bluuebunny/crossref_metadata_2025_split huggingface dataset:
DrawGlycan-SNFG and gpAnnotate: rendering glycans and annotating glycopeptide mass spectra
Authors: Cheng Kai , Pawlowski Gabrielle , Yu Xinheng , Zhou Yusen , Neelamegham Sriram 
Published: November 2019

Abstract

Summary
This manuscript describes an open-source program, DrawGlycan-SNFG (version 2), that accepts IUPAC (International Union of Pure and Applied Chemist)-condensed inputs to render Symbol Nomenclature For Glycans (SNFG) drawings. A wide range of local and global options enable display of various glycan/peptide modifications including bond breakages, adducts, repeat structures, ambiguous identifications etc. These facilities make DrawGlycan-SNFG ideal for integration into various glycoinformatics software, including glycomics and glycoproteomics mass spectrometry (MS) applications. As a demonstration of such usage, we incorporated DrawGlycan-SNFG into gpAnnotate, a standalone application to score and annotate individual MS/MS glycopeptide spectrum in different fragmentation modes.

Availability and implementation
DrawGlycan-SNFG and gpAnnotate are platform independent. While originally coded using MATLAB, compiled packages are also provided to enable DrawGlycan-SNFG implementation in Python and Java. All programs are available from https://virtualglycome.org/drawglycan; https://virtualglycome.org/gpAnnotate.

Supplementary information
Supplementary data are available at Bioinformatics online.
miR-155 as a novel clinical target for hematological malignancies
Authors: Witten Lisa , Slack Frank J 
Published: November 2019

Abstract
MicroRNAs (miRNAs), small non-coding RNAs that repress target genes, are a promising new focus of targeted therapeutics for cancer. miR-155 is a well-studied miRNA involved in inflammation that acts oncogenically in many hematological malignancies. Like other miRNAs, its role in these diseases is complex and nuanced, which gives particular power to its inhibition in diseased cells. This, together with increasing understanding of its key targets in cancer and the use of powerful mouse models of miR-155 in cancer, makes miR-155 an ideal target for therapeutic inhibition. Here, we review the role of miRNAs, and particularly miR-155, in cancers, and discuss progress on therapeutically targeting it, including the ongoing clinical trial of anti-miR-155 molecule Cobomarsen (MRG-106).
Transcription Factor 4 Safeguards Hippocampal Dentate Gyrus Development by Regulating Neural Progenitor Migration
Authors: Wang Yafei , Lu Zhiheng , Zhang Yilan , Cai Yuqun , Yun Di , Tang Tianxiang , Cai Zheping , Wang Chunyang , Zhang Yandong , Fang Fang , Yang Zhengang , Behnisch Thomas , Xie Yunli 
Published: November 2019

AbstractThe dentate gyrus (DG) of the hippocampal formation plays essential roles in learning and memory. Defective DG development is associated with neurological disorders. Here, we show that transcription factor 4 (Tcf4) is essential for DG development. Tcf4 expression is elevated in neural progenitors of the dentate neuroepithelium in the developing mouse brain. We demonstrate that conditional disruption of Tcf4 in the dentate neuroepithelium leads to abnormal neural progenitor migration guided by disorganized radial glial fibers, which further leads to hypoplasia in the DG. Moreover, we reveal that Wnt7b is a key downstream effector of Tcf4 in regulating neural progenitor migration. Behavioral analysis shows that disruption of integrity of the DG impairs the social memory highlighting the importance of proper development of the DG. These results reveal a critical role for Tcf4 in regulating DG development. As mutations in TCF4 cause Pitt–Hopkins syndrome (PTHS) characterized by severe intellectual disability, our data also potentially provide insights into the basis of neurological defects linked to TCF4 mutations.
Does environmental stress affect cortisol biodistribution in freshwater mussels?
Authors: Binder A Ronja D , Pfaffl Michael W , Hiltwein Felix , Geist Juergen , Beggel Sebastian 
Published: November 2019

Lay summaries:
Since little is known about invertebrate steroid hormones, we established a cortisol extraction and quantification protocol via ELISA in mussels, in the model organism Anodonta anatina. Additionally, we quantified cortisol biodistribution and redistribution in five different tissues after treatment with either copper (II) chloride, sodium chloride or algae feed.
Written Language Outcomes of Deaf Elementary Students Engaged in Authentic Writing
Authors: Wolbers Kimberly A , Dostal Hannah M , Cihak David , Holcomb Leala 
Published: November 2019

