bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model
Authors: Song Yidong , Yuan Qianmu , Chen Sheng , Chen Ken , Zhou Yaoqi , Yang Yuedong 
Published: May 2023

Abstract
Determining intrinsically disordered regions of proteins is essential for elucidating protein biological functions and the mechanisms of their associated diseases. As the gap between the number of experimentally determined protein structures and the number of protein sequences continues to grow exponentially, there is a need for developing an accurate and computationally efficient disorder predictor. However, current single-sequence-based methods are of low accuracy, while evolutionary profile-based methods are computationally intensive. Here, we proposed a fast and accurate protein disorder predictor LMDisorder that employed embedding generated by unsupervised pretrained language models as features. We showed that LMDisorder performs best in all single-sequence-based methods and is comparable or better than another language-model-based technique in four independent test sets, respectively. Furthermore, LMDisorder showed equivalent or even better performance than the state-of-the-art profile-based technique SPOT-Disorder2. In addition, the high computation efficiency of LMDisorder enabled proteome-scale analysis of human, showing that proteins with high predicted disorder content were associated with specific biological functions. The datasets, the source codes, and the trained model are available at https://github.com/biomed-AI/LMDisorder.
LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data
Authors: Chen Chia-Yu , Lӧber Ulrike , Forslund Sofia K 
Published: May 2023

Abstract

Summary
We introduce LongDat, an R package that analyzes longitudinal multivariable (cohort) data while simultaneously accounting for a potentially large number of covariates. The primary use case is to differentiate direct from indirect effects of an intervention (or treatment) and to identify covariates (potential mechanistic intermediates) in longitudinal data. LongDat focuses on analyzing longitudinal microbiome data, but its usage can be expanded to other data types, such as binary, categorical, and continuous data. We tested and compared LongDat with other tools (i.e., MaAsLin2, ANCOM, lgpr, and ZIBR) on both simulated and real data. We showed that LongDat outperformed these tools in accuracy, runtime, and memory cost, especially when there were multiple covariates. The results indicate that the LongDat R package is a computationally efficient and low-memory-cost tool for longitudinal data with multiple covariates and facilitates robust biomarker searches in high-dimensional datasets.

Availability and Implementation
The R package LongDat is available on CRAN (https://cran.r-project.org/web/packages/LongDat/) and GitHub (https://github.com/CCY-dev/LongDat).

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
The Next Generation of Population-Based DFNB16 Carrier Screening and Diagnosis: STRC Copy-Number Variant Analysis from Genome Sequencing Data
Authors: Xiang Jiale , Peng Jiguang , Sun Xiangzhong , Lin Zibin , Li Dongdong , Ye Haodong , Wang Sibao , Bai Yushi , Wang Xiaohong , Du Peina , Gao Ya , Sun Jun , Pan Silin , Peng Zhiyu 
Published: May 2023

Abstract

Background
Deafness, autosomal recessive 16 (DFNB16) is caused by compound heterozygous or homozygous variants in STRC and is the second most common form of genetic hearing loss. Due to the nearly identical sequences of STRC and the pseudogene STRCP1, analysis of this region is challenging in clinical testing.

Methods
We developed a method that accurately identifies the copy number of STRC and STRCP1 using standard short-read genome sequencing. Then, we used whole genome sequencing (WGS) data to investigate the population distribution of STRC copy number in 6813 neonates and the correlation between STRC and STRCP1 copy number.

Results
The comparison of WGS results with multiplex ligation-dependent probe amplification demonstrated high sensitivity (100%; 95% CI, 97.5%–100%) and specificity (98.8%; 95% CI, 97.7%–99.5%) in detecting heterozygous deletion of STRC from short-read genome sequencing data. The population analysis revealed that 5.22% of the general population has STRC copy number changes, almost half of which (2.33%; 95% CI, 1.99%–2.72%) were clinically significant, including heterozygous and homozygous STRC deletions. There was a strong inverse correlation between STRC and STRCP1 copy number.

