bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtifier: a deep learning-based identifier for viral sequences from metagenomes
Authors: Miao Yan , Liu Fu , Hou Tao , Liu Yun 
Published: December 2021

Abstract

Motivation
Viruses, the most abundant biological entities on earth, are important components of microbial communities, and as major human pathogens, they are responsible for human mortality and morbidity. The identification of viral sequences from metagenomes is critical for viral analysis. As massive quantities of short sequences are generated by next-generation sequencing, most methods utilize discrete and sparse one-hot vectors to encode nucleotide sequences, which are usually ineffective in viral identification.

Results
In this article, Virtifier, a deep learning-based viral identifier for sequences from metagenomic data is proposed. It includes a meaningful nucleotide sequence encoding method named Seq2Vec and a variant viral sequence predictor with an attention-based long short-term memory (LSTM) network. By utilizing a fully trained embedding matrix to encode codons, Seq2Vec can efficiently extract the relationships among those codons in a nucleotide sequence. Combined with an attention layer, the LSTM neural network can further analyze the codon relationships and sift the parts that contribute to the final features. Experimental results of three datasets have shown that Virtifier can accurately identify short viral sequences (&lt;500 bp) from metagenomes, surpassing three widely used methods, VirFinder, DeepVirFinder and PPR-Meta. Meanwhile, a comparable performance was achieved by Virtifier at longer lengths (&gt;5000 bp).

Availability and implementation
A Python implementation of Virtifier and the Python code developed for this study have been provided on Github https://github.com/crazyinter/Seq2Vec. The RefSeq genomes in this article are available in VirFinder at https://dx.doi.org/10.1186/s40168-017-0283-5. The CAMI Challenge Dataset 3 CAMI_high dataset in this article is available in CAMI at https://data.cami-challenge.org/participate. The real human gut metagenomes in this article are available at https://dx.doi.org/10.1101/gr.142315.112.

Supplementary information
Supplementary data are available at Bioinformatics online.
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses
Authors: Ferguson James M , Gamaarachchi Hasindu , Nguyen Thanh , Gollon Alyne , Tong Stephanie , Aquilina-Reid Chiara , Bowen-James Rachel , Deveson Ira W 
Published: December 2021

Abstract

Motivation
InterARTIC is an interactive web application for the analysis of viral whole-genome sequencing (WGS) data generated on Oxford Nanopore Technologies (ONT) devices. A graphical interface enables users with no bioinformatics expertise to analyze WGS experiments and reconstruct consensus genome sequences from individual isolates of viruses, such as SARS-CoV-2. InterARTIC is intended to facilitate widespread adoption and standardization of ONT sequencing for viral surveillance and molecular epidemiology.

Results
We demonstrate the use of InterARTIC for the analysis of ONT viral WGS data from SARS-CoV-2 and Ebola virus, using a laptop computer or the internal computer on an ONT GridION sequencing device. We showcase the intuitive graphical interface, workflow customization capabilities and job-scheduling system that facilitate execution of small- and large-scale WGS projects on any common virus.

Availability and implementation
InterARTIC is a free, open-source web application implemented in Python that executes best-practice command line workflows from the ARTIC network. The application can be downloaded as a set of pre-compiled binaries that are compatible with all common Linux distributions, Windows with Linux subsystems, MacOSX and ARM systems. All code can be found on GitHub at https://github.com/Psy-Fer/interARTIC/ and documentation can be found at https://github.com/Psy-Fer/interARTIC/.

Supplementary information
Supplementary data are available at Bioinformatics online.
ZDHHC19 localizes to the cell membrane of spermatids and is involved in spermatogenesis
Authors: Wu Yangyang , Zhang Xin , Zhang Xi , Liu Siyu , Zhang Jintao , Sun Shuya , Zhao Shuqin , Wang Zerui , Cui Yiqiang , Huang Xiaoyan , Liu Mingxi 
Published: December 2021

