bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thresholds for Safety of Cleft Lip Surgery in Premature Infants
Authors: Kalmar Christopher L. , Patel Vijay A. , Humphries Laura S. , Vu Giap H. , Zimmerman Carrie E. , Swanson Jordan W. , Taylor Jesse A. 
Published: September 2020

Summary:
The purpose of this study was to delineate optimal age to perform unilateral or bilateral cleft lip repair in premature patients. The American College of Surgeons National Surgical Quality Improvement Program Pediatric data set was queried for unilateral and bilateral cleft lip repairs performed between 2012 and 2017. Complications, readmissions, and reoperations were analyzed in the context of prematurity with appropriate statistics. Degree of prematurity was significantly associated with adverse events (p = 0.001, r
s = 0.44). Premature patients with unilateral cleft lip had a significantly decreased risk of adverse events when performing cleft lip repair after 150 days of age [OR, 18.1; p = 0.004; before cutoff, n = 10 of 140 (7.1 percent); after cutoff, n = 0 of 112 (0.0 percent)] in the absence of other risk factors. Premature patients with bilateral cleft lip had a significantly decreased risk of adverse events when performing cleft lip repair after 175 days of age (OR, 16.1; p = 0.010; before cutoff, n = 7 of 33 (21.2 percent); after cutoff, n = 0 of 28 (0.0 percent)] in the absence of other risk factors.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Risk, II.
Facial Fat Augmentation Finesse
Authors: Xue Amy S. , Dayan Erez , Rohrich Rod J. 
Published: September 2020

Summary:
Volume restoration with autologous fat augmentation has become a key technique in facial rejuvenation. It is highly versatile and useful as an independent operation or as an adjunct to rhytidectomy and blepharoplasty. The goal of this article and the accompanying videos is to provide a detailed step-by-step guide to achieving predictable and optimized surgical results.
OpenABM-Covid19 - an agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing
Authors: Hinch Robert , Probert William J M , Nurtay Anel , Kendall Michelle , Wymant Chris , Hall Matthew , Lythgoe Katrina , Cruz Ana Bulas , Zhao Lele , Stewart Andrea , Ferretti Luca , Montero Daniel , Warren James , Mather Nicole , Abueg Matthew , Wu Neo , Finkelstein Anthony , Bonsall David G , Abeler-Dörner Lucie , Fraser Christophe 
Published: September 2020

AbstractSARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including both manual and digital contact tracing. It can simulate a population of 1 million people in seconds per day allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 is its Python interface, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic.
Ruling In and Ruling Out COVID-19: Computing SARS-CoV-2 Infection Risk From Symptoms, Imaging and Test Data
Authors: D’Ambrosia Christopher , Christensen Henrik I. , Aronoff-Spencer Eliah 
Published: September 2020

ABSTRACTBackgroundAssigning meaningful probabilities of SARS-CoV-2 infection risk presents a diagnostic challenge across the continuum of care.MethodsWe integrated patient symptom and test data using machine learning and Bayesian inference to quantify individual patient risk of SARS-CoV-2 infection. We trained models with 100,000 simulated patient profiles based on thirteen symptoms, estimated local prevalence, imaging, and molecular diagnostic performance from published reports. We tested these models with consecutive patients who presented with a COVID-19 compatible illness at the University of California San Diego Medical Center over 14 days starting in March 2020.ResultsWe included 55 consecutive patients with fever (78%) or cough (77%) presenting for ambulatory (n=11) or hospital care (n=44). 51% (n=28) were female, 49% were age <60. Common comorbidities included diabetes (22%), hypertension (27%), cancer (16%) and cardiovascular disease (13%). 69% of these (n=38) were RT-PCR confirmed positive for SARS-CoV-2 infection, 11 had repeated negative nucleic acid testing and an alternate diagnosis. Bayesian inference network, distance metric-learning, and ensemble models discriminated between patients with SARS-CoV-2 infection and alternate diagnoses with sensitivities of 81.6 – 84.2%, specificities of 58.8 – 70.6%, and accuracies of 61.4 – 71.8%. After integrating imaging and laboratory test statistics with the predictions of the Bayesian inference network, changes in diagnostic uncertainty at each step in the simulated clinical evaluation process were highly sensitive to location, symptom, and diagnostic test choices.ConclusionsDecision support models that incorporate symptoms and available test results can help providers diagnose SARS-CoV-2 infection in real world settings.
The Gini Coefficient as a useful measure of malaria inequality among populations
Authors: Abeles Jonathan , Conway David J 
Published: September 2020

