bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary estimation of the novel coronavirus disease (COVID-19) cases in Iran: a modelling analysis based on overseas cases and air travel data
Authors: Zhuang Zian , Zhao Shi , Lin Qianying , Cao Peihua , Lou Yijun , Yang Lin , He Daihai 
Published: March 2020

AbstractAs of 1 March 2020, Iran has reported 987 COVID-19 cases and including 54 associated deaths. At least six neighboring countries (Bahrain, Iraq, Kuwait, Oman, Afghanistan and Pakistan) have reported imported COVID-19 cases from Iran. We used air travel data and the cases from Iran to other Middle East countries and estimated 16533 (95% CI: 5925, 35538) COVID-19 cases in Iran by 25 February, before UAE and other Gulf Cooperation Council countries suspended inbound and outbound flights from Iran.
A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19
Authors: Zhou Hong , Chen Xing , Hu Tao , Li Juan , Song Hao , Liu Yanran , Wang Peihan , Liu Di , Yang Jing , Holmes Edward C. , Hughes Alice C. , Bi Yuhai , Shi Weifeng 
Published: March 2020

SummaryThe unprecedented epidemic of pneumonia caused by a novel coronavirus, HCoV-19, in China and beyond has caused public health concern at a global scale. Although bats are regarded as the most likely natural hosts for HCoV-191,2, the origins of the virus remain unclear. Here, we report a novel bat-derived coronavirus, denoted RmYN02, identified from a metagenomics analysis of samples from 227 bats collected from Yunnan Province in China between May and October, 2019. RmYN02 shared 93.3% nucleotide identity with HCoV-19 at the scale of the complete virus genome and 97.2% identity in the 1ab gene in which it was the closest relative of HCoV-19. In contrast, RmYN02 showed low sequence identity (61.3%) to HCoV-19 in the receptor binding domain (RBD) and might not bind to angiotensin-converting enzyme 2 (ACE2). Critically, however, and in a similar manner to HCoV-19, RmYN02 was characterized by the insertion of multiple amino acids at the junction site of the S1 and S2 subunits of the Spike (S) protein. This provides strong evidence that such insertion events can occur in nature. Together, these data suggest that HCoV-19 originated from multiple naturally occurring recombination events among those viruses present in bats and other wildlife species.
Creating a Survey Instrument for Self-Assessed Menstrual Cycle Characteristics and Androgen Excess
Authors: Mahalingaiah Shruthi , Cosenza Carol , Cheng J. Jojo , Rodriguez Erika , Aschengrau Ann 
Published: March 2020

AbstractPolycystic ovary syndrome (PCOS) is the most common reproductive disorder in women, but tools for self-reported ascertainment are currently lacking. We created and evaluated an online survey instrument for identification of PCOS by incorporating clinically derived reproductive health questions and a novel pictorial tool for androgen excess. The survey was cognitively tested for question comprehension and usability. Comprehension problems included simplifying the PCOS definition and questions on bleeding duration. Recall and answer formation problems included beverage consumption and questions using symbols. Evaluation of this survey instrument via cognitive testing may help to accurately ascertain the prevalence of PCOS in general population settings.
Caution: The clinical characteristics of COVID-19 patients at admission are changing
Authors: Chen Zhaowei , Hu Jijia , Zhang Zongwei , Jiang Shan , Wang Tao , Shi Zhengli , Zhang Zhan 
Published: March 2020

