bluuebunny/crossref_metadata_2025_split huggingface dataset:
TBD (OWEN HOLLAND) LTD v SIMONS
Authors:   Court of Appeal
Published: March 2022

Abstract
H1 Copyright — Designs — Breach of confidence — Ex-employees — Baggage carts — Preservation of evidence — Search orders — Imaging orders — Review of imaged documents — Use of imaged documents — Appropriate safeguards — Interpretation of search orders — Committal proceedings — Applications for permission to commit — Litigation privilege — Common interest privilege — Waiver — Iniquity exception — Security for costs — Appeal to Court of Appeal
The phenomenon of the gender gap among gifted students: the situation in Italy based on analysis of results in mathematics competitions
Authors: Mazza Lorenzo , Gambini Alessandro 
Published: March 2022

Abstract
This paper deals with the gender gap phenomenon as displayed by Italian students participating in mathematical competitions—gifted students. In particular, the results obtained by the entire student population participating in district competitions from 2017 to 2020 were analysed. The combined analysis of the competition results and of the final questionnaire allowed us to highlight and deepen possible causes of the gender gap. It has been observed that girls underestimate themselves, sometimes giving up participating in competitions. Particularly, during the upper secondary school years, increasingly fewer girls choose to attend mathematical competitions. Analysing the results, although the percentage of correct answers between the two genders is fairly similar, the rate of girls who prefer not to answer to avoid mistakes is higher than that of boys.
A Model of Human Small Airway on a Chip for Studies of Subacute Effects of Inhalation Toxicants
Authors: Sakolish Courtney , Georgescu Andrei , Huh Dan Dongeun , Rusyn Ivan 
Published: March 2022

AbstractTesting for acute inhalation hazards is conducted in animals; however, a number of robust in vitro human cell-based alternatives have been developed and tested. These models range in complexity from cultures of cell lines or primary cells in air-liquid interface on Transwells, to more complex and physiologically relevant flow- and mechanical stimulation-enabled tissue chips. Although the former models are relatively straightforward to establish and can be tested in medium/high throughput, the latter require specialized equipment and lack in throughput. In this study, we developed a device that can be easily manufactured while allowing for the production of a differentiated lung tissue. This multilayered microfluidic device enables coculture of primary human small airway epithelial cells and lung microvascular endothelial cells under physiological conditions for up to 18 days and recreates the parenchymal-vascular interface in the distal lung. To explore the potential of this airway on a chip for applications in inhalation toxicology, we also devised a system that allows for direct gas/aerosol exposures of the engineered airway epithelium to noxious stimuli known to cause adverse respiratory effects, including dry flowing air, lipopolysaccharide, particulate matter, and iodomethane. This study generated quantitative, high-content data that were indicative of aberrant changes in biochemical (lactate dehydrogenase), barrier (dextran permeability), functional (ciliary beating), and molecular (imaging for various markers) phenotypes of the small airway epithelium due to inhalational exposures. This study is significant because it established an in vitro model of human small airway on a chip that can be used in medium/high-throughput studies of subacute effects of inhalation toxicants.
Surgical and Patient-Reported Outcomes of Autologous versus Implant-Based Reconstruction following Infected Breast Device Explantation
Authors: Asaad Malke , Slovacek Cedar , Mitchell David , Liu Jun , Selber Jesse C. , Clemens Mark W. , Chu Carrie K. , Mericli Alexander F. , Butler Charles E. 
Published: March 2022

Background:
Implant-based breast reconstruction infections often require implant explantation. Whereas some plastic surgeons pursue autologous reconstruction following the first implant-based breast reconstruction failure caused by infection, others argue that a second attempt is acceptable.

Methods:
The authors conducted a retrospective study of patients who underwent a second reconstruction attempt with implant-based or free flap breast reconstruction following explantation because of infection between 2006 and 2019. Surgical and patient-reported outcomes were compared between the two groups.

