bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing trait driver theory along abiotic gradients in tropical plant communities
Authors: Lourenço Jehová , Newman Erica A. , Dias Milanez Camilla Rozindo , Thomaz Luciana Dias , Enquist Brian J. 
Published: February 2020

ABSTRACTDespite the many studies using trait-based approaches to assess the impact of environmental gradients in forest trait composition, the relative roles of (i) intraspecific variation in community assembly and (ii) microclimatic or fine scale abiotic variation in shaping local trait diversity remain poorly understood. To advance their understanding we tested several assumptions and predictions of trait driver theory (TDT). We quantified the shape of trait distributions related to tree carbon, nutrient economics and stem hydraulics across a small-scale but steep gradient of soil water availability.We utilized a unique and steep environmental gradient in the coastal Brazilian Atlantic forest (restinga) communities that spans a very short distance (207 ±60 meters). We collected leaf and wood samples of tree species across 42 patches (or plots) ofrestingaforest. Furthermore, to detect if species directionally shift in niche space, we analyzed species composition in multidimensional hypervolume space.Despite short geographic distances, we observed large shifts in species replacement and intraspecific variation reflected by a directional shift in plant function. Consistent with TDT, we observe (i) trait distributions that are skewed in directions consistent with a forest responding to recent hotter and drier; (ii) peaked trait distributions, indicating strong functional convergence; and (iii) conditions decreasing means and variances of several leaf carbon and nutrient economic traits as well as stem hydraulic traits.Synthesis.Observed species replacements along the water table gradient and interspecific measures of functional diversity (community kurtosis and skewness) are consistent with strong phenotype/environmental matching of plant carbon, nutrient, and hydraulic strategies. We observe environmental filtering in both extremities of the gradient, selecting for acquisitive (wet) to conservative (dry) setup of traits. Similarly, species that span the entire water availability gradient are characterized by directional intraspecific shifts in multi-trait space that mirror interspecific shifts. Strong environmental gradients across short spatial scales provide unique systems to accurately assess assembly processes and address long-held assumptions and timely hypothesis predicted by trait driver theory.
Multivariate Analyses of Codon Usage of SARS-CoV-2 and other betacoronaviruses
Authors: Gu Haogao , Chu Daniel , Peiris Malik , Poon Leo L.M. 
Published: February 2020

AbstractCoronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genusBetacoronaviruswhich also includes severe acute respiratory syndrome related coronavirus (SARSr-CoV) and Middle East respiratory syndrome related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses can help identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, global correspondence analysis (CA), within-group correspondence analysis (WCA) and between-group correspondence analysis (BCA) were performed among different genes in coronavirus viral sequences. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.
SEIR Transmission dynamics model of 2019 nCoV coronavirus with considering the weak infectious ability and changes in latency duration
Authors: Pengpeng Shi , Shengli Cao , Peihua Feng 
Published: February 2020

ABSTRACTPneumonia patients of 2019-ncov in latent period are not easy to be effectively quarantined, but there is evidence that they have strong infectious ability. Here, the infectious ability of patients during the latent period is slightly less than that of the infected patients was assumed. We established a new SEIR propagation dynamics model, that considered the weak transmission ability of the incubation period, the variation of the incubation period length, and the government intervention measures to track and isolate comprehensively. Based on the raw epidemic data of China from January 23, 2020 to February 10, 2020, the dynamic parameters of the new present SEIR model are fitted. Through the Euler integration algorithm to solve the model, the effect of infectious ability of incubation patients on the theoretical estimation of the present SEIR model was analyzed, and the occurrence time of peak number in China was predicted.
A SMAD4-modulated gene profile predicts disease-free survival in stage II and III colorectal cancer
Authors: Szeglin Bryan C. , Wu Chao , Marco Michael R. , Park Hyun Sung , Zhang Zeda , Zhang Bing , Garcia-Aguilar Julio , Beauchamp R. Daniel , Chen Xi , Smith J. Joshua 
Published: February 2020

