bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-term Outcomes of Single-port Versus Multiport Laparoscopic Surgery for Colon Cancer
Authors: Lee Yoon Suk , Kim Ji Hoon , Kim Hyung Jin , Lee Sang Chul , Kang Byung Mo , Kim Chang Woo , Lim Sang Woo , Lee Suk-Hwan , Kim Jun Gi 
Published: March 2020

Objective:
To compare short-term perioperative outcomes of single-port laparoscopic surgery (SPLS) and multiport laparoscopic surgery (MPLS) for colon cancer.

Summary Background Data:
Although many studies reported short- and long-term outcomes of SPLS for colon cancer compared with MPLS, few have reported results of randomized controlled trials.

Methods:
This was a multicenter, prospective, randomized controlled trial with a noninferiority design. It was conducted between August 2011 and June 2017 at 7 sites in Korea. A total of 388 adults (aged 19–85 yrs) with clinical stage I, II, or III adenocarcinoma of the ascending or sigmoid colon were enrolled and randomized. The primary endpoint was 30-day postoperative complication rates. Secondary endpoints were the number of harvested lymph nodes, length of the resection margin, postoperative pain, and time to functional recovery (bowel movement and diet). Patients were followed for 30 days after surgery.

Results:
Among 388 patients, 359 (92.5%) completed the study (SPLS, n = 179; MPLS, n = 180). The 30-day postoperative complication rate was 10.6% in the SPLS group and 13.9% in the MPLS group (95% confidence interval, −10.05 to 3.05 percentage points; P < 0.0001). Total incision length was shorter in the SPLS group than in the MPLS group (4.6 cm vs 7.2 cm, P < 0.001), whereas the length of the specimen extraction site did not differ (4.4 cm vs 4.6 cm, P = 0.249). There were no significant differences between groups for all secondary endpoints and all other outcomes.

Conclusions:
Even though there was no obvious benefit to SPLS over MPLS when performing colectomy for cancer, our data suggest that SPLS is noninferior to MPLS and can be considered an option in selected patients, when performed by experienced surgeons.

Trial registration: ClinicalTrials.gov Identifier: NCT01480128.
Genome sequences of both organelles of the grapevine rootstock cultivar ‘Börner’
Authors: Frommer Bianca , Holtgräwe Daniela , Hausmann Ludger , Viehöver Prisca , Huettel Bruno , Töpfer Reinhard , Weisshaar Bernd 
Published: March 2020

AbstractGenomic long reads of the interspecific grapevine rootstock cultivar ‘Börner’ (Vitis ripariaGM183 xVitis cinereaArnold) were used to assemble its chloroplast and mitochondrion genome sequences. We annotated 133 chloroplast and 172 mitochondrial genes including the RNA-editing sites. The organellar genomes were maternally inherited to ‘Börner’ fromVitis riparia.
Broad anti-coronaviral activity of FDA approved drugs against SARS-CoV-2in vitroand SARS-CoVin vivo
Authors: Weston Stuart , Coleman Christopher M. , Haupt Rob , Logue James , Matthews Krystal , Frieman Matthew B. 
Published: March 2020

AbstractSARS-CoV-2 emerged in China at the end of 2019 and has rapidly become a pandemic with roughly 2.7 million recorded COVID-19 cases and greater than 189,000 recorded deaths by April 23rd, 2020 (www.WHO.org). There are no FDA approved antivirals or vaccines for any coronavirus, including SARS-CoV-2. Current treatments for COVID-19 are limited to supportive therapies and off-label use of FDA approved drugs. Rapid development and human testing of potential antivirals is greatly needed. A quick way to test compounds with potential antiviral activity is through drug repurposing. Numerous drugs are already approved for human use and subsequently there is a good understanding of their safety profiles and potential side effects, making them easier to fast-track to clinical studies in COVID-19 patients. Here, we present data on the antiviral activity of 20 FDA approved drugs against SARS-CoV-2 that also inhibit SARS-CoV and MERS-CoV. We found that 17 of these inhibit SARS-CoV-2 at a range of IC50 values at non-cytotoxic concentrations. We directly follow up with seven of these to demonstrate all are capable of inhibiting infectious SARS-CoV-2 production. Moreover, we have evaluated two of these, chloroquine and chlorpromazine,in vivousing a mouse-adapted SARS-CoV model and found both drugs protect mice from clinical disease.
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
Authors: Brann David H. , Tsukahara Tatsuya , Weinreb Caleb , Lipovsek Marcela , Van den Berge Koen , Gong Boying , Chance Rebecca , Macaulay Iain C. , Chou Hsin-jung , Fletcher Russell , Das Diya , Street Kelly , de Bezieux Hector Roux , Choi Yoon-Gi , Risso Davide , Dudoit Sandrine , Purdom Elizabeth , Mill Jonathan S. , Hachem Ralph Abi , Matsunami Hiroaki , Logan Darren W. , Goldstein Bradley J. , Grubb Matthew S. , Ngai John , Datta Sandeep Robert 
Published: March 2020