AbstractBackgroundWith the emergence of 4rd generation transmission, the prevention and treatment of the novel coronavirus disease 2019 (COVID-19) has entered a new period. We aimed to report several changes in the clinical characteristics at admission of patients with COVID-19.MethodsClinical records and laboratory results of patients suffering from COVID-19 were retrospectively reviewed and matched with the admission dates to analyze the changes in characteristics at the onset of illness.ResultsOf the 89 affected patients, 31 [34.8%] patients were admitted from January 16 to 22, and 58 [65.2%] were admitted from January 23 to 29. Patients were admitted with more systemic symptoms, such as fever (21 [67.7%] of 31), fatigue (13 [41.9%] of 31), and myalgia (7 [22.6%] of 31), before January 23. More patients (10 [32.3%] of 31) admitted before January 23 had a small amount of sputum production compared with a smaller proportion (4 [6.9%] of 58) of the patients admitted after January 23. Other symptoms, such as cough, nausea, diarrhea, and chest tightness, were not significantly different between the two groups. In addition, the group admitted before January 23 had a larger proportion of patients with reduced lymphocyte (13 [54.2%] of 24), CD3 (11 [54.4%] of 21), and CD8 (9 [42.9%] of 21) counts and elevated serum amyloid A (SAA, 18 [75%] of 24).ConclusionsThe initial symptoms of recently infected patients seem more insidious, indicating that the new coronavirus may gradually evolve into a virus similar to influenza and latent in asymptomatic carriers for a long time.SummaryCompared with the cases admitted earlier, more hidden initial symptoms and improved immune system disorders appeared in COVID-19 patients infected recently.
CoalQC - Quality control while inferring demographic histories from genomic data: Application to forest tree genomes
Authors: Patil Ajinkya Bharatraj , Shinde Sagar Sharad , Raghavendra S , Satish B.N , Kushalappa C.G , Vijay Nagarjun 
Published: March 2020

AbstractEstimating demographic histories using genomic datasets has proven to be useful in addressing diverse evolutionary questions. Despite improvements in inference methods and availability of large genomic datasets, quality control steps to be performed prior to the use of sequentially Markovian coalescent (SMC) based methods remains understudied. While various filtering and masking steps have been used by previous studies, the rationale for such filtering and its consequences have not been assessed systematically. In this study, we have developed a reusable pipeline called “CoalQC”, to investigate potential sources of bias (such as repeat regions, heterogeneous coverage, and callability). First, we demonstrate that genome assembly quality can affect the estimation of demographic history using the genomes of several species. We then use the CoalQC pipeline to evaluate how different repeat classes affect the inference of demographic history in the plant speciesPopulus trichocarpa.Next, we assemble a draft genome by generating whole-genome sequencing data forMesua ferrea(sampled from Western Ghats, India), a multipurpose forest plant distributed across tropical south-east Asia and use it as an example to evaluate several technical (sequencing technology, PSMC parameter settings) and biological aspects that need to be considered while comparing demographic histories. Finally, we collate the genomic datasets of 14 additional forest tree species to compare the temporal dynamics of Ne and find evidence of a strong bottleneck in all tropical forest plants during Mid-Pleistocene glaciations. Our findings suggest that quality control prior to the use of SMC based methods is important and needs to be standardised.
In vivox-ray diffraction and simultaneous EMG reveal the time course of myofilament lattice dilation and filament stretch
Authors: Malingen SA , Asencio AM , Cass JA , Ma W , Irving TC , Daniel TL 
Published: March 2020

ABSTRACTMuscle’s function within an organism depends on the feedback between molecular to meter-scale processes. While the motions of muscle’s contractile machinery are well described in isolated preparations, only a handful of experiments have documented the kinematics of the lattice occurring when multi-scale interactions are fully intact. We used time-resolved x-ray diffraction to record the kinematics of the myofilament lattice within a normal operating context: the tethered flight ofManduca sexta. Since the primary flight muscles ofManduca sextaare synchronous, we used these results to reveal the timing ofin vivocross-bridge recruitment, which occurred 24 (s.d. 26) ms following activation. In addition, the thick filaments stretched an average of 0.75 (s.d. 0.32)% and thin filaments stretched 1.11 (s.d. 0.65)%. In contrast to otherin vivopreparations, lattice spacing changed an average of 2.72 (s.d. 1.47)%. Lattice dilation of this magnitude significantly impacts shortening velocity and force generation, and filament stretching tunes force generation. While kinematics were consistent within individual trials, there was extensive variation between trials. Using a mechanism-free machine learning model we searched for patterns within and across trials. While lattice kinematics were predictable within trials, the model could not create predictions across trials. This indicates that the variability we see across trials may be explained by latent variables occurring in this naturally functioning system. The diverse kinematic combinations we documented mirror muscle’s adaptability and may facilitate its robust function in unpredictable conditions.
Kinome Profiling of Primary Endometrial Tumors Using Multiplexed Inhibitor Beads and Mass Spectrometry Identifies SRPK1 As Candidate Therapeutic Target
Authors: Johnson Katherine J. , Kumar Vikas , Kurimchak Alison M. , Srivastava Nishi , Peri Suraj , Cai Kathy Q. , Mantia-Smaldone Gina M. , Duncan James S. 
Published: March 2020