AbstractObjectiveLoss of SMAD4 is associated with worse outcomes for colorectal cancer patients. We used gene ontology and bioinformatics to identify an RNA-based SMAD4-modulated profile and test its association with patient outcome.DesignUsing a discovery dataset of 250 colorectal cancer patients, we analyzed expression of BMP/Wnt target genes for association with SMAD4 expression. Promoters of the BMP/Wnt genes were interrogated for SMAD-binding elements. 15 genes were implicated and three tested for modulation by SMAD4 in patient-derived colorectal cancer tumoroids. Expression of the 15 genes was used for unsupervised hierarchical clustering of a training dataset and two resulting clusters modeled in a centroid model. This model was applied to an independent validation dataset of stage II and III patients. Disease-free survival was analyzed by the Kaplan-Meier method.ResultsIn vitro analysis of three genes identified in the SMAD4-modulated profile (JAG1, TCF7, MYC) revealed modulation by SMAD4 consistent with the trend observed in the profile. In the training dataset (n = 553), the profile was not associated with outcome. However, among stage II and III patients (n = 461), distinct clusters were identified by unsupervised hierarchical clustering that were associated with disease-free survival (p = 0.02). The main model was applied to a validation dataset (n = 257) which confirmed the association of clustering with disease-free survival (p = 0.02).ConclusionsA SMAD4-modulated RNA-based gene profile identified high-risk stage II and III colorectal cancer patients, can predict disease-free survival, and has prognostic potential for stage II and III colorectal cancer patients.
BioTracs: A transversal framework for computational workflow standardization and traceability
Authors: Abi-Ghanem Joséphine , Ouattara Djomangan Adama 
Published: February 2020

AbstractBackgroundThe need of digital tools for integrative analysis is today important in most scientific areas. It leads to several community-driven initiatives to standardize the sharing of data and computational workflows. However, there exists no open agnostic framework to model and implement computation workflows, in particular in bioinformatics. It is therefore difficult for data scientists to share transparently and integrate heterogeneous analysis processes coming from different scientific domains, programing languages, projects or teams.ResultsWe present here BioTracs, a transversal framework for computational workflow standardization and traceability. It is based on PRISM architecture (Process Resource Interfacing SysteM), an agnostic open architecture we introduce here to standardize the way processes and resources can be modelled and interfaced in computational workflows to ensure traceability, reproducibility and facilitate sharing. BioTracs is today implemented in MATLAB and available under open source license on GitHub. Several BioTracs-derived applications are also available online. They were successfully applied to large-scale metabolomics and clinical studies and demonstrated flexibility and robustness.ConclusionsAs an implementation of the PRISM architecture, BioTracs paved the way to an open framework in which bioinformatics could specify ad model workflows. PRISM architecture is designed to provide scalability and transparency from the code to the project level we less efforts. It could also be implemented using open object-oriented languages such as Python, C++ or java.Abstract Figure
Auditory tests for characterizing hearing deficits in listeners with various hearing abilities: The BEAR test battery
Authors: Sanchez-Lopez Raul , Nielsen Silje Grini , El-Haj-Ali Mouhamad , Bianchi Federica , Fereczkowski Michal , Cañete Oscar M , Wu Mengfan , Neher Tobias , Dau Torsten , Santurette Sébastien 
Published: February 2020

ABSTRACTThe Better hEAring Rehabilitation (BEAR) project aims to provide a new clinical profiling tool – a test battery – for hearing loss characterization. Whereas the loss of sensitivity can be efficiently measured using pure-tone audiometry, the assessment of supra-threshold hearing deficits remains a challenge. In contrast to the classical ‘attenuation-distortion’ model, the proposed BEAR approach is based on the hypothesis that the hearing abilities of a given listener can be characterized along two dimensions, reflecting independent types of perceptual deficits (distortions). A data-driven approach provided evidence for the existence of different auditory profiles with different degrees of distortions. Ten tests were included in a test battery, based on their clinical feasibility, time efficiency and related evidence from the literature. The tests were divided into six categories: audibility, speech perception, binaural processing abilities, loudness perception, spectro-temporal modulation sensitivity and spectro-temporal resolution. Seventy-five listeners with symmetric, mild-to-severe sensorineural hearing loss were selected from a clinical population. The analysis of the results showed interrelations among outcomes related to high-frequency processing and outcome measures related to low-frequency processing abilities. The results showed the ability of the tests to reveal differences among individuals and their potential use in clinical settings.
The reproductive number R0 of COVID-19 based on estimate of a statistical time delay dynamical system
Authors: Shao Nian , Cheng Jin , Chen Wenbin 
Published: February 2020