Conclusions
We developed a novel and reliable method to determine STRC copy number based on standard short-read based WGS data. Incorporating this method into analytic pipelines would improve the clinical utility of WGS in the screening and diagnosis of hearing loss. Finally, we provide population-based evidence of pseudogene-mediated gene conversions between STRC and STRCP1.
Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit
Authors: Chen Nianhang , Zhang Rong , Zeng Tao , Zhang Xuting , Wu Ruibo 
Published: May 2023

Abstract
Terpenoids and their derivatives are collectively known as the terpenome and are the largest class of natural products, whose biosynthesis refers to various kinds of enzymes. To date, there is no terpenome-related enzyme database, which is a desire for enzyme mining, metabolic engineering and discovery of new natural products related to terpenoids. In this work, we have constructed a comprehensive database called TeroENZ (http://terokit.qmclab.com/browse_enz.html) containing 13 462 enzymes involved in the terpenoid biosynthetic pathway, covering 2541 species and 4293 reactions reported in the literature and public databases. At the same time, we classify enzymes according to their catalytic reactions into cyclase, oxidoreductase, transferase, and so on, and also make a classification according to species. This meticulous classification is beneficial for users as it can be retrieved and downloaded conveniently. We also provide a computational module for isozyme prediction. Moreover, a module named TeroMAP (http://terokit.qmclab.com/browse_rxn.html) is also constructed to organize all available terpenoid enzymatic reactions into an interactive network by interfacing with the previously established database of terpenoid compounds, TeroMOL. Finally, all these databases and modules are integrated into the web server TeroKit (http://terokit.qmclab.com/) to shed light on the field of terpenoid research.
Database URL http://terokit.qmclab.com/
Impact of a sugar-sweetened beverage tax on sugar producers in Ukraine
Authors: Mandeville Kate L , Nivievskyi Oleg , Neyter Roman , Martyshev Pavlo , Vakhitov Volodymyr , Warren Bethany , Doroshenko Olena 
Published: May 2023

Abstract
Taxes on sugar-sweetened beverages can promote health and raise revenue. Whether these taxes negatively impact domestic sugar producers, an argument often made by opponents, is understudied. We extended a simulation model based on a uniform specific volume-based tax of UAH 4/L in Ukraine. We estimated best- and worst-case scenarios for reductions in domestic sugar demand to be 162 and 23 000 metric tons. This is at worst ∼0.5% of current exports, meaning decreases in domestic demand could easily be absorbed by export markets given export trends. Due to highly protectionist sugar sector policy, sugar producers would not be able to fully substitute domestic sales revenues through increased export revenues, but the worst-case revenue gap was &lt;0.5% of total sectoral output in recent years. Overall, introducing a tax on sugar-sweetened beverages in Ukraine is likely to have a very limited impact on domestic sugar producers.
Theory-guided process evaluation of a multicomponent, technology-based ‘SMART Eating’ trial among Indian adults: an embedded mixed-methods study
Authors: Kaur Jasvir , Kaur Manmeet , Chakrapani Venkatesan , Kumar Rajesh 
Published: May 2023

Abstract
We report process evaluation findings from the ‘SMART Eating’ intervention trial, which significantly improved fat, sugar and salt (FSS), and fruits and vegetables (FVs) intake among adults. Intervention used information technology [short message service (SMS), WhatsApp and website] and interpersonal communication (distribution of SMART Eating kit) and pamphlet for comparison group. Guided by UK Medical Research Council’s framework, using embedded mixed-methods design, continuous process evaluation documented fidelity, dose, reach, acceptability and mechanisms. Intervention was implemented as intended, with high reach (91%) in both groups: ‘comparison group’ (n = 366): inadequate use of pamphlets (46%); ‘intervention group’ (n = 366): with timely remedial measures to remove implementation/usage barriers, dose of SMS (93%), WhatsApp (89%) and ‘SMART Eating’ kit (100%) was adequate, but website usage was low (50%); compliance was evident from participants’ interactions with the implementor and observations on kit usage. All these might have improved attitude, social influence, self-efficacy and household behaviours, which, in turn, mediated intervention’s effect on improving FSS and FV intake. Among poor performers, lack of effect on FV intake was perceived to be related to high cost/pesticides use and FSS intake was related to lack of family support. Low website usage, challenges with WhatsApp messaging and contextual factors (cost, pesticides abuse and family support) need to be considered while designing similar future interventions.
Molecular Pathogenesis of Colitis-associated Colorectal Cancer: Immunity, Genetics, and Intestinal Microecology
Authors: Yin Yue , Wan Jian , Yu Jingmin , Wu Kaichun 
Published: May 2023

