bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are female-dominated occupations a secure option? Occupational gender segregation, accompanied occupational characteristics, and the risk of becoming unemployed
Authors: Bächmann Ann-Christin 
Published: November 2022

Abstract
In the German labour market, research hints towards a reversal in gender-specific risk of becoming unemployed: While women previously faced higher risk than men, in recent years, they have consistently lower risk. This paper analyses this reversal by focusing on the role of occupational gender segregation. I discuss theoretical differences in the labour supply and demand structure and thus in the unemployment risk of male- and female-dominated occupations caused by crowding and technological and sectoral change. Using the German National Educational Panel Study combined with occupation level data, I analyse the transition to unemployment over three decades. The results confirm gender-specific trends over time: While women faced higher risk of becoming unemployed in the 1980s, they face significantly lower risk than men in the 21st century. A Karlson-Holm-Breen decomposition shows that the lower risk of women in the newest decade under observation is mediated by the unequal distribution of men and women over the occupational structure. Yet, the higher risk of women in the 1980s cannot be traced back to differences in male- and female-dominated occupations. On the contrary, the results suggest that women were more likely to become unemployed in that decade independent of their occupation.
Improving prescribing: a feasibility study of pharmacogenetic testing with clinical decision support in primary healthcare in Singapore
Authors: Smith Helen , Dawes Martin , Katzov-Eckert Hagit , Burrell Sarah , Xin Hui Sam , Winther Michael D 
Published: November 2022

Abstract

Background
The study of genetic variation as a factor influencing drug safety, efficacy, and effectiveness has brought about significant breakthroughs in understanding the clinical application of gene–drug interactions to better manage drug therapy.

Objective
This study was designed to assess the feasibility of collecting buccal samples by general practitioners (GPs) at private practices in Singapore within a usual consultation, incorporating use of a pharmacogenetics-based medical decision support system to guide subsequent drug dosing.

Methods
We used a prospective cohort study design, with GPs recruiting 189 patients between October 2020 and March 2021. The genotypes of 51 biallelic SNPs were determined using Illumina Infinium Global Screening Array.

Results
Seven GPs from 6 private practices recruited and obtained buccal samples from a total of 189 patients. All patients had at least one actionable variant. The prevalence of patients having 2, 3, or 4 variants was 37.0%, 32.8%, and 12.7%, respectively. Potential alterations to medications were identified using the Clinical Decision Support System. Patients were accepting and the GPs were enthusiastic about the potential of pharmacogenetics to personalize medicine for their patients.

Conclusion
This is the first study in Singapore to demonstrate the feasibility of pharmacogenetic testing in primary care. The high prevalence of genetic variants underscores the potential use of pharmacogenetics in this setting.
Association of Endothelial Protein C Receptor (EPCR) rs867186 Gene Polymorphism With Increased Levels of Soluble EPCR and High Risk of Severe Malaria and Fatality in Beninese Children
Authors: Blankson Samuel Odarkwei , Dikroh Liliane , Tettey Patrick , Tornyigah Bernard , Adamou Rafiou , Moussiliou Azizath , Alao Maroufou J , Amoussou Annick , Padounou Caroline , Milet Jacqueline , Mensah Benedicta Ayiedu , Aniweh Yaw , Ndam Nicaise Tuikue , Roussilhon Christian , Tahar Rachida 
Published: November 2022

Abstract
The endothelial protein C receptor (EPCR)–rs867186 G allele has been linked to high plasma levels of soluble EPCR (sEPCR) and controversially associated with either susceptibility or resistance to severe and cerebral malaria. In this study, quantitative enzyme-linked immunosorbent assay and sequencing were used to assess sEPCR levels and EPCR-rs867186 polymorphism in blood samples from Beninese children with different clinical presentations of malaria. Our findings show that sEPCR levels were higher at hospital admission than during convalescence and that EPCR-rs867186 G allele was associated with increased sEPCR plasma levels, malaria severity, and mortality rate (P &lt; .001, P = .03, and P = .04, respectively), suggesting a role of sEPCR in the pathogenesis of severe malaria.
Behavior Change in Water, Sanitation, and Hygiene: A 100-Year Perspective
Authors: Venis Robbie A 
Published: November 2022