Abstract
This study explores the impact of Strategic and Interactive Writing Instruction (SIWI) on six students’ written language skills through the application of a multiple-baseline probe single case design with embedded condition. This was part of a larger Institute of Education Sciences (IES)-funded project focused on the development and feasibility of implementation of SIWI. For the majority of skills analyzed, there were improvements in the mean level of performance with the implementation of SIWI, as well as more consistent responding and positive trends in the data. The study also revealed that teachers are in need of additional tools to aid the systematic identification and tracking of syntax skills in children’s written language development, and to distinguish these from other writing skills such as conventions or handwriting.
Merger Policy in a Quantitative Model of International Trade*
Authors: Breinlich Holger , Nocke Volker , Schutz Nicolas 
Published: November 2019

Abstract
In a two-country international trade model with oligopolistic competition, we study the conditions on market structure and trade costs under which a merger policy designed to benefit domestic consumers is too tough or too lenient from the viewpoint of the foreign country. We calibrate the model to match industry-level data in the U.S. and Canada. Our results suggest that at present levels of trade costs, merger policy is too tough in the vast majority of sectors. We also quantify the resulting externalities and study the impact of different regimes of coordinating merger policies at varying levels of trade costs.
Cancer statistics: a comparison between World Health Organization (WHO) and Global Burden of Disease (GBD)
Authors: Mattiuzzi Camilla , Lippi Giuseppe 
Published: November 2019

Abstract
This study aims to define comparability of 2016 statistics between Global Health Estimates (GHE) and Global Health Data Exchange (GHDx) registries for disability-adjusted life years (DALYs) and mortality of the 25 most frequent worldwide malignancies. An excellent correlation can be found between the two registries for both cancer DALYs (r = 0.988) and mortality (r = 0.993). Cancer-related DALYs are substantially equivalent (mean bias, −1.9%; P = 0.603), while cancer mortality is modestly but significantly overestimated in GDHx (mean bias, 9.1%; P = 0.004). These results suggest that cancer DALYs estimate appear almost overlapping between GHE and GHDx registries, while cancer mortality is slightly overestimated in GDHx.
Key amino acid residues of neuraminidase involved in influenza A virus entry
Authors: Chen Fangzhao , Liu Teng , Xu Jiagui , Huang Yingna , Liu Shuwen , Yang Jie 
Published: November 2019

ABSTRACT
Generally, influenza virus neuraminidase (NA) plays a critical role in the release stage of influenza virus. Recently, it has been found that NA may promote influenza virus to access the target cells. However, the mechanism remain unclear. Here, we reported that peramivir indeed possessed anti-influenza A virus (IAV) activity in the stage of viral entry. Importantly, we verified the critical residues of influenza NA involved in the viral entry. As a result, peramivir as an efficient NA inhibitor could suppress the initiation of IAV infection. Furthermore, mutational analysis showed NA might be associated with viral entry via amino acids residues R118, E119, D151, R152, W178, I222, E227, E276, R292 and R371. Our results demonstrated NA must contain the key amino acid residues can involve in IAV entry.
Partial anomalous pulmonary venous connection detected during right pneumonectomy
Authors: Yenigün Bülent Mustafa , Kocaman Gökhan , Gürsoy Çoruh Ayşegül , Akal Rıfat Murat 
Published: November 2019

Abstract
Partial anomalous pulmonary venous connection (PAPVC) is a rare congenital anomaly. Generally, it is seen on the right side and is associated with an atrial septal defect. Herein, we present a case of a 50-year-old male patient with a supracardiac type PAPVC detected during pneumonectomy for a right hilar mass. This is the second case report in the literature presenting surgical treatment of both lung cancer and PAPVC using pneumonectomy. Thoracic surgeons should be aware of this anomaly when they are planning to perform a major lung resection. If PAPVC and lung cancer are in the same lobe, anatomical lung resections including pneumonectomy can be safely performed.
Screening Strategies for a Sustainable Endpoint for Gambiense Sleeping Sickness
Authors: Castaño M Soledad , Aliee Maryam , Mwamba Miaka Erick , Keeling Matt J , Chitnis Nakul , Rock Kat S 
Published: November 2019

Abstract

Background
Gambiense human African trypanosomiasis ([gHAT] sleeping sickness) is a vector-borne disease that is typically fatal without treatment. Intensified, mainly medical-based, interventions in endemic areas have reduced the occurrence of gHAT to historically low levels. However, persistent regions, primarily in the Democratic Republic of Congo (DRC), remain a challenge to achieving the World Health Organization’s goal of global elimination of transmission (EOT).

