bluuebunny/crossref_metadata_2025_split huggingface dataset:
𝐵-rigidity of the property to be an almost Pogorelov polytope
Authors: Erokhovets Nikolai 
Published: October 2021

Toric topology assigns to eachnn-dimensional combinatorial simple convex polytopePPwithmmfacets an(m+n)(m+n)-dimensional moment-angle manifoldZP\mathcal {Z}_Pwith an action of the compact torus TmT^msuch thatZP/Tm\mathcal {Z}_P/T^mis a convex polytope of combinatorial typePP. We study the notion ofBB-rigidity. A property of a polytopePPis calledBB-rigid if each simplenn-polytope QQsuch that the graded ringsH∗(ZP,Z)H^*(\mathcal {Z}_P,\mathbb Z)andH∗(ZQ,Z)H^*(\mathcal {Z}_Q,\mathbb Z)are isomorphic also has this property. We study families of33-dimensional polytopes defined by their cyclickk-edge-connectivity. These families include flag polytopes and Pogorelov polytopes, that is, polytopes realizable as bounded right-angled polytopes in Lobachevsky space L3\mathbb L^3. Pogorelov polytopes include fullerenes—simple polytopes with only pentagonal and hexagonal faces. It is known that the properties to be flag and to be Pogorelov areBB-rigid. We focus on almost Pogorelov polytopes, which are strongly cyclically44-edge-connected polytopes. They correspond to right-angled polytopes of finite volume in L3\mathbb L^3. There is a subfamily of ideal almost Pogorelov polytopes corresponding to ideal right-angled polytopes. We prove that the properties to be an almost Pogorelov polytope and to be an ideal almost Pogorelov polytope areBB-rigid. As a corollary, we obtain that the33-dimensional associahedronAs3As^3and permutohedronPe3Pe^3areBB-rigid. We generalize methods known for Pogorelov polytopes. We obtain results onBB-rigidity of subsets inH∗(ZP,Z)H^*(\mathcal {Z}_P,\mathbb Z)and prove an analog of the so-called separable circuit condition (SCC).
Addressing Posttreatment Selection Bias in Comparative Effectiveness Research, Using Real-World Data and Simulation
Authors: Belviso Nicholas , Zhang Yichi , Aronow Herbert D , Wyss Richard , Barbour Marilyn , Kogut Stephen , Lawal Oluwadolapo D , Zhan Si Y , Don Prabhani Kuruppumullage , Wen Xuerong 
Published: October 2021

Abstract
To examine methodologies that address imbalanced treatment switching and censoring, 6 different analytical approaches were evaluated under a comparative effectiveness framework: intention-to-treat, as-treated, intention-to-treat with censor-weighting, as-treated with censor-weighting, time-varying exposure, and time-varying exposure with censor-weighting. Marginal structural models were employed to address time-varying exposure, confounding, and possibly informative censoring in an administrative data set of adult patients who were hospitalized with acute coronary syndrome and treated with either clopidogrel or ticagrelor. The effectiveness endpoint included first occurrence of death, myocardial infarction, or stroke. These methodologies were then applied across simulated data sets with varying frequencies of treatment switching and censoring to compare the effect estimate of each analysis. The findings suggest that implementing different analytical approaches has an impact on the point estimate and interpretation of analyses, especially when censoring is highly unbalanced.
Choice of Outcome in COVID-19 Studies and Implications for Policy: Mortality and Fatality
Authors: Westreich Daniel , Edwards Jessie K , Tennant Peter W G , Murray Eleanor J , van Smeden Maarten 
Published: October 2021

Abstract
In this brief communication, we discuss the confusion of mortality with fatality in the interpretation of evidence in the coronavirus disease 2019 (COVID-19) pandemic, and how this confusion affects the translation of science into policy and practice. We discuss how this confusion has influenced COVID-19 policy in France, Sweden, and the United Kingdom and discuss the implications for decision-making about COVID-19 vaccine distribution. We also discuss how this confusion is an example of a more general statistical fallacy we term the “Missing Link Fallacy.”
Management of patients with fibrosing interstitial lung diseases
Authors: Morrow Lee E , Hilleman Daniel , Malesker Mark A 
Published: October 2021

Abstract

Purpose
This article summarizes the appropriate use and pharmacology of treatments for fibrosing interstitial lung diseases, with a specific focus on the antifibrotic agents nintedanib and pirfenidone.

