bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effective Hamiltonian as a necessary basis of the open quantum optical system theory
Authors: Basharov A M 
Published: May 2021

Abstract
Based on a model open system, the kinetic equation obtained from the initial exact Hamiltonian with anti-rotating terms is shown to differ from the kinetic equation from the approximate effective Hamiltonian without anti-rotating terms. The paper proves necessity of transition from the exact Hamiltonian to the effective Hamiltonian, with the main idea of its construction being the requirement for the absence of rapidly varying terms in the interaction representation. This requirement is necessary to obtain the correct kinetic equation.
Anthropology of student research activities
Authors: Zinnurova A F 
Published: May 2021

Abstract
The purpose of the article is to identify problem areas of students’ research activities and to show ways to improve this activity. An anthropological analysis of the professional training of students shows that an imitation of research activities prevails at present. The issues of tutoring and mentoring support not only of a particular student’s research activities, but also of the entire process of his education are still relevant. The tutoring system has been adopted in Russia, but it still does not work fully: students lack basic training to conduct full-fledged research. The article analyzes the experience of basic training of outstanding scientists, a two-stage structure of immersion in knowledge.
A missing source of uncertainty: forcing-dependent model parameter sensitivity
Authors: Zhu Xiuhua 
Published: May 2021

Abstract
Climate modelling groups usually work with a handful of model versions (parameter combinations) that reproduce certain targeted aspects of observed climate within a certain validity range and apply them for studying future climate change. What is of concern is whether these retained model versions, with respect to their de-selected counterparts, continue being optimal for future climate that is supposed to distinctly differ from the present one. Extrapolating model performances beyond their validity range requires model parameter sensitivity (i.e., changes in model output due to changes in model parameters) remains more or less stationary despite different forcing conditions. This requirement, however, is shown to be ill-grounded by exemplified analyses of resolution sensitivity in an Earth System Model under different forcing conditions, whereby model resolution is handled as a model parameter in a wider sense: (i) Model resolution sensitivity depends on the forcing conditions applied; moreover, (ii) The further the forcing deviates from a reference state, the earlier one can detect a systematic change in model resolution sensitivity, in particular, in its spatial details. Therefore, model parameter sensitivity and forcing conditions should be evaluated as a compound; failure to account for this relation leads to a systematic underestimation of uncertainty in forced responses of climate models, thereby imposing hazardous impacts on practical applications of CMIP outputs.
Design and validation of a reconfigurable polysonic wind tunnel
Authors: Warning S , Christianer M , Evans W , Coffey F , McQuilling M , Ising E 
Published: May 2021

AbstractA new polysonic wind tunnel has been designed and constructed at Saint Louis University. The flow paths and flow conditioning needs were designed by PhD students and the structural design and manufacturing were accomplished by local pressure vessel and manufacturing firms. Starting with a set of two 25 hp air compressors, an air filter and dryer system with an operating pressure range between 100–200 psia, and a 14 m3storage tank, the total cost for additional components and labor was on the order of $750,000, where design and installation was completed in approximately 18 months. The facility is uniquely reconfigurable to accommodate straight and curved flow paths, with existing configurations supporting a supersonic shock wave-boundary layer interaction study in a rectangular channel and another study of a transonic linear cascade of high-pressure turbine airfoils. The design process and resulting components are described herein, and include how to improve supersonic nozzle design by adjusting for displacement thickness growth as well as how to diagnose and correct choked flow conditions which existed in the first iteration of the flow path circuit. Results also include a sample schlieren image of a normal shock wave-boundary layer interaction and airfoil static pressure distributions and total pressure ratio across the turbine showing successful configuration implementations.
Understanding star-fundamental algebras
Authors: Giambruno A. , La Mattina D. , Milies C. 
Published: May 2021

Star-fundamental algebras are special finite dimensional algebras with involution∗*over an algebraically closed field of characteristic zero defined in terms of multialternating∗*-polynomials.

