bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hummingbird: efficient performance prediction for executing genomic applications in the cloud
Authors: Bahmani Amir , Xing Ziye , Krishnan Vandhana , Ray Utsab , Mueller Frank , Alavi Amir , Tsao Philip S. , Snyder Michael P. , Pan Cuiping 
Published: March 2021

Abstract

Motivation
A major drawback of executing genomic applications on cloud computing facilities is the lack of tools to predict which instance type is the most appropriate, often resulting in an over- or under- matching of resources. Determining the right configuration before actually running the applications will save money and time. Here, we introduce Hummingbird, a tool for predicting performance of computing instances with varying memory and CPU on multiple cloud platforms.

Results
Our experiments on three major genomic data pipelines, including GATK HaplotypeCaller, GATK Mutect2 and ENCODE ATAC-seq, showed that Hummingbird was able to address applications in command line specified in JSON format or workflow description language (WDL) format, and accurately predicted the fastest, the cheapest and the most cost-efficient compute instances in an economic manner.

Availability and implementation
Hummingbird is available as an open source tool at: https://github.com/StanfordBioinformatics/Hummingbird.

Supplementary information
Supplementary data are available at Bioinformatics online.
Expression of Genes in the 16p11.2 Locus during Development of the Human Fetal Cerebral Cortex
Authors: Morson Sarah , Yang Yifei , Price David J , Pratt Thomas 
Published: March 2021

Abstract
The 593 kbp 16p11.2 copy number variation (CNV) affects the gene dosage of 29 protein coding genes, with heterozygous 16p11.2 microduplication or microdeletion implicated in about 1% of autism spectrum disorder (ASD) cases. The 16p11.2 CNV is frequently associated with macrocephaly or microcephaly indicating early defects of neurogenesis may contribute to subsequent ASD symptoms, but it is unknown which 16p11.2 transcripts are expressed in progenitors and whose levels are likely, therefore, to influence neurogenesis. Analysis of human fetal gene expression data revealed that KIF22, ALDOA, HIRIP3, PAGR1, and MAZ transcripts are expressed in neural progenitors with ALDOA and KIF22 significantly enriched compared to post-mitotic cells. To investigate the possible roles of ALDOA and KIF22 proteins in human cerebral cortex development we used immunohistochemical staining to describe their expression in late first and early second trimester human cerebral cortex. KIF22 protein is restricted to proliferating cells with its levels increasing during the cell cycle and peaking at mitosis. ALDOA protein is expressed in all cell types and does not vary with cell-cycle phase. Our expression analysis suggests the hypothesis that altered neurogenesis in the cerebral cortex contributes to ASD in 16p11.2 CNV patients.
Detecting Cyberbullying across Social Media Platforms in Saudi Arabia Using Sentiment Analysis: A Case Study
Authors: Fati Suliman Mohamed 
Published: March 2021

AbstractTwitter has become an open space for the users’ interactions and discussions on diverse trending topics. One of the issues raised on social media platforms is the misunderstanding of ‘freedom of speech’, which in turn, leads us to a new social and behavioral attack: cyberbullying. Cyberbully affects both individuals and societies. Despite tough sanctions globally and locally, cyberbullying is still a serious issue, which needs further consideration. Thus, this research aims to address this issue by proposing a framework, based on sentiment analysis, to detect cyberbullying in the tweets stream. The proposed framework in this paper extracts the tweets from Twitter. Then, the preprocessing through tweets tokenization was applied to remove noise from tweets and also symbols and phrases such as http, emoji faces, hash tag symbols, mention symbols and retweet. After data tokenization, the proposed system classifies the tweets, based on extracted keywords from both experts and potential victims, using deep-learning classification algorithm with 70% of dataset samples used for the training purpose, and 30% of the dataset samples used for the testing purpose. The experimental results show the ability of proposed methodology to detect cyberbullying effectively with accuracy 81%.
Linguistic but Not Cognitive Weaknesses in Deaf or Hard-of-Hearing Poor Comprehenders
Authors: Deng Qinli , Tong Shelley Xiuli 
Published: March 2021

