bluuebunny/crossref_metadata_2025_split huggingface dataset:
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats
Authors: Mikheenko Alla , Bzikadze Andrey V , Gurevich Alexey , Miga Karen H , Pevzner Pavel A 
Published: May 2020

Abstract

Motivation
Extra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.

Results
To address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.

Availability and implementation
https://github.com/ablab/TandemTools.

Supplementary information
Supplementary data are available at Bioinformatics online.
The string decomposition problem and its applications to centromere analysis and assembly
Authors: Dvorkina Tatiana , Bzikadze Andrey V , Pevzner Pavel A 
Published: May 2020

Abstract

Motivation
Recent attempts to assemble extra-long tandem repeats (such as centromeres) faced the challenge of translating long error-prone reads from the nucleotide alphabet into the alphabet of repeat units. Human centromeres represent a particularly complex type of high-order repeats (HORs) formed by chromosome-specific monomers. Given a set of all human monomers, translating a read from a centromere into the monomer alphabet is modeled as the String Decomposition Problem. The accurate translation of reads into the monomer alphabet turns the notoriously difficult problem of assembling centromeres from reads (in the nucleotide alphabet) into a more tractable problem of assembling centromeres from translated reads.

Results
We describe a StringDecomposer (SD) algorithm for solving this problem, benchmark it on the set of long error-prone Oxford Nanopore reads generated by the Telomere-to-Telomere consortium and identify a novel (rare) monomer that extends the set of known X-chromosome specific monomers. Our identification of a novel monomer emphasizes the importance of identification of all (even rare) monomers for future centromere assembly efforts and evolutionary studies. To further analyze novel monomers, we applied SD to the set of recently generated long accurate Pacific Biosciences HiFi reads. This analysis revealed that the set of known human monomers and HORs remains incomplete. SD opens a possibility to generate a complete set of human monomers and HORs for using in the ongoing efforts to generate the complete assembly of the human genome.

Availability and implementation
StringDecomposer is publicly available on https://github.com/ablab/stringdecomposer.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Practical Guide for Faecal Calprotectin Measurement: Myths and Realities
Authors: D’Amico Ferdinando , Nancey Stéphane , Danese Silvio , Peyrin-Biroulet Laurent 
Published: May 2020

Abstract

Background and Aims
Faecal calprotectin [FC] is a valid and non-invasive marker of mucosal inflammation. It is widely used both in clinical trials and in daily clinical practice for patients with inflammatory bowel diseases, but currently no accepted standardization for FC testing is available. Our primary aim here was to provide a clinician’s guide containing all the practical information on FC measurement in order to avoid any confounding factors, to minimize intra- and inter-individual variability in dosage, and to ensure a better and adequate interpretation of the results.

Methods
We conducted a detailed search of the scientific literature in the PubMed/MEDLINE, EMBASE and Cochrane databases up to January 2020 to find all relevant and available articles on pre-analytical and analytical phases of FC measurement.

Results
FC testing is a multi-step procedure consisting of a pre-analytical phase aimed to collect and process the stool sample and a subsequent analytical phase of FC measurement. Several factors can influence test results determining false positives or false negatives. Importantly, this faecal marker is mostly used for patient follow-up and as a predictor of treatment response. For this reason, any altered data may affect the physicians’ decisions, negatively impacting on patient management.

Conclusions
This review provides for the first time practical advice to minimize dosage variability, although further dedicated studies are needed to compare commercially available tests and identify the best tools for the most precise and accurate FC measurement.
5-Year prognostic value of the right ventricular strain-area loop in patients with pulmonary hypertension
Authors: Hulshof Hugo G , van Dijk Arie P , Hopman Maria T E , Heesakkers Hidde , George Keith P , Oxborough David L , Thijssen Dick H J 
Published: May 2020

Abstract

Aims
Patients with pre-capillary pulmonary hypertension (PH) show poor survival, often related to right ventricular (RV) dysfunction. In this study, we assessed the 5-year prognostic value of a novel echocardiographic measure that examines RV function through the temporal relation between RV strain (ϵ) and area (i.e. RV ϵ-area loop) for all-cause mortality in PH patients.

Methods and results
Echocardiographic assessments were performed in 143 PH patients (confirmed by right heart catheterization). Transthoracic echocardiography was utilized to assess RV ϵ-area loop. Using receiver operating characteristic curve-derived cut-off values, we stratified patients in low- vs. high-risk groups for all-cause mortality. Kaplan–Meier survival curves and uni-/multivariable cox-regression models were used to assess RV ϵ-area loop’s prognostic value (independent of established predictors: age, sex, N-terminal pro B-type natriuretic peptide, 6-min walking distance). During follow-up 45 (31%) patients died, who demonstrated lower systolic slope, peak ϵ, and late diastolic slope (all P &lt; 0.05) at baseline. Univariate cox-regression analyses identified early systolic slope, systolic slope, peak ϵ, early diastolic uncoupling, and early/late diastolic slope to predict all-cause mortality (all P &lt; 0.05), whilst peak ϵ possessed independent prognostic value (P &lt; 0.05). High RV loop-score (i.e. based on number of abnormal characteristics) showed poorer survival compared to low RV loop-score (Kaplan–Meier: P &lt; 0.01). RV loop-score improved risk stratification in high-risk patients when added to established predictors.