ABSTRACTBACKGROUNDUnderstanding inequality in infectious disease burden requires clear and unbiased indicators. The Gini coefficient, conventionally used as a macroeconomic descriptor of inequality, is potentially useful to quantify epidemiological heterogeneity. With a potential range from 0 (all populations equal) to 1 (populations having maximal differences), this coefficient is used here to show the extent and persistence of inequality of malaria infection burden at a wide variety of population levels.METHODSWe first applied the Gini coefficient to quantify variation among WHO world regions for malaria and other major global health problems. Malaria heterogeneity was then measured among countries within the geographical sub-region where burden is greatest, among the major administrative divisions in several of these countries, and among selected local communities. Data were analysed from previous research studies, national surveys, and global reports, and Gini coefficients were calculated together with confidence intervals using bootstrap resampling methods.RESULTSMalaria showed a very high level of inequality among the world regions (Gini coefficient, G = 0.77, 95% CI 0.66-0.81), more extreme than for any of the other major global health challenges compared at this level. Within the most highly endemic geographical sub-region, there was substantial inequality in estimated malaria incidence among countries of West Africa, which did not decrease between 2010 (G = 0.28, 95% CI 0.19-0.36) and 2018 (G = 0.31, 0.22-0.39). There was a high level of sub-national variation in prevalence among states within Nigeria (G = 0.30, 95% CI 0.26-0.35), but more moderate variation within Ghana (G = 0.18, 95% CI 0.12-0.25) and Sierra Leone (G = 0.17, 95% CI 0.12-0.22). There was also significant inequality in prevalence among local village communities, generally more marked during dry seasons when there was lower mean prevalence. The Gini coefficient correlated strongly with the Coefficient of Variation which has no finite range.CONCLUSIONSThe Gini coefficient is a useful descriptor of epidemiological inequality at all population levels, with confidence intervals and interpretable bounds. Wider use of the coefficient would give broader understanding of malaria heterogeneity revealed by multiple types of studies, surveys and reports, providing more accessible insight from available data.
Two-target quantitative PCR to predict library composition for shallow shotgun sequencing
Authors: Cho Matthew Y. , Oliva Marc , Spreafico Anna , Chen Bo , Wei Xu , Choi Yoojin , Kaul Rupert , Siu Lillian L. , Coburn Bryan , Schneeberger Pierre H. H. 
Published: September 2020

AbstractShotgun sequencing enables retrieving high resolution information 40 from complex microbial communities. However, the technique is limited by missing information about host-to-microbe ratios observed in different sample types. This makes it challenging to plan sequencing experiments, especially in the context of high sample multiplexing and/or limited sequencing output. We evaluated a qPCR-based assay to predict host-to microbe ratio prior to sequencing. Using a two-target assay aimed at conserved human and bacterial genes, we predicted human-to-microbe ratios in two sample types and validated it on independently collected samples. The assay enabled accurate prediction for a broad range of sample compositions.
The firstAntechinusreference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies
Authors: Brandies Parice A. , Tang Simon , Johnson Robert S.P. , Hogg Carolyn J. , Belov Katherine 
Published: September 2020

