bluuebunny/crossref_metadata_2025_split huggingface dataset:
genozip: a fast and efficient compression tool for VCF files
Authors: Lan Divon , Tobler Raymond , Souilmi Yassine , Llamas Bastien 
Published: April 2020

Abstract

Motivation
genozip is a new lossless compression tool for Variant Call Format (VCF) files. By applying field-specific algorithms and fully utilizing the available computational hardware, genozip achieves the highest compression ratios amongst existing lossless compression tools known to the authors, at speeds comparable with the fastest multi-threaded compressors.

Availability and implementation
genozip is freely available to non-commercial users. It can be installed via conda-forge, Docker Hub, or downloaded from github.com/divonlan/genozip.

Supplementary information
Supplementary data are available at Bioinformatics online.
Testis-specific serine kinase protein family in male fertility and as targets for non-hormonal male contraception†
Authors: Salicioni Ana M , Gervasi María G , Sosnik Julian , Tourzani Darya A , Nayyab Saman , Caraballo Diego A , Visconti Pablo E 
Published: April 2020

Abstract
Male contraception is a very active area of research. Several hormonal agents have entered clinical trials, while potential non-hormonal targets have been brought to light more recently and are at earlier stages of development. The general strategy is to target genes along the molecular pathways of sperm production, maturation, or function, and it is predicted that these novel approaches will hopefully lead to more selective male contraceptive compounds with a decreased side effect burden. Protein kinases are known to play a major role in signaling events associated with sperm differentiation and function. In this review, we focus our analysis on the testis-specific serine kinase (TSSK) protein family. We have previously shown that members of the family of TSSKs are postmeiotically expressed in male germ cells and in mature mammalian sperm. The restricted postmeiotic expression of TSSKs as well as the importance of phosphorylation in signaling processes strongly suggests that TSSKs have an important role in germ cell differentiation and/or sperm function. This prediction has been supported by the reported sterile phenotype of the Tssk6 knockout (KO) mice and of the double Tssk1 and Tssk2 KO mice and by the male subfertile phenotype observed in a Tssk4 KO mouse model.
Hyperdry human amniotic membrane application as a wound dressing for a full-thickness skin excision after a third-degree burn injury
Authors: Oba Jiro , Okabe Motonori , Yoshida Toshiko , Soko Chika , Fathy Moustafa , Amano Koji , Kobashi Daisuke , Wakasugi Masahiro , Okudera Hiroshi 
Published: April 2020

AbstractBackgroundSevere burn injuries create large skin defects that render the host susceptible to bacterial infections. Burn wound infection often causes systemic sepsis and severe septicemia, resulting in an increase in the mortality of patients with severe burn injuries. Therefore, appropriate wound care is important to prevent infection and improve patient outcomes. However, it is difficult to heal a third-degree burn injury. The aim of this study was to investigate whether hyperdry human amniotic membrane (HD-AM) could promote early granulation tissue formation after full-thickness skin excision in third-degree burn injury sites in mice.MethodsAfter the development of HD-AM and creation of a third-degree burn injury model, the HD-AM was either placed or not placed on the wound area in the HD-AM group or HD-AM group, respectively. The groups were prepared for evaluation on postoperative days 1, 4 and 7. Azan staining was used for granulation tissue evaluation, and estimation of CD163, transforming growth factor beta-1 (TGF-β1), vascular endothelial growth factor (VEGF), CD31, alpha-smooth muscle actin (α-SMA) and Iba1 expression was performed by immunohistochemical staining. Quantitative reverse-transcription polymerase chain reaction (PCR) was used to investigate gene expression of growth factors, cell migration chemokines and angiogenic and inflammatory markers.ResultsThe HD-AM group showed significant early and qualitatively good growth of granulation tissue on the full-thickness skin excision site. HD-AM promoted early-phase inflammatory cell infiltration, fibroblast migration and angiogenesis in the granulation tissue. Additionally, the early infiltration of cells of the immune system was observed.ConclusionsHD-AM may be useful as a new wound dressing material for full-thickness skin excision sites after third-degree burn injuries, and may be a new therapeutic technique for improving the survival rate of patients with severe burn injuries.
Structural Brain Architectures Match Intrinsic Functional Networks and Vary across Domains: A Study from 15 000+ Individuals
Authors: Luo Na , Sui Jing , Abrol Anees , Chen Jiayu , Turner Jessica A , Damaraju Eswar , Fu Zening , Fan Lingzhong , Lin Dongdong , Zhuo Chuanjun , Xu Yong , Glahn David C , Rodrigue Amanda L , Banich Marie T , Pearlson Godfrey D , Calhoun Vince D 
Published: April 2020

