bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enrichment analysis on regulatory subspaces: a novel direction for the superior description of cellular responses to SARS-CoV-2
Authors: Rodrigues Pedro , Costa Rafael S. , Henriques Rui 
Published: December 2021

AbstractStatementThe enrichment analysis of discriminative cell transcriptional responses to SARS-CoV-2 infection using biclustering produces a broader set of superiorly enriched GO terms and KEGG pathways against alternative state-of-the-art machine learning approaches, unraveling novel knowledge.Motivation and methodsThe comprehensive understanding of the impacts of the SARS-CoV-2 virus on infected cells is still incomplete. This work identifies and analyses the main cell regulatory processes affected and induced by SARS-CoV-2, using transcriptomic data from several infectable cell lines available in public databases and in vivo samples. We propose a new class of statistical models to handle three major challenges, namely the scarcity of observations, the high dimensionality of the data, and the complexity of the interactions between genes. Additionally, we analyse the function of these genes and their interactions within cells to compare them to ones affected by IAV (H1N1), RSV and HPIV3 in the target cell lines.ResultsGathered results show that, although clustering and predictive algorithms aid classic functional enrichment analysis, recent pattern-based biclustering algorithms significantly improve the number and quality of the detected biological processes. Additionally, a comparative analysis of these processes is performed to identify potential pathophysiological characteristics of COVID-19. These are further compared to those identified by other authors for the same virus as well as related ones such as SARS-CoV-1. This approach is particularly relevant due to a lack of other works utilizing more complex machine learning tools within this context.
White Matter β-Amyloid Precursor Protein Immunoreactivity in Autopsied Subjects With and Without COVID-19
Authors: Beach Thomas G. , DeTure Michael , Walker Jessica E. , Arce Richard , Glass Michael J. , Sue Lucia I. , Intorcia Anthony J. , Nelson Courtney M. , Suszczewicz Katsuko E. , Borja Claryssa I. , Serrano Geidy E. , Dickson Dennis W. 
Published: December 2021

ABSTRACTThe coronavirus SARS-CoV-2 causes COVID-19, a predominantly respiratory disease that has been reported to be associated with numerous neurological signs, symptoms and syndromes. More than 20 published studies have used RT-PCR methods to determine viral SARS-CoV-2 genomic presence in postmortem brain tissue and the overall impression is that viral brain invasion is relatively uncommon and occurs in low copy numbers, supporting indirect mechanisms as the cause of most neurological phenomena. Hypoxic-ischemic brain injury and stroke are one such possible indirect mechanism, as acute ischemia or stroke concurrence with COVID-19 has been reported as being 0.5% to 20%. Immunohistochemical stains for β-amyloid precursor protein (APP) have been suggested to be a “signature” change of hypoxic leukoencephalopathy or COVID-19 brain disease, although prior reports have not had a non-COVID-19 control group. We therefore compared the prevalence and intensity of white matter APP staining in the brains of subjects dying with and without COVID-19. Clinical and neuropathological results, including semi-quantitative assessment of the density of white matter APP staining, were compared between 20 COVID-19 cases and 20 pre-COVID-19 autopsy cases, including 10 cases with autopsy-proven non-COVID-19 pneumonia and 10 cases without pneumonia. Positive APP white matter staining in at least one of the two brain regions (precentral gyrus and cingulate gyrus) studied was not significantly more common in COVID-19 vs controls (14/20 vs 12/20). Comparing density scores from both brain regions combined, the mean scores for COVID-19 cases were higher than those for controls of both types together but not significantly different when restricting to controls with pneumonia. Among control cases, cases with pneumonia had significantly higher scores. The presence or absence of a major neuropathologically-defined neurodegenerative disorder did not significantly affect the APP scores. The major finding is that while APP white matter staining cannot be regarded as a specific marker of COVID-19, as it does not occur with significantly greater probability in in COVID-19 brains as compared to non-COVID-19 brains, it is possible that white matter APP staining, representing acute or subacute axonal damage, may be a common occurrence in the perimortem period, and that it may be more intense in subjects dying with pneumonia, regardless of cause.
NFL COVID-19 Return to Sport Injury Prevalence Comparison
Authors: Puga Troy , Schafer Josh , Agbedanu Prince , Treffer Kevin 
Published: December 2021