AbstractAltered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) – the causal agent in COVID-19 – affects olfaction directly by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing revealed that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing and immunostaining demonstrated ACE2 expression in support cells, stem cells, and perivascular cells; in contrast, neurons in both the olfactory epithelium and bulb did not express ACE2 message or protein. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
Markerless tracking of an entire insect colony
Authors: Bozek Katarzyna , Hebert Laetitia , Portugal Yoann , Stephens Greg J. 
Published: March 2020

AbstractWe present a comprehensive, computational method for tracking an entire colony of the honey beeApis melliferausing high-resolution video on a natural honeycomb background. We adapt a convolutional neural network (CNN) segmentation architecture to automatically identify bee and brood cell positions, body orientations and within-cell states. We achieve high accuracy (~10% body width error in position, ~10° error in orientation, and true positive rate > 90%) and demonstrate months-long monitoring of sociometric colony fluctuations. We combine extracted positions with rich visual features of organism-centered images to track individuals over time and through challenging occluding events, recovering ~79% of bee trajectories from five observation hives over a span of 5 minutes. The resulting trajectories reveal important behaviors, including fast motion, comb-cell activity, and waggle dances. Our results provide new opportunities for the quantitative study of collective bee behavior and for advancing tracking techniques of crowded systems.
Inflated citations and metrics of journals discontinued from Scopus for publication concerns: the GhoS(t)copus Project
Authors: Cortegiani Andrea , Ippolito Mariachiara , Ingoglia Giulia , Manca Andrea , Cugusi Lucia , Severin Anna , Strinzel Michaela , Panzarella Vera , Campisi Giuseppina , Manoj Lalu , Gregoretti Cesare , Einav Sharon , Moher David , Giarratano Antonino 
Published: March 2020

AbstractBackgroundScopus is a leading bibliometric database. It contains the largest number of articles cited in peer-reviewed publications. The journals included in Scopus are periodically re-evaluated to ensure they meet indexing criteria and some journals might be discontinued for publication concerns. These journals remain indexed and can be cited. Their metrics have yet to be studied. This study aimed to evaluate the main features and metrics of journals discontinued from Scopus for publication concerns, before and after their discontinuation, and to determine the extent of predatory journals among the discontinued journals.MethodsWe surveyed the list of discontinued journals from Scopus (July 2019). Data regarding metrics, citations and indexing were extracted from Scopus or other scientific databases, for the journals discontinued for publication concerns.ResultsA total of 317 journals were evaluated. Ninety-three percent of the journals (294/318) declared they published using an Open Access model. The subject areas with the greatest number of discontinued journals wereMedicine(52/317; 16%),Agriculture and Biological Science(34/317; 11%), andPharmacology, Toxicology and Pharmaceutics(31/317; 10%). The mean number of citations per year after discontinuation was significantly higher than before (median of difference 64 citations, p<0.0001), and so was the number of citations per document (median of difference 0.4 citations, p<0.0001). Twenty-two percent (72/317) were included in the Cabell’s blacklist. The DOAJ currently included only 9 journals while 61 were previously included and discontinued, most for “suspected editorial misconduct by the publisher’.Conclusions:The citation count of journals discontinued for publication concerns increases despite discontinuation and predatory behaviors seemed common. This paradoxical trend can inflate scholars’ metrics prompting artificial career advancements, bonus systems and promotion. Countermeasures should be taken urgently to ensure the reliability of Scopus metrics both at the journal- and author-level for the purpose of scientific assessment of scholarly publishing.
Burkholderia pseudomalleiclinical isolates are highly susceptiblein vitroto cefiderocol, a novel siderophore cephalosporin
Authors: Burnard Delaney , Robertson Gemma , Henderson Andrew , Falconer Caitlin , Bauer-Leo Michelle , Cottrell Kyra , Gassiep Ian , Norton Robert , Paterson David L. , Harris Patrick N. A. 
Published: March 2020

