bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics of Homeless Temporarily-Housed in Project RoomKey During the COVID-19 Pandemic
Authors: Sloan Kylie , Kogan Alexis Coulourides , Guller Jodie , Feldman Corinne T. , Feldman Brett J. 
Published: March 2024

Introduction: People experiencing unsheltered homelessness (PEUH) have higher disease burden yet limited access to healthcare. COVID-19 introduced even greater risk for PEUH aged 65+ years with an underlying chronic health condition and were temporarily housed in hotels/motels for Project RoomKey (PRK). This study aimed to characterize a PRK cohort who received primary care from a street medicine program. Methods: This observational case series study included a sample of 35 PRK participants receiving primary care from a street medicine team at a single site from July to September 2020. We used the HOUSED BEDS assessment tool for taking history on PEUH. Results: Participants were 63% male, 40% Hispanic/Latino/a, 40% white, 94% English-speaking, and 73% had chronic health conditions. Assessment revealed: average Homelessness (H) of 4 years; 76% had no prior social service Outreach (O); average Utilization (U) was 4 emergency department visits in prior 6-months; 68% received Salary (S) from government income; Food access or Eat (E) was commonly purchased (29%) or donated (26%); clean water to Drink (D) for 59% of participants; 86% had access to a Bathroom (B); Encampment (E) was varied and 38% reported safety concerns; Daily routine (D) showed 76% could access a telephone, 32% received social support from family; 79% reported past or current Substance use (S). No participants contracted COVID-19 during study period. Conclusions: This study describes health and demographic characteristics of PRK participants in Southern California. Findings inform policies to continue PRK that includes onsite healthcare such as via street medicine.
Integration of scRNA-seq data by disentangled representation learning with condition domain adaptation
Authors: Liu Renjing , Qian Kun , He Xinwei , Li Hongwei 
Published: March 2024

Abstract
Background
The integration of single-cell RNA sequencing data from multiple experimental batches and diverse biological conditions holds significant importance in the study of cellular heterogeneity.

Results
To expedite the exploration of systematic disparities under various biological contexts, we propose a scRNA-seq integration method called scDisco, which involves a domain-adaptive decoupling representation learning strategy for the integration of dissimilar single-cell RNA data. It constructs a condition-specific domain-adaptive network founded on variational autoencoders. scDisco not only effectively reduces batch effects but also successfully disentangles biological effects and condition-specific effects, and further augmenting condition-specific representations through the utilization of condition-specific Domain-Specific Batch Normalization layers. This enhancement enables the identification of genes specific to particular conditions. The effectiveness and robustness of scDisco as an integration method were analyzed using both simulated and real datasets, and the results demonstrate that scDisco can yield high-quality visualizations and quantitative outcomes. Furthermore, scDisco has been validated using real datasets, affirming its proficiency in cell clustering quality, retaining batch-specific cell types and identifying condition-specific genes.

Conclusion
scDisco is an effective integration method based on variational autoencoders, which improves analytical tasks of reducing batch effects, cell clustering, retaining batch-specific cell types and identifying condition-specific genes.
Using protein language models for protein interaction hot spot prediction with limited data
Authors: Sargsyan Karen , Lim Carmay 
Published: March 2024

Abstract
Background
Protein language models, inspired by the success of large language models in deciphering human language, have emerged as powerful tools for unraveling the intricate code of life inscribed within protein sequences. They have gained significant attention for their promising applications across various areas, including the sequence-based prediction of secondary and tertiary protein structure, the discovery of new functional protein sequences/folds, and the assessment of mutational impact on protein fitness. However, their utility in learning to predict protein residue properties based on scant datasets, such as protein–protein interaction (PPI)-hotspots whose mutations significantly impair PPIs, remained unclear. Here, we explore the feasibility of using protein language-learned representations as features for machine learning to predict PPI-hotspots using a dataset containing 414 experimentally confirmed PPI-hotspots and 504 PPI-nonhot spots.

Results
Our findings showcase the capacity of unsupervised learning with protein language models in capturing critical functional attributes of protein residues derived from the evolutionary information encoded within amino acid sequences. We show that methods relying on protein language models can compete with methods employing sequence and structure-based features to predict PPI-hotspots from the free protein structure. We observed an optimal number of features for model precision, suggesting a balance between information and overfitting.

