bluuebunny/crossref_metadata_2025_split huggingface dataset:
Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 From Adult Index Cases With and Without Human Immunodeficiency Virus in South Africa, 2020–2021: A Case-Ascertained, Prospective, Observational Household Transmission Study
Authors: Kleynhans Jackie , Walaza Sibongile , Martinson Neil A , Neti Mzimasi , von Gottberg Anne , Bhiman Jinal N , Toi Dylan , Amoako Daniel G , Buys Amelia , Ndlangisa Kedibone , Wolter Nicole , Genade Leisha , Maloma Lucia , Chewparsad Juanita , Lebina Limakatso , de Gouveia Linda , Kotane Retshidisitswe , Tempia Stefano , Cohen Cheryl 
Published: August 2022

Abstract

Background
In South Africa, 19% of adults are living with human immunodeficiency virus (HIV; LWH). Few data on the influence of HIV on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission are available.

Methods
We performed a case-ascertained, prospective household transmission study of symptomatic adult index SARS-CoV-2 cases LWH and not living with HIV (NLWH) and their contacts from October 2020 to September 2021. Households were followed up 3 times a week for 6 weeks to collect nasal swabs for SARS-CoV-2 testing. We estimated household cumulative infection risk (HCIR) and duration of SARS-CoV-2 positivity (at a cycle threshold value &lt;30 as proxy for high viral load).

Results
HCIR was 59% (220 of 373), not differing by index HIV status (60% LWH vs 58% NLWH). HCIR increased with index case age (35–59 years: adjusted OR [aOR], 3.4; 95% CI, 1.5–7.8 and ≥60 years: aOR, 3.1; 95% CI, 1.0–10.1) compared with 18–34 years and with contacts’ age, 13–17 years (aOR, 7.1; 95% CI, 1.5–33.9) and 18–34 years (aOR, 4.4; 95% CI, 1.0–18.4) compared with &lt;5 years. Mean positivity was longer in cases LWH (adjusted hazard ratio, 0.4; 95% CI, .1–.9).

Conclusions
Index HIV status was not associated with higher HCIR, but cases LWH had longer positivity duration. Adults aged &gt;35 years were more likely to transmit and individuals aged 13–34 to be infected SARS-CoV-2 in the household. As HIV infection may increase transmission, health services must maintain HIV testing and antiretroviral therapy initiation.
Severe Acute Respiratory Syndrome Coronavirus 2 Hyperimmune Intravenous Human Immunoglobulins Neutralizes Omicron Subvariants BA.1, BA.2, BA.2.12.1, BA.3, and BA.4/BA.5 for Treatment of Coronavirus Disease 2019
Authors: Awasthi Mayanka , Golding Hana , Khurana Surender 
Published: August 2022

Abstract
Our study demonstrates that neither 2020 convalescent plasma (CP) nor 2019/2020 intravenous immunoglobulin (IVIG) neutralizes Omicron subvariants BA.1 to BA.5. In contrast, 2020 hyperimmune anti–severe acute respiratory syndrome coronavirus 2 IVIG (hCoV-2IG) lots neutralized Omicron variants of concern, similar to results with 2022 CP from BA.1 breakthrough infections. Therefore, high-titer hCoV-2IG and CP could be evaluated for treatment of high-risk individuals infected with circulating Omicron subvariants.
Practical Attacks of Round-Reduced SIMON Based on Deep Learning
Authors: Hou Zezhou , Ren Jiongjiong , Chen Shaozhen 
Published: August 2022