AbstractThis study examined the reading comprehension profiles, and the related linguistic and cognitive skills, of 146 Chinese students in Grades 3–9 who are deaf or hard of hearing (d/Dhh). Employing a rigorous regression approach, the current study identified 19 unexpected poor comprehenders, 24 expected average comprehenders, and 16 unexpected good comprehenders. Compared to the expected average and unexpected good comprehenders, the unexpected poor comprehenders performed worse in broad linguistic skills (i.e., Chinese sign language comprehension, vocabulary, and segmental and suprasegmental phonological awareness), but their weaknesses in cognitive skills (i.e., working memory and executive function) were less severe. These findings suggest that weak linguistic skills are possible indicators of reading comprehension difficulties for students who are d/Dhh.
Pathological assessment of very late bare metal stent thrombosis in the left main coronary artery: a case report
Authors: Yuki Haruhito , Naganuma Toru , Nakazawa Gaku , Nakamura Sunao 
Published: March 2021

Abstract

Background
Late catch-up phenomenon following stent implantation is a well-known complication. However, no report has evaluated thrombosis after 9 years with multi-modality and pathological evaluation.

Case summary
A 71-year-old man with stable angina underwent elective percutaneous intervention of the left main coronary artery with implantation of a bare metal stent (BMS) 9 years ago. At the 9-year follow-up, coronary computed tomography (CCT) and coronary angiography (CAG) findings revealed a thrombus-like structure in the BMS slightly protruding into the sinus of Valsalva. Therefore, the previously prescribed double-antiplatelet therapy was replaced with an anticoagulant and clopidogrel, and a potent statin treatment was initiated. After the changes in drug treatment, follow-up examinations with CCT at 1 and 3 months suggested a decrease in the size of the thrombus; however, it appeared to increase after 6 months. Subsequently, the patient underwent surgical intervention. Pathological assessment of the explanted stent showed a proteoglycan-dominated extracellular matrix with few smooth muscle cells suggesting an organized thrombus.

Discussion
It should be emphasized that multiple factors might be responsible for very late stent thrombosis, such as peri-stent strut chronic inflammation involving proteoglycans, stent protrusion, and poorly controlled type 2 diabetes mellitus, possibly further inducing inflammatory cells.
The Antibiotic Dosage of Fastest Resistance Evolution: Gene Amplifications Underpinning the Inverted-U
Authors: Reding Carlos , Catalán Pablo , Jansen Gunther , Bergmiller Tobias , Wood Emily , Rosenstiel Phillip , Schulenburg Hinrich , Gudelj Ivana , Beardmore Robert 
Published: March 2021

Abstract
To determine the dosage at which antibiotic resistance evolution is most rapid, we treated Escherichia coli in vitro, deploying the antibiotic erythromycin at dosages ranging from zero to high. Adaptation was fastest just below erythromycin’s minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis: simultaneous selection for copy number variation in three resistance mechanisms which exhibited an “inverted-U” pattern of dose-dependence, as did several insertion sequences and an integron. Many genes did not conform to this pattern, however, reflecting changes in selection as dose increased: putative media adaptation polymorphisms at zero antibiotic dosage gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux amplifications dominated at the highest dosages. All treatments exhibited E. coli increases in the copy number of efflux operons acrAB and emrE at rates that correlated with increases in population density. For strains where the inverted-U was no longer observed following the genetic manipulation of acrAB, it could be recovered by prolonging the antibiotic treatment at subMIC dosages.
Four lenses on people management in the public sector: an evidence review and synthesis
Authors: Ali Aisha J , Fuenzalida Javier , Gómez Margarita , Williams Martin J 
Published: March 2021