ABSTRACTProtein kinases (collectively, termed the kinome) represent one of the most tractable drug targets in the pursuit of new and effective cancer treatments. However, less than 20% of the kinome is currently being explored as primary targets for cancer therapy, leaving the majority of the kinome untargeted for drug therapy. Chemical proteomics approaches such as Multiplexed Inhibitor Beads and Mass Spectrometry (MIB-MS) have been developed that measure the abundance of a significant portion of the kinome, providing a strategy to interrogate kinome landscapes and dynamics. Kinome profiling of cancer cell lines using MIB-MS has been extensively characterized, however, application of this method to measure tissue kinome(s) has not been thoroughly explored. Here, we present a quantitative proteomics workflow specifically designed for kinome profiling of tissues that pairs MIB-MS with a newly designed super-SILAC kinome standard. Using this workflow, we mapped the kinome landscape of endometrial carcinoma (EC) tumors and normal endometrial (NE) tissues and identified several kinases overexpressed in EC tumors, including Serine/Arginine-Rich Splicing Factor kinase, (SRPK1). Immunohistochemical (IHC) analysis of EC tumor TMAs confirmed MIB-MS findings and showed SRPK1 protein levels were highly expressed in endometrioid and uterine serous cancer (USC) histological subtypes. Querying large-scale genomics studies of EC tumors revealed high expression of SRPK1 correlated with poor survival. Inhibition of SRPK1 in USC cells altered mRNA splicing, downregulating several oncogenes including MYC and Survivin resulting in apoptosis. Taken together, we present a SILAC-based MIB-MS kinome profiling platform for measuring kinase abundance in tumor tissues, and demonstrate its application to identify SRPK1 as a plausible kinase drug target for the treatment of EC.
Biodiversity mediates the effects of stressors but not nutrients on litter decomposition
Authors: Beaumelle Léa , Laender Frederik De , Eisenhauer Nico 
Published: March 2020

AbstractUnderstanding the consequences of ongoing biodiversity changes for ecosystems is a pressing challenge. Controlled biodiversity-ecosystem function experiments with random biodiversity loss scenarios have demonstrated that more diverse communities usually provide higher levels of ecosystem functioning. However, it is not clear if these results predict the ecosystem consequences of environmental changes that cause non-random alterations in biodiversity and community composition. We synthesized 69 independent studies reporting 660 observations of the impacts of two pervasive drivers of global change (chemical stressors and nutrient enrichment) on animal and microbial decomposer diversity and litter decomposition. Using meta-analysis and structural equation modelling, we show that declines in decomposer diversity and abundance explain reduced litter decomposition in response to stressors but not to nutrients. While chemical stressors generally reduced biodiversity and ecosystem functioning, detrimental effects of nutrients occurred only at high levels of nutrient inputs. Thus, more intense environmental change does not always result in stronger responses, illustrating the complexity of ecosystem consequences of biodiversity change. Overall, these findings provide strong empirical evidence for significant real-world biodiversity-ecosystem functioning relationships when human activities decrease biodiversity. This highlights that the consequences of biodiversity change for ecosystems are nontrivial and depend on the kind of environmental change.
Population Stratification at the Phenotypic Variance level and Implication for the Analysis of Whole Genome Sequencing Data from Multiple Studies
Authors: Sofer Tamar , Zheng Xiuwen , Laurie Cecelia A. , Gogarten Stephanie M. , Brody Jennifer A. , Conomos Matthew P. , Bis Joshua C. , Thornton Timothy A. , Szpiro Adam , O’Connell Jeffrey R. , Lange Ethan M. , Gao Yan , Cupples L. Adrienne , Psaty Bruce M. ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Rice Kenneth M. 
Published: March 2020

