bluuebunny/crossref_metadata_2025_split huggingface dataset:
Training intensity distribution analysis by race pace vs. physiological approach in world‐class middle‐ and long‐distance runners
Authors: Kenneally Mark , Casado Arturo , Gomez‐Ezeiza Josu , Santos‐Concejero Jordan 
Published: May 2020

AbstractThis study aimed to analyse the training intensity distribution (TID) of a group of 7 world‐class middle‐ and long‐distance runners over 50 weeks using two different approaches to organise TID zones: (1) based on individual specific race pace and; (2) based on physiological parameters. Analysed training data included training volume, intensity and frequency. The average weekly volume for the group was 135.4 ± 29.4 km·week−1. Training volumes for Z1, Z2 and Z3 were 88.5 ± 1.1%, 7.4 ± 0.8% and 4.1 ± 0.7% respectively for race‐pace based approach, and 87.2 ± 1.2%, 6.1 ± 0.7% and 6.6 ± 0.9% respectively for the physiological approach. Differences were found between the approaches in Z2 (large effect, ES = 1.20) and Z3 (moderate effect, ES = 0.93). The approach based on race‐pace zones produced pyramidal distributions in both middle‐ and long‐distance runners across all phases of the season. The physiological approach produced polarised and pyramidal distributions depending of the phase of the season in the middle‐distance runners, and pyramidal type TID across all phases of the season in the long‐distance runners. The results of this study demonstrate that the training analysis in a world‐class group of runners shows different TID when assessed relative to race pace versus to physiological zones. This highlights a potential deficiency in training analysis and prescription methods which do not make reference to specific performance. An approach which makes reference to both physiological and performance measures may allow for a more consistent and logical analysis.
Audit logs to enforce document integrity in Skyline and Panorama
Authors: Rohde Tobias , Chupalov Rita , Shulman Nicholas , Sharma Vagisha , Eckels Josh , Pratt Brian S , MacCoss Michael J , MacLean Brendan X 
Published: May 2020

Abstract

Summary
Skyline is a Windows application for targeted mass spectrometry method creation and quantitative data analysis. Like most graphical user interface (GUI) tools, it has a complex user interface with many ways for users to edit their files which makes the task of logging user actions challenging and is the reason why audit logging of every change is not common in GUI tools. We present an object comparison-based approach to audit logging for Skyline that is extensible to other GUI tools. The new audit logging system keeps track of all document modifications made through the GUI or the command line and displays them in an interactive grid. The audit log can also be uploaded and viewed in Panorama, a web repository for Skyline documents that can be configured to only accept documents with a valid audit log, based on embedded hashes to protect log integrity. This makes workflows involving Skyline and Panorama more reproducible.

Availability and implementation
Skyline is freely available at https://skyline.ms.

Supplementary information
Supplementary data are available at Bioinformatics online.
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence
Authors: Sedova Mayya , Jaroszewski Lukasz , Alisoltani Arghavan , Godzik Adam 
Published: May 2020

AbstractMotivationAs the COVID-19 pandemic is spreading around the world, the SARS-CoV-2 virus is evolving with mutations that potentially change and fine-tune functions of the proteins coded in its genome.ResultsCoronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context.Availability and implementationCoronavirus3D server is freely available at https://coronavirus3d.org.
Broadening the ‘Survivor Capsule’ of Intimate Partner Violence Services
Authors: Baird Stephanie L , Alaggia Ramona , Maiter Sarah 
Published: May 2020