AbstractAntechinus are a genus of mouse-like marsupials that exhibit a rare reproductive strategy known as semelparity and also naturally develop age-related neuropathologies similar to those in humans. We provide the first annotated antechinus reference genome for the brown antechinus (Antechinus stuartii). The reference genome is 3.3Gb in size with a scaffold N50 of 73Mb and 93.3% complete mammalian BUSCOs. Using bioinformatic methods we assign scaffolds to chromosomes and identify 0.78Mb of Y-chromosome scaffolds. Comparative genomics revealed interesting expansions in the NMRK2 gene and the protocadherin gamma family, which have previously been associated with aging and age-related dementias respectively. Transcriptome data displayed expression of common Alzheimer’s related genes in the antechinus brain and highlight the potential of utilising the antechinus as a future disease model. The valuable genomic resources provided herein will enable future research to explore the genetic basis of semelparity and age-related processes in the antechinus.
Starvation-induced regulation of carbohydrate transport at the blood-brain barrier is TGF-β-signaling dependent
Authors: Hertenstein Helen , McMullen Ellen , Weiler Astrid , Volkenhoff Anne , Becker Holger M. , Schirmeier Stefanie 
Published: September 2020

AbstractDuring hunger or malnutrition animals prioritize alimentation of the brain over other organs to ensure its function and thus their survival. This so-called brain sparing is described from Drosophila to humans. However, little is known about the molecular mechanisms adapting carbohydrate transport. Here, we used Drosophila genetics to unravel the mechanisms operating at the blood-brain barrier (BBB) under nutrient restriction. During starvation, expression of the carbohydrate transporter Tret1-1 is increased to provide more efficient carbohydrate uptake. Two mechanisms are responsible for this increase. Similarly to the regulation of mammalian GLUT4, Rab-dependent intracellular shuttling is needed for Tret1-1 integration into the plasma membrane, even though Tret1-1 regulation is independent of insulin signaling. In addition, starvation induces transcriptional upregulation controlled by TGF-β signaling. Considering TGF-β-dependent regulation of the glucose transporter GLUT1 in murine chondrocytes, our study reveals an evolutionarily conserved regulatory paradigm adapting the expression of sugar transporters at the BBB.
Tricarboxylic acid cycle and proton gradient inPandoravirus massiliensis: Is it still a virus?
Authors: Aherfi Sarah , Brahim Belhaouari Djamal , Pinault Lucile , Baudoin Jean-Pierre , Decloquement Philippe , Abrahao Jonatas , Colson Philippe , Levasseur Anthony , Lamb David C. , Chabriere Eric , Raoult Didier , La Scola Bernard 
Published: September 2020

ABSTRACTSince the discovery ofAcanthamoeba polyphagaMimivirus, the first giant virus of amoeba, the historical hallmarks defining a virus have been challenged. Giant virion sizes can reach up to 2.3 µm, making them visible by optical microscopy. They have large genomes of up to 2.5 Mb that encode proteins involved in the translation apparatus. Herein, we investigated possible energy production inPandoravirus massiliensis, the largest of our giant virus collection. MitoTracker and TMRM mitochondrial membrane markers allowed for the detection of a membrane potential in virions that could be abolished by the use of the depolarizing agent CCCP. An attempt to identify enzymes involved in energy metabolism revealed that 8 predicted proteins ofP. massiliensisexhibited low sequence identities with defined proteins involved in the universal tricarboxylic acid cycle (acetyl Co-A synthase; citrate synthase; aconitase; isocitrate dehydrogenase; α-ketoglutarate decarboxylase; succinate dehydrogenase; fumarase). All 8 viral predicted ORFs were transcribed together during viral replication, mainly at the end of the replication cycle. Two of these proteins were detected in mature viral particles by proteomics. The product of the ORF132, a predicted protein ofP. massiliensis, cloned and expressed inEscherichia coli, provided a functional isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle, which converts isocitrate to α-ketoglutarate. We observed that membrane potential was enhanced by low concentrations of Acetyl-CoA, a regulator of the tricarboxylic acid cycle. Our findings show for the first time that energy production can occur in viruses, namely, pandoraviruses, and the involved enzymes are related to tricarboxylic acid cycle enzymes. The presence of a proton gradient inP. massiliensiscoupled with the observation of genes of the tricarboxylic acid cycle make this virus a form a life for which it is legitimate to question ‘what is a virus?’.
Reclassification ofCatabacter hongkongensisasChristensenella hongkongensiscomb.nov. based on whole genome analysis
Authors: Liu Xiaoying , Sutter Jessica L. , de la Cuesta-Zuluaga Jacobo , Waters Jillian L. , Youngblut Nicholas D. , Ley Ruth E. 
Published: September 2020