Abstract
Brain structural networks have been shown to consistently organize in functionally meaningful architectures covering the entire brain. However, to what extent brain structural architectures match the intrinsic functional networks in different functional domains remains under explored. In this study, based on independent component analysis, we revealed 45 pairs of structural-functional (S-F) component maps, distributing across nine functional domains, in both a discovery cohort (n = 6005) and a replication cohort (UK Biobank, n = 9214), providing a well-match multimodal spatial map template for public use. Further network module analysis suggested that unimodal cortical areas (e.g., somatomotor and visual networks) indicate higher S-F coherence, while heteromodal association cortices, especially the frontoparietal network (FPN), exhibit more S-F divergence. Collectively, these results suggest that the expanding and maturing brain association cortex demonstrates a higher degree of changes compared with unimodal cortex, which may lead to higher interindividual variability and lower S-F coherence.
Development of Dynamic Functional Architecture during Early Infancy
Authors: Wen Xuyun , Wang Rifeng , Yin Weiyan , Lin Weili , Zhang Han , Shen Dinggang 
Published: April 2020

Abstract
Uncovering the moment-to-moment dynamics of functional connectivity (FC) in the human brain during early development is crucial for understanding emerging complex cognitive functions and behaviors. To this end, this paper leveraged a longitudinal resting-state functional magnetic resonance imaging dataset from 51 typically developing infants and, for the first time, thoroughly investigated how the temporal variability of the FC architecture develops at the “global” (entire brain), “mesoscale” (functional system), and “local” (brain region) levels in the first 2 years of age. Our results revealed that, in such a pivotal stage, 1) the whole-brain FC dynamic is linearly increased; 2) the high-order functional systems tend to display increased FC dynamics for both within- and between-network connections, while the primary systems show the opposite trajectories; and 3) many frontal regions have increasing FC dynamics despite large heterogeneity in developmental trajectories and velocities. All these findings indicate that the brain is gradually reconfigured toward a more flexible, dynamic, and adaptive system with globally increasing but locally heterogeneous trajectories in the first 2 postnatal years, explaining why infants have rapidly developing high-order cognitive functions and complex behaviors.
Missed Opportunities for Human Immunodeficiency Virus (HIV) Testing During Injection Drug Use–Related Healthcare Encounters Among a Cohort of Persons Who Inject Drugs With HIV Diagnosed During an Outbreak—Cincinnati/Northern Kentucky, 2017–2018
Authors: Furukawa Nathan W , Blau Erin F , Reau Zach , Carlson David , Raney Zachary D , Johnson Tisha K , Deputy Nicholas P , Sami Samira , McClung Robert P , Neblett-Fanfair Robyn , de Fijter Sietske , Ingram Tim , Thoroughman Doug , Vogel Stephanie , Lyss Sheryl B 
Published: April 2020

Abstract

Background
Persons who inject drugs (PWID) have frequent healthcare encounters related to their injection drug use (IDU) but are often not tested for human immunodeficiency virus (HIV). We sought to quantify missed opportunities for HIV testing during an HIV outbreak among PWID.

Methods
PWID with HIV diagnosed in 5 Cincinnati/Northern Kentucky counties during January 2017–September 2018 who had ≥1 encounter 12 months prior to HIV diagnosis in 1 of 2 Cincinnati/Northern Kentucky area healthcare systems were included in the analysis. HIV testing and encounter data were abstracted from electronic health records. A missed opportunity for HIV testing was defined as an encounter for an IDU-related condition where an HIV test was not performed and had not been performed in the prior 12 months.