SummaryIn modern Whole Genome Sequencing (WGS) epidemiological studies, participant-level data from multiple studies are often pooled and results are obtained from a single analysis. We consider the impact of differential phenotype variances by study, which we term ‘variance stratification’. Unaccounted for, variance stratification can lead to both decreased statistical power, and increased false positives rates, depending on how allele frequencies, sample sizes, and phenotypic variances vary across the studies that are pooled. We describe a WGS-appropriate analysis approach, implemented in freely-available software, which allows study-specific variances and thereby improves performance in practice. We also illustrate the variance stratification problem, its solutions, and a corresponding diagnostic procedure in data from the Trans-Omics for Precision Medicine Whole Genome Sequencing Program (TOPMed), used in association tests for hemoglobin concentrations and BMI.
The physical form of microbial ligands bypasses the need for dendritic cell migration to stimulate adaptive immunity
Authors: Borriello Francesco , Spreafico Roberto , Poli Valentina , Chou Janet , Barrett Nora A. , Lacanfora Lucrezia , Franco Marcella E , Marongiu Laura , Iwakura Yoichiro , Pucci Ferdinando , Kruppa Michael D , Ma Zuchao , Wiliams David L , Zanoni Ivan 
Published: March 2020

AbstractA central paradigm of immunology is that the innate immune system first detects infectious agents in peripheral tissues, shortly after a pathogen has breached an epithelial barrier. This detection event is mediated by pattern recognition receptors in phagocytes, which then migrate to draining lymph nodes (dLNs), where information of a microbial encounter is conveyed to T and B lymphocytes to generate adaptive immunity. Through the study of fungal moieties, we present data that challenge this model. We found that soluble fungal polysaccharides are immunosilent in the periphery, but become potent immunogens in the dLN. These ligands completely bypass the need of phagocyte migration and, instead, directly activate an immune response that is most similar to those that typify viral infections. These data establish a class of microbial products that violate a central tenet of the immunological lexicon and illustrate that the physical form (not just the chemical structure) impacts innate and adaptive immunity.
Plagues of Desert Locust: No invasion risk to China
Authors: Wang Yun-Ping , Wu Ming-Fei , Lin Pei-Jiong , Wang Yao , Chen Ai-Dong , Jiang Yu-Ying , Zhai Bao-Ping , Chapman Jason W. , Hu Gao 
Published: March 2020

AbstractRecently, the most serious upsurge of desert locust (Schistocerca gregaria) in the last 25 years is spreading across eastern Africa and southwestern Asia. Parts of the desert locust ‘invasion area’, namely the northern border areas of Pakistan and India are very close to China, and whether locust swarms will invade China is of wide concern. To answer this question, we identified areas of potentially suitable habitat for the desert locust within China based on historical precipitation and temperature data, and found that parts of Xinjiang and Inner Mongolia provinces could provide ephemeral habitat in summer, but these places are remote from any other desert locust breeding area. Presently, the desert locust populations in Pakistan and India are mature and have laid eggs, and are less likely to spread long distances. The next generation of adults will appear in April and May, and so we examined twenty years’ historical wind data (2000–2019) for this period. Our results showed that winds at the height of locust swarm flight blew eastward during April and May, but the wind speeds were quite slow and would not facilitate desert locust eastward migration over large distances. Furthermore, simulated trajectories of desert locust swarms with 10 days’ migration mostly ended within India. The most easterly point of these trajectories just reached eastern India, close to the border between India and Myanmar, and this is very close to the eastern border of the invasion area of desert locust described in previous studies. In conclusion, the risk that the desert locust will invade China is very low.
Direction-selective motion discrimination by traveling waves in visual cortex
Authors: Heitmann Stewart , Ermentrout G. Bard 
Published: March 2020