Methods
We used stochastic models of gHAT transmission fitted to DRC case data and explored patterns of regional reporting and extinction. The time to EOT at a health zone scale (~100 000 people) and how an absence of reported cases informs about EOT was quantified.

Results
Regional epidemiology and level of active screening (AS) both influenced the predicted time to EOT. Different AS cessation criteria had similar expected infection dynamics, and recrudescence of infection was unlikely. However, whether EOT has been achieved when AS ends is critically dependent on the stopping criteria. Two or three consecutive years of no detected cases provided greater confidence of EOT compared with a single year (~66%–75% and ~82%–84% probability of EOT, respectively, compared with 31%–51%).

Conclusions
Multiple years of AS without case detections is a valuable measure to assess the likelihood that the EOT target has been met locally.
Duration of pretomanid/moxifloxacin/pyrazinamide therapy compared with standard therapy based on time-to-extinction mathematics
Authors: Srivastava Shashikant , Deshpande Devyani , Magombedze Gesham , van Zyl Johanna , Cirrincione Kayle , Martin Katherine , Bendet Paula , Berg Alexander , Hanna Debra , Romero Klaus , Hermann Dave , Gumbo Tawanda 
Published: November 2019

AbstractObjectivesAnimal models have suggested that the combination of pretomanid with pyrazinamide and moxifloxacin (PaMZ) may shorten TB therapy duration to 3–4 months. Here, we tested that in the hollow-fibre system model of TB (HFS-TB).MethodsA series of HFS-TB experiments were performed to compare the kill rates of the PaMZ regimen with the standard three-drug combination therapy. HFS-TB experiments were performed with bacilli in log-phase growth treated for 28 days, intracellular bacilli treated daily for 28 days and semi-dormant Mycobacterium tuberculosis treated with daily therapy for 56 days for sterilizing effect. Next, time-to-extinction equations were employed, followed by morphism transformation and Latin hypercube sampling, to determine the proportion of patients who achieved a time to extinction of 3, 4 or 6 months with each regimen.ResultsUsing linear regression, the HFS-TB sterilizing effect rates of the PaMZ regimen versus the standard-therapy regimen during the 56 days were 0.18 (95% credible interval=0.13–0.23) versus 0.15 (95% credible interval=0.08–0.21) log10 cfu/mL/day, compared with 0.16 (95% credible interval=0.13–0.18) versus 0.11 (95% credible interval=0.09–0.13) log10 cfu/mL/day in the Phase II clinical trial, respectively. Using time-to-extinction and Latin hypercube sampling modelling, the expected percentages of patients in which the PaMZ regimen would achieve sterilization were 40.37% (95% credible interval=39.1–41.34) and 72.30% (95% credible interval=71.41–73.17) at 3 and 4 months duration of therapy, respectively, versus 93.67% (95% credible interval=93.18–94.13) at 6 months for standard therapy.ConclusionsThe kill rates of the PaMZ regimen were predicted to be insufficient to achieve cure in less than 6 months in most patients.
Thinking outside the pelvis: benign peritoneal multicystic mesothelioma of the ascending colon
Authors: Murphy Brenda , Ismaeil Mohamed , Winter Des C 
Published: November 2019

AbstractBenign peritoneal multicystic mesothelioma is a rare tumor of the visceral peritoneum. The authors present an atypical case of a 74-year-old man who presented with a multicystic mesothelioma of the ascending colon.
Extensive hidradenitis suppurativa with dorsal foot involvement: a case report
Authors: Nisar Saira , Roberson Jeffrey L , Travis Taryn E , Johnson Laura S , Shupp Jeffrey W 
Published: November 2019

Abstract
Hidradenitis suppurativa (HS) is a highly morbid chronic inflammatory skin disease resulting in painful and purulent lesions classically occurring in areas with a high density of apocrine glands such as the groin and axillae. This is the case of a 53-year-old male with medically refractory Hurley stage III HS affecting multiple anatomical sites including the dorsum of the right foot, an atypical location. Throughout his hospital course, he underwent a series of surgical excision and graft procedures to treat extensive HS lesions on various anatomical locations. In patients with a history of HS, mechanical stress may result in atypical lesion locations. In addition to the standard medical and surgical treatment, management should include optimizing nutritional parameters, smoking cessation, wound care and reducing friction and pressure at the affected area.
Turning sugar into oil: making photosynthesis blind to feedback inhibition
Authors: Paul Matthew J , Eastmond Peter J 
Published: November 2019