Results
Among 109 PWID with HIV diagnosed who had ≥1 healthcare encounter, 75 (68.8%) had ≥1 IDU-related encounters in the 12 months before HIV diagnosis. These 75 PWID had 169 IDU-related encounters of which 86 (50.9%) were missed opportunities for HIV testing and occurred among 46 (42.2%) PWID. Most IDU-related encounters occurred in the emergency department (118/169; 69.8%). Using multivariable generalized estimating equations, HIV testing was more likely in inpatient compared with emergency department encounters (adjusted relative risk [RR], 2.72; 95% confidence interval [CI], 1.70–4.33) and at the healthcare system receiving funding for emergency department HIV testing (adjusted RR, 1.76; 95% CI, 1.10–2.82).

Conclusions
PWID have frequent IDU-related encounters in emergency departments. Enhanced HIV screening of PWID in these settings can facilitate earlier diagnosis and improve outbreak response.
Description of Sulfitobacter sediminilitoris sp. nov., isolated from a tidal flat
Authors: Park Sooyeon , Chen Siyu , Lee Jung-Sook , Kim Wonyong , Yoon Jung-Hoon 
Published: April 2020

ABSTRACT
A Gram-stain-negative bacterial strain, JBTF-M27T, was isolated from a tidal flat from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M27T fell within the clade comprising the type strains of Sulfitobacter species. Strain JBTF-M27T exhibited the highest 16S rRNA gene sequence similarity (98.8%) to the type strain of S. porphyrae. Genomic ANI and dDDH values of strain JBTF-M27T between the type strains of Sulfitobacter species were less than 76.1 and 19.2%, respectively. Mean DNA-DNA relatedness value between strain JBTF-M27T and the type strain of S. porphyrae was 21%. DNA G + C content of strain JBTF-M27T from genome sequence was 57.8% (genomic analysis). Strain JBTF-M27T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid. The major polar lipids of strain JBTF-M27T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M27T is separated from recognized Sulfitobacter species. On the basis of the data presented, strain JBTF-M27T ( = KACC 21648T = NBRC 114356T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter sediminilitoris sp. nov. is proposed.
Involvement of Pca1 in ROS-mediated apoptotic cell death induced by alpha-thujone in the fission yeast (Schizosaccharomyces pombe)
Authors: Agus Hizlan Hincal , Kok Gizem , Derinoz Ezgi , Oncel Didem , Yilmaz Sedanur 
Published: April 2020

ABSTRACT
Alpha-thujone, widely used in beverages (1–5 mg/kg), is known to have cytotoxic effects, but the mode of action and the role of potential apoptotic proteins in yeast cell death should be unraveled. In this study, we used Schizosaccharomyces pombe, which is a promising unicellular model organism in mechanistic toxicology and cell biology, to investigate the involvement of pro-apoptotic factors in alpha-thujone-induced cell death. We showed alpha-thujone-induced ROS accumulation-dependent cytotoxicity and apoptosis. In addition, we used superoxide dismutase-deficient cells (sod1 and sod2 mutants) to understand the effect of oxidative stress. Alpha-thujone caused significant cytotoxicity and apoptotic cell death, particularly in sod mutants. Moreover, two potential apoptotic factors, pca1 and pnu1 (pombe caspase-1 and pombe nuc1) were investigated to understand which factor mediates alpha-thujone-induced cell death. Pca1-deficient cells showed increased survival rates and reduced apoptosis in comparison to parental cells after chemical treatment while pnu1 mutation did not cause any significant change and the response was found identical as of parental cells. Yeast responded to alpha-thujone in caspase-dependent manner which was very similar to that for acetic acid. In conclusion, alfa-thujone-induced apoptosis and accounting mechanisms, which were mediated by ROS and driven by Pca1, were clarified in the unicellular model, S. pombe.
mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow
Authors: Liu Junfeng , Liu Qiao , Yang Qingzhu 
Published: April 2020