We prove that the upper-block matrix algebras with involution introduced in Di Vincenzo and La Scala [J. Algebra 317 (2007), pp. 642–657] are star-fundamental. Moreover, any finite dimensional algebra with involution contains a subalgebra mapping homomorphically onto one of such algebras.

We also give a characterization of star-fundamental algebras through the representation theory of the symmetric group.
IgM Plasma Cell Myeloma
Authors: Lu Haiyan , Durkin Lisa , Zhao Xiaoxian , Nakashima Megan O 
Published: May 2021

Abstract

Objectives
Immunoglobulin M plasma cell myeloma (IgMPCM) is a rare entity that is difficult to distinguish from other IgM-related neoplasms. The study aims to characterize the clinicopathologic features of IgMPCM, including MYD88 L265P and CXCR4 mutations.

Methods
From our institutional archives, bone marrow biopsy specimens from January 1, 2008, to December 1, 2018, with monotypic plasma cells (PCs) expressing IgM that met current International Myeloma Working Group/World Health Organization criteria for PCM were included. Sanger sequencing was used to test for MYD88 L265P and WHIM-like CXCR4 mutations.

Results
Nine cases of IgMPCM were identified. Serum IgM paraproteins were detected in eight cases. CD138-positive PC burden averaged 41.9% (5%-80%). In four cases, PCs had lymphoplasmacytic morphology with cyclin D1 expression by immunohistochemistry. Three of four tested cases were positive for t(11;14) by fluorescence in situ hybridization, one with monosomy 13. The remaining case was positive for del13q14. All were negative for MYD88 L265P and WHIM-like CXCR4 mutations. Eight patients received immunochemotherapy, with four receiving autologous hematopoietic stem cell transplant. Median follow-up was 61 months (range, 11-120). All patients were alive except one.

Conclusions
Distinguishing IgMPCM from other IgM-related disorders requires correlation with clinical, laboratory, and radiologic findings. Exclusion of MYD88 L265P and WHIM-like CXCR4 mutations may be useful to diagnose IgMPCM.
Clinicopathologic Features of Gynecologic Malignancies Presenting Clinically as Colonic Malignancies
Authors: Fuller Lanisha D , Dunn Andrew , Huber Aaron R , Vyas Monika , Gonzalez Raul S 
Published: May 2021

Abstract

Objectives
To systematically evaluate gynecologic malignancies (adnexal or uterine) causing gastrointestinal (GI) signs (eg, mass on colonoscopy) or symptoms (eg, bloody stools) clinically mimicking a GI primary malignancy.

Methods
The archives of 2 institutions were retrospectively reviewed for gynecologic malignancies clinically manifesting as colonic lesions. For each case, available radiologic, endoscopic, and histologic findings were recorded.

Results
We identified 16 cases: 13 biopsies and 3 resections. The masses were localized in the rectosigmoid (14 cases [88%]), right (1 case [6%]), and transverse (1 case [6%]) colon. Gastrointestinal-type complaints included abdominal pain, weight loss, hematochezia, and obstruction; 1 case was asymptomatic and found during screening colonoscopy. Nine patients (56%) had no known prior gynecologic malignancy, and in only 2 of these patients was there some clinical suspicion of a noncolonic primary malignancy. Most cases (13 [81%]) were serous carcinoma, usually high-grade adnexal or primary peritoneal. Six cases (38%) directly extended into the colon, and 7 (44%) metastasized; route of spread was unclear in the others. Only 1 case (6%) showed mucosal involvement, and none showed desmoplasia or dirty necrosis. Four of the 13 serous carcinomas (31%) showed psammoma bodies.

Conclusions
Advanced gynecologic malignancies, most commonly serous carcinoma, can rarely manifest as GI lesions. Clues to noncolonic origin on biopsy include lack of colonic mucosal involvement/dysplasia, desmoplasia, or dirty necrosis.
Adapting pharmacy experiential education during COVID-19: Innovating remote preceptor resources, tools, and patient care delivery beyond virtual meetings
Authors: Law Elaine , Scott Marie C , Moon Yong S K , Lee Audrey J , Bandy Veronica T , Haydon Andrew , Shek Allen , Kang-Birken S Lena 
Published: May 2021

Abstract

Purpose
To describe the innovative teaching practices, tools, and resources for remote learning developed by a school of pharmacy with a decentralized experiential program to empower and support preceptors in response to the coronavirus disease 2019 (COVID-19) pandemic.