Summary
The interstitial lung diseases are a heterogenous group of parenchymal lung disorders with a common feature—infiltration of the interstitial space with derangement of the normal capillary-alveolar anatomy. Diseases characterized by fibrosis of the interstitial space are referred to as the fibrosing interstitial lung diseases and often show progression over time: idiopathic pulmonary fibrosis is the most common fibrotic interstitial lung disease. Historically, therapies for fibrosing lung diseases have been limited in number, questionable in efficacy, and associated with potential harms. Food and Drug Administration (FDA) approval of the antifibrotic agents nintedanib and pirfenidone for idiopathic pulmonary fibrosis in 2014 heralded an era of reorganization of therapy for the fibrotic interstitial lung diseases. Subsequent investigations have led to FDA approval of nintedanib for systemic sclerosis–associated interstitial lung disease and interstitial lung diseases with a progressive phenotype. Although supportive care and pulmonary rehabilitation should be provided to all patients, the role(s) of immunomodulators and/or immune suppressing agents vary by the underlying disease state. Several agents previously used to treat fibrotic lung diseases (N-acetylcysteine, anticoagulation, and pulmonary vasodilators) lack efficacy or cause harm.

Conclusion
With the introduction of effective pharmacotherapy for fibrosing interstitial lung disease, pharmacists have an increasingly important role in the interdisciplinary team managing these patients.
Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics
Authors: Chen Lingxi , Qing Yuhao , Li Ruikang , Li Chaohui , Li Hechen , Feng Xikang , Li Shuai Cheng 
Published: October 2021

Abstract
The recent advance of single-cell copy number variation (CNV) analysis plays an essential role in addressing intratumor heterogeneity, identifying tumor subgroups and restoring tumor-evolving trajectories at single-cell scale. Informative visualization of copy number analysis results boosts productive scientific exploration, validation and sharing. Several single-cell analysis figures have the effectiveness of visualizations for understanding single-cell genomics in published articles and software packages. However, they almost lack real-time interaction, and it is hard to reproduce them. Moreover, existing tools are time-consuming and memory-intensive when they reach large-scale single-cell throughputs. We present an online visualization platform, single-cell Somatic Variant Analysis Suite (scSVAS), for real-time interactive single-cell genomics data visualization. scSVAS is specifically designed for large-scale single-cell genomic analysis that provides an arsenal of unique functionalities. After uploading the specified input files, scSVAS deploys the online interactive visualization automatically. Users may conduct scientific discoveries, share interactive visualizations and download high-quality publication-ready figures. scSVAS provides versatile utilities for managing, investigating, sharing and publishing single-cell CNV profiles. We envision this online platform will expedite the biological understanding of cancer clonal evolution in single-cell resolution. All visualizations are publicly hosted at https://sc.deepomics.org.
Cytogenetic, geographical, spore type and plastid haplotype data reveal cryptic patterns of species diversity in the cosmopolitanCystopteris fragiliscomplex (Polypodiopsida: Cystopteridaceae)
Authors: Ekrt Libor , Košnar Jiří , Rothfels Carl J , Hanušová Kristýna , Hornych Ondřej , Urfus Tomáš 
Published: October 2021

AbstractThe delimitation of lineages in the Cystopteris fragilis complex is complicated by the presence of multiple cytotypes and a lack of defining morphological characters. One character, the production of rugose instead of regular spiny spores, is sometimes associated with a potential Scottish endemic, C. dickieana; however, whether this character is associated with a distinct lineage is uncertain. To better understand the diversity in the C. fragilis complex, we selected 87 C. fragilis samples of known ploidy (4x, 5x, 6x) for sequencing of two plastid loci and we assessed their spore types. These samples represent the variability found in Northern Hemisphere populations, including the type locality of C. dickieana in Scotland. Our analyses revealed two haplotype lineages, which we label the hemifragilis and reevesiana clades, based on their potential relationship to the two presumed diploid parents of C. fragilis. Hexaploids and tetraploids were both polyphyletic. Rugose spores were rarer overall (26% of samples), but five times more prevalent in the hemifragilis clade. Although proper delimitation and understanding of C. fragilis remains a challenge, this study further describes great genotypic and cytotypic complexity present in this complex. Furthermore, rugose-spored plants are widely distributed and should not be associated with a single name.
Contemporary outcomes of anemia in US patients with chronic kidney disease
Authors: Wittbrodt Eric T , James Glen , Kumar Supriya , van Haalen Heleen , Chen Hungta , Sloand James A , Kalantar-Zadeh Kamyar 
Published: October 2021

