bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Trends of Monarch Butterflies (Lepidoptera: Nymphalidae) Migrating From the Core of Canada’s Eastern Breeding Population
Authors: Ethier Danielle M 
Published: August 2020

Abstract
The Monarch butterfly (Danaus plexippus) (Linnaeus 1758) is being considered for up-listing to Endangered under the Canadian federal Species-at-Risk Act due to population declines recorded throughout the annual life cycle. Understanding local population dynamics is therefore necessary to assess the effect of environmental and human induced stressors, and to establish a benchmark from which management success can be measured through time. Using fall count data collected along the Lake Erie shoreline, which captures migrants moving south from the core eastern breeding population in Canada, monarch abundance trends are quantified. Count data from three migration count sites and one roost site were analyzed following similar methods as Crewe and McCracken (2015) to make findings comparable. Two of these datasets are newly compiled and are analyzed here for the first time. Results suggest that during the past 10 yr, the number of migrating monarchs along the north shore of Lake Erie has been stable [mean: −3.05% per year, credibility interval (CI): −13.15, 9.97], which is consistent with changes being observed on the wintering grounds. Only migration counts collected between 1995 and 2018 at the Long Point sites demonstrated significant abundance declines (5.25% per year, CI: −8.60, −1.39), which is a similar results to previous analysis of this dataset. Opportunities for future research are discussed within the context of using monarch count data for future conservation efforts.
The OSPE
Authors: Belovarac Brendan J , Zabar Sondra R , Warfield Dana , Bannan Michael A , Rapkiewicz Amy V 
Published: August 2020

Abstract

Objectives
Resident assessment tends to consist of multiple-choice examinations, even in nuanced areas, such as quality assurance. Internal medicine and many other specialties use objective structured clinical examinations, or OSCEs, to evaluate residents. We adapted the OSCE for pathology, termed the Objective Structured Pathology Examination (OSPE).

Methods
The OSPE was used to evaluate first- and second-year residents over 2 years. The simulation included an anatomic pathology sign-out session, where the resident could be evaluated on diagnostic skills and knowledge of key information for cancer staging reports, as well as simulated frozen-section analysis, where the resident could be evaluated on communication skills with a “surgeon.” The OSPE also included smaller cases with challenging quality issues, such as mismatched slides or gross description irregularities. All cases were scored based on the Pathology Milestones created by the Accreditation Council for Graduate Medical Education.

Results
Using this OSPE, we were able to demonstrate that simulated experiences can be an appropriate tool for standardized evaluation of pathology residents.

Conclusions
Yearly evaluation using the OSPE could be used to track the progress of both individual residents and the residency program as a whole, identifying problem areas for which further educational content can be developed.
Improvement of Pediatric Liver Core Biopsy Adequacy by Reducing Laboratory-Related Tissue Fragmentation and Increasing Portal Tract Yield
Authors: Liang Jiancong , Abbuhl Mary F , Wang Huiying , Prasad Vinay , Coogan Alice 
Published: August 2020

Abstract

Objectives
We aimed to identify potential laboratory causes of suboptimal liver biopsy quality and sought to implement corresponding measures to improve biopsy adequacy.

Methods
We prospectively measured the number and size of tissue fragments and the amount of portal tracts in 200 consecutive pediatric medical liver biopsies before and after quality improvement processes were initiated.

Results
We identified laboratory-related tissue fragmentation as a significant cause of low biopsy adequacy. The principal approaches to reduce fragmentation included establishment of multistep monitoring of tissue integrity, adjustment of specimen-processing conditions, and laboratory staff education and awareness. These adjustments collectively led to lower overall tissue fragmentation (decreasing from 59% to 24%, P &lt; .01) and higher biopsy adequacy rates (increasing from 32% to 56%, P &lt; .01). The number of evaluable portal tracts increased from 4.4 to 5.7 portal tracts per centimeter of core biopsy tissue (P &lt; .01).