AbstractIn this paper, we estimate the reproductive number R0 of COVID-19 based on Wallinga and Lipsitch framework [11] and a novel statistical time delay dynamic system. We use the observed data reported in CCDC’s paper to estimate distribution of the generation interval of the infection and apply the simulation results from the time delay dynamic system as well as released data from CCDC to fit the growth rate. The conclusion is: Based our Fudan-CCDC model, the growth rate r of COVID-19 is almost in [0.30, 0.32] which is larger than the growth rate 0.1 estimated by CCDC [9], and the reproductive number R0 of COVID-19 is estimated by 3.25 ≤ R0 ≤ 3.4 if we simply use R = 1 + r ∗ Tc with Tc = 7.5, which is bigger than that of SARS. Some evolutions and predictions are listed.
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping
Authors: Cousminer Diana L. , Wagley Yadav , Pippin James A. , Elhakeem Ahmed , Way Gregory P. , McCormack Shana E. , Chesi Alessandra , Mitchell Jonathan A. , Kindler Joseph M. , Baird Denis , Hartley April , Howe Laura , Kalkwarf Heidi J. , Lappe Joan M. , Lu Sumei , Leonard Michelle , Johnson Matthew E. , Hakonarson Hakon , Gilsanz Vicente , Shepherd John A. , Oberfield Sharon E. , Greene Casey S. , Kelly Andrea , Lawlor Deborah , Voight Benjamin F. , Wells Andrew D. , Zemel Babette S. , Hankenson Kurt , Grant Struan F. A. 
Published: February 2020

Introductory paragraphBone accrual impacts lifelong skeletal health, but genetic discovery has been hampered by cross-sectional study designs and uncertainty about target effector genes. Here, we captured this dynamic phenotype by modeling longitudinal bone accrual across 11,000 bone scans followed by genome-wide association studies (GWAS). We revealed 40 loci (35 novel), half residing in topological associated domains harboring known bone genes. Variant-to-gene mapping identified contacts between GWAS loci and nearby gene promoters, and siRNA knockdown of gene expression clarified the putative effector gene at three specific loci in two osteoblast cell models. The resulting target genes highlight the cell fate decision between osteogenic and adipogenic lineages as important in normal bone accrual.
The Epidemiology of Plasmodium vivax Among Adults in the Democratic Republic of the Congo: A Nationally-Representative, Cross-Sectional Survey
Authors: Brazeau Nicholas F. , Mitchell Cedar L. , Morgan Andrew P. , Deutsch-Feldman Molly , Watson Oliver John , Thwai Kyaw L. , Waltmann Andreea , Emch Michael , Gartner Valerie , Redelings Ben , Wray Gregory A. , Mwandagalirwa Melchior K. , Tshefu Antoinette K. , Likwela Joris L. , Edwards Jess K. , Verity Robert , Parr Jonathan B. , Meshnick Steven R. , Juliano Jonathan J. 
Published: February 2020