Abstract
Sperm is the ultimate executor of male reproductive function. Normal morphology, quantity, and motility of sperm ensure the normal reproductive process. Palmitoylation is a posttranslational modification mediated by palmitoyltransferases whereby palmitoyl is added to proteins. Seven palmitoyltransferases have been identified in Saccharomyces cerevisiae and 23 in humans (including ZDHHC1–9 and ZDHHC11–24), with corresponding homologs in mice. We identified two testis-specific palmitoyltransferases ZDHHC11 and ZDHHC19 in mice. The Zdhhc11 and Zdhhc19-knockout mouse models were constructed, and it was found that the Zdhhc11 knockout males were fertile, while Zdhhc19 knockout males were sterile. ZDHHC19 is located in the cell membrane of step 4–9 spermatids in the mouse testis, and phenotypic analysis showed that the testicular weight ratio in the Zdhhc19−/− mice decreased along with the number and motility of the sperm decreased, while sperm abnormalities increased, mainly due to the “folded” abnormal sperm caused by sperm membrane fusion, suggesting the involvement of ZDHHC19 in maintaining membrane stability in the male reproductive system. In addition, Zdhhc19−/− mice showed abnormal sperm morphologies and apoptosis during spermatogenesis, suggesting that spermatogenesis in the Zdhhc19−/− mice was abnormal. These results indicate that ZDHHC19 promotes membrane stability in male germ cells.
A Sensitive Liquid Chromatography-Mass Spectrometry Method for Determination of Toosendanin in Rat Plasma and its Application to Pharmacokinetic Study
Authors: Shen Chuangpeng , Pan Zhisen , Wu Xiaojie , Zhong Chong , Li Qiao , Si Yuqi , Liu Changhui , Tu Haitao , Deng Zhijun , Zhu Zhangzhi , Guo Jiewen , Xin Xiaoyi , Liu Min 
Published: December 2021

Abstract
A simple, rapid and sensitive analytical method was developed for the determination of toosendanin in rat plasma using liquid chromatography tandem mass spectrometry (LC–MS/MS). Andrographolide was selected as the internal standard, and the plasma samples were extracted by liquid–liquid extraction with diethyl ether. Chromatographic separation was performed on a Dikma Spursil C18, 3.5 μm (150 × 2.1 mm i.d) analytical column with 85% methanol:water (v/v) containing 0.025% formic acid (pH = 3.9) as mobile phase. The flow rate was 0.25 mL/min, and the total run time was 3 min. Detection was performed with a triple-quadrupole tandem mass spectrometer using negative ion mode electrospray ionization (ESI) in the multiple reaction monitoring (MRM) mode. The MS/MS ion transitions monitored were m/z 573.1 → 531.1 and 349.0 → 287.0 for toosendanin and andrographolide, respectively. Good linearity was observed over the concentration range of 3.125–500 ng/mL in 100 μL of rat plasma with a correlation coefficient ˃0.9997. Intra- and inter-assay variabilities were ˂8.5% in plasma. The recovery and the matrix effect were in the range 71.8–73.5% and 96.4–103.8%, respectively. The analyte was stable under various conditions (at room temperature, during freeze–thaw settings, in the autosampler, and under deep-freeze conditions). The method was successfully applied to a pharmacokinetic study of toosendanin after its oral administration in rats at a dose of 10 mg/kg.
The last pre-pandemic European Renal Association Registry report: age at start of kidney replacement therapy in Europe
Authors: Carriazo Sol , Ortiz Alberto 
Published: December 2021

ABSTRACTThe European Renal Association (ERA) Registry Annual Report 2019 will be its last pre-pandemic report. From 2020 on, registry data will incorporate any potential impact of coronavirus disease 2019 (COVID-19) on kidney replacement therapy (KRT) practices in Europe. The 2019 report focussed on age comparisons and found substantial differences in the distribution of primary renal disease, treatment modality, kidney donor type and the survival probabilities for different age categories. The report presents data that support a correlation (R2 = 0.43, P &lt; 0.00001) between the incidence of KRT per million population (pmp) and the median age at the start of KRT in the different regions and countries, suggesting that initiating KRT at an older median age may be a determinant of KRT incidence. The causes of the lower age at KRT in some countries should be explored. These may include, but are not limited to, KRT not being offered to the elderly or the elderly refusing KRT. In this regard, there was a correlation between the median age at the start of KRT and per capita gross domestic product (GDP) (R2 = 0.26, P &lt; 0.0046), suggesting that the availability of resources may be a factor that limits the offer of KRT to the elderly. The UK may represent a case to study these issues. Both age at initiation of KRT and KRT incidence are below the European median and lower than that expected for GDP. Furthermore, there are differences between the various countries within the UK, as well as documented racial differences, the latter being a piece of information missing for most European countries.
Percutaneous versus surgical femoral access in minimally invasive cardiac operations
Authors: El-Sayed Ahmad Ali , Bayram Ali , Salamate Saad , Sirat Sami , Amer Mohamed , Bakhtiary Farhad 
Published: December 2021

Abstract

OBJECTIVES
Both surgical and percutaneous femoral accesses for the establishment of extracorporeal circulation are used in minimally invasive cardiac surgeries. The goal of this study was to compare the outcomes with the MANTA vascular closure device after percutaneous arterial decannulation via the surgical approach.