Conclusions
We demonstrated a sustainable improvement in the overall quality of pediatric needle core liver biopsies by reducing tissue fragmentation. Effective laboratory adjustments included monitoring of tissue integrity, modifications of processing conditions, and laboratory staff education.
The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer
Authors: Kim Soyeon , Bai YuLong , Fan Zhenjiang , Diergaarde Brenda , Tseng George C , Park Hyun Jung 
Published: August 2020

Abstract
Alternative polyadenylation (APA) in breast tumor samples results in the removal/addition of cis-regulatory elements such as microRNA (miRNA) target sites in the 3′-untranslated region (3′-UTRs) of genes. Although previous computational APA studies focused on a subset of genes strongly affected by APA (APA genes), we identify miRNAs of which widespread APA events collectively increase or decrease the number of target sites [probabilistic inference of microRNA target site modification through APA (PRIMATA-APA)]. Using PRIMATA-APA on the cancer genome atlas (TCGA) breast cancer data, we found that the global APA events change the number of the target sites of particular microRNAs [target sites modified miRNA (tamoMiRNA)] enriched for cancer development and treatments. We also found that when knockdown (KD) of NUDT21 in HeLa cells induces a different set of widespread 3′-UTR shortening than TCGA breast cancer data, it changes the target sites of the common tamoMiRNAs. Since the NUDT21 KD experiment previously demonstrated the tumorigenic role of APA events in a miRNA dependent fashion, this result suggests that the APA-initiated tumorigenesis is attributable to the miRNA target site changes, not the APA events themselves. Further, we found that the miRNA target site changes identify tumor cell proliferation and immune cell infiltration to the tumor microenvironment better than the miRNA expression levels or the APA events themselves. Altogether, our computational analyses provide a proof-of-concept demonstration that the miRNA target site information indicates the effect of global APA events with a potential as predictive biomarker.
CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase
Authors: Lu Yang Young , Bai Jiaxing , Wang Yiwen , Wang Ying , Sun Fengzhu 
Published: August 2020

Abstract

Motivation
Rapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, one primary step is sequence comparison. Alignment-free sequence comparison based on k-mer frequencies offers a computationally efficient solution, yet in practice, the k-mer frequency vectors for large k of practical interest lead to excessive memory and storage consumption.

Results
We report CRAFT, a general genomic/metagenomic search engine to learn compact representations of sequences and perform fast comparison between DNA sequences. Specifically, given genome or high throughput sequencing data as input, CRAFT maps the data into a much smaller embedding space and locates the best matching genome in the archived massive sequence repositories. With 102−104-fold reduction of storage space, CRAFT performs fast query for gigabytes of data within seconds or minutes, achieving comparable performance as six state-of-the-art alignment-free measures.

Availability and implementation
CRAFT offers a user-friendly graphical user interface with one-click installation on Windows and Linux operating systems, freely available at https://github.com/jiaxingbai/CRAFT.

Supplementary information
Supplementary data are available at Bioinformatics online.
iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features
Authors: Zhang Dan , Xu Zhao-Chun , Su Wei , Yang Yu-He , Lv Hao , Yang Hui , Lin Hao 
Published: August 2020

AbstractMotivationProtein carbonylation is one of the most important oxidative stress-induced post-translational modifications, which is generally characterized as stability, irreversibility and relative early formation. It plays a significant role in orchestrating various biological processes and has been already demonstrated to be related to many diseases. However, the experimental technologies for carbonylation sites identification are not only costly and time consuming, but also unable of processing a large number of proteins at a time. Thus, rapidly and effectively identifying carbonylation sites by computational methods will provide key clues for the analysis of occurrence and development of diseases.ResultsIn this study, we developed a predictor called iCarPS to identify carbonylation sites based on sequence information. A novel feature encoding scheme called residues conical coordinates combined with their physicochemical properties was proposed to formulate carbonylated protein and non-carbonylated protein samples. To remove potential redundant features and improve the prediction performance, a feature selection technique was used. The accuracy and robustness of iCarPS were proved by experiments on training and independent datasets. Comparison with other published methods demonstrated that the proposed method is powerful and could provide powerful performance for carbonylation sites identification.Availability and implementationBased on the proposed model, a user-friendly webserver and a software package were constructed, which can be freely accessed at http://lin-group.cn/server/iCarPS.Supplementary informationSupplementary data are available at Bioinformatics online.
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays
Authors: Li Po-E , Myers y Gutiérrez Adán , Davenport Karen , Flynn Mark , Hu Bin , Lo Chien-Chi , Player Jackson Elais , Shakya Migun , Xu Yan , Gans Jason D , Chain Patrick S G 
Published: August 2020