AbstractThe majority of neurons in primary visual cortex respond selectively to bars of light that have a specific orientation and move in a specific direction. The spatial and temporal responses of such neurons are non-separable. How neurons accomplish that computational feat without resort to explicit time delays is unknown. We propose a novel neural mechanism whereby visual cortex computes non-separable responses by generating endogenous traveling waves of neural activity that resonate with the space-time signature of the visual stimulus. The spatiotemporal characteristics of the response are defined by the local topology of excitatory and inhibitory lateral connections in the cortex. We simulated the interaction between endogenous traveling waves and the visual stimulus using spatially distributed populations of excitatory and inhibitory neurons with Wilson-Cowan dynamics and inhibitory-surround coupling. Our model reliably detected visual gratings that moved with a given speed and direction provided that we incorporated neural competition to suppress false motion signals in the opposite direction. The findings suggest that endogenous traveling waves in visual cortex can impart direction-selectivity on neural responses without resort to explicit time delays. They also suggest a functional role for motion opponency in eliminating false motion signals.Author summaryIt is well established that the so-called ‘simple cells’ of the primary visual cortex respond preferentially to oriented bars of light that move across the visual field with a particular speed and direction. The spatiotemporal responses of such neurons are said to be non-separable because they cannot be constructed from independent spatial and temporal neural mechanisms. Contemporary theories of how neurons compute non-separable responses typically rely on finely tuned transmission delays between signals from disparate regions of the visual field. However the existence of such delays is controversial. We propose an alternative neural mechanism for computing non-separable responses that does not require transmission delays. It instead relies on the predisposition of the cortical tissue to spontaneously generate spatiotemporal waves of neural activity that travel with a particular speed and direction. We propose that the endogenous wave activity resonates with the visual stimulus to elicit direction-selective neural responses to visual motion. We demonstrate the principle in computer models and show that competition between opposing neurons robustly enhances their ability to discriminate between visual gratings that move in opposite directions.
Noise Invariance in Inferior Colliculus Neurons is Dependant on the Input Noisy Conditions
Authors: Hosseini Maryam , Rodriguez Gerardo , Guo Hongsun , Lim Hubert H. , Plourde Éric 
Published: March 2020

AbstractThe auditory system is extremely efficient to extract audio information in the presence of background noise. However, the neural mechanisms related to this efficiency is still greatly misunderstood, especially in the inferior colliculus (IC). In fact, while noise processing under different conditions has been investigated at the auditory cortex level, studies in the IC have been much limited. One interesting observation has been that there seems to be some degree of noise invariance in the IC in the presence of white noise. We wish to broaden this knowledge by investigating if there is a difference in the activity of neurons in the IC, when presenting noisy vocalisations with different types of noises, input signal-to-noise ratios (SNR) and signal levels. We do so using a generalized linear model (GLM), which gives us the ability to study the neural activity under these different conditions at a per neuron level. We found that non-stationary noise is the only noise type that clearly contributes to the neural activity in the IC, regardless of the SNR, input level or vocalisation type. However, when presenting white or natural stationary noises, a great diversity of responses was observed for the different conditions, where the activity of some neurons was affected by the presence of noise and the activity of others was not. Therefore, there seems to be some level of background noise invariance as early as the IC level, as reported before, however, this invariance seems to be highly dependent on the noisy conditions.New & NoteworthyThe neural mechanisms of auditory perception in the presence of background noise are still not well understood, especially in the IC. We studied neural activity in the IC when presenting noisy vocalisations using different background noise types, SNRs and input sound levels. We observed that only the non-stationary noise type clearly contributes to the neural activity in the IC. The noise invariance previously observed in the IC thus seems dependent on the noisy conditions.