bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 surveillance - a descriptive study on data quality issues
Authors: Costa-Santos Cristina , Luísa Neves Ana , Correia Ricardo , Santos Paulo , Monteiro-Soares Matilde , Freitas Alberto , Ribeiro-Vaz Inês , Henriques Teresa , Rodrigues Pedro Pereira , Costa-Pereira Altamiro , Pereira Ana Margarida , Fonseca João 
Published: November 2020

AbstractBackgroundHigh-quality data is crucial for guiding decision making and practicing evidence-based healthcare, especially if previous knowledge is lacking. Nevertheless, data quality frailties have been exposed worldwide during the current COVID-19 pandemic. Focusing on a major Portuguese surveillance dataset, our study aims to assess data quality issues and suggest possible solutions.MethodsOn April 27th 2020, the Portuguese Directorate-General of Health (DGS) made available a dataset (DGSApril) for researchers, upon request. On August 4th, an updated dataset (DGSAugust) was also obtained. The quality of data was assessed through analysis of data completeness and consistency between both datasets.ResultsDGSAugust has not followed the data format and variables as DGSApril and a significant number of missing data and inconsistencies were found (e.g. 4,075 cases from the DGSApril were apparently not included in DGSAugust). Several variables also showed a low degree of completeness and/or changed their values from one dataset to another (e.g. the variable ‘underlying conditions’ had more than half of cases showing different information between datasets). There were also significant inconsistencies between the number of cases and deaths due to COVID-19 shown in DGSAugust and by the DGS reports publicly provided daily.ConclusionsThe low quality of COVID-19 surveillance datasets limits its usability to inform good decisions and perform useful research. Major improvements in surveillance datasets are therefore urgently needed - e.g. simplification of data entry processes, constant monitoring of data, and increased training and awareness of health care providers - as low data quality may lead to a deficient pandemic control.
Extensive and accurate benchmarking of DIA acquisition methods and software tools using a complex proteomic standard
Authors: Gotti Clarisse , Roux-Dalvai Florence , Joly-Beauparlant Charles , Mangnier Loïc , Leclercq Mickaël , Droit Arnaud 
Published: November 2020

ABSTRACTOver the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins mixture (UPS1 – Sigma) at 8 different concentrations in anE. coliproteome background, we tested 36 workflows including 4 different DIA window acquisition schemes and 6 different software tools (DIA-NN, DIA-Umpire, OpenSWATH, ScaffoldDIA, Skyline and Spectronaut) with or without the use of a DDA spectral library. Based on the number of proteins identified, quantification linearity and reproducibility, as well as sensitivity and specificity in 28 pairwise comparisons of different UPS1 concentrations, we summarize the major considerations and propose guidelines for choosing the DIA workflow best suited for LC-MS/MS proteomic analyses. Our 96 DIA raw files and software outputs have been deposited on ProteomeXchange for testing or developing new DIA processing tools.
New water and air pollution sensors added to the Sonic Kayak citizen science system for low cost environmental mapping
Authors: Griffiths Amber GF , Garrett Joanne K , Duffy James P , Matthews Kaffe , Visi Federico G , Eatock Claire , Robinson Mike , Griffiths David J 
Published: November 2020

AbstractSonic Kayaks are low-cost open-source systems for gathering fine-scale environmental data. The system is designed to be simple to fit on to standard kayaks or canoes, and full instructions have been made available for anyone wishing to build their own. The first version included temperature sensors and a hydrophone for recording underwater sound. Here we outline the design and integration of two new sensors, for underwater turbidity and above water air particulate pollution. All sensors record continually, and the GPS location, time and date are also stored for every data point, allowing fine-scale environmental data mapping. The data being collected by the sensors is sonified (turned into sound) in real-time, allowing the paddler to hear the data as they are collecting it, making it possible to locate and follow interesting occurrences. We present proof-of principle data for the first time for all the sensors, demonstrating how the system can be used for environmental mapping, and discuss potential future applications and adaptations. We believe the Sonic Kayak system offers particular promise for citizen science and environmental activism, as well as allowing professional researchers to gather data that was previously difficult or impossible to obtain.
Variant Calling Parallelization on Processor-in-Memory Architecture
Authors: Lavenier Dominique , Cimadomo Remy , Jodin Romaric 
Published: November 2020