Abstract We review the literature on people management and performance in organizations across a range of disciplines, identifying aspects of management where there is clear evidence about what works as well as aspects where the evidence is mixed or does not yet exist. We organize our discussion by four lenses, or levels of analysis, through which people management can be viewed: (i) individual extrinsic, intrinsic, and psychological factors; (ii) organizational people management, operational management, and culture; (iii) team mechanisms, composition and structural features; and (iv) relationships, including networks, leadership, and individuals’ relationships to their job and tasks. Each of these four lenses corresponds not only to a body of literature but also to a set of management tools and approaches to improving public employees’ performance; articulating the connections across these perspectives is an essential frontier for research. We find that existing people management evidence and practice have overemphasized formal management tools and financial motivations at the expense of understanding how to leverage a broader range of motivations, build organizational culture, and use informal and relational management practices. We suggest that foregrounding the role of relationships in linking people and performance—relational public management—may prove a fertile and interdisciplinary frontier for research and practices.
Fueling the Covid-19 pandemic: summer school holidays and incidence rates in German districts
Authors: Plümper Thomas , Neumayer Eric 
Published: March 2021

Abstract

Background
The Robert-Koch-Institute reports that during the summer holiday period a foreign country is stated as the most likely place of infection for an average of 27 and a maximum of 49% of new SARS-CoV-2 infections in Germany.

Methods
Cross-sectional study on observational data. In Germany, summer school holidays are coordinated between states and spread out over 13 weeks. Employing a dynamic model with district fixed effects, we analyze the association between these holidays and weekly incidence rates across 401 German districts.

Results
We find effects of the holiday period of around 45% of the average district incidence rates in Germany during their respective final week of holidays and the 2 weeks after holidays end. Western states tend to experience stronger effects than Eastern states. We also find statistically significant interaction effects of school holidays with per capita taxable income and the share of foreign residents in a district’s population.

Conclusions
Our results suggest that changed behavior during the holiday season accelerated the pandemic and made it considerably more difficult for public health authorities to contain the spread of the virus by means of contact tracing. Germany’s public health authorities did not prepare adequately for this acceleration.
Phenotypic analysis of pyrin-associated autoinflammation with neutrophilic dermatosis patients during treatment
Authors: Van Nieuwenhove Erika , De Langhe Ellen , Dooley James , Van Den Oord Joost , Shahrooei Mohammad , Parvaneh Nima , Ziaee Vahid , Savic Sinisa , Kacar Mark , Bossuyt Xavier , Humblet-Baron Stephanie , Liston Adrian , Wouters Carine 
Published: March 2021

Abstract

Objective
In 2016 specific heterozygous gain-of-function mutations in the Mediterranean fever gene MEFV were reported as causal for a distinct autoinflammatory disease coined pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). We sought to provide an extended report on clinical manifestations in PAAND patients to date and evaluate the efficacy and safety of treatment with the IL-1-blocking agent anakinra.

Methods
We undertook an open-label pilot study with anakinra. Three patients were recruited in a preliminary phase of the study with the intention to expand the treatment cohort in case of a favourable response. Acute-phase reactants and plasma cytokine levels were monitored throughout. Skin biopsies at baseline and at week 12 were stained for relevant cytokines. Available clinical data on treatment responses were retrospectively collected on additional patients.

Results
The three patients from the preliminary phase of the study [patients 1–3 (P1–P3)] demonstrated one failed and two partial treatment responses, where one patient opted to continue treatment with anakinra and the other favoured adalimumab. While a partial systemic response was observed, there was no appreciable effect of anakinra on the prominent cutaneous manifestations, reflected in residual local inflammatory cytokine expression in lesional skin. These observations did not warrant further expansion of the treatment cohort. Clinical data was retrospectively collected on an additional eight patients (P4–P11), highlighting both dominant and recessive inheritance with variable penetrance in PAAND and common gastrointestinal involvement that was not previously appreciated.

Conclusion
In our experience, while anakinra appears safe, it was not superior to biologicals targeting TNF-α in PAAND despite evidence directly implicating dysregulated IL-1β signalling.
“Everyone has the right to their opinion”: “Gender Ideology” Rhetoric and Epistemic Struggles in Slovak Policymaking
Authors: Valkovičová Veronika , Meier Petra 
Published: March 2021

Abstract
Through the case study of the Slovak Committee on Gender Equality, a governmental advisory body, this article draws upon the growing literature on “gender ideology” rhetoric in Central and Eastern Europe to study the efforts of advocates of that rhetoric to gain access to policymaking structures. With the aid of narrative research, we examine the Committee’s struggles over appropriate terminology and discourse, data and research, and ultimately the status of experts. This shows how “gender ideology” rhetoric serves to delegitimize gender knowledge, and how it eventually turns into knowledge itself.
Considérations sur le droit de rétention du transporteur routier de marchandises en droit OHADA
Authors: Tchamgwe Innocent 
Published: March 2021