AbstractCefiderocol is a novel cephalosporin designed to treat multidrug resistant Gram-negative infections. By forming a chelated complex with ferric iron, cefiderocol is transported into the periplasmic space via bacterial iron transport systems and primarily binds to penicillin-binding protein 3 (PBP3) to inhibit peptidoglycan synthesis. This mode of action results in cefiderocol having greaterin vitroactivity against many Gram-negative bacilli than currently used carbapenems, β-lactam/β-lactamase inhibitor combinations, and cephalosporins. Thus, we investigated thein vitroactivity of cefiderocol (S-649266) against a total of 271 clinical isolates ofBurkholderia pseudomalleifrom Australia. The collection was comprised of primary isolates (92.3%) and subsequent isolates (7.7%). Minimum inhibitory concentrations (MIC) of cefiderocol ranged from ≤0.03 to 32 mg/L, where the MIC90was 1 mg/L and 16 mg/L for primary and subsequent isolates, respectively. Based upon non-species specific (Gram-negative bacilli) clinical breakpoints for cefiderocol (MIC ≤ 4 mg/L), twelve isolates (4.4%) would be classified as non-susceptible. Further testing for co-resistance to meropenem, ceftazidime, trimethoprim-sulfamethoxazole, amoxicillin-clavulanate and doxycycline was performed on a subset of isolates with elevated cefiderocol MICs (≥2 mg/L, 4.8%) and 84.6% of these isolates exhibited resistance to at least one of these antimicrobials. Cefiderocol was found to be highly activein vitroagainstB. pseudomalleiprimary clinical isolates. This novel compound shows great potential for the treatment of melioidosis in endemic countries and should be explored further.
Anaerobic metabolism of Foraminifera thriving below the seafloor
Authors: Orsi William D. , Morard Raphaël , Vuillemin Aurele , Eitel Michael , Wörheide Gert , Milucka Jana , Kucera Michal 
Published: March 2020

AbstractForaminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the generaBolivinaandStainforthiadominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. The relative abundance of Foraminifera gene expression in anoxic sediment depths increased an order of magnitude, which was confirmed in a ten-day incubation experiment where the development of anoxia coincided with a 27-fold increase in the relative abundance of Foraminifera protein encoding transcripts. This indicates that many Foraminifera were not only surviving, but thriving under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, dissimilatory nitrate reduction, fumarate reduction, and dephosphorylation of creatine phosphate. This was co-expressed alongside genes involved in production of reticulopodia, phagocytosis, calcification, and clathrin-mediated-endocytosis (CME). Thus, Foraminifera may use CME under anoxic conditions to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These mechanisms help explain how some Foraminifera can thrive under anoxia, which would help to explain their ecological success documented in the fossil record since the Cambrian period more than 500 million years ago.
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning
Authors: Li Zhongxiao , Li Yisheng , Zhang Bin , Li Yu , Long Yongkang , Zhou Juexiao , Zou Xudong , Zhang Min , Hu Yuhui , Chen Wei , Gao Xin 
Published: March 2020