Abstract
At CRYPTO’19, Gohr built a bridge between deep learning and cryptanalysis. Based on deep neural networks, he trained neural distinguishers of SPECK32/64. Besides, with the help of neural distinguishers, he attacked 11-round SPECK32/64 using Bayesian optimization. Compared with the traditional attack, its complexity was reduced. Although his work opened a new direction of machine learning aided cryptanalysis, there are still two research gaps that researchers are eager to fill in. (i) Can the attack using neural distinguishers be used to other block ciphers? (ii) Are there effective key recovery attacks on large-size block ciphers adopting neural distinguishers? In this paper, our core target is to propose an effective neural-aided key recovery policy to attack large-size block ciphers. For large-size block ciphers, it costs too much time in pre-computation, especially in wrong key response profile, which is the main reason why there are almost no neural aided attacks on large-size block ciphers. Fortunately, we find that there is a fatal flaw in the wrong key profile. In the some experiments of SIMON32/64 and SIMON48/96, there is a regular of change in response profiles, which implies that we can use partial response instead of the complete response. Based on this, we propose a generic key recovery attack scheme which can attack large-size block ciphers. As an application, we perform a key recovery attack on 13-round SIMON64/128, which is the first practical attack using neural distinguishers to large-size ciphers. In addition, we also attack 13-round SIMON32/64 and SIMON48/96, which also shows that the neural distinguishers can be used to other block ciphers.
Echocardiographic predictors of presence of cardiac amyloidosis in aortic stenosis
Authors: Jaiswal Vikash , Ang Song Peng , Chia Jia Ee , Abdelazem Eman Muhammad , Jaiswal Akash , Biswas Monodeep , Gimelli Alessia , Parwani Purvi , Siller-Matula Jolanta M , Mamas Mamas A 
Published: August 2022

Abstract

Aims
Aortic stenosis (AS) and cardiac amyloidosis (CA) frequently coexist but the diagnosis of CA in AS patients remains a diagnostic challenge. We aim to evaluate the echocardiographic parameters that may aid in the detection of the presence of CA in AS patients.

Method and results
We performed a systematic literature search of electronic databases for peer-reviewed articles from inception until 10 January 2022. Of the 1449 patients included, 160 patients had both AS–CA whereas the remaining 1289 patients had AS-only. The result of our meta-analyses showed that interventricular septal thickness [standardized mean difference (SMD): 0.74, 95% CI: 0.36–1.12, P = 0.0001), relative wall thickness (SMD: 0.74, 95% CI: 0.17–1.30, P &lt; 0.0001), posterior wall thickness (SMD: 0.74, 95% CI 0.51 to 0.97, P = 0.0011), LV mass index (SMD: 1.62, 95% CI: 0.63–2.62, P = 0.0014), E/A ratio (SMD: 4.18, 95% CI: 1.91–6.46, P = 0.0003), and LA dimension (SMD: 0.73, 95% CI: 0.43–1.02, P &lt; 0.0001)] were found to be significantly higher in patients with AS–CA as compared with AS-only patients. In contrast, myocardial contraction fraction (SMD: −2.88, 95% CI: −5.70 to −0.06, P = 0.045), average mitral annular S′ (SMD: −1.14, 95% CI: −1.86 to −0.43, P = 0.0017), tricuspid annular plane systolic excursion (SMD: −0.36, 95% CI: −0.62 to −0.09, P = 0.0081), and tricuspid annular S′ (SMD: −0.77, 95% CI: −1.13 to −0.42, P &lt; 0.0001) were found to be significantly lower in AS–CA patients.

Conclusion
Parameters based on echocardiography showed great promise in detecting CA in patients with AS. Further studies should explore the optimal cut-offs for these echocardiographic variables for better diagnostic accuracy.
Trends in survival after cardiac arrest: a Swedish nationwide study over 30 years
Authors: Jerkeman Matilda , Sultanian Pedram , Lundgren Peter , Nielsen Niklas , Helleryd Edvin , Dworeck Christian , Omerovic Elmir , Nordberg Per , Rosengren Annika , Hollenberg Jacob , Claesson Andreas , Aune Solveig , Strömsöe Anneli , Ravn-Fischer Annica , Friberg Hans , Herlitz Johan , Rawshani Araz 
Published: August 2022

Abstract

Aims
Trends in characteristics, management, and survival in out-of-hospital cardiac arrest (OHCA) and in-hospital cardiac arrest (IHCA) were studied in the Swedish Cardiopulmonary Resuscitation Registry (SCRR).