ABSTRACT

Background
Long-term clinical outcome data from patients with non-dialysis-dependent (NDD) chronic kidney disease (CKD) are lacking. We characterized patients with NDD-CKD and anemia using real-world data from the USA.

Methods
This retrospective longitudinal observational study evaluated integrated Limited Claims and Electronic Health Record Data (IBM Health, Armonk, NY), including patients ≥18 years with two or more estimated glomerular filtration rate (eGFR) measures &lt;60 mL/min/1.73 m2 ≥90 days apart. Anemia was defined as the first observed hemoglobin &lt;10 g/dL within 6-month pre- and post-CKD index date. Data were analyzed from January 2012 to June 2018. Patients with documented iron-deficiency anemia at baseline were excluded.

Results
Comprising 22 720 patients (57.4% female, 63.9% CKD stage 3, median hemoglobin 12.5 g/dL), median (interquartile range) follow-up for patients with and without anemia were 2.9 (1.5–4.4) and 3.8 (2.2–4.8) years, respectively. The most prevalent comorbidities were dyslipidemia (57.6%), type 2 diabetes mellitus (38.8%) and uncontrolled hypertension (20.0%). Overall, 23.3% of patients had anemia, of whom 1.9% and &lt;0.1% received erythropoiesis-stimulating agents (ESAs) or intravenous iron, respectively. Anemia prevalence increased with CKD stage from 18.2% (stage 3a) to 72.8% (stage 5). Patients with anemia had a higher incidence rate of hospitalizations for heart failure (1.6 versus 0.8 per 100 patient-years), CKD stage advancement (43.5 versus 27.5 per 100 patient-years), and a 40% eGFR decrease (18.1 versus 7.3 per 100 patient-years) versus those without anemia.

Conclusions
Anemia, frequently observed in NDD-CKD and associated with adverse clinical outcomes, is rarely treated with ESAs and intravenous iron. These data suggest that opportunities exist for improved anemia management in patients with NDD-CKD.
Challenging indication of cardioverter defibrillator implantation after sudden cardiac arrest in the very young: a case series of catecholaminergic polymorphic ventricular tachycardia secondary to de novo calmodulin p.Asn98Ser
Authors: Maltret Alice , Benaich Fatima Azzahrae , Rendu John , Fressart Véronique , Roux-Buisson Nathalie , Bonnet Damien , Denjoy Isabelle 
Published: October 2021

Abstract

Background
Calmodulinopathy is an emerging group of primary electrical disease with various, severe, and early onset phenotype. Sudden cardiac arrest (SCA)/death can be the first symptom and current medical management seems insufficient to prevent recurrences. Implantable cardioverter-defibrillator (ICD) in the young is challenging and can be harmful.

Case summary
We report the management of two very young boys (aged 3.5 and 5.5 years old) who survived an SCA due to calmodulin mutation responsible of a catecholaminergic polymorphic ventricular tachycardia phenotype. In both case, SCA had an adrenergic trigger. Despite SCA, ICD implantation was denied by the parents. After thorough discussion with the family, the patients were managed with solely betablocker treatment and loop recorder implantation. At last follow-up of 30 and 23 months, respectively, there were no recurrence of any cardiac event.

