcript types, including long non-coding RNAs.
Neuroanatomy of transgender persons in a Non‐Western population and improving reliability in clinical neuroimaging

Although the neuroanatomy of transgender persons is slowly being charted, findings are presently discrepant. Moreover, the major body of work has focused on Western populations. One important factor is the issue of power and low signal‐to‐noise (SNR) ratio in neuroimaging studies of rare study populations including endocrine or neurological patient groups. The present study focused on the structural neuroanatomy of a Non‐Western (Iranian) sample of 40 transgender men (TM), 40 transgender women (TW), 30 cisgender men (CM), and 30 cisgender women (CW), while assessing whether the reliability of findings across structural anatomical measures including gray matter volume (GMV), cortical surface area (CSA), and cortical thickness (CTh) could be increased by using two back‐to‐back within‐session structural MRI scans. Overall, findings in transgender persons were more consistent with sex assigned at birth in GMV and CSA, while no group differences emerged for CTh. Repeated measures analysis also indicated that having a second scan increased SNR in all regions of interest, most notably bilateral frontal poles, pre‐ and postcentral gyri and putamina. The results suggest that a simple time and cost‐effective measure to improve SNR in rare clinical populations with low prevalence rates is a second anatomical scan when structural MRI is of interest.
Measurements show that marginal wells are a disproportionate source of methane relative to production

ABSTRACT Oil and natural gas wells are a prominent source of the greenhouse gas methane (CH4), but most measurements are from newer, high producing wells. There are nearly 700,000 marginal “stripper” wells in the US, which produce less than 15 barrels of oil equivalent (BOE) d−1. We made direct measurements of CH4 and volatile organic carbon (VOC) emissions from marginal oil and gas wells in the Appalachian Basin of southeastern Ohio, all producing < 1 BOE d−1. Methane and VOC emissions followed a skewed distribution, with many wells having zero or low emissions and a few wells responsible for the majority of emissions. The average CH4 emission rate from marginal wells was 128 g h−1 (median: 18 g h−1; range: 0– 907 g h−1). Follow-up measurements at five wells indicated high emissions were not episodic. Some wells were emitting all or more of the reported gas produced at each well, or venting gas from wells with no reported gas production. Measurements were made from wellheads only, not tanks, so our estimates may be conservative. Stochastic processes such as maintenance may be the main driver of emissions. Marginal wells are a disproportionate source of CH4 and VOCs relative to oil and gas production. We estimate that oil and gas wells in this lowest production category emit approximately 11% of total annual CH4 from oil and gas production in the EPA greenhouse gas inventory, although they produce about 0.2% of oil and 0.4% of gas in the US per year. Implications: Low producing marginal wells are the most abundant type of oil and gas well in the United States, and a surprising number of them are venting all or more of their reported produced gas to the atmosphere. This makes marginal wells a disproportionate greenhouse gas emissions source compared to their energy return, and a good target for environmental mitigation.
Association of the long fluoroscopy time with factors in contemporary primary percutaneous coronary interventions

Background Since the long fluoroscopy time in primary PCI for ST-segment elevation myocardial infarction (STEMI) could be an indicator of delayed reperfusion, it should be important to recognize which types of lesions require longer fluoroscopy-time in primary PCI. The purpose of this study was to investigate the association of the long fluoroscopy-time with clinical factors in primary percutaneous coronary interventions (PCI). Methods A total of 539 patients who underwent primary PCI were divided into the conventional fluoroscopy-time group (Q1-Q4: n = 434) and the long fluoroscopy-time group (Q5: n = 105) according to the quintile of the total fluoroscopy time in primary PCI. Univariate and multivariate logistic regression analyses were performed to find associations between clinical variables and the long fluoroscopy-time. Results In univariate logistic regression analysis, prevalence of diabetes mellitus, hemodialysis, and previous CABG were significantly associated with the long fluoroscopy-time. In addition, complex lesion characteristics such as lesion length, lesion angle, tortuosity, and calcification were associated with the long fluoroscopy-time. In multivariable logistic regression analysis, lesion length [per 10 mm incremental: odds ratio (OR) 1.751, 95% confidence interval (CI) 1.397–2.195, P<0.001], moderate-excessive tortuosity (vs. mild tortuosity: OR 4.006, 95% CI 1.498–10.715, P = 0.006), and moderate to severe calcification (vs. none-mild calcification: OR 1.865, 95% CI 1.107–3.140, P = 0.019) were significantly associated with the long fluoroscopy-time. Conclusions In primary PCI for STEMI, diffuse long lesion, tortuosity, and moderate-severe calcification were associated with the long fluoroscopy-time. These complex features require special attention to reduce reperfusion time in primary PCI.
Updates on defining and detecting diarrheagenic Escherichia coli pathotypes