AbstractThe generaCatabacter (family Catabacteraceae)andChristensenella(familyChristensenellaceae)are close relatives within the phylum Firmicutes. Members of these genera are strictly anaerobic, non-spore forming, short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest thatCatabactersplitsChristensenellainto a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species ofChristensenellaand two strains ofCatabacter hongkongensis. A concatenated alignment of 135 shared protein sequences indicates thatC. hongkongensisis indeed nested within theChristensenellaclade. Based on their evolutionary relationship, we propose the transfer ofCatabacter hongkongensisto the new genus asChristensenella hongkongensiscomb.nov.
FHOD formin and SRF promote striated muscle development through separate pathways inC. elegans
Authors: Yingling Curtis V. , Pruyne David 
Published: September 2020

AbstractPrevious work with cultured cells has shown transcription of muscle genes by serum response factor (SRF) can be stimulated by actin polymerization driven by proteins of the formin family. However, it is not clear if endogenous formins similarly promote SRF-dependent transcription during muscle developmentin vivo. We tested whether formin activity promotes SRF-dependent transcription in striated muscle in the simple animal model,Caenorhabditis elegans. Our lab has shown FHOD-1 is the only formin that directly promotes sarcomere formation in the worm’s striated muscle. We show here FHOD-1 and SRF homolog UNC-120 both support muscle growth and also muscle myosin II heavy chain expression. However, while a hypomorphicunc-120allele blunts transcription of a set of striated muscle genes, these genes are upregulated or unchanged by absence of FHOD-1. Instead, pharmacological inhibition of the proteasome restores myosin protein levels in worms lacking FHOD-1, suggesting elevated proteolysis accounts for their myosin deficit. Interestingly, proteasome inhibition does not restore normal muscle growth tofhod-1(Δ)mutants, suggesting formin contributes to muscle growth by some alternative mechanism. Overall, we find SRF does not depend on formin to promote muscle gene transcription in a simplein vivosystem.
Evidence for current circulation of an ancient West Nile virus strain (NY99) in Brazil
Authors: Siconelli Márcio Junio Lima , de Melo Jorge Daniel Macedo , de Castro-Jorge Luiza Antunes , Fonseca-Júnior Antônio Augusto , Nascimento Mateus Laguardia , Floriano Vitor Gonçalves , de Souza Fransérgio Rocha , de Queiroz-Júnior Eudson Maia , Camargos Marcelo Fernandes , Lara Costa Eliana Dea , Bianco Carvalho Adolorata Aparecida , da Fonseca Benedito Antonio Lopes 
Published: September 2020

AbstractIntroductionIn Brazil, West Nile virus (WNV) was first detected in 2018 from horses with neurological disease.AimHere we present the first reported case in Ceará state and complete genome sequence from an isolated in Espírito Santo state from 2019.MethodsThe virus was isolated from a horse that died with neurological signs in Espírito Santo and was sequenced by MiSeq.ResultsPhylogenetic analysis reveals that this isolate belongs to lineage 1a, clustering with NY99 strain, that disappeared from the USA since 2005.ConclusionsOur findings reinforce the hypothesis that WNV has been silently circulating in Brazil for many years.
Density modification of cryo-EM maps
Authors: Terwilliger Thomas C. , Sobolev Oleg V. , Afonine Pavel V. , Adams Paul D. , Read Randy J. 
Published: September 2020