Abstract
Patients with inflammatory bowel disease (IBD) have a high risk for colorectal cancer (CRC). This cancer type, which is strongly associated with chronic inflammation, is called colitis-associated CRC (CAC). Understanding the molecular pathogenesis of CAC is crucial to identify biomarkers necessary for early diagnosis and more effective treatment directions. The accumulation of immune cells and inflammatory factors, which constitute a complex chronic inflammatory environment in the intestinal mucosa, may cause oxidative stress or DNA damage to the epithelial cells, leading to CAC development and progression. An important feature of CAC is genetic instability, which includes chromosome instability, microsatellite instability, hypermethylation, and changes in noncoding RNAs. Furthermore, the intestinal microbiota and metabolites have a great impact on IBD and CAC. By clarifying immune, genetic, intestinal microecology, and other related pathogenesis, CAC may be more predictable and treatable.
Changes in Vaginal Bacteria and Inflammatory Mediators From Periconception Through the Early Postpartum Period in a Cohort of Kenyan Women Without HIV
Authors: Sabo Michelle C , Lokken Erica M , Srinivasan Sujatha , Kinuthia John , Richardson Barbra A , Fiedler Tina L , Munch Matthew , Proll Sean , Salano Clayton , John-Stewart Grace , Jaoko Walter , Fredricks David N , McClelland R Scott 
Published: May 2023

Abstract

Background
Women's increased risk of HIV acquisition during pregnancy and postpartum may be mediated by changes in vaginal microbiota and/or cytokines.

Methods
A cohort of 80 Kenyan women who were HIV-1 seronegative contributed 409 vaginal samples at 6 pregnancy time points: periconception, positive pregnancy test result, first trimester, second trimester, third trimester, and postpartum. Concentrations of vaginal bacteria linked with HIV risk and Lactobacillus spp were measured using quantitative polymerase chain reaction. Cytokines were measured by immunoassay.

Results
Based on Tobit regression, later pregnancy time points were associated with lower concentrations of Sneathia spp (P = .01), Eggerthella sp type 1 (P = .002), and Parvimonas sp type 2 (P = .02) and higher concentrations of Lactobacillus iners (P &lt; .001), Lactobacillus crispatus (P &lt; .001), Lactobacillus vaginalis (P &lt; .001), interleukin 6 (P &lt; .001), TNF (P = .004), C-X-C motif chemokine ligand 10 (CXCL10; P &lt; .001), C-C motif ligand 3 (P = .009), C-C motif ligand 4 (P &lt; .001), C-C motif ligand 5 (P = .002), interleukin 1β (P = .02), and interleukin 8 (P = .002). Most cervicovaginal cytokines and vaginal bacteria clustered separately in principal component analysis, except for CXCL10, which did not group with either cytokines or bacteria. The shift toward a Lactobacillus-dominated microbiota during pregnancy mediated the relationship between pregnancy time point and CXCL10.

Conclusions
Increases in proinflammatory cytokines, but not vaginal bacterial taxa linked with higher HIV risk, could provide an explanation for increased HIV susceptibility during pregnancy and postpartum.
Variation among populations ofTrichogramma euproctidis(Hymenoptera: Trichogrammatidae) revealed by life table parameters: perspectives for biological control
Authors: Tabebordbar Fatemeh , Formisano Giorgio , Shishehbor Parviz , Ebrahimi Ebrahim , Giorgini Massimo , Sørensen Jesper Givskov 
Published: May 2023

AbstractThe successful mass-rearing of potential biological control agents is a prerequisite for sustainable pest control. In this study, the performance of 3 Trichogramma euproctidis (Girault) (Hymenoptera: Trichogrammatidae) populations collected from different locations in Khuzestan (Southwest Iran) were evaluated to optimize the egg parasitoid mass-rearing for augmentative biological control of lepidopteran pests. We aimed to investigate the effects of both population origin and host quality on biological traits of ovipositing females (number of parasitized eggs) and of their progeny (development time, survival rate, sex ratio, longevity, and fecundity). The effect of host quality was assessed by allowing the parasitoid to oviposit into 1, 2, 3, or 4-day-old Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) eggs. The 3 T. euproctidis populations developed successfully regardless the age of the host eggs. However, we found significant variation among populations and a strong influence of host quality on the traits investigated. Progeny performance in all populations decreased with increasing host age. The best-performing population (collected in Mollasani) showed the highest parasitization rate, highest survival rate, and progeny sex ratio with the greatest percentage of females. A life table corroborated these findings with superior estimates of the net reproductive rate (R0), intrinsic rate of increase (r), and reduced generation time (T) for the Mollasani population on 1-day-old host eggs. We conclude that ample variation exists among T. euproctidis populations and that rearing the Mollasani population on young rather than old eggs of E. kuehniella would be recommended to implement the biological control programs to target lepidopteran pests in Southwestern Iran.
The United Nations convention on the rights of persons with disabilities, neuroscience, and criminal legal capacity
Authors: Barsky Benjamin A , Stein Michael Ashley 
Published: May 2023