ABSTRACTBackgroundReports of P. vivax infections among Duffy-negative hosts have begun to accumulate throughout sub-Saharan Africa. Despite this growing body of evidence, no nationally representative epidemiological surveys of P. vivax in sub-Saharan Africa nor population genetic analyses to determine the source of these infections have been performed.MethodsTo overcome this critical gap in knowledge, we screened nearly 18,000 adults in the Democratic Republic of the Congo (DRC) for P. vivax using samples from the 2013-2014 Demographic Health Survey. Infections were identified by quantitative PCR and confirmed with nested-PCR. P. vivax mitochondrial genomes were constructed after short-read sequencing. Risk factors, spatial distributions and population genetic analyses were explored.FindingsOverall, we found a 2.96% (95% CI: 2.28%, 3.65%) prevalence of P. vivax infections across the DRC. Nearly all infections were among Duffy-negative adults (486/489). Infections were not associated with typical malaria risk-factors and demonstrated small-scale heterogeneity in prevalence across space. Mitochondrial genomes suggested that DRC P. vivax is an older clade that shares its most recent common ancestor with South American isolates.InterpretationP. vivax is more prevalent across the DRC than previously believed despite widespread Duffy-negativity. Comparison to global and historical P. vivax sequences suggests that historic DRC P. vivax may have been transported to the New World on the wave of European expansion. Our findings suggest congolese P. vivax is an innocuous threat given its relatively flat distribution across space, lack of malaria risk factors, and potentially ancestral lineage.FundingNational Institutes of Health and the Wellcome Trust.
Identifying candidate detoxification genes in the ecdysteroid kinase-like (EcKL) and cytochrome P450 gene families inDrosophila melanogasterby integrating evolutionary and transcriptomic data
Authors: Scanlan Jack L. , Gledhill-Smith Rebecca S. , Battlay Paul , Robin Charles 
Published: February 2020

AbstractThe capacity to detoxify toxic compounds is essential for adaptation to the ecological niches of many organisms, especially insects. However, detoxification in insects is often viewed through the lens of mammalian detoxification research, even though the organ and enzyme systems involved have diverged for over half a billion years. Phosphorylation is a non-canonical phase II detoxification reaction that, among animals, occurs near exclusively in insects, but the enzymes responsible have never been cloned or otherwise identified. We propose the hypothesis that members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene family in 12 species ofDrosophilaand explored their evolution within the genus. Many ancestral EcKL clades are evolutionarily unstable and have experienced repeated gene gain and loss events, while others are conserved as single copy orthologs. Leveraging multiple published gene expression datasets fromD. melanogaster, and using the cytochrome P450s—a canonical detoxification family—as a test case, we demonstrate relationships between xenobiotic induction, detoxification tissue-enriched expression and evolutionary instability in the EcKLs and the P450s. We also found previously unreported genomic and transcriptomic variation in a number of EcKLs and P450s associated with toxic stress phenotypes using a targeted phenome-wide association study (PheWAS) approach. Lastly, we devised a systematic method for identifying candidate detoxification genes in large gene families that is concordant with experimentally determined functions of P450 genes inD. melanogaster. Applying this method to the EcKLs suggested a significant proportion of these genes play roles in detoxification, and that the EcKLs may constitute a detoxification gene family in insects. Additionally, we estimate that between 11–16 uncharacterisedD. melanogasterP450s are strong detoxification candidates.HighlightsThe poorly characterised ecdysteroid kinase-like (EcKL) gene family is hypothesised to encode enzymes responsible for detoxification by phosphorylation in insects.An integrative ‘detoxification score’ method accurately categorises the known functions of a canonical detoxification family, the cytochrome P450s, and suggests many EcKLs are also involved in detoxification.A targeted phenome-wide association study finds novel associations between EcKL/P450 variation and a number of toxic stress phenotypes, such as two unlinked EcKL paralogs that are both associated with developmental methylmercury resistance.
Height differences in clonal stands ofTussilago farfarapromote outcrossing by influencing pollinator behaviour
Authors: Dolezal Aleksandra J. 
Published: February 2020