Summary
As the pandemic has continued, there have been significant shifts in pharmacy workflow, staffing, and patient care delivery. Pharmacy students are slowly being reintegrated into these learning environments. Although preceptors are willing and eager to teach, many lack the resources, tools, and support to create remote learning experiences at their facilities. The University of the Pacific Thomas J. Long School of Pharmacy has a decentralized experiential education model in which faculty regional coordinators with clinical practices and diverse expertise are disseminated throughout California. This model allowed us to collaborate and understand preceptor needs from a local level. We created a preceptor COVID-19 guidance document, introduced innovative virtual playbooks to pivot up to 100% remote rotations, and promoted the layered learning model to integrate pharmacy residents into the remote teaching space. Communication and flexibility are key to ensure student and preceptor safety while maintaining high-quality advanced pharmacy practice experiences and preserving patient-student relationships in telehealth.

Conclusion
Overall, we successfully created innovative solutions and leveraged our decentralized experiential model to meet the teaching and learning demands during an unanticipated crisis. We continue to adapt and plan to assess the effectiveness of the tools by administering surveys of preceptors and pharmacy students.
V—The Linguistic Approach to Ontology
Authors: Walters Lee 
Published: May 2021

AbstractWhat are the prospects for a linguistic approach to ontology? Given that it seems that there are true subject-predicate sentences containing empty names, traditional linguistic approaches to ontology appear to be flawed. I argue that in order to determine what there is, we need to determine which sentences ascribe properties (and relations) to objects, and that there does not appear to be any formal criterion for this. This view is then committed to giving an account of what predicates do in sentences when they do not ascribe properties. I sketch an approach to the varieties of predication.
Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions
Authors: Nain Zulkar , Barman Shital K , Sheam Md Moinuddin , Syed Shifath Bin , Samad Abdus , Quinn Julian M W , Karim Mohammad Minnatul , Himel Mahbubul Kabir , Roy Rajib Kanti , Moni Mohammad Ali , Biswas Sudhangshu Kumar 
Published: May 2021

Abstract
Despite the association of prevalent health conditions with coronavirus disease 2019 (COVID-19) severity, the disease-modifying biomolecules and their pathogenetic mechanisms remain unclear. This study aimed to understand the influences of COVID-19 on different comorbidities and vice versa through network-based gene expression analyses. Using the shared dysregulated genes, we identified key genetic determinants and signaling pathways that may involve in their shared pathogenesis. The COVID-19 showed significant upregulation of 93 genes and downregulation of 15 genes. Interestingly, it shares 28, 17, 6 and 7 genes with diabetes mellitus (DM), lung cancer (LC), myocardial infarction and hypertension, respectively. Importantly, COVID-19 shared three upregulated genes (i.e. MX2, IRF7 and ADAM8) with DM and LC. Conversely, downregulation of two genes (i.e. PPARGC1A and METTL7A) was found in COVID-19 and LC. Besides, most of the shared pathways were related to inflammatory responses. Furthermore, we identified six potential biomarkers and several important regulatory factors, e.g. transcription factors and microRNAs, while notable drug candidates included captopril, rilonacept and canakinumab. Moreover, prognostic analysis suggests concomitant COVID-19 may result in poor outcome of LC patients. This study provides the molecular basis and routes of the COVID-19 progression due to comorbidities. We believe these findings might be useful to further understand the intricate association of these diseases as well as for the therapeutic development.
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction
Authors: Kim QHwan , Ko Joon-Hyuk , Kim Sunghoon , Park Nojun , Jhe Wonho 
Published: May 2021

Abstract

Motivation
Characterizing drug–protein interactions (DPIs) is crucial to the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict DPIs without human trial and error. However, because data labeling requires significant resources, the available protein data size is relatively small, which consequently decreases model performance. Here, we propose two methods to construct a deep learning framework that exhibits superior performance with a small labeled dataset.

