bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building trust in research through information and intent transparency with health information: representative cross-sectional survey of 502 US adults
Authors: Mangal Sabrina , Park Leslie , Reading Turchioe Meghan , Choi Jacky , Niño de Rivera Stephanie , Myers Annie , Goyal Parag , Dugdale Lydia , Masterson Creber Ruth 
Published: June 2022

Abstract

Objective
Participation in healthcare research shapes health policy and practice; however, low trust is a barrier to participation. We evaluated whether returning health information (information transparency) and disclosing intent of data use (intent transparency) impacts trust in research.

Materials and Methods
We conducted an online survey with a representative sample of 502 US adults. We assessed baseline trust and change in trust using 6 use cases representing the Social-Ecological Model. We assessed descriptive statistics and associations between trust and sociodemographic variables using logistic and multinomial regression.

Results
Most participants (84%) want their health research information returned. Black/African American participants were more likely to increase trust in research with individual information transparency (odds ratio (OR) 2.06 [95% confidence interval (CI): 1.06–4.34]) and with intent transparency when sharing with chosen friends and family (3.66 [1.98–6.77]), doctors and nurses (1.96 [1.10–3.65]), or health tech companies (1.87 [1.02–3.40]). Asian, Native American or Alaska Native, Native Hawaiian or Pacific Islander, Multirace, and individuals with a race not listed, were more likely to increase trust when sharing with health policy makers (1.88 [1.09–3.30]). Women were less likely to increase trust when sharing with friends and family (0.55 [0.35–0.87]) or health tech companies (0.46 [0.31–0.70]).

Discussion
Participants wanted their health information returned and would increase their trust in research with transparency when sharing health information.

Conclusion
Trust in research is influenced by interrelated factors. Future research should recruit diverse samples with lower baseline trust levels to explore changes in trust, with variation on the type of information shared.
Interlocking joint shape optimization for structurally informed design of block assemblages
Authors: Mousavian Elham , Bagi Katalin , Casapulla Claudia 
Published: June 2022

AbstractThis paper presents a computer aided design tool that analyses the structural feasibility of interlocking assemblages with orthotropic sliding resistance and automatically adjusts the assemblage shape to remove the infeasibility. First, the static problem of limit analysis is extended to the corrugated interfaces. To model different bond patterns and openings, an assemblage is abstracted to different types of joints representing the dry joints between the blocks, joints inside the blocks, and the excluded joints where the openings are located. This problem is then reformulated to measure the structural infeasibility due to the sliding constraint violation. The so-called sliding infeasibility measure shows how far an infeasible model is to become feasible. This problem is used as the objective function of a shape optimization algorithm that minimizes the sliding infeasibility measure through automated change of the interlocking joints, by which the model becomes structurally feasible. The optimization is validated using the discrete element analysis.
Sebaceous carcinoma of trunk with bilateral axillary lymph node metastasis: a rare presentation of malignant adnexal tumor in young adult
Authors: Jaiswal Lokesh Shekher , Neupane Durga , Lageju Nimesh , Khadka Sarada , Sah Bijay , Pradhan Anju 
Published: June 2022

Abstract
Malignant adnexal tumors of skin are rare. Sebaceous carcinoma—a rare and aggressive cutaneous tumor—is frequently located in the periorbital region. Malignant adnexal tumors of sebaceous carcinoma type on trunk with axillary lymph node and distant metastasis in young adult is rare. The incidence of extraocular sebaceous carcinoma has been expected to be 0.06 per 100 000 person-years with an increased incidence in elderly patients and men. With a note of mimicking benign dermatologic conditions, definitive diagnosis of sebaceous carcinomas is often hindered, increasing morbidity and mortality for patients. Herein, we present a case of a 35-year-old man with a large ulcero-proliferating lesion of trunk region previously resected for a small swelling and eventually presented with the recurrent lesion and diagnosed as sebaceous carcinoma of trunk with bilateral axillary lymphnode and distant bone metastasis demonstrating several diagnostic and management challenges.
Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses
Authors: Zhang Chuanyi , Sashittal Palash , Xiang Michael , Zhang Yichi , Kazi Ayesha , El-Kebir Mohammed 
Published: June 2022