This article comments on:
Beechey-Gradwell Z, Cooney L, Winichayakul S, Andrews M, Hea SY, Crowther T, Roberts N. 2020. Storing carbon in leaf lipid sinks enhanced perennial ryegrass carbon capture especially under high N and elevated CO2. Journal of Experimental Botany 71, 2351–2361.
The European Nucleotide Archive in 2019
Authors: Amid Clara , Alako Blaise T F , Balavenkataraman Kadhirvelu Vishnukumar , Burdett Tony , Burgin Josephine , Fan Jun , Harrison Peter W , Holt Sam , Hussein Abdulrahman , Ivanov Eugene , Jayathilaka Suran , Kay Simon , Keane Thomas , Leinonen Rasko , Liu Xin , Martinez-Villacorta Josue , Milano Annalisa , Pakseresht Amir , Rahman Nadim , Rajan Jeena , Reddy Kethi , Richards Edward , Smirnov Dmitriy , Sokolov Alexey , Vijayaraja Senthilnathan , Cochrane Guy 
Published: November 2019

Abstract
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory’s European Bioinformatics Institute provides open and freely available data deposition and access services across the spectrum of nucleotide sequence data types. Making the world’s public sequencing datasets available to the scientific community, the ENA represents a globally comprehensive nucleotide sequence resource. Here, we outline ENA services and content in 2019 and provide an insight into selected key areas of development in this period.
Rapid in vitro production of single-stranded DNA
Authors: Minev Dionis , Guerra Richard , Kishi Jocelyn Y , Smith Cory , Krieg Elisha , Said Khaled , Hornick Amanda , Sasaki Hiroshi M , Filsinger Gabriel , Beliveau Brian J , Yin Peng , Church George M , Shih William M 
Published: November 2019

Abstract
There is increasing demand for single-stranded DNA (ssDNA) of lengths >200 nucleotides (nt) in synthetic biology, biological imaging and bionanotechnology. Existing methods to produce high-purity long ssDNA face limitations in scalability, complexity of protocol steps and/or yield. We present a rapid, high-yielding and user-friendly method for in vitro production of high-purity ssDNA with lengths up to at least seven kilobases. Polymerase chain reaction (PCR) with a forward primer bearing a methanol-responsive polymer generates a tagged amplicon that enables selective precipitation of the modified strand under denaturing conditions. We demonstrate that ssDNA is recoverable in ∼40–50 min (time after PCR) with >70% yield with respect to the input PCR amplicon, or up to 70 pmol per 100 μl PCR reaction. We demonstrate that the recovered ssDNA can be used for CRISPR/Cas9 homology directed repair in human cells, DNA-origami folding and fluorescent in-situ hybridization.
Contrasting diurnal patterns in antioxidant capacities, but not in expression of stress protein genes among copepod populations from clear versus glacially fed alpine and subalpine lakes
Authors: Tartarotti Barbara , Sommaruga Ruben , Saul Nadine 
Published: November 2019

Abstract
Short-term changes in environmental conditions largely influence planktonic organisms, but their responses will depend on the habitat characteristics. Here we studied diurnal patterns in antioxidative metabolites (lipophilic and hydrophilic antioxidant capacities) and in the expression of stress protein genes (heat shock proteins, hsp) of copepods to identify short-term stress responses in clear and turbid alpine lakes, as well as in less transparent subalpine ones. Cyclops abyssorum tatricus showed diurnal variation in antioxidant capacities with maxima around noon in clear, but not in glacially fed, turbid lakes. Low fluctuations of these metabolites were also observed in another copepod, Acanthodiaptomus denticornis. Although levels of hsp genes differed between populations living in clear or glacially fed lakes, there was no diurnal rhythmicity in gene expression. Our data show that when planktonic organisms may be at greatest risk of oxidative damage, such as during the daytime in high UV radiation environments, they activate antioxidant responses. Conversely, in less transparent lakes, the physiological response seems to be unnecessary. The difference in gene expression levels suggests an ecological, albeit not acute, role of these genes in copepods experiencing daily environmental fluctuations.
Identifying phenotypes of patients with antiphospholipid antibodies: results from a cluster analysis in a large cohort of patients
Authors: Sciascia Savino , Radin Massimo , Cecchi Irene , Bertolaccini Maria Laura , Bertero Maria Tiziana , Rubini Elena , Vaccarino Antonella , Bazzan Mario , Giachino Osvaldo , Baldovino Simone , Rossi Daniela , Mengozzi Giulio , Roccatello Dario 
Published: November 2019