AbstractThe current methodological paradigm for addressing water, sanitation, and hygiene (WaSH) inaccessibility in rural sub-Saharan Africa is achieving insufficient progress. This essay evaluates WaSH-related policy, programming, and discourse from 1918 to 2021 to identify how this paradigm evolved and how it may reform. I argue that political–economic environments have strongly influenced existing sectoral praxis, shaping both programmatic methods and means. Colonial occupations generated rural–urban material inequalities, which were maintained and exacerbated during postwar reconstruction (1950–1970) and the proliferation of neoliberalism (1970–1990s). Meanwhile, modernization theory, a fundamental feature of colonial thought, has persisted discursively and practically. That is, rural resource limitations led WaSH practitioners to promote lower-cost appropriate technologies in the 1980s. Then, with challenges regarding technological disuse and misuse, behavior change–oriented methodologies responsively emerged in the 2000s and continue today. Yet, much like colonial predecessors, this latter turn presupposes that its programmatic benefactors must adapt to access WaSH services. Behavior change programs thus fail to critically consider the role of technological inadequacies and associated risk exposures in perpetuating existing inequities. Investigation of utility-style service models, where WaSH services adapt to the lives of its benefactors and behavioral persuasion is substituted for nonuser technological management, is recommended.
Automated deidentification of radiology reports combining transformer and “hide in plain sight” rule-based methods
Authors: Chambon Pierre J , Wu Christopher , Steinkamp Jackson M , Adleberg Jason , Cook Tessa S , Langlotz Curtis P 
Published: November 2022

Abstract

Objective
To develop an automated deidentification pipeline for radiology reports that detect protected health information (PHI) entities and replaces them with realistic surrogates “hiding in plain sight.”

Materials and Methods
In this retrospective study, 999 chest X-ray and CT reports collected between November 2019 and November 2020 were annotated for PHI at the token level and combined with 3001 X-rays and 2193 medical notes previously labeled, forming a large multi-institutional and cross-domain dataset of 6193 documents. Two radiology test sets, from a known and a new institution, as well as i2b2 2006 and 2014 test sets, served as an evaluation set to estimate model performance and to compare it with previously released deidentification tools. Several PHI detection models were developed based on different training datasets, fine-tuning approaches and data augmentation techniques, and a synthetic PHI generation algorithm. These models were compared using metrics such as precision, recall and F1 score, as well as paired samples Wilcoxon tests.

Results
Our best PHI detection model achieves 97.9 F1 score on radiology reports from a known institution, 99.6 from a new institution, 99.5 on i2b2 2006, and 98.9 on i2b2 2014. On reports from a known institution, it achieves 99.1 recall of detecting the core of each PHI span.

Discussion
Our model outperforms all deidentifiers it was compared to on all test sets as well as human labelers on i2b2 2014 data. It enables accurate and automatic deidentification of radiology reports.

Conclusions
A transformer-based deidentification pipeline can achieve state-of-the-art performance for deidentifying radiology reports and other medical documents.
China-MENA Energy Cooperation under the Belt and Road Initiative: Megaprojects, Economic Planning, and a Pragmatic Approach to the ‘Green’ Transition
Authors: Zoppolato Davide Giacomo , Jiang Shisong 
Published: November 2022

Abstract
Cooperation between China and the Middle East and North Africa (MENA) in the energy field reached a new impetus with the launch of the Belt and Road Initiative (BRI). Specific cooperation plans and strategies have been implemented both at the regional and bilateral levels to strengthen the cooperation in this area between the two blocks. Despite this progress, crucial questions remain unanswered regarding the approaches, characteristics and rationale behind the green transition in the MENA context. This article focuses on the cooperation between five North African countries—Morocco, Algeria, Tunisia, Libya and Egypt—and China under the BRI. It highlights how the initiative mobilizes funding and expertise urgently needed for developing and deploying clean technologies in North Africa. China’s ‘pragmatic’ approach to energy could speed up the transition in the region, but only if appropriate manufacturing capacities and a solid industrial base are developed in parallel with the deployment of renewables. We argue that an advancement in the cooperation between China and MENA could facilitate the achievement of Sustainable Development Goal 7: ‘Ensure access to affordable, reliable, sustainable and modern energy for all’.
Functions and mechanisms of RNA helicases in plants
Authors: Li Xindi , Li Changhao , Zhu Jiaying , Zhong Songxiao , Zhu Hongliang , Zhang Xiuren 
Published: November 2022

AbstractRNA helicases (RHs) are a family of ubiquitous enzymes that alter RNA structures and remodel ribonucleoprotein complexes typically using energy from the hydrolysis of ATP. RHs are involved in various aspects of RNA processing and metabolism, exemplified by transcriptional regulation, pre-mRNA splicing, miRNA biogenesis, liquid–liquid phase separation, and rRNA biogenesis, among other molecular processes. Through these mechanisms, RHs contribute to vegetative and reproductive growth, as well as abiotic and biotic stress responses throughout the life cycle in plants. In this review, we systematically characterize RH-featured domains and signature motifs in Arabidopsis. We also summarize the functions and mechanisms of RHs in various biological processes in plants with a focus on DEAD-box and DEAH-box RNA helicases, aiming to present the latest understanding of RHs in plant biology.
MeerKAT follow-up of enigmatic GLEAM 4-Jy (G4Jy) sources
Authors: Sejake Precious K , White Sarah V , Heywood Ian , Thorat Kshitij , Bester Hertzog L , Makhathini Sphesihle , Fanaroff Bernie 
Published: November 2022