Abstract
Transcription regulatory sequences (TRSs), which occur upstream of structural and accessory genes as well as the 5′ end of a coronavirus genome, play a critical role in discontinuous transcription in coronaviruses. We introduce two problems collectively aimed at identifying these regulatory sequences as well as their associated genes. First, we formulate the TRS Identification problem of identifying TRS sites in a coronavirus genome sequence with prescribed gene locations. We introduce CORSID-A, an algorithm that solves this problem to optimality in polynomial time. We demonstrate that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses. Second, we demonstrate for the first time how TRS sites can be leveraged to identify gene locations in the coronavirus genome. To that end, we formulate the TRS and Gene Identification problem of simultaneously identifying TRS sites and gene locations in unannotated coronavirus genomes. We introduce CORSID to solve this problem, which includes a web-based visualization tool to explore the space of near-optimal solutions. We show that CORSID outperforms state-of-the-art gene finding methods in coronavirus genomes. Furthermore, we demonstrate that CORSID enables de novo identification of TRS sites and genes in previously unannotated coronavirus genomes. CORSID is the first method to perform accurate and simultaneous identification of TRS sites and genes in coronavirus genomes without the use of any prior information.
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp
Authors: Takada Hiraku , Mandell Zachary F , Yakhnin Helen , Glazyrina Anastasiya , Chiba Shinobu , Kurata Tatsuaki , Wu Kelvin J Y , Tresco Ben I C , Myers Andrew G , Aktinson Gemma C , Babitzke Paul , Hauryliuk Vasili 
Published: June 2022

Abstract
Since antibiotic resistance is often associated with a fitness cost, bacteria employ multi-layered regulatory mechanisms to ensure that expression of resistance factors is restricted to times of antibiotic challenge. In Bacillus subtilis, the chromosomally-encoded ABCF ATPase VmlR confers resistance to pleuromutilin, lincosamide and type A streptogramin translation inhibitors. Here we show that vmlR expression is regulated by translation attenuation and transcription attenuation mechanisms. Antibiotic-induced ribosome stalling during translation of an upstream open reading frame in the vmlR leader region prevents formation of an anti-antiterminator structure, leading to the formation of an antiterminator structure that prevents intrinsic termination. Thus, transcription in the presence of antibiotic induces vmlR expression. We also show that NusG-dependent RNA polymerase pausing in the vmlR leader prevents leaky expression in the absence of antibiotic. Furthermore, we demonstrate that induction of VmlR expression by compromised protein synthesis does not require the ability of VmlR to rescue the translational defect, as exemplified by constitutive induction of VmlR by ribosome assembly defects. Rather, the specificity of induction is determined by the antibiotic's ability to stall the ribosome on the regulatory open reading frame located within the vmlR leader. Finally, we demonstrate the involvement of (p)ppGpp-mediated signalling in antibiotic-induced VmlR expression.
The Drosophila hnRNP F/H homolog Glorund recruits dFMRP to inhibit nanos translation elongation
Authors: Peng Yingshi , Gavis Elizabeth R 
Published: June 2022