AbstractThis study responds to a need to expand current understandings of the ways in which counselling services for intimate partner violence (IPV) address trauma. From the perspectives of fifteen women who accessed IPV counselling services in Ontario, Canada, this feminist intersectional study used constructivist grounded theory methods to explore how services help women heal from trauma. Specifically, the study aimed to understand how counselling services meet the needs of survivors of IPV and respond to their complex identities and experiences of trauma and oppression. Findings exemplify the theoretical concept of a survivor capsule, illustrating ways in which women’s unique lives often do not fit into current IPV services, showing a need for more complex intersectional understandings of women’s experiences of IPV and trauma. These study findings demonstrate the importance of recognising women’s individual needs for multiple services as well as the harm caused when women have to fight to access the services they need. Findings also illustrate the instrumental role of counsellors who provide validation, are connected with women’s experiences, and are knowledgeable about IPV and trauma. Finally, suggestions are put forward for ways in which service providers can create spaces of acceptance rather than services that are stigmatising.
Message in a bottle: the Mediterranean Sea currents acted as protagonists in shaping the distribution of the sea daffodil (Pancratium maritimum, Amaryllidaceae)
Authors: De Castro Olga , Innangi Michele , Menale Bruno 
Published: May 2020

AbstractThe Mediterranean Basin can be considered as a natural laboratory with which to study the effects of sea currents in the dispersal of coastal plant species that use hydrochory. Pancratium maritimum is a perennial geophyte, with a wide distribution along Mediterranean coasts. We aim to provide a timeframe for the origin of the diversification of this plant, to clarify its phylogeographical structure and to investigate the role of currents in the Mediterranean Sea in influencing spatial patterns of its genetic distribution. The phylogeographic history was analysed using 50 populations. A genetic structure analysis and divergence time estimation was performed using plastid sequences. Five haplotypes were detected, of which two were the most abundant; a third was observed in the central Mediterranean, and two rare haplotypes were present in the eastern Mediterranean. The genetic breaks were concordant with the direction of the major Mediterranean currents. The divergence time estimation for the origin of P. maritimum was located at the end of the Neogene (mid Pliocene to mid Pleistocene). We showed the importance of sea currents in the Mediterranean in acting both as a means of dispersal and as a barrier to the distribution and evolution of P. maritimum due to the special adaptations of its seeds.
High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display
Authors: O’Donovan Brian , Mandel-Brehm Caleigh , Vazquez Sara E , Liu Jamin , Parent Audrey V , Anderson Mark S , Kassimatis Travis , Zekeridou Anastasia , Hauser Stephen L , Pittock Sean J , Chow Eric , Wilson Michael R , DeRisi Joseph L 
Published: May 2020

AbstractParaneoplastic neurological disorders are immune-mediated diseases understood to manifest as part of a misdirected anti-tumor immune response. Paraneoplastic neurological disorder-associated autoantibodies can assist with diagnosis and enhance our understanding of tumor-associated immune processes. We designed a comprehensive library of 49-amino-acid overlapping peptides spanning the entire human proteome, including all splicing isoforms and computationally predicted coding regions. Using this library, we optimized a phage immunoprecipitation and sequencing protocol with multiple rounds of enrichment to create high-resolution epitope profiles in serum and cerebrospinal fluid (CSF) samples from patients suffering from two common paraneoplastic neurological disorders, the anti-Yo (n = 36 patients) and anti-Hu (n = 44 patients) syndromes. All (100%) anti-Yo patient samples yielded enrichment of peptides from the canonical anti-Yo (CDR2 and CDR2L) antigens, while 38% of anti-Hu patients enriched peptides deriving from the nELAVL (neuronal embryonic lethal abnormal vision like) family of proteins, the anti-Hu autoantigenic target. Among the anti-Hu patient samples that were positive for nELAVL, we noted a restricted region of immunoreactivity. To achieve single amino acid resolution, we designed a novel deep mutational scanning phage library encoding all possible single-point mutants targeting the reactive nELAVL region. This analysis revealed a distinct preference for the degenerate motif, RLDxLL, shared by ELAVL2, 3 and 4. Lastly, phage immunoprecipitation sequencing identified several known autoantigens in these same patient samples, including peptides deriving from the cancer-associated antigens ZIC and SOX families of transcription factors. Overall, this optimized phage immunoprecipitation sequencing library and protocol yielded the high-resolution epitope mapping of the autoantigens targeted in anti-Yo and anti-Hu encephalitis patients to date. The results presented here further demonstrate the utility and high-resolution capability of phage immunoprecipitation sequencing for both basic science and clinical applications and for better understanding the antigenic targets and triggers of paraneoplastic neurological disorders.
Ligation-assisted endoscopic mucosal resection for esophageal granular cell tumors is safe and effective
Authors: Kumar Shria , Chandrasekhara Vinay , Kochman Michael L , Ahmad Nuzhat , Attalla Sara , Ho Immanuel K , Jaffe David L , Lee Peter J , Panganamamula Kashyap V , Saumoy Monica , Fortuna Danielle , Ginsberg Gregory G 
Published: May 2020