Conclusion
Our data demonstrate the potential for RV ϵ-area loops to independently predict all-cause mortality in patients with pre-capillary PH. The non-invasive nature and simplicity of measuring the RV ϵ-area loop, support the potential clinical relevance of (repeated) echocardiography assessment of PH patients.
The SAFE-T upper endoscopy tool: a web-based application for the point-of-care evaluation of gastroenterology fellow performance in upper endoscopy
Authors: Kumar Navin L , Kugener Guillaume , Hathorn Kelly E , Perencevich Molly L , Jajoo Kunal , Saltzman John R 
Published: May 2020

Abstract

Background
Attending assessment is a critical part of endoscopic education for gastroenterology fellows. The aim of this study was to develop and validate a concise, web-based assessment tool to evaluate real-time fellow performance in upper endoscopy.

Methods
We developed the Skill Assessment in Fellow Endoscopy Training (SAFE-T) upper endoscopy tool to capture both summative and formative feedback in a concise, five-part questionnaire. The tool mirrors the previously validated SAFE-T colonoscopy tool and is administered electronically via a web-based application. We evaluated the tool in a prospective study of 15 gastroenterology fellows (5 fellows each from Years 1–3 of training) over the 2018–2019 academic year. An independent reviewer evaluated a subset of these procedures and completed both the SAFE-T and Assessment of Competency in Endoscopy (ACE) upper endoscopy forms for reliability testing.

Results
Twenty faculty completed 413 SAFE-T evaluations of the 15 fellows in the study. The mean SAFE-T overall score differentiated each sequential fellow year of training, with first-year cases having lower performance than second-year cases (3.31 vs 4.25, P &lt; 0.001) and second-year cases having lower performance than third-year cases (4.25 vs 4.56, P &lt; 0.001). The mean SAFE-T overall score decreased with increasing case-complexity score, with straightforward compared with average cases (3.98 vs 3.39, P &lt; 0.001) and average compared with challenging cases (3.39 vs 2.84, P = 0.042). In dual-observed procedures, the SAFE-T tool showed excellent inter-rater reliability with a Kappa agreement statistic of 0.815 (P = 0.001). The SAFE-T overall score also highly correlated with the ACE upper endoscopy overall hands-on score (r = 0.76, P = 0.011).

Conclusions
We developed and validated the SAFE-T upper endoscopy tool—a concise and web-based means of assessing real-time gastroenterology fellow performance in upper endoscopy.
Citizenry and Nationality: the Participation of Immigrants in Urban Politics in Later Medieval England
Authors: Lambert Bart 
Published: May 2020

Abstract
This article explores the participation of immigrants, or people born outside the kingdom, in urban politics in later medieval England. It demonstrates that the nationality of these newcomers was of only secondary importance. What mattered most was whether immigrants’ economic and political interests aligned with those of the civic political elites. If they did not, aliens’ nationality could be mobilized to exclude them from urban politics. If, however, immigrants’ activities complemented those of the urban elites economically and politically, they had every chance to engage with all aspects of civic political life and be elected into the highest civic offices.
Factorization of Noncommutative Polynomials and Nullstellensätze for the Free Algebra
Authors: Helton J , Klep Igor , Volčič Jurij 
Published: May 2020