Abstract

Summary
Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons.

Availability and implementation
The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics.org/#/assayValidation, https://github.com/jgans/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation.

Supplementary information
Supplementary data are available at Bioinformatics online.
Copulatory behaviour increases sperm viability in female spiders
Authors: Cargnelutti Franco , Calbacho-Rosa Lucia , Uñates Diego , Costa-Schmidt Luiz Ernesto , Córdoba-Aguilar Alex , Peretti Alfredo Vicente 
Published: August 2020

AbstractOne remarkable reproductive feature in animals with internal fertilization is a reduction in sperm viability over time in females. Whether this reduction is driven by male–male competition and/or cryptic female choice is unclear. From the perspective of cryptic female choice, we postulated that sperm viability is affected by a particular male copulatory behaviour. In this study, we investigated the following aspects: (1) sperm viability in mated females vs. males; (2) whether sperm viability varies temporally after mating; and (3) whether male copulatory behaviour covaries positively with sperm viability within females. We used the spider Holocnemus pluchei, whose males use several copulatory behaviours to court females. We found that females that stored sperm for 4 or 15 days showed no difference in sperm viability but had lower sperm viability compared with males, and males that performed a longer post-insemination behaviour had higher sperm viability inside the female. It is unclear how sperm viability is reduced and how male post-insemination behaviour affects this. It is possible that extending copulation allows males to induce females to keep sperm alive for longer. This result is predicted by theory whereby males induce females to facilitate sperm to reach and fertilize eggs based on male postcopulatory behaviour.
Sulcal Depth in the Medial Ventral Temporal Cortex Predicts the Location of a Place-Selective Region in Macaques, Children, and Adults
Authors: Natu Vaidehi S , Arcaro Michael J , Barnett Michael A , Gomez Jesse , Livingstone Margaret , Grill-Spector Kalanit , Weiner Kevin S 
Published: August 2020

Abstract
The evolution and development of anatomical–functional relationships in the cerebral cortex is of major interest in neuroscience. Here, we leveraged the fact that a functional region selective for visual scenes is located within a sulcus in the medial ventral temporal cortex (VTC) in both humans and macaques to examine the relationship between sulcal depth and place selectivity in the medial VTC across species and age groups. To do so, we acquired anatomical and functional magnetic resonance imaging scans in 9 macaques, 26 human children, and 28 human adults. Our results revealed a strong structural–functional coupling between sulcal depth and place selectivity across age groups and species in which selectivity was strongest near the deepest sulcal point (the sulcal pit). Interestingly, this coupling between sulcal depth and place selectivity strengthens from childhood to adulthood in humans. Morphological analyses suggest that the stabilization of sulcal–functional coupling in adulthood may be due to sulcal deepening and areal expansion with age as well as developmental differences in cortical curvature at the pial, but not the white matter surfaces. Our results implicate sulcal features as functional landmarks in high-level visual cortex and highlight that sulcal–functional relationships in the medial VTC are preserved between macaques and humans despite differences in cortical folding.
Management of Asymptomatic Terminal Ileitis
Authors: Donet Jean A , Charabaty Aline , Moss Alan C 
Published: August 2020