Abstract
Translational control of maternal mRNAs generates spatial and temporal patterns of protein expression necessary to begin animal development. Translational repression of unlocalized nanos (nos) mRNA in late-stage Drosophila oocytes by the hnRNP F/H homolog, Glorund (Glo), is important for embryonic body patterning. While previous work has suggested that repression occurs at both the translation initiation and elongation phases, the molecular mechanism by which Glo regulates nos translation remains elusive. Here, we have identified the Drosophila fragile X mental retardation protein, dFMRP, as a Glo interaction partner with links to the translational machinery. Using an oocyte-based in vitro translation system, we confirmed that Glo regulates both initiation and elongation of a nos translational reporter and showed that dFMRP specifically represses translation elongation and promotes ribosome stalling. Furthermore, we combined mutational analysis and in vivo and in vitro binding assays to show that Glo's qRRM2 domain specifically and directly interacts with dFMRP. Our findings suggest that Glo regulates nos translation elongation by recruiting dFMRP and that Glo's RNA-binding domains can also function as protein-protein interaction interfaces critical for its regulatory functions. Additionally, they reveal a mechanism for targeting dFMRP to specific transcripts.
Structural variation and parallel evolution of apomixis in citrus during domestication and diversification
Authors: Wang Nan , Song Xietian , Ye Junli , Zhang Siqi , Cao Zhen , Zhu Chenqiao , Hu Jianbing , Zhou Yin , Huang Yue , Cao Shuo , Liu Zhongjie , Wu Xiaomeng , Chai Lijun , Guo Wenwu , Xu Qiang , Gaut Brandon S , Koltunow Anna M G , Zhou Yongfeng , Deng Xiuxin 
Published: June 2022

Abstract
Apomixis, or asexual seed formation, is prevalent in Citrinae via a mechanism termed nucellar or adventitious embryony. Here, multiple embryos of a maternal genotype form directly from nucellar cells in the ovule and can outcompete the developing zygotic embryo as they utilize the sexually derived endosperm for growth. Whilst nucellar embryony enables the propagation of clonal plants of maternal genetic constitution, it is also a barrier to effective breeding through hybridization. To address the genetics and evolution of apomixis in Citrinae, a chromosome-level genome of the Hongkong kumquat (Fortunella hindsii) was assembled following a genome-wide variation map including structural variants (SVs) based on 234 Citrinae accessions. This map revealed that hybrid citrus cultivars shelter genome-wide deleterious mutations and SVs into heterozygous states free from recessive selection, which may explain the capability of nucellar embryony in most cultivars during Citrinae diversification. Analyses revealed that parallel evolution may explain the repeated origin of apomixis in different genera of Citrinae. Within Fortunella, we found that apomixis of some varieties originated via introgression. In apomictic Fortunella, the locus associated with apomixis contains the FhRWP gene, encoding an RWP-RK domain-containing protein previously shown to be required for nucellar embryogenesis in Citrus. We found the heterozygous SV in the FhRWP and CitRWP promoters from apomictic Citrus and Fortunella, due to either two or three miniature inverted transposon element (MITE) insertions. A transcription factor, FhARID, encoding an AT-rich interaction domain-containing protein binds to the MITEs in the promoter of apomictic varieties, which facilitates induction of nucellar embryogenesis. This study provides evolutionary genomic and molecular insights into apomixis in Citrinae and has potential ramifications for citrus breeding.
Anxieties of the Dominant: Legal, Social, and Religious in the Politics of Religious Conversion in India
Authors: Kumar Mukesh , Yadav Garima 
Published: June 2022

Abstract
The promulgation of the new state-level conversion laws in India or some changes in already existing ones by ordinances is premised upon various conspiracy theories of Hindu fundamentalists against Muslims. Implicit in and placed at the centre of these new anti-conversion laws and public debates thereof is the conspiracy theory of love-jihad that Muslim men lure Hindu women on the pretext of love and get them convert to Islam to eventually outnumber the Hindu majority. This article argues that the anti-conversion laws in India result from anxieties of the dominant caste and class regarding gender and caste, leading to the imposition of the mainstream orthodox religious and political will upon the marginalized. The creation of anti-conversion laws is based on assumptions, fears, conspiracy theories, and moral and religious values primarily shared by the ‘upper-caste’ section across the political spectrum. Furthermore, it also shows a growing nexus between conservative religious forces and state apparatuses that restricts religious and social mobility of the marginalized sections through legal changes.
GREEN FLUORESCENT PROTEIN variants with enhanced folding are more efficiently imported into chloroplasts
Authors: Jeong Jinseung , Moon Byeongho , Hwang Inhwan , Lee Dong Wook 
Published: June 2022