Abstract
This article gives a class of Nullstellensätze for noncommutative polynomials. The singularity set of a noncommutative polynomial $f=f(x_1,\dots ,x_g)$ is $\mathscr{Z}(\,f)=(\mathscr{Z}_n(\,f))_n$, where $\mathscr{Z}_n(\,f)=\{X \in{\operatorname{M}}_{n}({\mathbb{C}})^g \colon \det f(X) = 0\}.$ The 1st main theorem of this article shows that the irreducible factors of $f$ are in a natural bijective correspondence with irreducible components of $\mathscr{Z}_n(\,f)$ for every sufficiently large $n$. With each polynomial $h$ in $x$ and $x^*$ one also associates its real singularity set $\mathscr{Z}^{{\operatorname{re}}}(h)=\{X\colon \det h(X,X^*)=0\}$. A polynomial $f$ that depends on $x$ alone (no $x^*$ variables) will be called analytic. The main Nullstellensatz proved here is as follows: for analytic $f$ but for $h$ dependent on possibly both $x$ and $x^*$, the containment $\mathscr{Z}(\,f) \subseteq \mathscr{Z}^{{\operatorname{re}}} (h)$ is equivalent to each factor of $f$ being “stably associated” to a factor of $h$ or of $h^*$. For perspective, classical Hilbert-type Nullstellensätze typically apply only to analytic polynomials $f,h $, while real Nullstellensätze typically require adjusting the functions by sums of squares of polynomials (sos). Since the above “algebraic certificate” does not involve a sos, it seems justified to think of this as the natural determinantal Hilbert Nullstellensatz. An earlier paper of the authors (Adv. Math. 331 (2018): 589–626) obtained such a theorem for special classes of analytic polynomials $f$ and $h$. This paper requires few hypotheses and hopefully brings this type of Nullstellensatz to near final form. Finally, the paper gives a Nullstellensatz for zeros ${\mathcal{V}}(\,f)=\{X\colon f(X,X^*)=0\}$ of a hermitian polynomial $f$, leading to a strong Positivstellensatz for quadratic free semialgebraic sets by the use of a slack variable.
Neutrophils Are Required During Immunization With the Pneumococcal Conjugate Vaccine for Protective Antibody Responses and Host Defense Against Infection
Authors: Tchalla Essi Y I , Bhalla Manmeet , Wohlfert Elizabeth A , Bou Ghanem Elsa N 
Published: May 2020

AbstractNeutrophils can shape adaptive immunity; however, their role in vaccine-induced protection against infections in vivo remains unclear. Here, we tested their role in the clinically relevant polysaccharide conjugate vaccine against Streptococcus pneumoniae (pneumococcus). We antibody depleted neutrophils during vaccination, allowed them to recover, and 4 weeks later challenged mice with pneumococci. We found that while isotype-treated vaccinated controls were protected against an otherwise lethal infection in naive mice, full protection was lost upon neutrophil depletion. Compared to vaccinated controls, neutrophil-depleted mice had higher lung bacterial burdens, increased incidence of bacteremia, and lower survival rates. Sera from neutrophil-depleted mice had less antipneumococcal IgG2c and IgG3, were less efficient at inducing opsonophagocytic killing of bacteria by neutrophils in vitro, and were worse at protecting naive mice against pneumococcal pneumonia. In summary, neutrophils are required during vaccination for optimal host protection, which has important implications for future vaccine design against pneumococci and other pathogens.
Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle
Authors: Purfield Deirdre C , Evans Ross D , Berry Donagh P 
Published: May 2020

Abstract
Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P &lt; 5 × 10−8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P &gt; × 10−6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P &lt; 5 × 10−8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.
Age-Based Characteristics of Pediatric Burn Injuries From Outdoor Recreational Fires
Authors: Trotter Zola , Foster Kevin , Khetarpal Shailesh , Sinha Madhumita 
Published: May 2020

Abstract
Accidental burns from outdoor recreational activities, such as campfires, bonfires, ceremonial fires, and firepits, are not uncommon; however, few studies describe the nature of such injuries in children. The objective of this study was to examine the age-based pattern of pediatric burn injuries from outdoor fires. Children and adolescents 0 to 18 years, admitted to the Burn Center between 2008 and 2018 with acute burn injuries from outdoor fires, were included in the current study. Demographic and clinical data were obtained from the burn injury database. Patients were categorized into three age groups: 0 to 5 years, 5 to 10 years, and 10 to 18 years. One hundred and sixty-seven children were included in the data analysis, the mean age of the cohort was 6.4 (SD ± 4.9) years, and the majority (66.5%) were males. More than half (52.1%) were less than 5 years of age, they commonly sustained hand burns and frequently required inpatient burn management. Burn severity varied between age groups, and the mean total burn surface area (TBSA) was significantly higher in adolescents (10.9%). Almost half the injuries (49.7%) resulted from a fall onto a campfire, bonfire, or a firepit. In this study, we found age-specific variation in the mechanism and pattern of burn injuries. Children at least 5 years and adolescents were least common victims of burns due to outdoor fires but suffered from more serious injuries with significantly higher TBSA involvement, longer intensive care unit, and ventilator days. Raising awareness among parents, caregivers, and children about outdoor fire safety is important for the prevention of such injuries.
Breast Imaging Second Opinion Consultation: A Single Institution’s Process of Improvement and Reform
Authors: Freiburg Luke , Bhole Sonya , Liko Hazizi Elona , Friedewald Sarah M 
Published: May 2020

Abstract

Objective
To review a single institution’s second opinion breast imaging process, data tracking, and metrics before and after implementing quality improvement changes and the effect on report turnaround time.