AbstractIn this paper, we introduce a new combination of software and hardware PIM (Process-in-Memory) architecture to accelerate the variant calling genomic process. PIM translates into bringing data intensive calculations directly where the data is: within the DRAM, enhanced with thousands of processing units. The energy consumption, in large part due to data movement, is significantly lowered at a marginal additional hardware cost. Such design allows an unprecedented level of parallelism to process billions of short reads. Experiments on real PIM devices developed by the UPMEM company show significant speed-up compared to pure software implementation. The PIM solution also compared nicely to FPGA or GPU based acceleration bringing similar to twice the processing speed but most importantly being 5 to 8 times cheaper to deploy with up to 6 times less power consumption.
Geographic microevolution ofMycobacterium ulceranssustains Buruli ulcer extension, Australia
Authors: Saad Jamal , Hammoudi Nassim , Zgheib Rita , Anani Hussein , Drancourt Michel 
Published: November 2020

AbstractThe reason why severe cases of Buruli ulcers caused byMycobacterium ulceransare emerging in some South Australia counties has not been determined. In this study, we measured the diversity ofM. ulceranscomplex whole genome sequences (WGS) and reported a marker of this diversity. Using this marker as a probe, we compared WGS diversity in Buruli ulcer-epidemic South Australia counties versus non-epidemic Australian counties and further refined comparisons at the level of counties where severe Buruli ulcer cases have been reported. Analyzing 218 WGS (35 complete and 183 reconstructed WGS, including 174 Australian WGS) yielded 15M. ulceranscomplex genotypes, including three genotypes specific to Australia and one genotype specific to South Australia. A 1,068-bp PPE family protein gene exhibiting genotype-specific sequence variations was employed to further probe 13 minority clones hidden in sequence reads. The repartition of these clones significantly differed between South Australia and the rest of Australia. In addition, a significantly higher prevalence of 3/13 clones was observed in South Australia counties of the Mornington Peninsula, Melbourne and Bellarine Peninsula than in other South Australia counties. The data presented in this report suggest that the microevolution of threeM. ulceranscomplex clones drove the emergence of severe Buruli ulcer cases in some South Australia counties. Sequencing one specificPPEgene served to efficiently probeM. ulceranscomplex clones. Further functional studies may balance the environmental adaptation and virulence of these clones.
Immediate impact of transcranial magnetic stimulation on brain structure: short-term neuroplasticity following one session of cTBS
Authors: Jung JeYoung , Lambon Ralph Matthew A. 
Published: November 2020

AbstractRecent evidence demonstrates that activation-dependent neuroplasticity on a structural level can occur in a short time (2 hour or less) in humans. However, the exact time scale of structural plasticity in adult human brain remains unclear. Using voxel-based morphometry (VBM), we investigated changes in gray matter (GM) after one session of continuous theta-burst stimulation (cTBS) delivered to the anterior temporal lobe (ATL). Twenty-five participants were received cTBS over the left ATL or occipital pole as a control site outside of the scanner and had structural and functional imaging. During functional imaging, participants performed a semantic association task. VBM result revealed decreased GM in the left ATL and right cerebellum after ATL stimulation compared to the control stimulation. In addition, cTBS over the left ATL induced slower reaction time in sematic task performance, reduced regional activity at the target site, and altered functional connectivity between the left and right ATL during semantic processing. Furthermore, the ATL GM changes were associated with the functional connectivity changes in the ATL-connectivity during semantic processing. These structural alterations are mirrored by functional changes in cortical excitability attributed to the GM changes and demonstrate the rapid dynamics of cortical plasticity. Our findings support fast adjusting neuronal systems, such as postsynaptic morphology changes and neuronal turnover. Our results suggest that TBS is able to produce powerful changes in regional synaptic activity in human adult brain.
Spatial management can significantly reduce dFAD beachings in Indian and Atlantic Ocean tropical tuna purse seine fisheries
Authors: Imzilen Taha , Lett Christophe , Chassot Emmanuel , Kaplan David M. 
Published: November 2020