Methods and results
The SCRR was used to study 106 296 cases of OHCA (1990–2020) and 30 032 cases of IHCA (2004–20) in whom resuscitation was attempted. In OHCA, survival increased from 5.7% in 1990 to 10.1% in 2011 and remained unchanged thereafter. Odds ratios [ORs, 95% confidence interval (CI)] for survival in 2017–20 vs. 1990–93 were 2.17 (1.93–2.43) overall, 2.36 (2.07–2.71) for men, and 1.67 (1.34–2.10) for women. Survival increased for all aetiologies, except trauma, suffocation, and drowning. OR for cardiac aetiology in 2017–20 vs. 1990–93 was 0.45 (0.42–0.48). Bystander cardiopulmonary resuscitation increased from 30.9% to 82.2%. Shockable rhythm decreased from 39.5% in 1990 to 17.4% in 2020. Use of targeted temperature management decreased from 42.1% (2010) to 18.2% (2020). In IHCA, OR for survival in 2017–20 vs. 2004–07 was 1.18 (1.06–1.31), showing a non-linear trend with probability of survival increasing by 46.6% during 2011–20. Myocardial ischaemia or infarction as aetiology decreased during 2004–20 from 67.4% to 28.3% [OR 0.30 (0.27–0.34)]. Shockable rhythm decreased from 37.4% to 23.0% [OR 0.57 (0.51–0.64)]. Approximately 90% of survivors (IHCA and OHCA) had no or mild neurological sequelae.

Conclusion
Survival increased 2.2-fold in OHCA during 1990–2020 but without any improvement in the final decade, and 1.2-fold in IHCA during 2004–20, with rapid improvement the last decade. Cardiac aetiology and shockable rhythms were halved. Neurological outcome has not improved.
Modulation of the cell wall protein Ecm33p in yeast Saccharomyces cerevisiae improves the production of small metabolites
Authors: Ramos-Viana Verónica , Møller-Hansen Iben , Kempen Paul , Borodina Irina 
Published: August 2022

Abstract
The cell wall is a dynamic organelle that determines the shape and provides the cell with mechanical strength. This study investigated whether modulation of cell wall composition can influence the production or secretion of small metabolites by yeast cell factories. We deleted and upregulated several cell wall-related genes KRE2, CWP1, CWP2, ECM33, PUN1, and LAS21 in yeast Saccharomyces cerevisiae engineered for p-coumaric acid or β-carotene production. Deletions of las21∆ and ecm33∆ impaired the yeast growth on medium with cell wall stressors, calcofluor white, and caffeine. Both overexpression and deletion of ECM33 significantly improved the specific yield of p-coumaric acid and β-carotene. We observed no change in secretion in any cell wall-altered mutants, suggesting the cell wall is not a limiting factor for small molecule secretion at the current production levels. We evaluated the cell wall morphology of the ECM33 mutant strains using transmission electron microscopy. The ecm33∆ mutants had an increased chitin deposition and a less structured cell wall, while the opposite was observed in ECM33-overexpressing strains. Our results point at the cell wall-related gene ECM33 as a potential target for improving production in engineered yeast cell factories.
The
Rat de l’Opéra
and the Social Imaginary of Labour: Dance in July Monarchy Popular Culture
Authors: Sabee Olivia 
Published: August 2022

Abstract

Mid-nineteenth-century literary and theatrical depictions of
rats de l’Opéra
(young girls training and performing with the Paris Opéra) emphasize their physical and material hardships, dubious morals, and shapeshifting abilities.
Physiologies
, tell-all histories of the Paris Opéra, and vaudeville livrets each underscore these qualities of the
rat
in their portrayals of her, yet they also emphasize her role as a labourer. Taken together, these representations of the
rat
connect ensemble dancers with the idea of labour in the social imaginary, crafting an image of the ensemble dancer as physical labourer, juxtaposed with the star dancer, considered to be an artist.
Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast
Authors: Chatfield-Reed Kate , Marno Jones Kurtis , Shah Farah , Chua Gordon 
Published: August 2022

Abstract
In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.
Multitrait Bayesian shrinkage and variable selection models with the BGLR-R package
Authors: Pérez-Rodríguez Paulino , de los Campos Gustavo 
Published: August 2022