Methods
This Institutional Review Board approved retrospective quality improvement project was performed at a tertiary-care academic medical center and included patients 18 years or older who submitted their outside facility imaging for reinterpretation (any combination of mammography, breast ultrasonography, and/or magnetic resonance imaging performed within the last six months) with finalized second opinion reports between June 1, 2016, and July 17, 2017. Significant intradepartmental changes were implemented March 2017 with the goal to improve second opinion report turnaround time. Key metrics from 399 studies were analyzed before and after implemented changes. Two-sided Fisher’s exact test was used to assess the significance of results.

Results
After department interventions, the percentage of outside reports available at the time of surgical consultation improved from 82% (213/259) to 91% (127/140), an 11% improvement (P &lt; 0.05). The average number of days from initial second opinion consultation to the availability of final report improved from 10.2 days to 9 days, a 12% improvement. Prior to the changes, the number of days it took a radiologist to complete a report varied from 1 to 4 days, but afterwards was consistently 1 day or less.

Conclusion
Implementation of second opinion intradepartmental changes demonstrated a significant improvement in report turnaround time and the number of finalized reports available at the time of surgical consultation. An efficient second opinion process is crucial to a breast imaging center, as it ultimately expedites patient surgical and oncological care.
Baseline Susceptibility of a Laboratory Strain of Northern Corn Rootworm, Diabrotica barberi (Coleoptera: Chrysomelidae) to Bacillus thuringiensis Traits in Seedling, Single Plant, and Diet-Toxicity Assays
Authors: Pereira Adriano E , Huynh Man P , Sethi Amit , Miles Ashley L , Wade French B , Ellersieck Mark R , Coudron Thomas A , Shelby Kent S , Hibbard Bruce E 
Published: May 2020

AbstractThe northern corn rootworm (NCR), Diabrotica barberi Smith & Lawrence, is an economic pest of maize in the U.S. Corn Belt. The objective of this study was to determine the baseline susceptibility of a laboratory NCR strain to Bt proteins eCry3.1Ab, mCry3A, Cry3Bb1, and Cry34/35Ab1 using seedling, single plant, and diet-toxicity assays. Plant assays were performed in greenhouse using corn hybrids expressing one of the Bt proteins and each respective near-isoline. Diet-toxicity assays, consisting of Bt proteins overlaid onto artificial diet were also conducted. In both plant assays, significantly more larvae survived Cry34/35Ab1-expressing corn compared with all other Bt-expressing corn, and larvae that survived eCry3.1Ab-expressing corn had significantly smaller head capsule widths compared with larvae that survived Cry34/35Ab1-expressing corn. In seedling assays, larvae surviving eCry3.1Ab-expressing corn also had significantly smaller head capsule widths compared with larvae that survived mCry3A-expressing corn. Additionally, larvae that survived mCry3A-expressing corn weighed significantly more than larvae surviving eCry3.1Ab- and Cry34/35Ab1-expressing corn. In single plant assays, no significant differences in larval dry weight was observed between any of the Bt-expressing corn. In diet assays, LC50s ranged from 0.14 (eCry3.1Ab) to 10.6 µg/cm2 (Cry34/35Ab1), EC50s ranged from 0.12 (Cry34/35Ab1) to 1.57 µg/cm2 (mCry3A), IC50s ranged from 0.08 (eCry3.1Ab) to 2.41 µg/cm2 (Cry34/35Ab1), and MIC50s ranged from 2.52 (eCry3.1Ab) to 14.2 µg/cm2 (mCry3A). These results establish the toxicity of four Bt proteins to a laboratory diapausing NCR strain established prior to the introduction of Bt traits and are important for monitoring resistance evolution in NCR field populations.
Asymptomatic colonic intussusception in ulcerative colitis: a case report
Authors: Tanabe Taro , Furukawa Satomi , Masuda Tomoyuki , Morimoto Koji , Yamana Tetsuo , Sahara Rikisaburo 
Published: May 2020

Abstract
Intussusception in adults is, especially with ulcerative colitis (UC), rare and only described in a few cases. Most adult patients with intussusception develop abdominal pain or other symptoms of bowel obstruction. This case describes an 18-year-old male with UC who treated with 5-aminosalycilicacid and underwent annual screening colonoscopies. Two attempts revealed that it was impossible to achieve total surveillance through the colonoscopy because multiple polyps were preventing the colonoscope from traversing the entire colon. Therefore, CT scan was performed and colonic intussusception was discovered incidentally, and the patient underwent elective laparoscopic total colectomy. To the best of our knowledge, this is the first reported case of asymptomatic intussusception in the adult patient with UC. When total surveillance colonoscopy fails to yield results, a CT may be advisable to pick up such an asymptomatic intussusception.