Results:
A total of 6093 implant-based breast reconstructions were performed during the study period, of which 130 breasts met our inclusion criteria [implant-based, n = 86 (66 percent); free flap, n = 44 (34 percent)]. No significant differences in rates of overall (25 percent versus 36 percent; p = 0.2) or major (20 percent versus 21 percent; p = 0.95) complications were identified between the free flap and implant-based cohorts, respectively. Implant-based breast reconstruction patients were more likely to experience a second infection (27 percent versus 2 percent; p = 0.0007) and reconstruction failure (21 percent versus 5 percent; p = 0.019). Among irradiated patients, reconstruction failure was reported in 44 percent of the implant-based and 7 percent of the free flap cohorts (p = 0.02). Free flap patients reported significantly higher scores for Satisfaction with Breasts (73.7 ± 20.1 versus 48.5 ± 27.9; p = 0.0046).

Conclusions:
Following implant-based breast reconstruction explantation because of infection, implant-based and free flap breast reconstruction had similar rates of overall and major complications; however, implant-based breast reconstruction had considerably higher rates of infection and reconstructive failures and lower patient-reported scores for Satisfaction with Breasts. Given the high rates of implant-based breast reconstruction failure in patients with prior radiotherapy and infection-based failure, plastic surgeons should strongly consider autologous reconstruction in this patient population.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Rising Trend in Waitlisting for Alcoholic Hepatitis With More Favorable Outcomes Than Other High Model for End-stage Liver Disease in the Current Era
Authors: Bittermann Therese , Mahmud Nadim , Weinberg Ethan M. , Reddy K. Rajender 
Published: March 2022

Background.
In the appropriate candidate, liver transplantation (LT) is a viable treatment for alcoholic hepatitis (AH). We compared the waitlisting trends and outcomes of AH patients in the context of others with high Model for End-stage Liver Disease (MELD) score.

Methods.
LT listings for AH between January 1, 2008, and June 12, 2020 were identified in the United Network for Organ Sharing database. Temporal trends in listings for AH were assessed. Covariate adjusted competing risks models evaluated waitlist mortality and LT rates between AH candidates and others with listing native MELD ≥30.

Results.
Between 2008 and 2019, waitlist additions for AH increased 6.5-fold. Waiting time for AH candidates was short (median 10 d). Delisting for clinical improvement was infrequent in AH, albeit higher than MELD ≥30 patients (3.3% versus 0.8%; P < 0.001). Among 99 centers with ≥1 AH listing, AH patients accounted for 0.2%–18.2% of all alcohol-related listings and 0.6%–25.0% of those with native listing MELD ≥30. Overall listing volume was larger at these 99 centers than the 40 with no AH listings (P < 0.001). AH candidates in 2014–2020 experienced improved waitlist survival (adjusted subhazard ratio, 0.67; 95% confidence interval, 0.52-0.86; P = 0.002) and higher transplant rates (adjusted subhazard ratio, 1.14; 95% confidence interval, 1.04-1.25; P = 0.006) versus other MELD ≥30 candidates.

Conclusions.
There has been a rising trend in waitlisting patients with AH and high MELD score. Liver disease causes influence waitlist outcomes and those of AH candidates are more favorable. Further research and allocation adjustments may be needed to ensure equitable organ allocation, based on liver disease cause, for those on the LT waitlist.
Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
Authors: Won Miyoung , Hong Seung-Beom , Han Byeong-Hak , Kwon Soon-Wo 
Published: March 2022

A Gram-negative, non-motile, strictly aerobic and rod- or filamentous-shaped strain, CJU-R4T, was isolated from a flower of royal azalea (Rhododendron schlippenbachii) collected in the Republic of Korea. Strain CJU-R4T was catalase-positive and oxidase-negative, and grew at 15–33 °C (optimum, 28–20 °C), at pH 5.0–8.0 (optimum, pH 7.0–8.0), and in the presence of 0–1 % NaCl (w/v; optimum, 0 %). Strain CJU-R4T had the highest 16S rRNA gene sequence similarity to

Spirosoma oryzae

RHs22T (96.6 %), revealing less than 93 % sequence similarity to other type strains. Phylogenetic and phylogenomic analysis also revealed strain CJU-R4T formed a robust cluster with

S. oryzae

RHs22T. The major fatty acids were summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c; 33.0 %), C16 : 1
ω5c (22.1 %), iso-C15 : 0 (12.6 %) and C16 : 0 (10.7 %). The polar lipids were composed of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. Menaquinone-7 was detected as the sole respiratory quinone. The genomic DNA G+C content was 55.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain CJU-R4T and