SUMMARY
Given their malignant potential, resection of esophageal granular cell tumors (GCTs) is often undertaken, yet the optimal technique is unknown. We present a large series of dedicated endoscopic resection using band ligation (EMR-B) of esophageal GCTs. Patients diagnosed with esophageal GCTs between 2002 and 2019 were identified using a prospectively collected pathology database. Endoscopic reports were reviewed, and patients who underwent dedicated EMR-B of esophageal GCTs were included. Medical records were queried for demographics, findings, adverse events, and follow-up. We identified 21 patients who underwent dedicated EMR-B for previously identified esophageal GCT. Median age was 39 years; 16 (76%) were female. Eight (38%) had preceding signs or symptoms, potentially attributable to the GCT. Upon endoscopic evaluation, 12 (57%) were found in the distal esophagus. Endoscopic ultrasound was used in 15 cases (71%). Median lesion size was 7 mm, interquartile range 4 mm—8 mm. The largest lesion was 12 mm. A total of 20 (95%) had en bloc resection confirmed with pathologic examination. The only patient with tumor extending to the resection margin underwent surveillance endoscopy that showed no residual tumor. No patients experienced bleeding, perforation, or stricturing in our series. No patients have had known recurrence of their esophageal GCT. EMR-B of esophageal GCT achieves complete histopathologic resection with minimal adverse events. EMR-B is safe and effective and seems prudent compared with observation for what could be an aggressive and malignant tumor. EMR-B should be considered first-line therapy when resecting esophageal GCT up to 12 mm in diameter.
Prevalence of Early- and Late-Season Pest Damage to Corn in Cover Crop-Based Reduced-Tillage Organic Systems
Authors: Regan Karly H , Voortman Christina A , Wallace John M , Barbercheck Mary E 
Published: May 2020

Abstract
In organic agronomic cropping systems, the use of synthetic insecticides and transgenic varieties are prohibited and producers rely mainly on biological control, tillage, crop rotation, and other cultural practices to manage pests. We measured damage to organic corn (Zea mays L.) from multiple invertebrate pests, including slugs (Gastropoda: Mollusca), European corn borer (Ostrinia nubilalis Hübner), corn earworm (Helicoverpa zea Boddie), and fall armyworm (Spodoptera frugiperda Smith), early and late in the growing season in four cropping systems that varied in tillage frequency and intensity and in winter cover crop species. Specific management tactics included two cover crop mixtures preceding corn, the use of a roller-crimper or tillage to terminate cover crops preceding corn, and the establishment of interseeded cover crops after corn emergence. Prevalence of early-season damage was high, but severity of damage was very low and unrelated to corn yield. The proportion of corn plants affected by chewing pests early in the season was lower in plots in which tillage compared to a roller-crimper was used to terminate cover crops. Cropping system did not affect the numbers of late-season caterpillar pests or corn yield. Predation by natural enemies appeared to effectively maintain damage from chewing pests below yield-damaging levels. These results support the inclusion of winter and interseeded cover crops in organic agronomic crop rotations to gain environmental benefits without increasing risks of damage by insect pests.
The implications of catheter ablation for solitary atrial flutter in preventing stroke risk: a nationwide population-based cohort study
Authors: Lin Yu-Sheng , Wu Victor Chien-Chia , Wang Hui-Ting , Chen Huang-Chung , Chen Mien-Cheng , Chang Shih-Tai , Chu Pao-Hsien , Chen Yung-Lung 
Published: May 2020

Abstract

Aims
The implications of ablation for atrial fibrillation in preventing stroke are controversial, and no studies have investigated whether ablation prevents ischaemic stroke (IS) in atrial flutter (AFL).