Purpose of review Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize diarrheagenic Escherichia coli (DEC) pathotype definitions and discuss existing and emerging molecular, genomic, and gut microbiome methods to detect, define, and study DEC pathotypes. Recent findings DEC pathotypes are currently diagnosed by molecular detection of unique virulence genes. However, some pathotypes have defied coherent molecular definitions because of imperfect gene targets, and pathotype categories are complicated by hybrid strains and isolation of pathotypes from asymptomatic individuals. Recent progress toward more efficient, sensitive, and multiplex DEC pathotype detection has been made using emerging PCR-based technologies. Genomics and gut microbiome detection methods continue to advance rapidly and are contributing to a better understanding of DEC pathotype diversity and functional potential. Summary DEC pathotype categorizations and detection methods are useful but imperfect. The implementation of molecular and sequence-based methods and well designed epidemiological studies will continue to advance understanding of DEC pathotypes. Additional emphasis is needed on sequencing DEC genomes from regions of the world where they cause the most disease and from the pathotypes that cause the greatest burden of disease globally.
A Study on Genetic Variability, Character Association and Path Co-Efficient Analysis on Morphological and Yield Attributing Characters of Taro (Colocasia esculenta (L.) Schott)

The study investigated genotypic and phenotypic co-efficients of variation, heritability, genetic advance at 5% selection intensity and in percentage of population mean of nine characters (plant height, leaf number, length and width of leaf lamina, number and weight of cormels per plant, weight of corm per plant, dry matter percentage in the tubers and tuber yield per from 14 cultivars of taro [Colocasia esculenta (L.) Schott]). Results indicated highest genotypic co-efficient of variation for dry matter percentage (47.91), which was 95.78% of the phenotypic co-efficient of variation, whereas tuber yield per plant showed the widest range (819.37). Number of cormels per plant and dry matter percentage ehibited considerably higher heritability (84.90% and 91.70%, respectively) and genetic advance (81.19 and 79.00, respectively), indicating the potentiality of selection for improvement of such characters. These two characters were found to be positively correlated to tuber yield per plant. Path analysis revealed that weight of cormels per plant possessed the highest direct effect on tuber yield, indicating the importance of selection based on this character to increase tuber yield per plant.
Colony sizes, roost use and foraging ecology of Hipposideros diadema reginae, a rare bat from tropical Australia

Hipposideros diadema reginae is a rare subspecies of Diadem Leafnosed Bat confined to tropical Queensland. Few data are available on its population size or ecology. From July, 1990 to December, 1993, I conducted colony counts at Chillagoe and Iron Range to assess its abundance, and radio-tagged six males at Chillagoe to provide data on roosting and foraging ecology for management purposes. I recorded the subspecies in nine of 18 caves surveyed at Chillagoe. Two or more bats were regularly observed in only four caves, each of which had greater or equal 250 m of passage, large chambers with high domed ceilings, and multiple entrances. The largest colony was found in Trezkinn Cave (range of 6-65 bats). Both Trezkinn and a nearby cave, Donna, were fully developed tourist caves, but were frequently used as day roosts by radio-tagged bats. Each cave had a gate at its entrance. At Iron Range, between 70 and 250 bats roosted in Gordon's Mine. Bats used multiple day roosts, but did not change roost every day. The main foraging behaviour was perch hunting, with continuous flight as a secondary behaviour. The mean foraging range of tagged bats was 1.08 km from the day roost (range of 0.3-2.5 km). Foraging occurred within all available types of vegetation; use of vegetation showed intraspecific variation. Hipposideros d. reginae exhibits flexibility in its foraging ecology, but has specific roost requirements. Recommended management actions are: prevent or regulate human access to roosts, search for additional colonies at Chillagoe by targeting potentially suitable caves, and ban scientific collecting at both sites.
Roles for the chloroplast-localized PPR Protein 30 and the "Mitochondrial" Transcription Termination Factor 9 in chloroplast quality control.

Chloroplasts constantly experience photo-oxidative stress while performing photosynthesis. This is particularly true under abiotic stresses that lead to the accumulation of reactive oxygen species (ROS) that oxidize DNA, proteins, and lipids. ROS can also act as signals to induce acclimation through chloroplast degradation, cell death, and nuclear gene expression. To better understand the mechanisms behind ROS signaling from chloroplasts we have used the Arabidopsis thaliana mutant plastid ferrochelatase two (fc2) that conditionally accumulates the ROS singlet oxygen (1 O2 ) leading to chloroplast degradation and eventually cell death. Here we have mapped mutations that suppress chloroplast degradation in the fc2 mutant and demonstrate that they affect two independent loci (PPR30 and mTERF9) encoding chloroplast proteins predicted to be involved in post-transcriptional gene expression. These mutants exhibited broadly reduced chloroplast gene expression, impaired chloroplast development, and reduced chloroplast stress signaling. 1 O2 levels, however, could be uncoupled to chloroplast degradation suggesting that PPR30 and mTERF9 are involved in ROS signaling pathways. In the wild type background, ppr30 and mTERF9 mutants were also observed to be less susceptible to cell death induced by excess light stress. While broadly inhibiting plastid transcription with rifampicin was also able to suppress cell death in fc2 mutants, specific reductions in plastid gene expression using other mutations was not always sufficient. Together these results suggest that plastid gene expression, or the expression of specific plastid genes by PPR30 and mTERF0, is a necessary prerequisite for chloroplasts to activate 1 O2 signaling pathways to induce chloroplast quality control pathways and/or cell death.