Abstract1.PurposeDuring the COVID 19 Pandemic, the NFL teams have been reported to have limited training sections in preparation for their games. This study compares the prevalence of injury during the 2018, 2019, and 2020 NFL seasons, with the aim to determine the potential causes of the differences in prevalence.2.MethodOfficial injury reports from each team were counted during the 17-week regular season of each year (2018, 2019, and 2020). The data was analyzed using an unpaired t-test to compare the injury prevalence between each of the three seasons.3.ResultsThe 2018 season produced a total of 1,561 injuries and a mean of 48.78 injuries per team. The 2019 season produced a total of 1,897 injuries and mean of 59.28 injuries per team, while the 2020 season produced a total of 2, 484 injuries and mean of 77.63 injuries per team. An unpaired t-test was performed using the data to compare the mean number of injuries per team of each of the seasons. Comparison of the 2020 season against the 2019 season showed a statistically significant difference (P=.0003). Comparison of the 2020 season to the 2018 season found a statistically significant difference (P=.0001). Comparison between the 2019 and the 2018 seasons found a statistically significant difference (P=.0314).ConclusionAlthough the 2019 and 2018 season showed a statistically significant difference (P=0.0314), this difference is not as astronomical when we compare the 2020 seasons vs 2019 and 2018 seasons (P=0.0003 and P=0.0001, respectively) (Figure 2). The astronomical increase in injury prevalence in the 2020 season over the previous years does raise the possibility that there was reduced physiological adaption to stress, due to the limited amount of training embarked on. The limited amount of training was the result of closure of practice facilities during the COVID-19 pandemic. More physiological investigation involving players must be done at the professional and amateur levels to determine if there is a lack of physiological adaptation due to limited use of practice and training facilities during the COVID-19 pandemic.
Identifying weather variables as important clinical predictors of bacterial diarrhea among international travelers to Nepal and Thailand
Authors: Pender Melissa A. , Smith Timothy , Brintz Ben J. , Pandey Prativa , Shrestha Sanjaya , Anuras Sinn , Demons Samandra , Sornsakrin Siriporn , Platts-Mills James A. , Bodhidatta Ladaporn , Leung Daniel T. 
Published: December 2021

AbstractBackgroundClinicians and travelers often have limited tools to differentiate bacterial from non-bacterial causes of travelers’ diarrhea (TD). Development of a clinical prediction rule assessing the etiology of TD may help identify episodes of bacterial diarrhea and limit inappropriate antibiotic use. We aimed to identify predictors of bacterial diarrhea among clinical, demographic, and weather variables, as well as to develop and cross-validate a parsimonious predictive model.MethodsWe collected de-identified clinical data from 457 international travelers with acute diarrhea presenting to two healthcare centers in Nepal and Thailand. We used conventional microbiologic and multiplex molecular methods to identify diarrheal etiology from stool samples. We used random forest and logistic regression to determine predictors of bacterial diarrhea.ResultsWe identified 195 cases of bacterial etiology, 63 viral, 125 mixed pathogens, 6 protozoal/parasite, and 68 cases without a detected pathogen. Random forest regression indicated that the strongest predictors of bacterial over viral or non-detected etiologies were average location-specific environmental temperature and RBC on stool microscopy. In 5-fold cross-validation, the parsimonious model with the highest discriminative performance had an AUC of 0.73 using 3 variables with calibration intercept -0.01 (SD 0.31) and slope 0.95 (SD 0.36).ConclusionsWe identified environmental temperature, a location-specific parameter, as an important predictor of bacterial TD, among traditional patient-specific parameters predictive of etiology. Future work includes further validation and the development of a clinical decision-support tool to inform appropriate use of antibiotics in TD.
Role of immigrant males and muzzle contacts in the uptake of a novel food by wild vervet monkeys
Authors: Dongre Pooja , Lanté Gaëlle , Cantat Mathieu , Canteloup Charlotte , van de Waal Erica 
Published: December 2021