METHODS
Between November 2018 and January 2021, a total of 490 consecutive patients underwent minimally invasive cardiac operations at our institution. Cannulation and decannulation of femoral vessels were under direct vision surgically or percutaneously. The MANTA system was used to close the femoral artery in all patients with percutaneous cannulation. Demographic, clinical and procedural data were collected retrospectively.

RESULTS
Surgical cut-down and suture closure of the femoral artery was performed in 222 patients (45.3%); percutaneous access and closure with the MANTA system was used in 268 patients (54.7%). The surgical group presented a significantly higher incidence of any access site complication compared to the percutaneous group [18 patients (8.1%) vs 6 patients (2.2%); P = 0.003]. Lymph fistula and wound healing disorders occurred more frequently in the surgical group (3.2% vs 0% [P = 0.004] and 3.6% vs 0% [P = 0.002], respectively). Median procedural duration and stays in the intensive care unit were significantly lower in the percutaneous group {127 [interquartile range (IQR) 97–158] min vs 150 (IQR 117–185) min (P &lt; 0.001) and 1 (IQR 1–2) day vs 2 (IQR 1–3) days (P = 0.008), respectively}.

CONCLUSIONS
Percutaneous access and closure with the MANTA system are feasible, safe and associated with lower incidences of all-cause access site complications and shorter stays in the intensive care unit compared to surgical access and closure in minimally invasive cardiac surgeries.
Genotyping-by-sequencing and genomic selection applications in hexaploid triticale
Authors: Ayalew Habtamu , Anderson Joshua D , Krom Nick , Tang Yuhong , Butler Twain J , Rawat Nidhi , Tiwari Vijay , Ma Xue-Feng 
Published: December 2021

Abstract
Triticale, a hybrid species between wheat and rye, is one of the newest additions to the plant kingdom with a very short history of improvement. It has very limited genomic resources because of its large and complex genome. Objectives of this study were to generate dense marker data, understand genetic diversity, population structure, linkage disequilibrium (LD), and estimate accuracies of commonly used genomic selection (GS) models on forage yield of triticale. Genotyping-by-sequencing (GBS), using PstI and MspI restriction enzymes for reducing genome complexity, was performed on a triticale diversity panel (n = 289). After filtering for biallelic loci with more than 70% genome coverage, and minor allele frequency (MAF) &gt; 0.05, de novo variant calling identified 16,378 single nucleotide polymorphism (SNP) markers. Sequences of these variants were mapped to wheat and rye reference genomes to infer their homologous groups and chromosome positions. About 45% (7430), and 58% (9500) of the de novo identified SNPs were mapped to the wheat and rye reference genomes, respectively. Interestingly, 28.9% (2151) of the 7430 SNPs were mapped to the D genome of hexaploid wheat, indicating substantial substitution of the R genome with D genome in cultivated triticale. About 27% of marker pairs were in significant LD with an average r2 &gt; 0.18 (P &lt; 0.05). Genome-wide LD declined rapidly to r2 &lt; 0.1 beyond 10 kb physical distance. The three sub-genomes (A, B, and R) showed comparable LD decay patterns. Genetic diversity and population structure analyses identified five distinct clusters. Genotype grouping did not follow prior winter vs spring-type classification. However, one of the clusters was largely dominated by winter triticale. GS accuracies were estimated for forage yield using three commonly used models with different training population sizes and marker densities. GS accuracy increased with increasing training population size while gain in accuracy tended to plateau with marker densities of 2000 SNPs or more. Average GS accuracy was about 0.52, indicating the potential of using GS in triticale forage yield improvement.
The genome of the zebra mussel,Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol
Authors: McCartney Michael A , Auch Benjamin , Kono Thomas , Mallez Sophie , Zhang Ying , Obille Angelico , Becker Aaron , Abrahante Juan E , Garbe John , Badalamenti Jonathan P , Herman Adam , Mangelson Hayley , Liachko Ivan , Sullivan Shawn , Sone Eli D , Koren Sergey , Silverstein Kevin A T , Beckman Kenneth B , Gohl Daryl M 
Published: December 2021

AbstractThe zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments, we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact steamer-like elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.
Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions
Authors: Salavati Mazdak , Woolley Shernae A , Cortés Araya Yennifer , Halstead Michelle M , Stenhouse Claire , Johnsson Martin , Ashworth Cheryl J , Archibald Alan L , Donadeu Francesc X , Hassan Musa A , Clark Emily L 
Published: December 2021