Abstract
Gene flow between species may cause variations in branch length and topology of gene tree, which are beyond the expected variations from ancestral processes. These additional variations make it difficult to estimate parameters during speciation with gene flow, as the pattern of these additional variations differs with the relationship between isolation and migration. As far as we know, most methods rely on the assumption about the relationship between isolation and migration by a given model, such as the isolation-with-migration model, when estimating parameters during speciation with gene flow. In this article, we develop a multispecies coalescent approach which does not rely on any assumption about the relationship between isolation and migration when estimating parameters and is called mstree. mstree is available at https://github.com/liujunfengtop/MStree/ and uses some mathematical inequalities among several factors, which include the species divergence time, the ancestral population size, and the number of gene trees, to estimate parameters during speciation with gene flow. Using simulations, we show that the estimated values of ancestral population sizes and species divergence times are close to the true values when analyzing the simulation data sets, which are generated based on the isolation-with-initial-migration model, secondary contact model, and isolation-with-migration model. Therefore, our method is able to estimate ancestral population sizes and speciation times in the presence of different modes of gene flow and may be helpful to test different theories of speciation.
Gauging oxygen risk and tolerance for the megafauna of the Southern California shelf based on in situ observation, species mobility, and seascape
Authors: Parnell P Ed , Levin Lisa A , Navarro Michael O 
Published: April 2020

AbstractOxygen decline poses increasing risks to global shelf communities. This study was conducted to measure species oxygen exposures in situ and to assess risks of low oxygen based on the hypothesis that species risk varies spatially and is dependent on the interaction of shelf oxygen dynamics with habitat pattern, species mobility, and tolerance to low oxygen. Here, we report concomitant observations of oxygen, depth, and habitat for the most common benthic and epibenthic megafauna on the southern California shelf (30–125 m). The study was conducted when oxygen concentrations were the lowest observed within the previous 30 years off southern California (2012–2014), yet hypoxic conditions (&lt;1.42 ml l−1) were not observed. No significant oxygen exposure differences were observed among highly mobile, mobile, and sessile species due to the dynamic nature of the oxycline. Habitat affinities for the most abundant benthic megafauna (53 taxa) were discriminated among four different habitats. Highly mobile rockfish (Sebastidae) exhibited distributions suggesting less tolerance to low oxygen than most other taxa. Given the mosaic of consolidated and coarse-grained habitats that rockfish prefer, the onset of hypoxic conditions near the shelf break (∼90–120 m) would likely compress local rockfish populations into less favourable habitat in a non-linear fashion.
Hermite interpolation on the unit sphere and limits of Lagrange projectors
Authors: Van Manh Phung 
Published: April 2020

Abstract
We construct new Hermite and Lagrange interpolation schemes on the unit sphere in $\mathbb R^3$. We give Newton-type formulas for interpolation polynomials and use them to show that the Hermite projectors are the limits of Lagrange projectors when interpolation points coalesce.
Teledentistry in the diagnosis of oral lesions: A systematic review of the literature
Authors: Flores Anacláudia Pereira da Costa , Lazaro Samara Andreolla , Molina-Bastos Cynthia Goulart , Guattini Verônica Lucas de Oliveira , Umpierre Roberto Nunes , Gonçalves Marcelo Rodrigues , Carrard Vinicius Coelho 
Published: April 2020

Abstract

Objective
The purpose of this systematic review is to summarize information on the use of teledentistry in the diagnosis of oral lesions.

Materials and Methods
A systematic literature search conducted in August 2018 included articles published until December 2018 in 4 databases. Two reviewers evaluated the search results separately. If they were uncertain as to whether to include an article, a third reviewer made the final decision. Studies related to the diagnosis of oral lesions using teledentistry were included. The methodological quality of the studies was analyzed using the Quality Assessment of Studies of Diagnostic Accuracy.

Results
Eleven articles were included in the study. The selected articles were published between 1999 and 2018, predominantly in developing countries. The professionals acting as patient examiners are dental students and dentists, as well as other health professionals. Most of the patients evaluated in the studies were from rural populations or locations distant from large centers. The tools used to obtain patient data were smartphones, videoconference, email, questionnaires, histopathological exams, and telemedicine applications and systems. Most studies concluded that there is a high level of agreement between teledentistry and clinical consultation and that the use of this resource for diagnostic purposes can reduce costs and the travel time to consult a specialist personally. Nine of the 11 studies were of good quality.