ABSTRACT
We present the results from studying 140 radio sources in the GLEAM (GaLactic and Extragalactic All-sky MWA [Murchison Widefield Array]) 4-Jy (G4Jy) Sample. These sources were followed-up with MeerKAT to assess their radio morphology and enable host-galaxy identification, as existing radio images of 25 to 45-arcsec resolution do not provide sufficient information. We refer to these sources as the MeerKAT-2019 subset. The aim is to identify the host galaxy of these sources by visually inspecting the overlays comprising radio data from four surveys (at 150, 200, 843/1400, and 1300 MHz). Our morphological classification and host-galaxy identification relies upon the ∼7-arcsec resolution images from MeerKAT (1300 MHz). Through the visual inspection of the overlays, 14 radio sources in the MeerKAT-2019 subset have wide-angle tail morphology, 10 are head-tail, and 5 have X-, S-/Z-shaped morphology. Most of the remaining sources have the radio morphology of typical symmetric lobes. Of 140 sources, we find host galaxies for 98 sources, leaving 42 with no identified host galaxy. These 42 sources still have ambiguous identification even with higher resolution images from MeerKAT.
Hepatic veno-occlusive disease accompanied by thrombotic microangiopathy developed during treatment of juvenile dermatomyositis and macrophage activation syndrome: A case report
Authors: Mouri Mariko , Kanamori Toru , Tanaka Eriko , Hiratoko Kanako , Okubo Mariko , Inoue Michio , Morio Tomohiro , Shimizu Masaki , Nishino Ichizo , Okiyama Naoko , Mori Masaaki 
Published: November 2022

ABSTRACT
Hepatic veno-occlusive disease (VOD) is a complication of haematopoietic stem cell transplantation. VOD is associated with the occurrence of thrombotic microangiopathy (TMA). In haematopoietic stem cell transplantation, VOD and TMA are endothelial syndromes resulting from endothelial cell activation and dysfunction. In rheumatic disease, while TMA is not rare, there are few reports of VOD. In idiopathic myositis, only one case with VOD and TMA complications has been reported, and there are no published cases in juvenile dermatomyositis (JDM). We report a case of JDM manifesting VOD and TMA complications during the treatment for myositis and macrophage activation syndrome (MAS). A 5-year-old boy diagnosed as anti-nuclear matrix protein 2 antibody–positive JDM was complicated by MAS. He received pulsed methylprednisolone, prednisolone, and tacrolimus, but JDM and MAS progressed. He was then treated with intravenous cyclophosphamide and cyclosporine A, with improvement in myositis symptoms and MAS. After initiation of cyclophosphamide and cyclosporine A, he developed haemolysis, painful hepatomegaly, liver damage, and ascites. He was diagnosed with VOD and TMA. Cyclophosphamide and cyclosporine A were discontinued, with recovery from VOD and TMA. The patient remained well on treatment with methotrexate, without any relapse of JDM and MAS to date. The presence of vasculopathy and hypercytokinaemia because of JDM and MAS exacerbated endothelial cell damage. In the present case, we suggest that the main cause of VOD was medication with CY and CsA, which had been used to treat acute exacerbation of MAS and JDM.
A rare presentation of antisynthetase syndrome requiring intensive care in the midst of a COVID wave
Authors: Arya Akhila , Anand Sanu , Kumar Sandesh , Britto Carl 
Published: November 2022

ABSTRACT
A 24-year-old female with pneumonia two months prior presented with fever, cough, and worsening dyspnoea in the midst of a COVID-19 spike. Her initial episode was treated as COVID-19 pneumonia. On presentation, her chest computed tomography was suggestive of bilateral lower zone organising pneumonia with mild fibrosis and was attributed to post-COVID sequelae with an infective exacerbation. Oral steroids and antibiotics were administered, following which she had initial improvement and then subsequent deterioration requiring intensive care unit (ICU) care. A detailed clinical examination (in-person and virtually) at this point revealed the presence of pigmented rashes over the knuckles and weakness of hip muscles. Laboratory work showed elevated creatine kinase levels and positive anti-Ro and anti-Jo1 antibodies, which pointed to a diagnosis of antisynthetase syndrome. Unique attributes of this case include younger age of presentation in an atypical ethnic group, which are possibly incited by COVID-19 infection in the peak of a COVID-19 wave. The work-up, diagnosis, and initial management of this patient were carried out through a hybrid ICU model, which functioned as a traditional ICU in the day and a tele-ICU at night with an appropriate network of subspecialists including rheumatologists consulting, thus highlighting a collaborative model in a low-resource setting capable of managing rare cases even in the midst of increasing critical care needs during the pandemic.
GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets
Authors: Guo Shipeng , Xu Zhougeng , Dong Xiangjun , Hu Dongjie , Jiang Yanshuang , Wang Qunxian , Zhang Jie , Zhou Qian , Liu Shengchun , Song Weihong 
Published: November 2022