Results
At first, we use transfer learning in encoding protein sequences with a pretrained model, which trains general sequence representations in an unsupervised manner. Second, we use a Bayesian neural network to make a robust model by estimating the data uncertainty. Our resulting model performs better than the previous baselines at predicting interactions between molecules and proteins. We also show that the quantified uncertainty from the Bayesian inference is related to confidence and can be used for screening DPI data points.

Availability and implementation
The code is available at https://github.com/QHwan/PretrainDPI.

Supplementary information
Supplementary data are available at Bioinformatics online.
CONSTAX2: improved taxonomic classification of environmental DNA markers
Authors: Liber Julian A , Bonito Gregory , Benucci Gian Maria Niccolò 
Published: May 2021

Abstract

Summary
CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials.

Availability and implementation
CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code.

Supplementary information
Supplementary data are available at Bioinformatics online.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity by Viral Load, S Gene Variants and Demographic Factors, and the Utility of Lateral Flow Devices to Prevent Transmission
Authors: Lee Lennard Y W , Rozmanowski Stefan , Pang Matthew , Charlett Andre , Anderson Charlotte , Hughes Gareth J , Barnard Matthew , Peto Leon , Vipond Richard , Sienkiewicz Alex , Hopkins Susan , Bell John , Crook Derrick W , Gent Nick , Walker A Sarah , Peto Tim E A , Eyre David W 
Published: May 2021

Abstract

Background
How severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity varies with viral load is incompletely understood. Whether rapid point-of-care antigen lateral flow devices (LFDs) detect most potential transmission sources despite imperfect clinical sensitivity is unknown.

Methods
We combined SARS-CoV-2 testing and contact tracing data from England between 1 September 2020 and 28 February 2021. We used multivariable logistic regression to investigate relationships between polymerase chain reaction (PCR)-confirmed infection in contacts of community-diagnosed cases and index case viral load, S gene target failure (proxy for B.1.1.7 infection), demographics, SARS-CoV-2 incidence, social deprivation, and contact event type. We used LFD performance to simulate the proportion of cases with a PCR-positive contact expected to be detected using 1 of 4 LFDs.

Results
In total, 231 498/2 474 066 (9%) contacts of 1 064 004 index cases tested PCR-positive. PCR-positive results in contacts independently increased with higher case viral loads (lower cycle threshold [Ct] values), for example, 11.7% (95% confidence interval [CI] 11.5–12.0%) at Ct = 15 and 4.5% (95% CI 4.4–4.6%) at Ct = 30. B.1.1.7 infection increased PCR-positive results by ~50%, (eg, 1.55-fold, 95% CI 1.49–1.61, at Ct = 20). PCR-positive results were most common in household contacts (at Ct = 20.1, 8.7% [95% CI 8.6–8.9%]), followed by household visitors (7.1% [95% CI 6.8–7.3%]), contacts at events/activities (5.2% [95% CI 4.9–5.4%]), work/education (4.6% [95% CI 4.4–4.8%]), and least common after outdoor contact (2.9% [95% CI 2.3–3.8%]). Contacts of children were the least likely to test positive, particularly following contact outdoors or at work/education. The most and least sensitive LFDs would detect 89.5% (95% CI 89.4–89.6%) and 83.0% (95% CI 82.8–83.1%) of cases with PCR-positive contacts, respectively.

Conclusions
SARS-CoV-2 infectivity varies by case viral load, contact event type, and age. Those with high viral loads are the most infectious. B.1.1.7 increased transmission by ~50%. The best performing LFDs detect most infectious cases.
Gender differences in complications following catheter ablation of atrial fibrillation
Authors: Ngo Linh , Ali Anna , Ganesan Anand , Woodman Richard , Adams Robert , Ranasinghe Isuru 
Published: May 2021

Abstract

Aims
Population studies that provide unbiased estimates of gender differences in risk of complications following catheter ablation of atrial fibrillation (AF) are sparse. We sought to evaluate the association of female gender and risk of complications following AF ablation in a nationwide cohort.