Methods and results
This study analysed data contained in the Taiwan National Health Insurance Research Database for 16 765 patients with a first diagnosis of solitary AFL during 2001–2013. Eligible patients were divided into two groups according to whether or not they had received ablation. Propensity score matching (PSM) was performed to mitigate the effects of potential confounding factors. The primary outcome was occurrence of IS during follow-up. After 1:2 PSM, the analysis included 1037 patients in the ablation group and 2074 patients in the non-ablation group. The incidence of IS was lower in the ablation group compared to the non-ablation group [subdistribution hazard ratio (SHR) 0.61, 95% confidence interval (CI) 0.41–0.90] during the 2-year follow-up period but not thereafter (SHR 1.03, 95% CI 0.72–1.48). When grouping by stroke history, it revealed that ablation affected the incidence of stroke in patients without history of stroke (SHR 0.59, 95% CI 0.38–0.91) but not in patients with history of stroke. When each group was stratified by CHA2DS2-VASc score, ablation lowered the incidence of stroke in patients with CHA2DS2-VASc ≤3 (SHR 0.31, 95% CI 0.16–0.60) but not in patients with CHA2DS2-VASc ≥4 in the initial 2-year follow-up.

Conclusion
The different incidence of IS in patients with/without ablation indicates that ablation reduces the risk of IS in AFL patients.
Electrocardiographic imaging for cardiac arrhythmias and resynchronization therapy
Authors: Pereira Helder , Niederer Steven , Rinaldi Christopher A 
Published: May 2020

AbstractUse of the 12-lead electrocardiogram (ECG) is fundamental for the assessment of heart disease, including arrhythmias, but cannot always reveal the underlying mechanism or the location of the arrhythmia origin. Electrocardiographic imaging (ECGi) is a non-invasive multi-lead ECG-type imaging tool that enhances conventional 12-lead ECG. Although it is an established technology, its continuous development has been shown to assist in arrhythmic activation mapping and provide insights into the mechanism of cardiac resynchronization therapy (CRT). This review addresses the validity, reliability, and overall feasibility of ECGi for use in a diverse range of arrhythmias. A systematic search limited to full-text human studies published in peer-reviewed journals was performed through Medline via PubMed, using various combinations of three key concepts: ECGi, arrhythmia, and CRT. A total of 456 studies were screened through titles and abstracts. Ultimately, 42 studies were included for literature review. Evidence to date suggests that ECGi can be used to provide diagnostic insights regarding the mechanistic basis of arrhythmias and the location of arrhythmia origin. Furthermore, ECGi can yield valuable information to guide therapeutic decision-making, including during CRT. Several studies have used ECGi as a diagnostic tool for atrial and ventricular arrhythmias. More recently, studies have tested the value of this technique in predicting outcomes of CRT. As a non-invasive method for assessing cardiovascular disease, particularly arrhythmias, ECGi represents a significant advancement over standard procedures in contemporary cardiology. Its full potential has yet to be fully explored.
Orthostatic Blood Pressure Recovery Is Associated With the Rate of Cognitive Decline and Mortality in Clinical Alzheimer’s Disease
Authors: de Heus Rianne A A , de Jong Daan L K , Rijpma Anne , Lawlor Brian A , Olde Rikkert Marcel G M , Claassen Jurgen A H R 
Published: May 2020

Abstract

Background
Impaired recovery of blood pressure (BP) after standing has been shown to be related to cognitive function and mortality in people without dementia, but its role in people with Alzheimer’s disease (AD) is unknown. The aim of this study was to investigate the association of the orthostatic BP response with cognitive decline and mortality in AD.