Abstract
Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.
ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design
Authors: Tao Xavier B , LaFrance Sarah , Xing Yifei , Nava Alberto A , Martin Hector Garcia , Keasling Jay D , Backman Tyler W H 
Published: November 2022

Abstract
Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical ‘starters’ and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.
Stem Cell Basis of Shoot Branching
Authors: Yang Tingting , Jiao Yuling , Wang Ying 
Published: November 2022

AbstractDuring their postembryonic development, plants continuously form branches to conquer more space and adapt to changing environments. In seed plants, this is achieved by lateral branching, in which axillary meristems (AMs) initiate at the leaf axils to form axillary buds. The developmental potential of AMs to form shoot branches is the same as that of embryonic shoot apical meristems (SAMs). Recent studies in Arabidopsis thaliana have revealed the cellular origin of AMs and have identified transcription factors and phytohormones that regulate sequential steps leading to AM initiation. In particular, a group of meristematic cells detached from the SAM are key to AM initiation, which constitutes an excellent system for understanding stem cell fate and de novo meristem formation.
Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation
Authors: Gao Zhiyan , Yang Xingyu , Chen Jinming , Rausher Mark D , Shi Tao 
Published: November 2022

AbstractBoth cis- and trans-regulatory mutations drive changes in gene expression that underpin plant phenotypic evolution. However, how and why these two major types of regulatory mutations arise in different genes and how gene expression is inherited and associated with these regulatory changes are unclear. Here, by studying allele-specific expression in F1 hybrids of pink-flowered sacred lotus (Nelumbo nucifera) and yellow-flowered American lotus (N. lutea), we reveal the relative contributions of cis- and trans-regulatory changes to interspecific expression rewiring underlying petal color change and how the expression is inherited in hybrids. Although cis-only variants influenced slightly more genes, trans-only variants had a stronger impact on expression differences between species. In F1 hybrids, genes under cis-only and trans-only regulatory effects showed a propensity toward additive and dominant inheritance, respectively, whereas transgressive inheritance was observed in genes carrying both cis- and trans-variants acting in opposite directions. By investigating anthocyanin and carotenoid coexpression networks in petals, we found that the same category of regulatory mutations, particularly trans-variants, tend to rewire hub genes in coexpression modules underpinning flower color differentiation between species; we identified 45 known genes with cis- and trans-regulatory variants significantly correlated with flower coloration, such as ANTHOCYANIN 5-AROMATIC ACYLTRANSFERASE (ACT), GLUTATHIONE S-TRANSFERASE F11 (GSTF11), and LYCOPENE Ε-CYCLASE (LCYE). Notably, the relative abundance of genes in different categories of regulatory divergence was associated with the inferred magnitude of constraints like expression level and breadth. Overall, our study suggests distinct selective constraints and modes of gene expression inheritance among different regulatory mutations underlying lotus petal color divergence.
Immunophilin CYN28 is required for accumulation of photosystem II and thylakoid FtsH protease in Chlamydomonas
Authors: Fu Weihan , Cui Zheng , Guo Jia , Cui Xiayu , Han Guomao , Zhu Yunpeng , Hu Jinju , Gao Xiaoling , Li Yeqing , Xu Min , Fu Aigen , Wang Fei 
Published: November 2022

Abstract
Excess light causes severe photodamage to photosystem II (PSII) where the primary charge separation for electron transfer takes place. Dissection of mechanisms underlying the PSII maintenance and repair cycle in green algae promotes the usage of genetic engineering and synthetic biology to improve photosynthesis and biomass production. In this study, we systematically analyzed the high light (HL) responsive immunophilin genes in Chlamydomonas (Chlamydomonas reinhardtii) and identified one chloroplast lumen-localized immunophilin, CYN28, as an essential player in HL tolerance. Lack of CYN28 caused HL hypersensitivity, severely reduced accumulation of PSII supercomplexes and compromised PSII repair in cyn28. The thylakoid FtsH (filamentation temperature-sensitive H) is an essential AAA family metalloprotease involved in the degradation of photodamaged D1 during the PSII repair cycle and was identified as one potential target of CYN28. In the cyn28 mutant, the thylakoid FtsH undergoes inefficient turnover under HL conditions. The CYN28-FtsH1/2 interaction relies on the FtsH N-terminal proline residues and is strengthened particularly under HL. Further analyses demonstrated CYN28 displays peptidyl–prolyl isomerase (PPIase) activity, which is necessary for its physiological function. Taken together, we propose that immunophilin CYN28 participates in PSII maintenance and regulates the homeostasis of FtsH under HL stress via its PPIase activity.