Abstract
En raison de son caractère synallagmatique, le contrat de transport met à la charge de l’expéditeur ou du destinataire, selon le cas, l’obligation de payer le prix du déplacement des marchandises. Ainsi, en cas de refus de paiement du prix du transport le transporteur a le droit de retenir les marchandises transportées jusqu’à complet paiement de sa créance. Mais malgré que le droit de rétention du transporteur ait été érigé au rang de sûreté, c’est parfois avec peine que son exercice par le transporteur débouche sur un paiement spontané du débiteur du prix du transport. La réalisation de la sûreté n’étant pas en principe possible, le désintéressement du transporteur ne peut être assuré que grâce au secours des autres moyens qui lui sont offerts par la loi. Et là encore, c’est à prendre avec des réserves.
Due to its synallagmatic nature, the transport contract places the responsibility of the sender or the recipient, as the case may be, with the obligation to pay the price of moving the goods. Thus, in the event of refusal to pay the price of the transport, the carrier has the right to withhold the goods transported until full payment of his debt. But despite the fact that the carrier's lien has been raised to the rank of security, it is sometimes with difficulty that its exercise by the carrier leads to a spontaneous payment by the debtor of the transport price. The realization of the security is not in principle possible; the disinterestedness of the carrier can be assured only thanks to the help of the other means which are offered to him by the law. And there again, it is to be taken with reservations.
Where Did All the Appendicitis Go? Impact of the COVID-19 Pandemic on Volume, Management, and Outcomes of Acute Appendicitis in a Nationwide, Multicenter Analysis
Authors: Rosenthal Martin G. , Fakhry Samir M. , Morse Jennifer L. , Wyse Ransom J. , Garland Jeneva M. , Duane Therese M. , Slivinski Andrea , Wilson Nina Y. , Watts Dorraine D. , Shen Yan , Tabrizi Maryam Bita 
Published: March 2021

Objective:
The study objective was to evaluate effects of the COVID-19 pandemic on rates of emergency department (ED) acute appendicitis presentation, management strategies, and patient outcomes.

Summary Background Data:
Acute appendicitis is the most commonly performed emergency surgery in the United States and is unlikely to improve without medical or surgical intervention. Dramatic reductions in ED visits prompted concern that individuals with serious conditions, such as acute appendicitis, were deferring treatment for fear of contracting COVID-19.

Methods:
Patients from 146 hospitals with diagnosed appendicitis and arrival between March 2016 and May 2020 were selected. Electronic medical records data were retrospectively reviewed to retrieve patient data. Daily admissions were averaged from March 2016 through May 2019 and compared with March 2020. April-specific admissions were compared across the 5-year pre-COVID-19 period to April 2020 to identify differences in volume, demographics, disease severity, and outcomes.

Results:
Appendicitis patient admissions in 2020 decreased throughout March into April, with April experiencing the fewest admissions. April 2020 experienced a substantial decrease in patients who presented with appendicitis, dropping 25.4%, from an average of 2030 patients (2016–2019) to 1516 in 2020. An even greater decrease of 33.8% was observed in pediatric patients (age <18). Overall, 77% of the 146 hospitals experienced a reduction in appendicitis admissions. There were no differences between years in percent of patients treated nonoperatively (P = 0.493) incidence of shock (P = 0.95), mortality (P = 0.24), or need for postoperative procedures (P = 0.81).

Conclusions:
Acute appendicitis presentations decreased significantly during the COVID-19 pandemic, while overall management and patient outcomes did not differ from previous years. Further research is needed focusing on putative explanations for decreased hospital presentations unrelated to COVID-19 infection and possible implications for surgical management of uncomplicated acute appendicitis.