Conclusions
This study underscores the potential of transformer-based protein language models to extract critical knowledge from sparse datasets, exemplified here by the challenging realm of predicting PPI-hotspots. These models offer a cost-effective and time-efficient alternative to traditional experimental methods for predicting certain residue properties. However, the challenge of explaining why specific features are important for determining certain residue properties remains.
A new sphenodontian (Diapsida: Lepidosauria) from the Upper Triassic (Norian) of Germany and its implications for the mode of sphenodontian evolution
Authors: Freisem Lisa S. , Müller Johannes , Sues Hans-Dieter , Sobral Gabriela 
Published: March 2024

AbstractThe Arnstadt Formation of Saxony-Anhalt, Germany has yielded some of Germany’s most substantial finds of Late Triassic tetrapods, including the sauropodomorph Plateosaurus and the stem-turtle Proganochelys quenstedti. Here, we describe an almost complete skull of a new sphenodontian taxon from this formation (Norian, 227–208 Ma), making it the oldest known articulated sphenodontian skull from Europe and one of the oldest in the world. The material is represented by the dermal skull roof and by the complete maxilla and temporal region, as well as parts of the palate, braincase, and lower jaw. A phylogenetic assessment recovers it as a basal sphenodontian closely related to Planocephalosaurus robinsonae and to Eusphenodontia, making it the earliest-diverging sphenodontian known with an articulated skull. Its cranial anatomy is generally similar to the well-known Diphydontosaurus avonis from the Rhaetian of England, showing that this successful phenotype was already established in the clade around 10 myr earlier than assumed. An analysis of evolutionary change rates recovers high rates of evolution in basal sphenodontians, with decreasing rates throughout the evolution of the group. However, contrary to previous studies, reversals in this trend were identified, indicating additional peaks of evolutionary change. These results improve our understanding of the early sphenodontian diversity in Europe, providing critical information on evolutionary trends throughout the history of the clade and sparking renewed interest in its evolution.
Serum electrolyte concentrations and risk of atrial fibrillation: an observational and mendelian randomization study
Authors: Wu Yang , Kong Xiang-Jun , Ji Ying-Ying , Fan Jun , Ji Cheng-Cheng , Chen Xu-Miao , Ma Yue-Dong , Tang An-Li , Cheng Yun-Jiu , Wu Su-Hua 
Published: March 2024

Abstract
Background
Atrial fibrillation (AF) is a prevalent arrhythmic condition resulting in increased stroke risk and is associated with high mortality. Electrolyte imbalance can increase the risk of AF, where the relationship between AF and serum electrolytes remains unclear.

Methods
A total of 15,792 individuals were included in the observational study, with incident AF ascertainment in the Atherosclerosis Risk in Communities (ARIC) study. The Cox regression models were applied to calculate the hazard ratio (HR) and 95% confidence interval (CI) for AF based on different serum electrolyte levels. Mendelian randomization (MR) analyses were performed to examine the causal association.

Results
In observational study, after a median 19.7 years of follow-up, a total of 2551 developed AF. After full adjustment, participants with serum potassium below the 5th percentile had a higher risk of AF relative to participants in the middle quintile. Serum magnesium was also inversely associated with the risk of AF. An increased incidence of AF was identified in individuals with higher serum phosphate percentiles. Serum calcium levels were not related to AF risk. Moreover, MR analysis indicated that genetically predicted serum electrolyte levels were not causally associated with AF risk. The odds ratio for AF were 0.999 for potassium, 1.044 for magnesium, 0.728 for phosphate, and 0.979 for calcium, respectively.