AbstractThe BGLR-R package implements various types of single-trait shrinkage/variable selection Bayesian regressions. The package was first released in 2014, since then it has become a software very often used in genomic studies. We recently develop functionality for multitrait models. The implementation allows users to include an arbitrary number of random-effects terms. For each set of predictors, users can choose diffuse, Gaussian, and Gaussian–spike–slab multivariate priors. Unlike other software packages for multitrait genomic regressions, BGLR offers many specifications for (co)variance parameters (unstructured, diagonal, factor analytic, and recursive). Samples from the posterior distribution of the models implemented in the multitrait function are generated using a Gibbs sampler, which is implemented by combining code written in the R and C programming languages. In this article, we provide an overview of the models and methods implemented BGLR’s multitrait function, present examples that illustrate the use of the package, and benchmark the performance of the software.
The bHLH1-DTX35/DFR module regulates pollen fertility by promoting flavonoid biosynthesis in Capsicum annuum L.
Authors: Zhang Zhishuo , Liu Yi , Yuan Qiaoling , Xiong Cheng , Xu Hao , Hu Bowen , Suo Huan , Yang Sha , Hou Xilin , Yuan Fang , Pei Zhenming , Dai Xiongze , Zou Xuexiao , Liu Feng 
Published: August 2022

Abstract
High pollen fertility can ensure the yield and efficiency of breeding work, but factors that affect the fertility of pepper pollen have not been studied extensively. In this work, we screened the reduced pollen fertility 1 (rpf1) mutant of Capsicum annuum with reduced pollen fertility and yellow anthers from an EMS (ethyl methanesulfonate)-mutagenized pepper population. Through construction of an F2 population followed by BSA (bulked segregant analysis) mapping and KASP genotyping, we identified CabHLH1 as a candidate gene for control of this trait. A G → A mutation at a splice acceptor site in CabHLH1 causes a frameshift mutation in the mutant, and the translated protein is terminated prematurely. Previous studies on CabHLH1 have focused on the regulation of flavonoid synthesis. Here, we found that CabHLH1 also has an important effect on pollen fertility. Pollen vigor, anther flavonoid content, and seed number were lower in CabHLH1-silenced pepper plants, whereas anther H2O2 and MDA (malondialdehyde) contents were higher. RNA-seq analyses showed that expression of the flavonoid synthesis genes DFR, ANS, and RT was significantly reduced in anthers of CabHLH1-silenced plants and rpf1 plants, as was the expression of DTX35, a gene related to pollen fertility and flavonoid transport. Yeast one-hybrid and dual-luciferase reporter assays showed that CabHLH1 can directly bind to the promoters of DTX35 and DFR and activate their expression. These results indicate that CabHLH1 regulates reactive oxygen species homeostasis by promoting the synthesis of anther flavonoids and acts as a positive regulator of pepper pollen fertility.
Patient representatives need various methods to be involved in clinical practice guidelines: a qualitative study in Finland
Authors: Sipilä Raija , Hämeen-Anttila Katri , Komulainen Jorma 
Published: August 2022

Abstract

Objectives
The aim of the study was to identify POs’ views on the best ways to involve patient representatives and POs’ potential roles in the guideline process. Patient involvement in guideline development has been endorsed. The international guideline community has developed a toolkit to describe methods and facilitate patient involvement. The most used methods are commentary on the draft guideline and acting as guideline panel members. However, knowledge of the patient organizations’ (POs) perception of involvement is scarce.

Methods
Representatives from 12 POs (n = 20) in Finland were invited to group interviews (n = 4, á 1.5 h). In the qualitative analysis, we deductively identified using the Guidelines International Network public toolkit the best ways to involve patient representatives and inductively analyzed general principles for involvement and how the POs consider their potential roles.

Results
The interviewees raised three major principles for organizing patient involvement in guideline development: (i) different means of involvement, (ii) representativeness, and (iii) genuine and equal interaction. The interviewees endorsed involvement through statements and comments throughout the guideline process, and instead of participating in guideline panels as a member, they preferred reference groups or patients’ networks. The interviewees saw various roles for POs in guideline development, for example acting as confidants for patient representatives, information production, active participation, commenting, and communicative activities to population.