AbstractDebris from fisheries pose significant threats to coastal marine ecosystems worldwide. Tropical tuna purse seine fisheries contribute to this problem via the construction and deployment of thousands of man-made drifting fish aggregating devices (dFADs) annually, many of which end up beaching in coastal areas. Here, we analyzed approximately 40 000 dFAD trajectories in the Indian Ocean (IO) and 12 000 dFAD trajectories in the Atlantic Ocean (AO) deployed over the decade 2008-2017 to identify where and when beachings occur. We find that there is tremendous promise for reducing beaching events by prohibiting deployments in areas most likely to lead to a beaching. For example, our results indicate that around 40% of beachings can be prevented if deployments are prohibited in areas in the south of 8°S latitude, the Somali zone in winter, and the western Maldives in summer for the IO, and in an elongated strip of areas adjacent to the western African coast for the AO. In both oceans, the riskiest areas for beaching are not coincident with areas of high dFAD deployment activity, suggesting that these closures could be implemented with relatively minimal impact to fisheries. Furthermore, the existence of clear hotspots for beaching likelihood and the high rates of putative recovery of dFAD buoys by small-scale fishers in some areas suggests that early warning systems and dFAD recovery programs may be effective in areas that cannot be protected via closures if appropriate incentives can be provided to local partners for participating in these programs.
Variations in photoreceptor throughput to mouse visual cortex and the unique effects on tuning
Authors: Rhim I. , Coello-Reyes G. , Nauhaus I. 
Published: November 2020

ABSTRACTVisual input to primary visual cortex (V1) depends on highly adaptive filtering in the retina. In turn, isolation of V1 computations to study cortical circuits requires control over retinal adaption and its corresponding spatio-temporal-chromatic output. Here, we first measure the balance of input to V1 from the three main photoreceptor opsins – M-opsin, S-opsin, and rhodopsin – as a function of light adaption and retinotopy. Results show that V1 is rod-mediated in common laboratory settings, yet cone-mediated in natural daylight, as evidenced by exclusive sensitivity to UV wavelengths via cone S-opsin in the upper visual field. Next, we show that cone-mediated V1 responds to 2.5-fold higher temporal frequencies than rod-mediated V1. Furthermore, cone-mediated V1 has smaller RFs, yet similar spatial frequency tuning. V1 responses in rod-deficient (Gnat1−/−) mice confirm that the effects are due to differences in photoreceptor contribution. This study provides foundation for using mouse V1 to study cortical circuits.
Conjunctive spatial and idiothetic codes are topographically organized in the GABAergic cells of the lateral septum
Authors: van der Veldt Suzanne , Etter Guillaume , Mosser Coralie-Anne , Manseau Frédéric , Williams Sylvain 
Published: November 2020

AbstractThe hippocampal spatial code’s relevance for downstream neuronal populations – particularly its major subcortical output the lateral septum (LS) - is still poorly understood. Here, using calcium imaging combined with unbiased analytical methods, we functionally characterized and compared the spatial tuning of LS GABAergic cells to those of dorsal CA3 and CA1 cells. We identified a significant number of LS cells that are modulated by place, speed, acceleration, and direction, as well as conjunctions of these properties, directly comparable to hippocampal CA1 and CA3 spatially modulated cells. Interestingly, Bayesian decoding of position based on LS spatial cells reflected the animal’s location as accurately as decoding using the activity of hippocampal pyramidal cells. A portion of LS cells showed stable spatial codes over the course of multiple days, potentially reflecting long-term episodic memory. The distributions of cells exhibiting these properties formed gradients along the anterior-posterior and dorsal-ventral axes of the LS, directly reflecting the topographical organization of hippocampal inputs to the LS. Finally, we show using trans-synaptic tracing that LS neurons receiving CA3 and CA1 excitatory input send projections to the hypothalamus and medial septum, regions that are not targeted directly by principal cells of the dorsal hippocampus. Together, our findings demonstrate that the LS accurately and robustly represents spatial, directional as well as self-motion information and is uniquely positioned to relay this information from the hippocampus to its downstream regions, thus occupying a key position within a distributed spatial memory network.
Photoperiod Sensitive Energy Sorghum Responses to Environmental and Nitrogen Variabilities
Authors: Schetter August , Lin Cheng-Hsien , Zumpf Colleen , Jang Chunhwa , Hoffmann Leo , Rooney William , Lee D.K. 
Published: November 2020