Keywords: acute appendicitis, COVID-19, decreasing volumes, multicenter study
Multistakeholder Collaborative Effort to Enhance Long-Term Follow-Up in the Abdominal Core Health Quality Collaborative
Authors: Poulose Benjamin K. , Schwartzman Harriet , Huang Li-Ching , Chouinard Scott , Coelho Donald , Macarios David , Master Sundeep , Rosen Michael J. 
Published: March 2021

Objective:
To determine the effectiveness of a clinical call center in performing focused long-term patient reported outcome (PRO)-based follow-up for ventral hernia patients in routine practice.

Background:
Long-term follow-up remains the mainstay of assessing quality of care in hernia management. Achieving acceptable rates of long-term follow-up outside of clinical trials in the routine care of patients has been very difficult to achieve.

Methods:
A prospective quality improvement intervention using a clinical call center in 1000 random patients eligible for long-term (1 year or greater) follow-up after ventral hernia repair in the Abdominal Core Health Quality Collaborative was performed. The primary outcome measure was the proportion of patients with successfully completed PRO-based long-term follow-up.

Results:
Between 2013 and 2017, the baseline long-term follow-up PRO completion rate was 2167/13,950 (15.5%). For the Focus on Follow-Up initiative, 890 patients were eligible for contact; a completion rate of 450/890 (50.6%, P < 0.001) was achieved.

Conclusions:
Clinical call center-based patient contact can greatly facilitate the completion of PROs utilized for long-term follow-up in ventral hernia repair. This has important implications for quality improvement programs and postmarket device surveillance.
Targeting the IL-2 inducible kinase in melanoma; a phase 2 study of ibrutinib in systemic treatment-refractory distant metastatic cutaneous melanoma: preclinical rationale, biology, and clinical activity (NCI9922)
Authors: Moschos Stergios J. , Eroglu Zeynep , Khushalani Nikhil I. , Kendra Kari L. , Ansstas George , In Gino K. , Wang Peng , Liu Glenn , Collichio Frances A. , Googe Paul B. , Carson Craig C. , McKinnon Karen , Wang Hsing-Hui , Nikolaishvilli-Feinberg Nana , Ivanova Anastasia , Arrowood Christy C. , Garrett-Mead Nancy , Conway Kathleen C. , Edmiston Sharon N. , Ollila David W. , Serody Jonathan S. , Thomas Nancy E. , Ivy S. Percy , Agrawal Lokesh , Dees Elizabeth C. , Abbruzzese James L. 
Published: March 2021

Background
IL-2 inducible kinase (ITK) is highly expressed in metastatic melanomas and its inhibition suppresses melanoma cell proliferation. We hypothesize that ibrutinib has a direct antitumor effect in melanoma cell lines and that treatment of metastatic melanomas with ibrutinib induces antitumor responses.

Methods
We assessed the ibrutinib effect on melanoma cell proliferation, apoptosis, and motility. Patients with metastatic melanoma refractory to PD-1 and MAPK inhibitors (if BRAFV600-mutant) were treated with ibrutinib, 840 mg PO QD, as part of a phase II clinical trial (clinicaltrials.gov NCT02581930).

Results
Melanoma cell lines frequently express ITK, YES1, and EGFR. Ibrutinib suppressed cell motility and proliferation in most cell lines. Eighteen patients (13 male; median age 63.5 years, range 37–82; 12 with ipilimumab resistance) were enrolled. The most frequent side effects were fatigue (61%), anorexia (50%), hyponatremia (28%), nausea, and vomiting (22% each). No antitumor responses were seen. At a median follow-up of 6 months (0.3–35.8 months), the median progression-free survival was 1.3 months (range 0.2–5.5 months). Fifteen patients were discontinued from the study due to progression, and 14 patients had died from metastatic melanoma. All archived tumors expressed ITK, 41% had no expression of p16 and PTEN, and 61% had absent tumor-infiltrating lymphocytes (TILs). Ibrutinib significantly suppressed proliferating (Ki67+) CD19+ peripheral blood mononuclear cells and had no significant effect on other lymphocyte subsets.

Conclusion
Ibrutinib did not induce any meaningful clinical benefit. ITK expression may not be clinically relevant. Treatment-refractory metastatic melanomas have other fundamental defects (i.e. absent PTEN and p16 expression, absent TILs) that may contribute to an adverse prognosis.