Density modification uses expectations about features of a map such as a flat solvent and expected distributions of density in the region of the macromolecule to improve individual Fourier terms representing the map. This process transfers information from one part of a map to another and can improve the accuracy of a map. Here, the assumptions behind density modification for maps from electron cryomicroscopy are examined and a procedure is presented that allows the incorporation of model-based information. Density modification works best in cases where unfiltered, unmasked maps with clear boundaries between the macromolecule and solvent are visible, and where there is substantial noise in the map, both in the region of the macromolecule and the solvent. It also is most effective if the characteristics of the map are relatively constant within regions of the macromolecule and the solvent. Model-based information can be used to improve density modification, but model bias can in principle occur. Here, model bias is reduced by using ensemble models that allow an estimation of model uncertainty. A test of model bias is presented that suggests that even if the expected density in a region of a map is specified incorrectly by using an incorrect model, the incorrect expectations do not strongly affect the final map.
Utilising social networking services as a collective medium to support design communication in team collaboration
Authors: Kim Mi Jeong , Hwang Yeon Sook , Hwang Ha Sung 
Published: September 2020

PurposeA variety of collaborative technologies have been developed to support design communication among members of design teams, and understanding the affordances of these technologies is critical to effective design collaboration. This research explores the potential of social networking as a collective medium that encourages design communication among student designers at the conceptual stage of design in a studio course.Design/methodology/approachFor one semester, the student participants used different social networking services to communicate with their team members, and the authors analysed how they collaborated when solving a given problem using the collaborative tools.FindingsThe results show that various social networking platforms support students' communication of design and exploration of problems differently by affecting their clarification of ideas and information sharing. Collective discussion and online support are useful for framing problems and ideation in collaborative design.Originality/valueThis research proposes that social networking services appropriate to the activities needed to be chosen and provided to enable design communication to promote students' active learning through team collaboration.
Improving China's alfalfa industry development: an economic analysis
Authors: Wang Wenxin 
Published: September 2020

PurposeThis study analyzes the factors which affect the alfalfa cultivation acreage in China and estimates the development of alfalfa planting by the supply model.Design/methodology/approachBased on the characteristics and actual conditions of alfalfa cultivation in China, a naïve empirical model was created to analyze the impact of various influencing factors on the cultivation acreage of alfalfa.FindingsThe analysis of influential factors shows that China's alfalfa planting conforms to naïve price behavior. The prices of alfalfa and per capita arable land occupancy have a positive effect on the cultivation acreage, while the price of competitive crops and transportation costs have a negative effect on the production of alfalfa. Lastly, the 2012 alfalfa subsidy policy has a significant negative impact on alfalfa cultivation acreage.Research limitations/implicationsDue to the limited research on alfalfa supply in China, there is a lack of available research data and statistical data. A large number of data in this study are mainly indirect data derived and calculated from other industrial data. The measurement results may not be fully accurate.Originality/valueThis study represents the first empirical analysis of the characteristics of the factors influencing alfalfa cultivation acreage in China. The secondary data were used to analyze the influence of various control variables on the cultivation acreage of alfalfa, which is different from existing research.
Firm and industry effects: the importance of sample design
Authors: López-López Vicente , Iglesias Antelo Susana , Sousa Carlos M.P. 
Published: September 2020

Purpose
This paper aims to examine how sample design affects the relative importance of firm and industry factors in explaining performance variations.

Design/methodology/approach
Using a sample of 14,204 Spanish firms over a 10-year time frame, this study uses partial sensitivity analysis to examine the biases in results as a consequence of three methodological relevant concerns: outliers, industry classification and period.

Findings
Results indicate that the industry effect, supported by the industrial organization theory, has been underestimated in the empirical tests.

Originality/value
This study examines the biases in results as a consequence of three methodological relevant concerns (outliers, sector classification and period), which have not been sufficiently studied to date. Moreover, the study provides some new evidence favourable to the Industrial Organization (IO) perspective, which could have been biased and underestimated by the literature, as most of the analyses do not consider the methodological issues studied in this paper.