Abstract
The United Nations Convention on the Rights of Persons with Disabilities requires states parties to ‘recognize that persons with disabilities enjoy legal capacity on an equal basis with others in all aspects of life.’ This mandate has sparked debate about the interpretation of legal capacity, including within the criminal context as applied to the retrogressively named ‘insanity defense.’ Yet, under-examined are two questions: First, what defenses should defendants with psychosocial disabilities be able to invoke during criminal prosecutions? Second, what kind of evidence is consistent with, on the one hand, determining a defendant’s decision-making capacity to establish culpability and, on the other hand, the right to equal recognition before the law? Developments in neuroscience offer a unique prism to grapple with these issues. We argue that neuroscientific evidence of impaired decision-making, insofar as it presents valid and interpretable diagnostic information, can be a useful tool for influencing judicial decision-making and outcomes in criminal court. In doing so, we oppose the argument espoused by significant members of the global disability rights community that bioscientific evidence of psychosocial disability should be inadmissible to negate criminal responsibility. Such a position risks more defendants being punished harshly, sentenced to death, and placed in solitary confinement.
The 2022 dengue outbreak in Bangladesh: hypotheses for the late resurgence of cases and fatalities
Authors: Haider Najmul , Hasan Mohammad Nayeem , Khalil Ibrahim , Tonge Daniel , Hegde Shivanand , Chowdhury Muhammad Abdul Baker , Rahman Mahbubur , Khan Manjur Hossain , Ansumana Rashid , Zumla Alimuddin , Uddin Md Jamal 
Published: May 2023

Abstract
Bangladesh reported the highest number of annual deaths (n = 281) related to dengue virus infection in 2022 since the virus reappeared in the country in 2000. Earlier studies showed that &gt;92% of the annual cases occurred between the months of August and September. The 2022 outbreak is characterized by late onset of dengue cases with unusually higher deaths in colder months, that is, October–December. Here we present possible hypotheses and explanations for this late resurgence of dengue cases. First, in 2022, the rainfall started late in the season. Compared to the monthly average rainfall for September and October between 2003 and 2021, there was 137 mm of additional monthly rainfall recorded in September and October 2022. Furthermore, the year 2022 was relatively warmer with a 0.71°C increased temperature than the mean annual temperature of the past 20 yr. Second, a new dengue virus serotype, DENV-4, had recently reintroduced/reappeared in 2022 and become the dominant serotype in the country for a large naïve population. Third, the post-pandemic return of normalcy after 2 yr of nonpharmaceutical social measures facilitates extra mosquito breeding habitats, especially in construction sites. Community engagement and regular monitoring and destruction of Aedes mosquitoes’ habitats should be prioritized to control dengue virus outbreaks in Bangladesh.
The Development and Initial Validation of Items to Assess Parent Fear of Nighttime Hypoglycemia
Authors: Monzon Alexandra D , Cushing Christopher C , McDonough Ryan , Clements Mark , Gonder-Frederick Linda , Patton Susana R 
Published: May 2023

Abstract

Objective
Parents of youth with type 1 diabetes (T1D) are fearful their children will experience nighttime hypoglycemia. Currently, the Hypoglycemia Fear Survey for Parents (HFS-P) lacks items that specifically assess parents’ nighttime fear. This study aimed to fill this gap by rigorously identifying new items to specifically assess parent fear of nighttime hypoglycemia and then examine the psychometric properties of the revised Hypoglycemia Fear Survey for Parents including Nighttime Fear (HFS-P-NF).

Methods
For Phase 1, we recruited 10 pediatric diabetes providers and 15 parents/caregivers of youth with T1D to generate items related to fear of nighttime hypoglycemia. For Phase 2, we recruited an additional 20 parents/caregivers to pilot-test the newly generated items. For Phase 3, we recruited another 165 parents/caregivers to evaluate structural validity via confirmatory factor analyses, reliability, and content validity of the revised HFS-P-NF.