AbstractPlants with mixed mating systems balance the advantages of selfing and the costs of inbreeding. Previous studies have shown that plant species with the ability to self-pollinate and cross pollinate have strategies to promote outcrossing to increase genetic diversity. Various features of floral morphology are thought to be deliberate mechanisms to manipulate plant mating systems. I hypothesized that within-plant variation in flower stem height is a morphological trait that can reduce geitonogamy by increasing pollinator movement among plants. This hypothesis was tested using coltsfoot (Tussilago farfara); coltsfoot plants host several flowering stems that differ in height, with each stem having a single, terminal flowerhead. I used cut flowers to create ‘populations’ of coltsfoot in which each plant had four inflorescences with equal or unequal flower stalk lengths and measured frequency of insect pollinators that would stay among flowers within a plant or move to other plants. All pollinators (bee flies, hover flies, solitary bees and wasps) showed a marked discrimination in favor of leaving plants with flowers of different heights and stayed when plants had flowers of the same height. This study shows that variation in flower heights is important for reducing geitonogamy in coltsfoot and suggests that the evolution of this morphological trait should be considered in studies of mating systems.
Investigating the dynamics of microbial consortia in spatially structured environments
Authors: Gupta Sonali , Ross Tyler D. , Gomez Marcella M. , Grant Job L. , Romero Philip A. , Venturelli Ophelia S. 
Published: February 2020

ABSTRACTThe spatial organization of microbial communities arises from a complex interplay of biotic and abiotic interactions and is a major determinant of ecosystem functions. We design a microfluidic platform to investigate how the spatial arrangement of microbes impacts gene expression and growth. We elucidate key biochemical parameters that dictate the mapping between spatial positioning and gene expression patterns. We show that distance can establish a low-pass filter to periodic inputs, and can enhance the fidelity of information processing. Positive and negative feedback can play disparate roles in the synchronization and robustness of a genetic oscillator distributed between two strains to spatial separation. Quantification of growth and metabolite release in an amino-acid auxotroph community demonstrates that the interaction network and stability of the community are highly sensitive to temporal perturbations and spatial arrangements. In sum, our microfluidic platform can quantify spatiotemporal parameters influencing diffusion-mediated interactions in microbial consortia.
Kidney impairment is associated with in-hospital death of COVID-19 patients
Authors: Cheng Yichun , Luo Ran , Wang Kun , Zhang Meng , Wang Zhixiang , Dong Lei , Li Junhua , Yao Ying , Ge Shuwang , Xu Gang 
Published: February 2020

AbstractBackgroundInformation on kidney impairment in patients with coronavirus disease 2019 (COVID-19) is limited. This study aims to assess the prevalence and impact of abnormal urine analysis and kidney dysfunction in hospitalized COVID-19 patients in Wuhan.MethodsWe conducted a consecutive cohort study of COVID-19 patients admitted in a tertiary teaching hospital with 3 branches following a major outbreak in Wuhan in 2020. Hematuria, proteinuria, serum creatinine concentration and other clinical parameters were extracted from the electronic hospitalization databases and laboratory databases. Incidence rate for acute kidney injury (AKI) was examined during the study period. Association between kidney impairment and in-hospital death was analyzed.ResultsWe included 710 consecutive COVID-19 patients, 89 (12.3%) of whom died in hospital. The median age of the patients was 63 years (inter quartile range, 51-71), including 374 men and 336 women. On admission, 44% of patients have proteinuria hematuria and 26.9% have hematuria, and the prevalence of elevated serum creatinine and blood urea nitrogen were 15.5% and 14.1% respectively. During the study period, AKI occurred in 3.2% patients. Kaplan–Meier analysis demonstrated that patients with kidney impairment have higher risk for in-hospital death. Cox proportional hazard regression confirmed that elevated serum creatinine, elevated urea nitrogen, AKI, proteinuria and hematuria was an independent risk factor for in-hospital death after adjusting for age, sex, disease severity, leukocyte count and lymphocyte count.ConclusionsThe prevalence of kidney impairment (hematuria, proteinuria and kidney dysfunction) in hospitalized COVID-19 patients was high. After adjustment for confounders, kidney impairment indicators were associated with higher risk of in-hospital death. Clinicians should increase their awareness of kidney impairment in hospitalized COVID-19 patients.