AbstractAlternative polyadenylation (APA) is a crucial step in post-transcriptional regulation. Previous bioinformatic works have mainly focused on the recognition of polyadenylation sites (PAS) in a given genomic sequence, which is a binary classification problem. Recently, computational methods for predicting the usage level of alternative PAS in a same gene have been proposed. However, all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PAS into account. To address this, here we propose a deep learning architecture, DeeReCT-APA, to quantitatively predict the usage of all alternative PAS of a given gene. To accommodate different genes with potentially different numbers of PAS, DeeReCT-APA treats the problem as a regression task with a variable-length target. Based on a CNN-LSTM architecture, DeeReCT-APA extracts sequence features with CNN layers, uses bidirectional LSTM to explicitly model the interactions among competing PAS, and outputs percentage scores representing the usage levels of all PAS of a gene. In addition to the fact that only our method can predict quantitatively the usage of all the PAS within a gene, we show that our method consistently outperforms other existing methods on three different tasks for which they are trained: pairwise comparison task, highest usage prediction task and ranking task. Finally, we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and shed light on future mechanistic understanding in APA regulation. Our code and data are available athttps://github.com/lzx325/DeeReCT-APA-repo.
Maternal DNMT3A-dependent de novo methylation of the zygotic paternal genome inhibits gene expression in the early embryo
Authors: Albert Julien Richard , Yeung Wan Kin Au , Toriyama Keisuke , Kobayashi Hisato , Hirasawa Ryutaro , Brind’Amour Julie , Bogutz Aaron , Sasaki Hiroyuki , Lorincz Matthew 
Published: March 2020

ABSTRACTDe novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. Following fertilization, the paternal genome undergoes widespread DNAme loss before the first S-phase. Paradoxically, recent mass spectrometry analysis revealed that a low level of de novo DNAme occurs exclusively on the zygotic paternal genome. However, the loci involved and impact on genic transcription was not addressed. Here, we employ allele-specific analysis of wholegenome bisulphite sequencing (WGBS) data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome in 2-cell embryos. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with zygotic paternal DNAme acquisition (PDA), many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Strikingly, PDA is lost following maternal deletion ofDnmt3a. Furthermore, a subset of promoters showing PDA which are normally transcribed from the paternal allele in blastocysts show premature transcription at the 4-cell stage in maternalDnmt3aknockout embryos. These observations uncover an unexpected role for maternal DNMT3A activity in postfertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.
Large-scale Phenotypic Drug Screen Identifies Neuroprotectants in Zebrafish and Mouse Models of Retinitis Pigmentosa
Authors: Zhang Liyun , Chen Conan , Fu Jie , Lilley Brendan , Berlinicke Cynthia , Hansen Baranda , Ding Ding , Wang Guohua , Wang Tao , Shou Daniel , Ye Ying , Saxena Meera T. , Hall Kelsi R. , Sharrock Abigail V. , Brandon Carlene , Shim Joong Sup , Hanes Justin , Ji Hongkai , Liu Jun O. , Qian Jiang , Ackerley David F. , Rohrer Baerbel , Zack Donald J. , Mumm Jeff S. 
Published: March 2020

ABSTRACTRetinitis pigmentosa (RP) and associated inherited retinal diseases (IRDs) are caused by rod photoreceptor degeneration, necessitating therapeutics promoting rod photoreceptor survival. To address this, we tested compounds for neuroprotective effects in zebrafish and mouse RP models, reasoning drugs effective across species may translate better clinically. We first performed a large-scale phenotypic drug screen using a larval zebrafish model of inducible RP. 2,934 compounds, mostly human-approved drugs, were tested across six concentrations. Statistically, 113 compounds achieved “hit” status. Secondary tests of 42 high-priority hits confirmed eleven lead compounds. Nine leads were then evaluated in mouse RP models, with six exhibiting neuroprotective effects. An analysis of potential mechanisms of action suggested complementary activities. Paired lead compound assays in zebrafish showed additive neuroprotective effects for the majority. These results highlight the value of cross-species phenotypic drug discovery and suggest combinatorial drug therapies may provide enhanced therapeutic benefits for patients with RP and IRDs.
Pancreatlas™: applying an adaptable framework to map the human pancreas in health and disease
Authors: Saunders Diane C. , Messmer James , Kusmartseva Irina , Beery Maria L. , Yang Mingder , Atkinson Mark A. , Powers Alvin C. , Cartailler Jean-Philippe , Brissova Marcela 
Published: March 2020