ABSTRACTThe entry into and uptake of information in social groups is critical for behavioural adaptation by long-lived species in rapidly changing environments. We exposed five groups of wild vervet monkeys to a novel food to investigate innovation of processing and consuming it. We report that immigrant males innovated in two groups, and an infant innovated in one group. In two other groups, immigrant males imported the innovation from their previous groups. We compared uptake between groups with respect to the initial innovator to examine the extent to which dispersing males could introduce an innovation into groups. Uptake of the novel food was faster in groups where immigrant males ate first rather than the infant. Younger individuals were more likely overall, and faster, to subsequently acquire the novel food. We also investigated the role of muzzle contact behaviour in information seeking around the novel food. Muzzle contacts decreased in frequency over repeated exposures to the novel food. Muzzle contacts were initiated the most by naïve individuals, high rankers and juveniles; and were targeted most towards knowledgeable individuals and high rankers, and the least towards infants. We highlight the potential importance of dispersers in rapidly exploiting novel resources among populations.
Long term exposure of human gut microbiota with high and low emulsifier sensitivity to soy lecithin in M-SHIME model
Authors: Miclotte Lisa , De Paepe Ellen , Li Qiqiong , Van Camp John , Rajkovic Andreja , Van de Wiele Tom 
Published: December 2021

AbstractIn the context of the potential health hazards related to food processing, dietary emulsifiers have been shown to alter the structure and function of the gut microbial community, both in vivo and in vitro. In mouse models, these emulsifier exposed gut microbiota were shown to contribute to gut inflammation. Several knowledge gaps remain to be addressed though. As such, the impact from a longer timeframe of exposure on the gut microbiota is not known and interindividual variability in microbiome response needs to be measured.To answer these research questions, in this study the faecal microbiota from two individuals, previously selected for high and low emulsifier sensitivity, were exposed to two concentrations of soy lecithin during a 7 day treatment phase in the dynamic mucosal simulator of the human intestinal microbial ecosystem (M-SHIME). The results showed mild effects from soy lecithin on the composition and functionality of these microbial communities, which depended on the original microbial composition. The effects also mostly levelled off after 3 days of exposure. The emulsifier sensitivity for which the microbiota were selected, was preserved. Some potentially concerning effects were also registered: butyrate levels, positively correlating with Faecalibacterium abundance, were lowered by soy lecithin. Also the abundance of the beneficial Bifidobacterium genus was lowered, while the abundance of the notorious unclassified Enterobacteriaceae was increased. Within the family of the unclassified Lachnospiraceae, several genera were either suppressed or stimulated.The effects that these microbial alterations would have on a living host is not yet certain, especially given the fact that large fractions of soy lecithin’s constituents can be absorbed. Nevertheless, choline and phosphatidylcholine, both primary and absorbable constituents of soy lecithin, have recently been linked to cardiovascular disease via the generation of TMA by the gut microbiota. Further studies that validate our findings and link them to potential health outcomes are thus justified.
A seasonal pulse of ungulate neonates influences space use by carnivores in a multi-predator, multi-prey system
Authors: Ruprecht Joel , Forrester Tavis D. , Jackson Nathan J. , Clark Darren A. , Wisdom Michael J. , Rowland Mary M. , Smith Joshua B. , Stewart Kelley M. , Levi Taal 
Published: December 2021