AbstractRecently introduced photoperiod-sensitive (PS) biomass sorghum (Sorghum bicolorL. Moench) needs to be investigated for their yield potentials under different cultivation environments with reasonable nitrogen (N) inputs. The objectives of this study were to 1) evaluate the biomass yield and feedstock quality of four sorghum hybrids with different levels of PS ranging from very PS (VPS) hybrids and to moderate PS (MPS) hybrids, and 2) determine the optimal N inputs (0~168 kg N ha−1) under four environments: combinations of both temperate (Urbana, IL) and subtropical (College Station, TX) regions during 2018 and 2019. Compared to TX, the PS sorghums in central IL showed higher yield potential and steady feedstock production with an extended daylength and with less precipitation variability, especially for the VPS hybrids. The mean dry matter (DM) yields of VPS hybrids were 20.5 Mg DM ha−1and 17.7 Mg DM ha−1in IL and TX, respectively. The highest N use efficiency occurred at a low N rate of 56 kg N ha−1by improving approximately 33 kg DM ha−1per 1.0 kg N ha−1input. Approximately 70% of the PS sorghum biomass can be utilized for biofuel production, consisting of 58-65% of the cell wall components and 4-11% of the soluble sugar. This study demonstrated that the rainfed temperate area (e.g., IL) has a great potential for the sustainable cultivation of PS energy sorghum due their observed high yield potential, stable production, and low N requirements.
Muscle Atrophy: Different Strains of Mice Respond Differently to Single Limb Immobilization
Authors: Maroni Camilla Reina , Friedman Michael A , Zhang Yue , McClure Michael J , Fulle Stefania , Farber Charles R. , Donahue Henry J. 
Published: November 2020

AbstractTo examine whether genetic variability plays a role in muscle adaption to its mechanical environment, we examined hind limb immobilization in five different strains of mice: CAST/EiJ, NOD/ShiLtJ, NZO/HILtJ, 129S1/SvImJ and A/J. Mice had one limb immobilized by a cast for three weeks. The response to immobilization was dependent on the strain of mice examined. A/J mice lost the most body weight following immobilization and displayed a significant decrease in physical activity. None of the other strains displayed a significant decrease in activity. Food consumption was significantly increased in NOD/ShiLtJ mice. All other strains had non-significant changes in food consumption. Muscle mass/body weight was decreased by immobilization, to varying degrees, in all strains except 1291/SvImJ. Casting decreased absolute muscle mass in both quadriceps and gastrocnemius in NOD/ShiltJ and NZO/HILtJ mice, two strains that can develop diabetes, but not in the other strains. Three weeks of immobilization caused a significant increase in quadriceps levels of atrogenes in CAST/EiJ mice but not in other strains. Immobilization caused a significant increase in quadriceps and gastrocnemius levels ofMyh4in CAST/EiJ mice but not in any other strain. A similar trend was observed forMyh7in gastrocnemius muscle. Immobilization resulted in a decrease the p-p70S6K1/total p706SK1 ratio in quadriceps of NOD/ShiLtJ mice and the gastrocnemius of A/J mice, but not in other strains. Immobilization did not affect the p-4EBP1/total 4EBP1 ratio in quadriceps of any of the strains examined. However, the p-4EBP1/total 4EBP1 ratio in gastrocnemius was greater in immobilized, relative to control, limbs in CAST/EiJ mice. Muscle mass normalized to body weight in both gastrocnemius and quadriceps displayed the greatest degree of heritability. These results reveal remarkable variability in responsiveness to immobilization across five different genetic strains of mice.
Geographic variation in the seed mycobiome ofPseudotsuga menziesiivar.menziesiiacross the Pacific Northwest, USA
Authors: Bergmann Gillian E. , Busby Posy E. 
Published: November 2020