Abstract

Objectives
To identify the aggregation of patients with aPL into different subgroups sharing common features in terms of clinical and laboratory phenotypes.

Methods
We applied a hierarchical cluster analysis from the multiple correspondence analysis to determine subgroups of patients according to clinical and laboratory characteristics in a cohort of subjects with confirmed aPL positivity who presented to our outpatient clinics from 2006 to 2018.

Results
A total of 486 patients [403 women; age 41.7 years (26)] were included, resulting in five clusters. Cluster 1 (n= 150) presented with thrombotic events (65.3% with venous thrombosis), with triple aPL positivity found in 34.7% of them (the highest rate among the different clusters). All the patients from cluster 2 (n = 91) had a confirmed diagnosis of SLE and the highest rate of anti-dsDNA positivity (91.7%). Cluster 3 included 79 women with pregnancy morbidity. Triple positivity was present in 3.8%, significantly lower when compared with Cluster 1 (34.7% versus 3.8%, P &lt;0.01). Cluster 4 included 67 patients, 28 (41.8%) of whom with APS. Thrombotic events were observed in 23.9% patients. Cluster 4 had the highest rate of cytopenia, with thrombocytopenia as high 41.8% with no anti-dsDNA antibodies. Cluster 5 included 94 asymptomatic aPL carriers.

Conclusion
While clusters 1, 2, 3 and 5 corresponded to well-known entities, cluster 4 might represent a bridging condition between pure primary APS and defined SLE, with lower thrombotic risk when compared with primary APS but higher general features such as ANA and cytopenia (mainly thrombocytopenia).
The effect of calf jackets on the health, performance, and skin temperature of dairy origin beef calves
Authors: Rutherford Naomi H , Gordon Alan W , Arnott Gareth , Lively Francis O 
Published: November 2019

Abstract
Variations and extremities in climatic conditions can result in cold stress for dairy calves during the preweaning period. The objective of this study was to investigate the effect of calf jackets on the health, performance, and skin temperature of dairy-origin beef calves. This study took place in a designated calf rearing unit, spanned for a duration of 1 yr, and consisted of five batches of calves. Calves (30.9 ± 1.68 d of age; 55.9 ± 0.20 kg live weight) were assigned to one of four treatment groups on arrival at the rearing unit. Treatments consisted of control (no jacket), arrival (jacket for 2 wk postarrival), weight (jacket for a minimum of 2 wk and until 65 kg live weight), and wean (jacket until 5 d postweaning). Ambient conditions differed significantly (P &lt; 0.001) during each of the five batches; batch 4 was the coldest with a mean ambient temperature of 6.16 °C. Significant differences were observed between the five batches for day 50 weight (P &lt; 0.01) and disease incidence (P &lt; 0.05). However, treatment had no significant effect on calf health or performance (P &gt; 0.05) during any of the five batches. Skin temperature was significantly greater (P &lt; 0.001) for calves wearing a jacket. Furthermore, there was a significant (P &lt; 0.001) relationship between ambient temperature-humidity index and skin temperature for calves with and without a calf jacket. Therefore, although calf jackets had no benefit in terms of health or performance, they did act as a barrier to environmental conditions.
Reducing Older Workers’ Sickness Absence: The Moderating Role of Perceived Fairness
Authors: Goštautaitė Bernadeta , Shao Yiduo 
Published: November 2019

AbstractAlthough aging is often associated with higher vulnerability for illness, research has reported mixed results regarding the relationship between workers’ age and sickness absence. Drawing on social exchange theory, we propose that perceived fairness may attenuate the positive association between employee age and sickness absence. We tested our hypotheses by matching employee survey data with organizational archival data on sickness absence from a public sector organization in Lithuania (n = 458). Our findings showed that perceived fairness buffered the negative effect of age on sickness absence, which provides important implications.