Abstract
Chloroplasts and mitochondria are subcellular organelles that evolved from cyanobacteria and α-proteobacteria, respectively. Although they have their own genomes, the majority of their proteins are encoded by nuclear genes, translated by cytosolic ribosomes, and imported via outer and inner membrane translocon complexes. The unfolding of mature regions of proteins is thought to be a prerequisite for the import of the proteins into these organelles. However, it is not fully understood how protein folding properties affect their import into these organelles. In this study, we examined the import behavior of chloroplast and mitochondrial reporters with normal green fluorescent protein (GFP) and two GFP variants with enhanced folding propensity, superfolder GFP (sfGFP) and extra-superfolder GFP (esGFP), which is folded better than sfGFP. sfGFP and esGFP were less dependent on the sequence motifs of the transit peptide (TP) and import machinery during protein import into Arabidopsis (Arabidopsis thaliana) chloroplasts, compared with normal GFP. sfGFP and esGFP were efficiently imported into chloroplasts by a mutant TP with an alanine substitution in the N-terminal MLM motif, whereas the same mutant TP showed a defect in importing normal GFP into chloroplasts. Moreover, sfGFP and esGFP were efficiently imported into plastid protein import 2 (ppi2) and heat shock protein 93-V (hsp93-V) plants, which have mutations in atToc159 and Hsp93-V, respectively. In contrast, the presequence-mediated mitochondrial import of sfGFP and esGFP was severely impaired. Based on these results, we propose that the chloroplast import machinery is more tolerant to different folding states of preproteins, whereas the mitochondrial machinery is more specialized in the translocation of unfolded preproteins.
Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota
Authors: Sadiq Sabrina , Chen Yan-Mei , Zhang Yong-Zhen , Holmes Edward C 
Published: June 2022

Abstract
The RNA virus phylum Lenarviricota is composed of the fungi-associated families Narnaviridae and Mitoviridae, the RNA bacteriophage Leviviridae, and the plant and fungi-associated Botourmiaviridae. Members of the Lenarviricota are abundant in most environments and boast remarkable phylogenetic and genomic diversity. As this phylum includes both RNA bacteriophage and fungi- and plant-associated species, the Lenarviricota likely mark a major evolutionary transition between those RNA viruses associated with prokaryotes and eukaryotes. Despite the remarkable expansion of this phylum following metagenomic studies, the phylogenetic relationships among the families within the Lenarviricota remain uncertain. Utilising a large data set of relevant viral sequences, we performed phylogenetic and genomic analyses to resolve the complex evolutionary history within this phylum and identify patterns in the evolution of virus genome organisation. Despite limitations reflecting very high levels of sequence diversity, our phylogenetic analyses suggest that the Leviviridae comprise the basal lineage within the Lenarviricota. Our phylogenetic results also support the construction of a new virus family—the Narliviridae—comprising a set of diverse and phylogenetically distinct species, including a number of uniquely encapsidated viruses. We propose a taxonomic restructuring within the Lenarviricota to better reflect the phylogenetic relationships documented here, with the Botourmiaviridae and Narliviridae combined into the order Ourlivirales, the Narnaviridae remaining in the order Wolframvirales, and these orders combined into the single class, the Amabiliviricetes. In sum, this study provides insights into the complex evolutionary relationships among the diverse families that make up the Lenarviricota.
PREDICTIVE PERFORMANCE OF MACHINE LEARNING MODELS FOR DETECTION OF INCIDENT HEART FAILURE USING MULTI-CENTRE DATA
Authors: Sabovcik Frantisek , Ntalianis Evangelos , Cauwenberghs Nicholas , Kuznetsova Tatiana 
Published: June 2022

Objective:
To mitigate the health and economic burden associated with heart failure (HF), primary prevention is of utmost importance. To effectively address the diverse range of individual health profiles, prediction models must be trained and validated on a wide range of population-based cohorts. We evaluated the predictive performance of Survival Gradient Boosting (SGB) and Coxnet (CN) for the detection of incident HF. In addition, we compared the models’ performance trained only on a single-centre cohort with those trained on diverse multi-centre cohorts.