AbstractThe behavioral mechanisms by which predators encounter prey are poorly resolved. In particular, the extent to which predators engage in active search for prey versus incidentally encountering them is unknown. The distinction between search and incidental encounter influences prey population dynamics with active search exerting a stabilizing force on prey populations by alleviating predation pressure on low-density prey and increasing it for high-density prey.Parturition of many large herbivores occurs during a short and predictable temporal window in which young are highly vulnerable to predation. Our study aims to determine how a suite of carnivores responds to the seasonal pulse of newborn ungulates using contemporaneous GPS locations of four species of predators and two species of prey.We used step-selection functions to assess whether coyotes, cougars, black bears, and bobcats actively searched for parturient females in a low-density population of mule deer and a high-density population of elk. We then assessed whether searching carnivores shifted their habitat use toward areas exhibiting a high probability of encountering neonates.None of the four carnivore species encountered parturient mule deer more often than expected by chance suggesting that predation of young resulted from incidental encounters. By contrast, we determined that cougar and male bear movements positioned them in proximity of parturient elk more often than expected by chance which is evidence of searching behavior. Although both male bears and cougars searched for neonates, only male bears used elk parturition habitat in a way that dynamically tracked the phenology of the elk birth pulse suggesting that maximizing encounters with juvenile elk was a motivation when selecting resources.Our results support the existence of a stabilizing mechanism to prey populations through active search behavior by predators because carnivores in our study searched for the high-density prey species (elk) but ignored the low-density species (mule deer). We conclude that prey density must be high enough to warrant active search, and that there is high interspecific and intersexual variability in foraging strategies among large mammalian predators and their prey.
Aberrant Fucosylation of Saliva Glycoprotein Defining Lung Adenocarcinomas Malignancy
Authors: Gao Ziyuan , Wu Zhen , Han Ying , Zhang Xumin , Hao Piliang , Xu Mingming , Huang Shan , Li Shuwei , Xia Jun , Jiang Junhong , Yang Shuang 
Published: December 2021

AbstractAberrant glycosylation is a hallmark of cancer found during tumorigenesis and tumor progression. Lung cancer induced by oncogene mutations has been detected in the patient’s saliva, and saliva glycosylation has been altered. Saliva contains highly glycosylated glycoproteins, the characteristics of which may be related to various diseases. Therefore, elucidating cancer-specific glycosylation in the saliva of healthy, non-cancer, and cancer patients can reveal whether tumor glycosylation has unique characteristics for early diagnosis. In this work, we used a solid-phase chemoenzymatic method to study the glycosylation of saliva glycoproteins in clinical specimens. The results showed that the α1,6-core fucosylation of glycoproteins in cancer patients was significant increased. The fucosylation of α1,2 or α1,3 is also increased in cancer patients. We further analyzed the expression of fucosyltransferases responsible for α1,2, α1,3, α1,6 fucosylation. The fucosylation of the saliva of cancer patients is drastically different from that of non-cancer or health controls. These results indicate that the glycoform of saliva fucosylation distinguishes lung cancer from other diseases, and this feature has the potential to diagnose lung adenocarcinoma.TOCFucosylation biosynthesis in lung cancer. Saliva fucosylation contains α1,2-linked, α1,3-linked, α1,6-linked fucosylation in lung cancer.
Predicting biomass of resident kōkopu (Galaxias) populations using local habitat composition
Authors: Crichton Ben R. J. , Hickford Michael J.H. , McIntosh Angus R. , Schiel David R. 
Published: December 2021

AbstractWith the global decline of freshwater fishes, quantifying the body size-specific habitat use of vulnerable species is crucial for accurately evaluating population health, identifying the effects of anthropogenic stressors, and directing effective habitat restoration. Populations of New Zealand’s endemic kōkopu species (Galaxias fasciatus, G. argenteus, and G. postvectis) have declined substantially over the last century in response to anthropogenic stressors, including habitat loss and fragmentation, invasive species, and over-exploitation. Despite well-understood habitat associations, key within-habitat features driving the reach-scale biomass of small and large kōkopu remain unclear. Here, we investigated whether the total biomass of small (≤ 90 mm) and large (> 90 mm) kōkopu was associated with total pool area, average pool depth, total bank cover, average substrate size, and average forest canopy cover across fifty-seven 50 m reaches. These features were selected because generally pool habitats are productive feeding areas, bank cover and substrate interstices are important refuges, and forest cover provides greater food availability. Because kōkopu are nocturnal, populations were sampled with removal at night using headlamps and hand-nets until reaches were visually depleted. Using Akaike’s information criterion, it was found that increases in large kōkopu biomass were most parsimoniously explained by greater pool area and bank cover, whereas increases in small kōkopu biomass were best explained by low bank cover and greater average forest cover. This study demonstrated the importance of considering the ontogenetic shift in species’ habitat use and provided an effective modelling approach for quantifying the size-specific habitat use of these stream-dwelling fish.
Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference
Authors: Westbury Michael V. , Lorenzen Eline D. 
Published: December 2021