Conclusions
Guideline developers should offer various and easy ways of patient involvement. POs’ representatives considered reference groups to be a superior method of participation compared to guideline panel members. Organizations are willing to support guideline development and patient representatives.
Association Between Prolonged Shedding of Zika Virus in Human Semen and Male Reproductive Tract Inflammation
Authors: Vogt Megan B , McDonald Erin M , Delorey Mark , Mead Paul S , Hook Sarah A , Hinckley Alison F , Werre Stephen R , Brault Aaron C , Duggal Nisha K 
Published: August 2022

Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that causes congenital defects. Sexual transmission of ZIKV was confirmed in a recent epidemic; however, mechanisms behind ZIKV infection and persistence in the male reproductive tract (MRT) are unknown. Previously, we found that approximately 33% of men with symptomatic ZIKV infections shed ZIKV RNA in semen, and some men shed ZIKV RNA for &gt;3 months. Here, we evaluated the semen of 49 ZIKV-infected men to identify immune factors correlating with long-term ZIKV shedding in semen and ZIKV-infected cell types in semen. We found that prolonged ZIKV RNA shedding in semen was associated with MRT inflammation, indicated by higher leukocyte counts and inflammatory cytokine concentrations in semen of long-term versus short-term shedders. In addition, we found ZIKV RNA in seminal leukocytes and epithelial cells. This study of human semen from ZIKV-infected men provides critical insights into the effects of ZIKV on MRT health.
ReviewR: a light-weight and extensible tool for manual review of clinical records
Authors: Mayer David A , Rasmussen Luke V , Roark Christopher D , Kahn Michael G , Schilling Lisa M , Wiley Laura K 
Published: August 2022

AbstractObjectivesManual record review is a crucial step for electronic health record (EHR)-based research, but it has poor workflows and is error prone. We sought to build a tool that provides a unified environment for data review and chart abstraction data entry.Materials and MethodsReviewR is an open-source R Shiny application that can be deployed on a single machine or made available to multiple users. It supports multiple data models and database systems, and integrates with the REDCap API for storing abstraction results.ResultsWe describe 2 real-world uses and extensions of ReviewR. Since its release in April 2021 as a package on CRAN it has been downloaded 2204 times.Discussion and ConclusionReviewR provides an easily accessible review interface for clinical data warehouses. Its modular, extensible, and open source nature afford future expansion by other researchers.
Cyclic proofs for the first-order µ-calculus
Authors: Afshari Bahareh , Enqvist Sebastian , Leigh Graham E 
Published: August 2022

Abstract
We introduce a path-based cyclic proof system for first-order $\mu $-calculus, the extension of first-order logic by second-order quantifiers for least and greatest fixed points of definable monotone functions. We prove soundness of the system and demonstrate it to be as expressive as the known trace-based cyclic systems of Dam and Sprenger. Furthermore, we establish cut-free completeness of our system for the fragment corresponding to the modal $\mu $-calculus.
Neutron star crust in Voigt approximation II: general formula for electron screening correction for effective shear modulus
Authors: Chugunov Andrey I 
Published: August 2022

ABSTRACT
The main contribution to the effective shear modulus of neutron star crust can be calculated within Coulomb solid model and can be approximated by simple analytical expression for arbitrary (even multicomponent) composition. Here I consider correction associated with electron screening within Thomas–Fermi approximation. In particular, I demonstrate that for relativistic electrons (density ρ &gt; 106 g cm−3) this correction can be estimated as $\delta \mu _\mathrm{eff}^\mathrm{V}= -9.4\times 10^{-4}\sum _Z n_Z Z^{7/3} e^2/a_\mathrm{e},$ where summation is taken over ion species, nZ is number density of ions with charge Ze, kTF is Thomas–Fermi screening wavenumber. Finally, ae = (4πne/3)−1/3 is electron sphere radius. Quasi-neutrality condition ne = ∑ZZnZ is assumed. This result holds true for arbitrary (even multicomponent and amorphous) matter and can be applied for neutron star crust and (dense) cores of white dwarfs. For example, the screening correction reduces shear modulus by ∼9 per cent for Z ∼ 40, which is typical for inner layers of neutron star crust.