Abstract
Ileal intubation is often performed during screening colonoscopies. This had led to the recognition of mild ileitis in many asymptomatic patients. The natural history and clinical significance of this finding are not well established, and there are no guidelines on whether these patients merit further work-up or an interval surveillance colonoscopy. This conundrum was presented and discussed on @MondayNightIBD. In this article, we review the specific literature on the topic and make reference to the informed opinions of the convo participants. We propose an #IBDAlgorithm for management of asymptomatic ileitis.
The Impact of Rectal Stump Inflammation After Subtotal Colectomy on Pouch Outcomes in Ulcerative Colitis Patients
Authors: Wasmann Karin A , van der Does de Willebois Eline M , Koens Lianne , Duijvestein Marjolijn , Bemelman Willem A , Buskens Christianne J 
Published: August 2020

Abstract

Background and Aims
Proctitis after subtotal colectomy with ileostomy for ulcerative colitis [UC] is common, but its impact on short- and long-term outcome after pouch surgery is unknown. The aim of this study was to determine the incidence of proctitis after subtotal colectomy and its impact on postoperative morbidity and pouchitis.

Methods
The distal margin of the rectal stump of all consecutive patients undergoing completion proctectomy and pouch procedure for UC, between 1999 and 2017, was revised and scored for active inflammation according to the validated Geboes score, and for diversion proctitis. Pathological findings were correlated to complications after pouch surgery and pouchitis [including therapy-refractory] using multivariate analyses.

Results
Out of 204 included patients, 167 [82%] had active inflammation in the rectal stump and diversion colitis was found in 170 specimens [83%]. Overall postoperative complications and anastomotic leakage rates were not significantly different between patients with and without active inflammation in the rectal stump [34.7% vs 32.4%, p = 0.79, and 10.2% vs 5.4%, p = 0.54, respectively]. Active inflammation of the rectal stump was significantly associated with the development of pouchitis [54.3% vs 25.5%, plog = 0.02], as well as with therapy refractory pouchitis [14% vs 0%, plog = 0.05]. Following multivariate analysis, active inflammation was an independent predictor for the development of pouchitis. Diversion proctitis showed no association with these outcome parameters.

Conclusions
Active inflammation in the rectal stump after subtotal colectomy occurs in 80% of UC patients and is a predictor for the development of pouchitis and therapy-refractory pouchitis.
Sampling Flower Chafer Beetles (Coleoptera: Cetoniidae) in the Amazon Rainforest: The Role of Bait Types and Trap Installation Heights
Authors: Puker Anderson , Ferreira Kleyton R , Correa César M A 
Published: August 2020

Abstract
The role of different bait types and trap installation heights for an accurate trapping of flower chafer beetles (Coleoptera: Cetoniidae) is still poorly understand worldwide, especially in the Neotropical region. Therefore, in this study, we evaluated how the type of bait and trap installation height can influence flower chafer beetle sampling in the Amazon rainforest. For this, we sampled flower chafer beetles monthly from June to December 2019 in five Amazon forest fragments, in Juína, Mato Grosso, Brazil. In each collecting fragment, we installed aerial traps at different heights (i.e., 1.5, 4.5, 7.5, and 10.5 m above ground) and randomly baited with 300 ml of each of the following bait types: banana + sugarcane juice mixture; pineapple + sugarcane juice mixture; beer; or red wine. We collected 412 individuals belonging to 12 species of Cetoniidae beetles. Traps baited with pineapple + sugarcane juice mixture captured greater abundance and species richness of flower chafer beetles. Moreover, traps at 4.5, 7.5, and 10.5 m caught a similar number of individuals and species, and significantly more than traps at 1.5 m. Thus, our results provide evidence that for an accurate sampling of flower chafer beetle assemblages in tropical forests, traps baited preferably with a ripe fruit (e.g., pineapple) and sugarcane juice mixture should are installed at least 4.5 m above ground.
Optimization of atrial fibrillation care: management strategies and quality measures
Authors: Ritchie Leona A , Lip Gregory Y H , Lane Deirdre A 
Published: August 2020