AbstractWithin evolutionary biology, mitochondrial genomes (mitogenomes) provide useful insights at both population and species level. Several approaches are available to assemble mitogenomes. However, most are not suitable for divergent, extinct species, due to the requirement of a reference mitogenome from a conspecific or close relative, and relatively high-quality DNA.Iterative mapping can overcome the lack of a close reference sequence, and has been applied to an array of extinct species. Despite its widespread use, the accuracy of the reconstructed assemblies are yet to be comprehensively assessed. Here, we investigated the influence of mapping software (BWA or MITObim), parameters, and bait reference phylogenetic distance on the accuracy of the reconstructed assembly using two simulated datasets: (i) spotted hyena and various mammalian bait references, and (ii) southern cassowary and various avian bait references. Specifically, we assessed the accuracy of results through pairwise distance (PWD) to the reference conspecific mitogenome, number of incorrectly inserted base pairs (bp), and total length of the reconstructed assembly.We found large discrepancies in the accuracy of reconstructed assemblies using different mapping software, parameters, and bait references. PWD to the reference conspecific mitogenome, which reflected the level of incorrect base calls, was consistently higher with BWA than MITObim. The same was observed for the number of incorrectly inserted bp. In contrast, the total sequence length was lower. Overall, the most accurate results were obtained with MITObim using mismatch values of 3 or 5, and the phylogenetically closest bait reference sequence. Accuracy could be further improved by combining results from multiple bait references.We present the first comprehensive investigation of how mapping software, parameters, and bait reference influence mitogenome reconstruction from ancient DNA through iterative mapping. Our study provides information on how mitogenomes are best reconstructed from divergent, short-read data. By obtaining the most accurate reconstruction possible, one can be more confident as to the reliability of downstream analyses, and the evolutionary inferences made from them.
Invasive slipper limpets Crepidula fornicata act like a sink, rather than source, of Vibrio spp.
Authors: Quinn Emma A. , Malkin Sophie H. , Thomas Jessica E. , Poole Ryan , Davies Charlotte E. , Rowley Andrew F. , Coates Christopher J. 
Published: December 2021

AbstractA large knowledge gap exists regarding the disease profile and pathologic condition of the invasive, non-native, slipper limpet Crepidula fornicata. To help address this, we performed a yearlong health survey across two sites in South Wales UK – subtidal Swansea Bay and intertidal Milford Haven. In total, 1,800 limpets were screened systematically for haemolymph bacterial burdens using both general and vibrio-selective growth media (TSA +2% NaCl and TCBS, respectively), haemolymph (blood) inspection using microscopy, a PCR-based assay targeting Vibrio spp., and multi-tissue histology. Over 99% of haemolymph samples contained cultivable bacterial colony forming units, and 83% of limpets tested positive for the presence of vibrios via PCR (confirmed via Sanger sequencing). Vibrio presence did not vary greatly across sites, yet a strong temporal (seasonal) effect was observed – significantly higher bacterial loads during the summer. Binomial logistic regression models revealed larger (older) limpets were more likely to harbour vibrios, and the growth of bacteria on TCBS was a key predictor for PCR-based vibrio detection. Histological assessment of >340 animals revealed little evidence of inflammation, sepsis, or immune reactivity despite the gross bacterial numbers. We contend that slipper limpets are not susceptible to bacteriosis at either site surveyed, or do not to harbour vibrios known to be pathogenic to humans. The lack of susceptibility to local pathogenic bacteria may explain, in part, the invasion success of C. fornicata across this region.