Discussion
The benefits of ICD implantation at a very young age must be weighed against the risk complication. In the youngest, whom recreative activities are under constant supervision, the decision, jointly made with the parents, could be to postpone ICD.
Sodium-glucose cotransporter 2 inhibitors in patients with heart failure: a systematic review and meta-analysis of randomized trials
Authors: Ahmad Yousif , Madhavan Mahesh V , Stone Gregg W , Francis Darrel P , Makkar Raj , Bhatt Deepak L , Howard James P 
Published: October 2021

Abstract

Aims
Sodium-glucose cotransporter 2 (SGLT-2) inhibitors have now been evaluated for the treatment of heart failure in several placebo-controlled randomized controlled trials (RCTs) across various ejection fraction ranges, but these trials were powered for composite outcomes rather than individual clinical endpoints. We therefore performed a meta-analysis to assess their safety and efficacy on all-cause mortality, cardiovascular mortality, and heart failure hospitalizations.

Methods and results
We performed a prospectively registered random-effects meta-analysis of all RCTs comparing SGLT-2 inhibitors to placebo in patients with heart failure. The pre-specified primary endpoint was all-cause mortality. Secondary endpoints included cardiovascular mortality, heart failure hospitalizations, and the composite of cardiovascular mortality or heart failure hospitalization. Four trials with 15 684 patients were eligible. The SGLT-2 inhibitor tested was empagliflozin in two trials, dapagliflozin in one trial, and sotagliflozin in one trial. The weighted-mean follow-up was 20.0 months. The hazard ratio (HR) for all-cause mortality was 0.91, 95% confidence interval (CI) 0.82–1.01, P = 0.071. There was a 12% reduction in cardiovascular mortality (HR 0.88, 95% CI 0.79 to 0.97, P = 0.012), and a 30% reduction in heart failure hospitalization (HR 0.70, 95% CI 0.64 to 0.77, P &lt; 0.001).

Conclusion
SGLT-2 inhibitors significantly reduced cardiovascular mortality and heart failure hospitalizations in patients with heart failure. The effect appears consistent across three drugs studied in four trials. SGLT-2 inhibitors should become standard care for patients with heart failure.
A novel hybrid technique for the repair of an atrioesophageal fistula post-atrial radiofrequency ablation
Authors: Kronenberger Rani , Mana Fazia , Chierchia Gian-Battista , La Meir Mark 
Published: October 2021

Abstract
An atrioesophageal fistula is an uncommon complication of atrial ablation with a mortality rate of 40–100%. Uniform treatment guidelines have yet to be established. Herein, we illustrate the successful surgical management of an atrioesophageal fistula, avoiding the need for an oesophageal surgical intervention by sealing and clipping of the oesophagus. This novel single-step hybrid approach combining cardiac surgical and gastroenterological techniques provides a less aggressive strategy with potentially a more favourable prognosis.
Portfolio rebalancing based on time series momentum and downside risk
Authors: Guo Xiaoshi , Ryan Sarah M 
Published: October 2021

AbstractTo examine the familiar tradeoff between risk and return in financial investments, we use a rolling two-stage stochastic program to compare mean-risk optimization models with time series momentum strategies. In a backtest of allocating investment between a market index and a risk-free asset, we generate scenarios of future return according to a momentum-based stochastic process model. A new hybrid approach, time series momentum strategy controlling downside risk (TSMDR), frequently dominates traditional approaches by generating trading signals according to a modified momentum measure while setting the risky asset position to control the conditional value-at-risk (CVaR) of return. For insight into the outperformance of TSMDR, we decompose each strategy into two aspects, the trading signal and the asset allocation model that determines the risky asset position. We find that 1) weighted moving average can better capture the trend of the stock market than time series momentum computed as past 12-month excess return, 2) mean-risk strategies generally provide better returns whereas risk parity strategies have less investment risk and 3) controlling CVaR limits the investment risk better than controlling variance does.
Recent Immigrant Insect Fauna—Another Look at a Classic Analysis
Authors: Takeuchi Yu , Koch Frank H , Nelson Stacy A C 
Published: October 2021