Spirosoma oryzae

DSM 28354T were 81.5 and 23.9 %, respectively. Based on the results of the phenotypic and genotypic analyses, strain CJU-R4T is considered to represent a novel species of the genus

Spirosoma

, for which the name Spirosoma rhododendri sp. nov. is proposed. The type strain is CJU-R4T (=KACC 21264T=NBRC 114513T).
A Rapid, High Throughput, Viral Infectivity Assay using Automated Brightfield Microscopy with Machine Learning
Authors: Dodkins Rupert , Delaney John R. , Overton Tess , Scholle Frank , Frias Alba , Crisci Elisa , Huq Nafisa , Jordan Ingo , Kimata Jason T. , Goldberg Ilya G. 
Published: March 2022

AbstractInfectivity assays are essential for the development of viral vaccines, antiviral therapies and the manufacture of biologicals. Traditionally, these assays take 2–7 days and require several manual processing steps after infection. We describe an automated assay (AVIA™), using machine learning (ML) and high-throughput brightfield microscopy on 96 well plates that can quantify infection phenotypes within hours, before they are manually visible, and without sample preparation. ML models were trained on HIV, influenza A virus, coronavirus 229E, vaccinia viruses, poliovirus, and adenoviruses, which together span the four major categories of virus (DNA, RNA, enveloped, and non-enveloped). A sigmoidal function, fit to virus dilution curves, yielded an R2 higher than 0.98 and a linear dynamic range comparable to or better than conventional plaque or TCID50 assays. Because this technology is based on sensitizing AIs to specific phenotypes of infection, it may have potential as a rapid, broad-spectrum tool for virus identification.
Nucleic Acid Adductomics – the Next Generation of Adductomics for Assessing Environmental Health Risk
Authors: Cooke Marcus S. , Chang Yuan-Jhe , Chen Yet-Ran , Hu Chiung-Wen , Chao Mu-Rong 
Published: March 2022

AbstractThe exposome describes the totality of internal and external environmental exposures, across the life course. Components of the exposome have been linked to an increased risk of various, major diseases. To identify the precise nature, and size, of risk, in this complex mixture of exposures, powerful tools are needed to link exposure, cellular consequences, and health/disease. The most biologically informative biomarkers of the exposome should, to varying extents, reflect the dose of the exposure on the body or target organ(s), a subsequent effect on the biological system and, ideally, possess a role in disease. Modification of nucleic acids (NA) is a key consequence of environmental exposures, and while cellular DNA adductomics aims to evaluate the totality to DNA modifications in the genome, an approach which encompasses modifications of all nucleic acids, would be far more comprehensive, and therefore informative. To address this, we propose a cellular and urinary NA adductomics approach for the assessment of both DNA and RNA modifications, including modified (2’-deoxy)ribonucleosides (2’dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks (DDCL, RRCL, DRCL, DPCL, and RPCL, respectively). Supporting the feasibility of this approach, we presented preliminary, proof-of-principle results, which revealed the presence of over 1,000 modified NA moieties, and at least six types of NA modifications, in a representative, pooled urine from healthy subjects, including modified 2’-dN, modified rN, modified nB, DRCL, RRCL and RPCL, many of which were novel/unexpected. We suggest that NA adductomics will provide a more comprehensive approach to the study of nucleic acid modifications, which will facilitate a range of advances, including the identification of novel, unexpected modifications e.g., RNA-RNA, and DNA-RNA crosslinks; key modifications associated with mutagenesis; agent-specific mechanisms; and adductome signatures of key environmental agents, leading to the dissection of the exposome, and its role in human health/disease, across the life course.
Price and Tax Elasticity of Alcohol Consumption: Evidence from Seven Indian States
Authors: Gupta Samarth , Chowdhury Soumi Roy , Pohit Sanjib , Tullu Fikru Tesfaye , Joshi Pradeep 
Published: March 2022