SummaryHuman tissue phenotyping generates complex spatial information from numerous imaging modalities, yet images typically become static figures for publication and original data and metadata are rarely available. While comprehensive image maps exist for some organs, most resources have limited support for multiplexed imaging or have non-intuitive user interfaces. Therefore, we built a Pancreatlas™ resource that integrates several technologies into a novel interface, allowing users to access richly annotated web pages, drill down to individual images, and deeply explore data online. The current version of Pancreatlas contains over 800 unique images acquired by whole-slide scanning, confocal microscopy, and imaging mass cytometry, and is available athttps://www.pancreatlas.org. To create this human pancreas-specific biological imaging resource, we developed a React-based web application and Python-based application programming interface, collectively called Flexible Framework for Integrating and Navigating Data (FFIND), which can be adapted beyond Pancreatlas to meet countless imaging or other structured data management needs.
Characterization of theCorynebacterium glutamicumdehydroshikimate dehydratase QsuB and its potential for microbial production of protocatechuic acid
Authors: Shmonova Ekaterina A. , Voloshina Olga V. , Ovsienko Maksim V. , Smirnov Sergey V. , Doroshenko Vera G. 
Published: March 2020

AbstractThe dehydroshikimate dehydratase (DSD) fromCorynebacterium glutamicumencoded by theqsuBgene is related to the previously described QuiC1 protein (39.9% identity) fromPseudomonas putida. QuiC1 and QsuB are both two-domain bacterial DSDs. The N-terminal domain provides dehydratase activity, while the C-terminal domain has sequence identity with 4-hydroxyphenylpyruvate dioxygenase. Here, the QsuB protein and its DSD domain (N-QsuB) were expressed in the T7 system, purified and characterized. QsuB was present mainly in octameric form (60%), while N-QsuB had a predominantly monomeric structure (80%) in solution. Both proteins possessed DSD activity with one of the following cofactors (listed in order of decreasing activity): Co2+, Mg2+, Mn2+or Ca2+. The Kmand kcatvalues for QsuB were two and three times higher, respectively (Km~ 1 mM, kcat~ 61 s−1) than those for N-QsuB. Notably, 3,4-DHBA inhibited both enzymes via an uncompetitive mechanism. QsuB and N-QsuB were tested for 3,4-DHBA production from glucose inE. coli. MG1655ΔaroEPlac–qsuBproduced at least two times more 3,4-DHBA than MG1655ΔaroEPlac–n-qsuBin the presence of isopropyl β-D-1-thiogalactopyranoside.
EphA7 Isoforms Differentially Regulate Cortical Dendrite Development
Authors: Leonard Carrie E. , Baydyuk Maryna , Stepler Marissa A. , Burton Denver A. , Donoghue Maria J. 
Published: March 2020

AbstractThe shape of a neuron reflects its cellular function and ultimately, how it operates in neural circuits. Dendrites receive and integrate incoming signals, including excitatory input onto dendritic spines, so understanding how dendritic development proceeds is fundamental for discerning neural function. Using loss- and gain-of-function paradigms, we previously demonstrated that EphA7 receptor signaling during cortical development impacts dendrites in two ways: restricting growth early and promoting spine formation later. Here, the molecular basis for this shift in EphA7 function is defined. Expression analyses reveal that both full-length (EphA7-FL) and truncated (EphA7-T1; lacking kinase domain) isoforms of EphA7 are expressed in the developing cortex, with peak expression of EphA7-FL overlapping with dendritic elaboration and highest levels of EphA7-T1 coinciding with spine formation. Overexpression studies in cultured neurons demonstrate that EphA7-FL inhibits both dendritic growth and spine formation, while EphA7-T1 increases spine density. Furthermore, signaling downstream of EphA7 varies during development;in vivoinhibition of kinase-dependent mTOR by rapamycin in EphA7 mutant neurons rescues the dendritic branching, but not the dendritic spine phenotypes. Finally, interaction and signaling modulation was examined. In cells in culture, direct interaction between EphA7-FL and EphA7-T1 is demonstrated which results in EphA7- T1-based modulation of EphA7-FL phosphorylation.In vivo, both isoforms are colocalized to cortical synapses and levels of phosphorylated EphA7-FL decrease as EphA7-T1 levels rise. Thus, the phenotypes of EphA7 during cortical dendrite development are explained by divergent functions of two variants of the receptor.