AbstractThere is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the “Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)” to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, &gt;50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
Sea level instantaneous budget for 2003–2015
Authors: Mu Dapeng , Xu Tianhe , Guan Meiqian 
Published: December 2021

SUMMARYMost studies of sea level budget only indicate the stationary causes for the global mean sea level (GMSL) rise over the course of a time span of interest, providing limited information on temporary changes in the GMSL budget. In this contribution, we present an instantaneous budget of the GMSL for the period of 2003–2015, which offers new insights on the time evolution of the GMSL budget. We use a space-state model to compute the instantaneous rates of GMSL and their contributing sources (barystatic and steric contributions), to investigate the causes of the GMSL instantaneous budget, which accounts for and quantifies low-frequency variations in GMSL rise. Combining the barystatic GMSL instantaneous rates (estimated from satellite gravimetry) along with a particular choice of steric GMSL instantaneous rates (inferred from an Argo product) achieves closure of the GMSL instantaneous budget with a standard deviation of 0.4 mm yr−1. We find that the barystatic GMSL rate is primarily responsible for the striking fluctuations in the GMSL instantaneous rates between 2009 and 2015. For example, over only 20 months (July 2010 to February 2012), the GMSL (barystatic) rate increases from 0.32 (0.71) to 6.12 (4.55) mm yr−1. These strong fluctuations mainly result from hydrology and mountain glacier mass variations rather than mass loss in ice sheet, for instance, Australia slowed ∼1.2 mm yr−1 equivalent contribution to GMSL rise over the year 2010, which is approximately four times the linear rate of Antarctica mass loss.
Innovative actions in oceans and human health for Europe
Authors: Pellens Noortje , Boelee Eline , Veiga Joana M , Fleming Lora E , Blauw Anouk 
Published: December 2021

Summary
Innovative actions are local initiatives which leverage the interactions between the ocean and human health to reduce the risks and enhance the benefits for the stakeholders and the natural environment. These initiatives can have strong positive effects on human health and wellbeing as well as on the marine environment. We analysed 150 such innovative actions in Europe. Using a combined case study and survey approach, innovative actions were identified using interviews and content analysis of websites and compiled into a database. Quantitative data were analysed according to the Drivers, Pressures, State, Impact and Response (DPSIR) framework, guided by selected in-depth interviews. Overall, the innovative actions provided a positive impact on the health of both the ocean and humans through increasing food provision, water quality and tourism opportunities; and addressing environmental issues such as commercial fish stock depletion, pollution and climate change. Innovative actions contributed to meeting various targets of the Sustainable Development Goals (SDGs) 3, 13 and 14. These actions played a potential role ahead of and alongside policy. Some of the innovative actions may have potential to be put in place elsewhere. Such up-scaling would need to be adapted to local circumstances and could be facilitated by an innovative action exchange platform.
A retrospect of the structure determination of Taka-amylase A
Authors: Kusunoki Masami 
Published: December 2021

Abstract
The 3D structure of Taka-amylase A was determined by X-ray crystal analysis at 3 Å resolution by Masao Kakudo’s laboratory at the Institute for Protein Research, Osaka University, in 1980. Seven kinds of heavy atom derivatives were used for phase determination. There are three copies of Taka-amylase molecules in the asymmetric unit, which improved the quality of electron density maps, leading to the completion of a molecular model with 478 amino acids. The structure determination process in those days is described briefly.
The Hidden Danger of Lithium Battery-Powered Electric Bicycles and Scooters: A Case Series of the Israeli National Burn Center Experience
Authors: Segalovich Matan , Berl Ariel , Aviv Uri , Jaffe Eli , Shelef Ran , Haik Josef , Cleary Michelle , Kornhaber Rachel , Harats Moti 
Published: December 2021

Abstract
Electric-powered bicycles and scooters that use rechargeable lithium batteries are an urban transportation alternative and have become increasingly popular. However, in recent years, there has been an increase in patient admissions to the Israeli National Burn Center with burns associated with their use. In this case series of all patients (n = 9) referred to the Emergency Department (February 2016–October 2020) with lithium-related battery burns from electric-powered bicycles and scooters, we present burn depth, size, treatment, inhalation injuries, and hospitalization. All patients were admitted to the Israeli National Burn Center for treatment. The average TBSA was 27.5% (range 3%–57%). All but one patient had a combination of partial to full-thickness burns affecting the upper and lower limbs. Three patients sustained inhalation injuries and a total of four patients required intubation. Seven patients required surgery that included debridement and, in most cases, skin grafting. The availability and increase in the use of battery-powered bicycles and scooters may lead to an increase in injuries and death if consumers are not aware of the potential dangers related to the safe use of lithium batteries.