ABSTRACTFungal symbionts occur in all plant tissues, and many aid their host plants with critical functions, including nutrient acquisition, defense against pathogens, and tolerance of abiotic stress. “Core” taxa in the plant mycobiome, defined as fungi present across individuals, populations, or time, may be particularly crucial to plant survival during the challenging seedling stage. However, studies on core seed fungi are limited to individual sampling sites, raising the question of whether core taxa exist across large geographic scales. We addressed this question using both culture-based and culture-free techniques to identify the fungi found in individual seeds collected from nine provenances across the range of Coastal Douglas-fir (Pseudotsuga menziesiivar.menziesii), a foundation tree species in the Pacific Northwest and a globally important timber crop that is propagated commercially by seed. Two key findings emerged: 1) Seed mycobiome composition differed among seed provenances. 2) Despite spatial variation in the seed mycobiome, we detected four core members, none of which is a known pathogen of Douglas-fir:Trichodermaspp.,Hormonema macrosporum,Mucor plumbeusandTalaromyces rugulosus. Our results support the concept of a core seed microbiome, yet additional work is needed to determine the functional consequences of core taxa for seedling germination, growth, survival and competition.
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences
Authors: Rasekh Marzieh Eslami , Hernandez Yozen , Drinan Samantha D. , Bass Juan I. Fuxman , Benson Gary 
Published: November 2020

ABSTRACTVariable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2,770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35,638 VNTR loci and classified 5,676 as commonly polymorphic (i.e., with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e., transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1,096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.
9p21 Loss Defines the Evolutionary Patterns of Aggressive Renal Cell Carcinomas
Authors: Carbone Federica , Huang Justin K. , Perelli Luigi , Poggetto Edoardo Del , Gutschner Tony , Tomihara Hideo , Soeung Melinda , Lam Truong Nguyen Anh , Xia Ruohan , Zhu Cihui , Song Xingzhi , Zhang Jianhua , Sircar Kanishka , Malouf Gabriel G. , Sgambato Alessandro , Karam Jose A. , Gao JianJun , Jonasch Eric , Viale Andrea , Draetta Giulio F. , Futreal Andrew , Bakouny Ziad , Van Allen Eliezer M. , Choueiri Toni , Msaouel Pavlos , Litchfield Kevin , Turajlic Samra , Heffernan Timothy P. , Chen Ying Bei , DiNatale Renzo G. , Hakimi A. Ari , Bristow Christopher A. , Tannir Nizar M. , Carugo Alessandro , Genovese Giannicola 
Published: November 2020

AbstractDedifferentiation and acquisition of chromosomal instability in renal cell carcinoma portends dismal prognosis and aggressive clinical behavior. However, the absence of reliable experimental models dramatically impacts the understanding of mechanisms underlying malignant progression. Here we established anin vivogenetic platform to rapidly generate somatic mosaic genetically engineerd immune-competent mouse models of renal tumors, recapitulating the genomic and phenotypic features of these malignancies. Leveraging somatic chromosomal engineering, we demonstrated that ablation of the murine locus syntenic to human 9p21 drives the rapid expansion of aggressive mesenchymal clones with prominent metastatic behavior, characterized by early emergence of chromosomal instability, whole-genome duplication, and conserved patterns of aneuploidy. This model of punctuated equilibrium provides a remarkable example of cross-species convergent evolution.SignificanceTo better understand the role of 9p21 in malignant progression, we generated a somatic mosaic GEMM of renal cancer, capturing the histological, genomic and evolutionary features of human disease. With this technology we demonstrated a critica role of 9p21 loss in metastatic evolution of RCC and provide a unique tool for testing new therapeutic treatments.