Abstract
In 1978, Reece Sailer published a seminal retrospective entitled ‘Our Immigrant Insect Fauna.’ His goals were to better understand the origins and historical patterns of alien insect species introductions into the United States and establish a baseline for future work to improve our ability to respond to environmental and agricultural well-being threats. We updated Sailer’s study to include information on species introduced recently into the United States and that are now targeted by regulatory agencies. The recent trends (recorded through 2016) are different from those reported by Sailer. Asian-origin species are much more important than in 1978 and predominate today. Nevertheless, introductions from all parts of the world have continued. Although the diversity of alien species’ origins has increased through time, there has not been a corresponding change in the rate of introductions of species of phytosanitary importance. This finding is inconsistent with our original assumption of a positive nonlinear relationship with international trade imports. Our findings will assist in identifying and prioritizing potential high-risk plant pests as well as enhancing biosecurity capacities.
Polycomb group proteins in cancer: multifaceted functions and strategies for modulation
Authors: Wang Sijie , C. Ordonez-Rubiano Sandra , Dhiman Alisha , Jiao Guanming , Strohmier Brayden P , Krusemark Casey J , Dykhuizen Emily C 
Published: October 2021

AbstractPolycomb repressive complexes (PRCs) are a heterogenous collection of dozens, if not hundreds, of protein complexes composed of various combinations of subunits. PRCs are transcriptional repressors important for cell-type specificity during development, and as such, are commonly mis-regulated in cancer. PRCs are broadly characterized as PRC1 with histone ubiquitin ligase activity, or PRC2 with histone methyltransferase activity; however, the mechanism by which individual PRCs, particularly the highly diverse set of PRC1s, alter gene expression has not always been clear. Here we review the current understanding of how PRCs act, both individually and together, to establish and maintain gene repression, the biochemical contribution of individual PRC subunits, the mis-regulation of PRC function in different cancers, and the current strategies for modulating PRC activity. Increased mechanistic understanding of PRC function, as well as cancer-specific roles for individual PRC subunits, will uncover better targets and strategies for cancer therapies.
DeepT3 2.0: improving type III secreted effector predictions by an integrative deep learning framework
Authors: Jing Runyu , Wen Tingke , Liao Chengxiang , Xue Li , Liu Fengjuan , Yu Lezheng , Luo Jiesi 
Published: October 2021

AbstractType III secretion systems (T3SSs) are bacterial membrane-embedded nanomachines that allow a number of humans, plant and animal pathogens to inject virulence factors directly into the cytoplasm of eukaryotic cells. Export of effectors through T3SSs is critical for motility and virulence of most Gram-negative pathogens. Current computational methods can predict type III secreted effectors (T3SEs) from amino acid sequences, but due to algorithmic constraints, reliable and large-scale prediction of T3SEs in Gram-negative bacteria remains a challenge. Here, we present DeepT3 2.0 (http://advintbioinforlab.com/deept3/), a novel web server that integrates different deep learning models for genome-wide predicting T3SEs from a bacterium of interest. DeepT3 2.0 combines various deep learning architectures including convolutional, recurrent, convolutional-recurrent and multilayer neural networks to learn N-terminal representations of proteins specifically for T3SE prediction. Outcomes from the different models are processed and integrated for discriminating T3SEs and non-T3SEs. Because it leverages diverse models and an integrative deep learning framework, DeepT3 2.0 outperforms existing methods in validation datasets. In addition, the features learned from networks are analyzed and visualized to explain how models make their predictions. We propose DeepT3 2.0 as an integrated and accurate tool for the discovery of T3SEs.
Deep learning identifies erroneous microarray-based, gene-level conclusions in literature
Authors: Qin Yanan , Yi Daiyao , Chen Xianghao , Guan Yuanfang 
Published: October 2021

Abstract
More than 110 000 publications have used microarrays to decipher phenotype-associated genes, clinical biomarkers and gene functions. Microarrays rely on digital assaying the fluorescence signals of arrays. In this study, we retrospectively constructed raw images for 37 724 published microarray data, and developed deep learning algorithms to automatically detect systematic defects. We report that an alarming amount of 26.73% of the microarray-based studies are affected by serious imaging defects. By literature mining, we found that publications associated with these affected microarrays have reported disproportionately more biological discoveries on the genes in the contaminated areas compared to other genes. 28.82% of the gene-level conclusions reported in these publications were based on measurements falling into the contaminated area, indicating severe, systematic problems caused by such contaminations. We provided the identified published, problematic datasets, affected genes and the imputed arrays as well as software tools for scanning such contamination that will become essential to future studies to scrutinize and critically analyze microarray data.