Design and method:
We utilized 6 cohorts from the Heart ‘omics’ in AGEing (HOMAGE) project to evaluate two computational approaches. The dataset consists of 31,382 individuals (mean age 66 ± 10 years old), free of HF at the baseline. During a median follow-up of 5.36 years, 1,130 non-fatal HF events occurred. SGB is a non-linear machine learning method based on training regression trees with the objective of optimizing Cox partial likelihood. Coxnet is a standard linear Cox proportional hazard model, regularized by both L1 and L2 norms. To estimate the predictive accuracy of a single-centre model on a specific test cohort, we averaged the performance of single models trained on remaining cohorts one at a time. To develop models in multi-centre settings, we used 5 cohorts in every iteration as a training set and the remaining 1 cohort as a test set. We used 33 features, including clinical, ECG, and biochemical data.

Results:
Overall, multi-centre models achieved a higher c-index than those trained on single cohorts (Figure). For example, in the FLEMENGHO cohort, multi-centre SGB achieved 0.819, while only 0.664 in a single-centre setting. Additionally, non-linear SGB achieved a considerably higher c-index than linear CN in all but one cohort, especially in multi-centre settings, for example in the HVC cohort (SGB 0.689, CN 0.614).

Conclusions:
With a greater number and variety of training cohorts, the model learns a wider range of specific individual health characteristics. Flexible machine learning algorithms such as gradient boosting can be used to capture these diverse distributions and produce more precise, personalized models for the prediction of adverse events.
TIME SERIES CLUSTERING OF LEFT ATRIAL STRAIN CURVES FOR RISK STRATIFICATION IN THE GENERAL POPULATION
Authors: Ntalianis Evangelos , Sabovcik Frantisek , Daels Yne , Couwenberghs Nicholas , Kuznetsova Tatiana 
Published: June 2022

Objective:
Currently, only the peak reservoir left atrial (LA) strain has been in use while a huge amount of useful information during different phases of cardiac cycle has been ignored. In this study, therefore, we tested the hypothesis that an unsupervised time series analysis utilizing the whole LA deformation curves will identify distinct clusters associated to risk factors and improve cardiovascular (CV) risk prediction over the traditionally used covariables in the general population.

Design and method:
We prospectively studied 929 community-dwelling individuals (mean age, 51.6 years; 52.9% women), in whom we acquired clinical and echocardiographic data including LA strain traces at baseline and collected cardiac events on average 7.2 years later. We employed two unsupervised time series techniques such as Self-Organizing map and Variational Autoencoder with Convolutional Neural Network as building block to cluster spatiotemporal patterns of LA strain curves. Clinical characteristics and cardiac outcome were used to evaluate the validity of the clusters (k).

Results:
According to the quantization error value for every k, the optimal number of clusters was 5 for applied methods. Overall, both methods agreed with respect to cluster assignment. Figure (left panel) presents centroid LA strain curves which represent each cluster. The first three clusters had differences in sex distribution and heart rate, but had similar low CV risk profiles. On the other hand, cluster 5 had the worst CV risk factors combination, and higher prevalence of left ventricular remodelling and diastolic dysfunction (ie, lowest e’ velocity and highest E/e’) compared to other clusters. We also observed an increase in the risk for incidence of adverse events between cluster 5 and other clusters (Figure, right panel). After adjustment for traditional risk factors, cluster 5 had the highest risk of cardiac events as compared to cluster 1, 2 and 3 (HR: 1.34; 95%CI: 1.05–1.73); P = 0.020).

Conclusions:
Unsupervised Machine/Deep Learning algorithms employed on time series LA strain curves identifies clinically meaningful clusters of LA deformation, and provides incremental prognostic information over traditional risk stratification.