Methods
In this post hoc analysis of a randomized controlled trial (Nilvad), we measured the beat-to-beat response of BP upon active standing in mild-to-moderate AD. This included the initial drop (nadir within 40 seconds) and recovery after 1 minute, both expressed relative to resting values. We examined the relationship between a small or large initial drop (median split) and unimpaired (≥100%) or impaired recovery (&lt;100%) with 1.5-year change in Alzheimer’s Disease Assessment—cognitive subscale (ADAS-cog) scores and all-cause mortality.

Results
We included 55 participants (age 73.1 ± 6.2 years). Impaired BP recovery was associated with higher increases in ADAS-cog scores (systolic: β [95% confidence interval] = 5.6 [0.4–10.8], p = .035; diastolic: 7.6 [2.3–13.0], p = .006). During a median follow-up time of 49 months, 20 participants died. Impaired BP recovery was associated with increased mortality (systolic: HR [95% confidence interval] = 2.9 [1.1–7.8], p = .039; diastolic: HR [95% confidence interval] = 5.5 [1.9–16.1], p = .002). The initial BP drop was not associated with any outcome. Results were adjusted for age, sex, and intervention group.

Conclusions
Failure to fully recover BP after 1 minute of standing is associated with cognitive decline and mortality in AD. As such, BP recovery can be regarded as an easily obtained marker of progression rate of AD.
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
Authors: Kuhl Heiner , Li Ling , Wuertz Sven , Stöck Matthias , Liang Xu-Fang , Klopp Christophe 
Published: May 2020

Abstract

Background
Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce.

Result
Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads.

Conclusions
CSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects.
Erythema Nodosum: As an Extraintestinal Manifestation or Complication in Ulcerative Colitis?
Authors: Valdés Delgado Teresa , Maldonado Pérez Belén , Castro Laria Luisa 
Published: May 2020

Abstract
In our case, we want to highlight the importance of screening for opportunistic infectious diseases in these immunosuppressed patients. We present the case of an erythema nodosum triggered by reactivation of Herpes Simplex Virus (HSV) in a patient with ulcerative colitis.
Identification of compounds active against quiescent artemisinin-resistant Plasmodium falciparum parasites via the quiescent-stage survival assay (QSA)
Authors: Reyser Thibaud , Paloque Lucie , Ouji Manel , Nguyen Michel , Ménard Sandie , Witkowski Benoit , Augereau Jean-Michel , Benoit-Vical Françoise 
Published: May 2020

Abstract

Background
Quiescence is an unconventional mechanism of Plasmodium survival, mediating artemisinin resistance. This phenomenon increases the risk of clinical failures following artemisinin-based combination therapies (ACTs) by slowing parasite clearance and allowing the selection of parasites resistant to partner drugs.

Objectives
To thwart this multiresistance, the quiescent state of artemisinin-resistant parasites must be taken into consideration from the very early stages of the drug discovery process.

Methods
We designed a novel phenotypic assay we have named the quiescent-stage survival assay (QSA) to assess the antiplasmodial activity of drugs on quiescent parasites. This assay was first validated on quiescent forms from different artemisinin-resistant parasite lines (laboratory strain and field isolates), using two reference drugs with different mechanisms of action: chloroquine and atovaquone. Furthermore, the efficacies of different partner drugs of artemisinins used in ACTs were investigated against both laboratory strains and field isolates from Cambodia.

Results
Our results highlight that because of the mechanism of quiescence and the respective pharmacological targets of drugs, drug efficacies on artemisinin-resistant parasites may be different between quiescent parasites and their proliferating forms.

Conclusions
These data confirm the high relevance of adding the chemosensitivity evaluation of quiescent parasites by the specific in vitro QSA to the antiplasmodial drug development process in the current worrisome context of artemisinin resistance.