Conclusions
Teledentistry has the potential to improve the care quality related to diagnosis and management of oral lesions, shortening distances between patients who need specialized diagnoses and specialists.
Regression-Based Expected Shortfall Backtesting
Authors: Bayer Sebastian , Dimitriadis Timo 
Published: April 2020

AbstractThis article introduces novel backtests for the risk measure Expected Shortfall (ES) following the testing idea of Mincer and Zarnowitz (1969). Estimating a regression model for the ES stand-alone is infeasible and thus, our tests are based on a joint regression model for the Value at Risk (VaR) and the ES, which allows for different test specifications. These ES backtests are the first which solely backtest the ES in the sense that they only require ES forecasts as input variables. As the tests are potentially subject to model misspecification, we provide asymptotic theory under misspecification for the underlying joint regression. We find that employing a misspecification robust covariance estimator substantially improves the tests’ performance. We compare our backtests to existing joint VaR and ES backtests and find that our tests outperform the existing alternatives throughout all considered simulations. In an empirical illustration, we apply our backtests to ES forecasts for 200 stocks of the S&P 500 index.
The legal and medical necessity of abortion care amid the COVID-19 pandemic
Authors: Donley Greer , Chen Beatrice A , Borrero Sonya 
Published: April 2020

Abstract
In response to the COVID-19 pandemic, states have ordered the cessation of non-essential healthcare. Unfortunately, many conservative states have sought to capitalize on those orders to halt abortion care. In this short paper, we argue that abortion should not fall under any state’s non-essential healthcare order. Major medical organizations recognize that abortion is essential healthcare that must be provided even in a pandemic, and the law recognizes abortion as a time-sensitive constitutional right. Finally, we examine the constitutional arguments as to why enforcing these orders against abortion providers should not stand constitutional scrutiny. We conclude that no public health purpose can be served by this application because abortion uses less scarce resources and involves fewer contacts with healthcare professionals than prenatal care and delivery assistance, which is continuing to be provided in this public health emergency.
Ultra wide field angiography documented peripheral retinal eovascularization as cause of vitreous hemorrhage after scleral buckle surgery#
Authors: Enghelberg Moises , Chalam K V 
Published: April 2020

Abstract
We describe an unusual case of ultra wide fluorescein angiography (UWFA) documented peripheral retinal neovascularization (NVE) with delayed vitreous hemorrhage after placement of an encircling scleral buckle (a common procedure for repair of retinal detachment). Anterior segment ischemia is a rare complication after scleral buckle surgery for the treatment of retinal detachment and results from altered choroidal flow through the impingement of the anterior and long posterior ciliary arteries. UWFA performed for the evaluation of vitreous hemorrhage confirmed ischemia anterior to the scleral buckle and consequential NVE. This case represents the utility of UWFA in evaluating and managing this exceptionally rare complication associated with a common procedure in the field of vitreoretinal surgery.
Severe snakebite envenomation revealed by an acute abdomen
Authors: Kassegne Iroukora , Mouzou Tabana Essohanam , Kanassoua Kokou , Dossouvi Tamegnon , Amouzou Yawod Efoé-Ga , Sakiye Aboza , Adabra Komlan , Alassani Fousseni , Amavi Ayi Kossigan , Tchangai Boyodi , Dosseh Ekoué David Joseph 
Published: April 2020

Abstract
Acute abdomens are common conditions, with many aetiologies in developing countries. Abdominal bleeding due to snake envenomation is an extremely rare aetiology. A 11-year-old girl was admitted for acute abdominal pains. She had a history of foot bite of unknown origin. Physical examination revealed palor and abdominal tenderness. At laparotomy, there were peritoneal and retroperitoneal diffuse hematomas. Laboratory studies revealed abnormal coagulation profile. Retroperitoneal and peritoneal hematomas’ diagnosis, by consumptive coagulopathy, due to snakebite envenomation, was made. Polyvalent antivenom administration permitted a normalization of coagulation profile, however, with persistent surgical site bleeding. Whole blood transfusion was administered with bleeding stop. Sudden abdominal pain, palor and signs of peritonism suggest an acute abdomen. However, abdominal bleeding due to snakebite envenomation should be considered, especially in child with unidentified bite history. Imaging modalities may helpful to confirm the abdominal bleeding. Antivenom is the mainstay of the treatment.