AbstractAtrial fibrillation (AF) is the most common cardiac arrhythmia and a leading cause of mortality and morbidity. Optimal management of AF is paramount to improve quality of life and reduce the impact on health and social care services. Owing to its strong associations with other cardiovascular and non-cardiovascular comorbidities, a holistic management approach to AF care is advocated but this is yet to be clearly defined by international clinical guidelines. This ambiguity has prompted us to review the available clinical evidence on different management strategies to optimize AF care in the context of performance and quality measures, which can be used to objectively assess standards of care.
Beyond Naming and Shaming: Accusations and International Law in Cybersecurity
Authors: Finnemore Martha , Hollis Duncan B 
Published: August 2020

Abstract
Accusations of bad state behaviour in cyberspace are proliferating, yet this increase in naming has not obviously produced much shame. Accused states uniformly deny the accusation or decline to comment, without changing behaviour. For international lawyers, the problem is compounded by the absence of international law in these charges. States are not invoking international law when they complain of other states’ behaviour, suggesting the law is weak – or worse, irrelevant – in holding states accountable for their cyber operations. In lieu of ‘naming and shaming’, we introduce and examine the broader concept of ‘accusation’ as a social, political and legal practice with diverse uses in cyberspace and beyond. Accusers must make strategic choices about how they frame their accusations, and we unpack various elements accusers may manipulate to their advantage. Accusations also have many purposes. They may seek to ‘name and shame’ an accused into conforming to certain behavioural expectations, but they may also aim at defensive or deterrent effects on both the accused and, crucially, on third parties. Particularly important, accusations may play a constitutive role, constructing new norms, including customary international law, within the international community. In short, accusations offer states and other stakeholders a menu of strategic options beyond those identified by the extant literature on naming and shaming.
Dental arch changes comparison between expander with differential opening and fan-type expander: a randomized controlled trial
Authors: Massaro Camila , Janson Guilherme , Miranda Felicia , Aliaga-Del Castillo Aron , Pugliese Fernando , Lauris José Roberto Pereira , Garib Daniela 
Published: August 2020

Summary

Objectives
To compare posterior crossbite correction frequency and dentoalveolar changes of the expander with differential opening (EDO) and the fan-type expander (FE).

Trial design
Two-arm parallel randomized controlled trial.

Methods
Forty-eight patients from 7 to 11 years of age were allocated into two groups. Twenty-four patients were treated with the EDO and 24 patients were treated with the FE. Block randomization was performed. The study was single blind. Digital dental models were acquired before treatment and 6 months after rapid maxillary expansion. The primary outcomes were crossbite correction rate and maxillary arch width changes. Secondary outcomes were interincisal diastema, arch perimeter, length, size and shape, and mandibular dental arch changes.

Results
The final sample comprised 24 patients (13 female and 11 male; mean initial age of 7.62 years) in the EDO group and 24 patients (14 female and 10 male; mean initial age of 7.83 years) in the FE group. The crossbites were corrected in 100 per cent of subjects from EDO group and in 75 per cent of patients in FE group. EDO showed greater increases in maxillary intermolar region (P &lt; 0.001), while the FE demonstrated greater increases in the intercanine distance (P = 0.008). Increase in mandibular inter-first permanent molar distance was slightly greater in the EDO group (mean difference of 0.8 mm). Changes in arch length and perimeter were similar in both groups. Both expanders changed the maxillary arch shape. The post-treatment arch shape was larger in the anterior region for FE and in the posterior region in the EDO group.

Harms
Discomfort during activation was reported by 54 per cent of the participants. A temporary change in the nasal bridge was reported by one patient from FE group.

Conclusions
Maxillary arch width and shape changes were distinct between the EDO and the FE. Greater transversal increases of the anterior and posterior regions were observed for the FE and the EDO, respectively. A slightly greater mandibular spontaneous expansion was observed for the EDO only at the molar region.

Trial registration
NCT03705871.