Methods and results
We identified 35 211 patients (29.5% females) undergoing AF ablations from 2008 to 2017 using national hospitalization data from Australia and New Zealand. The primary outcome was any procedural complication occurring up to 30-days after discharge. Logistic regression was used to adjust for differences in baseline characteristics between sexes. Compared with males, females were older (mean age 64.9 vs. 61.2 years), had higher rates of hypertension (14.0% vs. 11.6%) and haematological disorders (5.3% vs. 3.8%) and experienced a higher rate of procedural complications (6.96% vs. 5.41%) (all P &lt; 0.001). This gender disparity remained significant after adjustment [odds ratio (OR) 1.25 (95% confidence interval 1.14–1.38), P &lt; 0.001] and was driven by an increased risk of vascular injury [OR 1.86 (1.23–2.82), P = 0.003], pericarditis [OR 1.86 (1.16–2.67), P = 0.008], pericardial effusion [OR 1.71 (1.35–2.17), P &lt; 0.001), and bleeding [OR 1.30 (1.15–1.46), P &lt; 0.001]. Notably, the gender difference persisted over time [OR for the most recent period 1.19 (1.003-1.422), P = 0.046] despite a declining complication rate in both men and women.

Conclusion
Females undergoing AF ablations experienced a 25% higher risk of procedural complications compared with males, a disparity that has persisted over time despite a falling complication rate. Efforts to reduce this gender disparity should focus on reducing the incidence of pericardial effusion, pericarditis, vascular injury, and bleeding.
Swordplay: Lord Mountbatten, Count Terauchi and the Japanese Surrender in Southeast Asia
Authors: Sturma Michael 
Published: May 2021

Abstract
Field Marshal Count Terauchi’s personal surrender of swords to Admiral Lord Louis Mountbatten in November 1945 highlights some of the complexities related to the Japanese surrender in Southeast Asia. Japanese swords served as important symbols for both their owners and the Allies. Mountbatten’s determination to dispossess the Japanese of their swords reflected his views on Japan’s militarism and a desire to impress upon soldiers their subservience to British authority when most had not been directly defeated in battle. On the other hand, Mountbatten was constrained by the huge area placed under his command, the lack of resources at his disposal and rising nationalist resistance. In these circumstances, Mountbatten sought the co-operation of surrendered Japanese personnel in British interests. The issue of surrendering Japanese swords underlines Mountbatten’s conflicting objectives and Count Terauchi’s efforts to manipulate the situation.
‘Distrust all Advice … and Make No Exception in Favour of our Advice’: Financial Knowledge and Knowingness in Late Victorian Britain
Authors: Taylor James 
Published: May 2021

Abstract
Over the past two decades, our understanding of the development of financial markets in the nineteenth century has been transformed by scholars working in two broad areas. Economic sociologists and literary scholars have explored the discursive underpinnings of the institutions of modern finance, deftly tracing the ways in which stock markets were legitimised through a growing association with science and statistics, and a simultaneous distancing from gambling and chance. From a very different perspective, quantitative analysis of shareholder registers and other archival records by economic historians and historical geographers has provided rich data giving a more precise picture of who invested and what they invested in. Valuable though this work has been, the gulf between the two approaches has resulted in a dearth of empirically grounded studies of the social and cultural dimensions of investment. An area particularly in need of greater exploration is the booming late Victorian print culture which purported to explain finance to new investors. This article offers a close reading of the financial journalism of Henry Labouchere, better known for his subsequent political career as a Liberal MP. Labouchere’s writings are deliberately riddled with contradictions, simultaneously legitimising and questioning the stock market, and switching between the roles of moral crusader and self-interested speculator. This carefully crafted performance encouraged an attitude of ‘knowingness’ towards finance among his readers which helps to explain why the stock market was able to grow in popularity even when it remained so closely associated with fraud.