AbstractIn this paper, we develop a novel methodology for constructing price indices of India Made Foreign Liquor (IMFL), which account for incompatible state-level taxation structure and policies across seven states in India. We use this price index to compute price and tax elasticity of IMFL in the seven states. We find that a 1% increase in price leads to only a 0.057% decline in consumption while a 1% increase in tax reduces alcohol consumption by 0.14%. We extend our estimates to show that a 10% increase in taxes will lead to an 8.4% increase in tax revenue. Our results are the most updated estimates of alcohol consumption elasticities, which overcomes several challenges such as varying manufacturing costs across states and varying tax across types of products within states, which other papers do not.
A complete MAPK cascade, a calmodulin, and a protein phosphatase act downstream of CRK receptor kinases and regulate Arabidopsis innate immunity
Authors: Bai Fangwen , Stratmann Johannes W. , Matton Daniel P. 
Published: March 2022

AbstractMitogen-activated protein kinase (MAPK) cascades are critical signal transduction modules in stress responses, but how their composition and mode of activation induces a stress response is poorly understood. We showed in Arabidopsis that CRK21, a cysteine-rich receptor-like protein kinase (CRK), phosphorylates MAPK kinase kinase 20 (MKKK20) and thus directly activates a novel MAPK cascade, consisting of MKKK20, the MAPK kinase MKK3, and the MAPK MPK6. Furthermore, the protein phosphatase PP2C76 and the calmodulin CaM7 were identified as negative and positive modulators of the cascade, respectively. Loss-of-function in components of the MAPK cascade or in CaM7 led to susceptibility to the bacterial pathogen Pseudomonas syringae and the fungal pathogen Botrytis cinerea. In contrast, loss-of-function of PP2C76 as well as transient overexpression of the genes in the MAPK cascade and CaM7 conferred resistance to the pathogens. Moreover, seven additional CRKs interacted with MKKK20 in vivo, and four of these were highly expressed after inoculation with P. syringae. In summary, our findings demonstrate that the novel CRK21-MKKK20-MKK3-MPK6 signaling pathway functions in immunity to fungal and bacterial pathogens and that CRKs may function in directly activating MKKKs.
vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework
Authors: Nagraj V. P. , Scholz Matthew , Jessa Shakeel , Ge Jianye , Woerner August E. , Budowle Bruce , Huang Meng , Turner Stephen D. 
Published: March 2022

AbstractMotivationGenotyping error can impact downstream SNP-based analyses. Simulating various modes and and levels of error can help investigators better understand potential biases caused by miscalled genotypes.ResultsWe have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missigness in VCF files. We demonstrate how vcferr could be used to address a research question by introducing varying levels of error of different type into a sample in a simulated pedigree, and assessed how kinship analysis degrades as a function of kind and type of error.Software Availabilityvcferr is available for installation via PyPi (https://pypi.org/project/vcferr/) or conda (https://anaconda.org/bioconda/vcferr). The software is released under the MIT license with source code available on GitHub (https://github.com/signaturescience/vcferr).
Molecular characterization of cell types in the squid Loligo vulgaris
Authors: Duruz Jules , Sprecher Marta , Kaldun Jenifer C. , Alsoudy Alsayed , Tschanz-Lischer Heidi , van Geest Geert , Nicholson Pamela , Bruggmann Rémy , Sprecher Simon G. 
Published: March 2022

AbstractCephalopods have long been getting a lot of attention for their fascinating behavioral abilities and for the complexity of their nervous systems that set them apart from other mollusks. Because of the great evolutionary distance that separates vertebrates from mollusks, it is evident that higher cognitive features have evolved independently in this clade although they sometimes resemble cognitive functions of vertebrates. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Gaining a better understanding of the biology of various species of cephalopods can significantly improve our knowledge of how these animals evolved and better identify the mechanisms that drive the astonishing faculties of their nervous systems. In this study, we performed single-cell transcriptomics of whole heads of Loligo vulgaris pre-hatchlings. We characterized the different cell types in the head of these animals and explored the expression patterns of core cell type markers by hybridization chain reaction. We were able to thoroughly describe some major components of the squid nervous that play important roles for the maintenance, development and sensory function in the nervous system of these animals.
Identification of a novel chalcone reductase gene for isoliquiritigenin biosynthesis in dahlia (Dahlia variabilis)
Authors: Ohno Sho , Yamada Haruka , Maruyama Kei , Deguchi Ayumi , Kato Yasunari , Yokota Mizuki , Tatsuzawa Fumi , Hosokawa Munetaka , Doi Motoaki 
Published: March 2022