Results
In Phase 1, we generated 54 items. In Phase 2, we removed 34 items due to violations of distributional normality and nonsignificant correlations. In Phase 3, a four-factor model reflecting behaviors maintaining high glucose, helplessness, negative social consequences, and nighttime worries was the best fitting model for the HFS-P-NF. The new items demonstrated strong internal consistency (α = 0.96) and strong to moderate relationships with criterion and content validity measures.

Conclusion
The current study provides initial evidence of validity and reliability for new items on the HFS-P-NF that broadened the conceptualization of parent fear of nighttime hypoglycemia. These findings are important to clinicians who may consider screening for parent fear of nighttime hypoglycemia more comprehensively.
Effects of low-dose/high-dose-rate X-irradiation on oxidative stress in organs following forced swim test and its combined effects on alcohol-induced liver damage in mice
Authors: Naoe Shota , Fujimoto Yuki , Murakami Kaito , Yukimine Ryohei , Tanaka Ayumi , Yamaoka Kiyonori , Kataoka Takahiro 
Published: May 2023

Abstract
The liver’s susceptibility to oxidative stress after a combination of forced swim test (FST) and low-dose-rate γ-irradiation has been observed. Therefore, this study aims to clarify the effects of low-dose (0.1 and 0.5 Gy)/high-dose-rate (1.2 Gy/min) irradiation on combined oxidative stressors—liver damage associated with FST and alcohol administration. In addition, the effects of similar irradiation on FST-induced immobility, which induces psychomotor retardation, and antioxidative effects on the brain, lungs, liver and kidneys were investigated, and the results were compared with those of a similar previous study that utilized low-dose-rate irradiation. Low-dose/high-dose-rate (especially 0.5 Gy) irradiation temporarily worsened liver antioxidant function and hepatic function with FST- and alcohol administration-related oxidative damage; however, the damages improved soon after. In addition, the increase in total glutathione content in the liver contributed to the early improvement of hepatic functions. However, pre-irradiation did not suppress immobility during the FST. The results also suggested that the effects of low-dose/high-dose-rate irradiation on the antioxidant functions of each organ after the FST were different from those of low-dose/low-dose-rate irradiation. Overall, this study provides further insights into the effects of low-dose irradiation on exposure to a combination of different oxidative stressors. It will also contribute to the elucidation of dose rate effects on oxidative stress in the low-dose irradiation range.
Metagenomic surveillance in Jinan, China, reveals serum microbiome and biochemistry features in fever of unknown origin (FUO) patients
Authors: Liu Ming , Liu Hui , Li Fenghua , Shen Yang , Zhang Liwen , Wang Gang , Wang Haitao , Qu Chunmei , Chen Gonghai , Zhao Xiulan , Liu Lanzheng , Zhou Jun 
Published: May 2023

Abstract
Here we aim to build up a metagenomics-centered surveillance on the infectious microbiome showing in the fever of unknown origin (FUO) patients. We collected venous blood, bronchoalveolar lavage fluid, cerebrospinal fluid, tissue block, sputum, bone marrow biopsy, and purulent liquid samples from 123 patients. Metagenomic sequencing (mNGS) for both DNA and RNA sequences was performed to profile the total pathogenic microbiome in the samples. A large pool of infectious or conditional infectious bacteria was found, belonging to Enterobacteriaceae, Staphylococcaceae (10.55%), Burkholderiaceae (10.05%), and Comamonadaceae (4.25%). The major virus families detected from mNGS analysis include Adenoviridae, Anelloviridae, Peribunyaviridae, Flaviviridae, and Herpesviridae, showing up in 34.96%, 47.37%, 30.89%, 5.69%, 3.25%, and 1.63% of patients, respectively. Using the Ward clustering method, two clusters of patients were organized: high-variety group and low-variety group. The patients in the high-variety group demonstrated higher levels of immune cells and inflammatory indicators such as lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase. The patients in the low-variety group showed higher levels of inflammatory lipids such as 13,14-dihy-15-keto PGE2 (fold &gt; 10, P = 0.021); tetra-PGDM (fold = 5.29, P = 0.037); and 20-HETE (fold &gt; 10, P = 0.02). The mNGS surveillance system demonstrated remarkable potential in preventing infectious diseases using mNGS data.