AbstractButein is one of flavonoids conferring bright yellow flower color and is a precursor of aurone in some species. Butein is synthesized by two steps, 3-malonyl CoA and 4-coumaloyl CoA are converted to isoliquiritigenin in the first step, and then isoliquiritigenin is converted to butein in the second step. In the first step, chalcone synthase (CHS) and chalcone reductase (CHR) catalyze this reaction, however, CHR has been reported for the isoflavone biosynthesis pathway in legumes, and CHR for butein biosynthesis has not yet been isolated. In this study, we report CHR that is evolutionally different gene from legume species is involved in isoliquiritigenin biosynthesis in dahlia. To isolate CHR gene, we conducted comparative RNA-seq analysis between ‘Shukuhai’ and its butein-loss lateral mutant ‘Rinka’. We found DvCHR showed significant difference in expression levels that encodes an aldo-keto reductase (AKR) 13 family protein, which was phylogenetically different from legume CHRs belonging to AKR4A family. Gene expression levels and genotype of DvCHR were correlated with butein accumulation among various dahlia cultivars. Though single over expression of DvCHR was not able to accumulate isoliquiritigenin in tobacco, co-overexpression of DvCHR with a chalcone glucosyltransferase Am4′CGT and a MYB transcription factor CaMYBA successfully induced isoliquiritigenin accumulation. In addition, DvCHR homologous gene expression was detected from butein or aurone accumulating Coreopsideae species but not from non-butein or non-aurone accumulating Asteraceae species. These results indicated DvCHR functions as chalcone reductase for butein biosynthesis in dahlia, and isoliquiritigenin biosynthesis in Coreopsideae species has been developed independently from legume species.
High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD phenotypes in human lung fibroblasts
Authors: Schwartz Uwe , Prada Maria Llamazares , Pohl Stephanie T. , Richter Mandy , Tamas Raluca , Schuler Michael , Keller Corinna , Mijosek Vedrana , Muley Thomas , Schneider Marc A. , Quast Karsten , Hey Joschka , Heußel Claus P. , Warth Arne , Winter Hauke , Serçin Özdemirhan , Karmouty-Quintana Harry , Herth Felix , Koch Ina , Petrosino Giuseppe , Mardin Balca R. , Weichenhan Dieter , Jurkowski Tomasz P. , Imbusch Charles D. , Brors Benedikt , Benes Vladimir , Jung Brigit , Wyatt David , Stahl Heiko , Plass Christoph , Jurkowska Renata Z. 
Published: March 2022

AbstractPatients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering the environmental cause of COPD (e.g., cigarette smoke) and disease phenotypes, including stem-cell senescence and impaired differentiation, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. The epigenetic landscape is markedly changed in lung fibroblasts across COPD stages, with DNA methylation changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization. Notably, we identified epigenetic and transcriptional dysregulation already in mild COPD patients, providing unique insights into early disease. Integration of profiling data identified 110 candidate regulators of disease phenotypes, including epigenetic factors. Using phenotypic screens, we verified the regulator capacity of multiple candidates and linked them to repair processes in the human lung.Our study provides first integrative high-resolution epigenetic and transcriptomic maps of human lung fibroblasts across stages of COPD. We reveal novel transcriptomic and epigenetic signatures associated with COPD onset and progression and identify new candidate regulators involved in the pathogenesis of chronic respiratory diseases. The presence of various epigenetic factors among the candidates demonstrates that epigenetic regulation in COPD is an exciting research field that holds promise for novel therapeutic avenues for patients.
A widely applicable and cost-effective method for general and specific RNA-protein complex isolation
Authors: Balzarini Sam , Van Ende Roosje , Voet Arnout , Geuten Koen 
Published: March 2022

ABSTRACTDespite important methodological advances made in the past few years, a widely applicable, cost-effective and easily scalable procedure that can be routinely used to isolate ribonucleoprotein complexes (RNPs) remains elusive. We describe a versatile method that connects aspects of existing methods in a workflow optimized to reach the above goals and called it “Silica-based Acidic Phase Separation (SAPS)-capture”. To validate the method, the 18S rRNP of S. cerevisiae was captured. To illustrate its applicability, we isolated a repertoire of RNPs in A. thaliana. This procedure can provide the community with a powerful tool to advance the study of ribonomes and RNPs in any organism or tissue type.