Conclusions
Serum electrolyte disorders such as hypokalemia, hypomagnesemia and hyperphosphatemia were associated with an increased risk of AF and may also serve to be prognostic factors. However, the present study did not support serum electrolytes as causal mediators for AF development.
Molecular adaptations underlying high-frequency hearing in the brain of CF bats species
Authors: Li Xintong , Wang Hui , Wang Xue , Bao Mingyue , Sun Ruyi , Dai Wentao , Sun Keping , Feng Jiang 
Published: March 2024

AbstractBackgroundThe majority of bat species have developed remarkable echolocation ability, especially for the laryngeally echolocating bats along with high-frequency hearing. Adaptive evolution has been widely detected for the cochleae in the laryngeally echolocating bats, however, limited understanding for the brain which is the central to echolocation signal processing in the auditory perception system, the laryngeally echolocating bats brain may also undergo adaptive changes.ResultIn order to uncover the molecular adaptations related with high-frequency hearing in the brain of laryngeally echolocating bats, the genes expressed in the brain ofRhinolophus ferrumequinum(CF bat) andMyotis pilosus(FM bat) were both detected and also compared. A total of 346,891 genes were detected and the signal transduction mechanisms were annotated by the most abundant genes, followed by the transcription. In hence, there were 3,088 DEGs were found between the two bat brains, with 1,426 highly expressed in the brain ofR. ferrumequinum, which were significantly enriched in the neuron and neurodevelopmental processes. Moreover, we found a key candidate hearing gene,ADCY1, playing an important role in theR. ferrumequinumbrain and undergoing adaptive evolution in CF bats.ConclusionsOur study provides a new insight to the molecular bases of high-frequency hearing in two laryngeally echolocating bats brain and revealed different nervous system activities during auditory perception in the brain of CF bats.
High prevalence of ST5-SCCmec II-t311 clone of methicillin-resistant Staphylococcus aureus isolated from bloodstream infections in East China
Authors: Zhan Qing , Teng Gaoqin , Chen Weiwei , Yu Xiao 
Published: March 2024

Abstract
Objectives
Methicillin-resistant Staphylococcus aureus (MRSA) is a challenging global health threat, resulting in significant morbidity and mortality worldwide. This study aims to determine the molecular characteristics and antimicrobial susceptibility of 263 MRSA isolates in Zhejiang Province, east China.

Methods
From 2014 to 2019, a total of 263 MRSA isolates from bloodstream infections (BSIs) were collected from 6 hospitals in 4 cities in Zhejiang province, east China. Antimicrobial susceptibility tests were conducted according to the guidelines set forth by the Clinical and Laboratory Standards Institute (CLSI). To characterize and analyze these isolates, multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) typing and virulence genes gene profiles were performed.

Results
The most predominant clone was ST5-SCCmec II-t311, which accounted for 41.8% (110/263), followed by ST59 (44/263, 16.7%). Compared with non-ST5-II-t311 isolates, ST5-II-t311 isolates were more resistant to erythromycin, tetracycline, levofloxacin, moxifloxacin, and ciprofloxacin, but more susceptible to clindamycin. Moreover, the rates of multidrug resistance were higher in ST5-II-t311 isolates compared to the non-ST5-II-t311 isolates. In comparison to the non-ST5-II-t311 isolates, ST5-II-t311 isolates showed no significant difference in virulence genes detected.

Conclusions
MRSA ST5-II-t311 clone has become the most predominant clone in Zhejiang Province, east China and has higher rates of multidrug resistance than other isolates, that should be kept in mind when treating BSI. Moreover, MRSA ST59 clone shows an upward trend and has begun to spread into hospitals. Our findings highlight the importance of epidemiological studies of S. aureus carriage in the eastern region.
High-throughput sequencing reveals differences in microbial community structure and diversity in the conjunctival tissue of healthy and type 2 diabetic mice
Authors: Li Fengjiao , Yang Shuo , Ma Ji , Zhao Xiaowen , Chen Meng , Wang Ye 
Published: March 2024

Abstract
Background
To investigate the differences in bacterial and fungal community structure and diversity in conjunctival tissue of healthy and diabetic mice.

Methods
RNA-seq assays and high-throughput sequencing of bacterial 16 S rDNA and fungal internal transcribed spacer (ITS) gene sequences were used to identify differentially expressed host genes and fungal composition profiles in conjunctival tissues of diabetic BKS-db/db mice and BKS (control) mice. Functional enrichment analysis of differentially expressed genes and the correlation between the relative abundance of bacterial and fungal taxa in the intestinal mucosa were also performed.

Results
Totally, 449 differential up-regulated genes and 1,006 down-regulated genes were identified in the conjunctival tissues of diabetic mice. The differentially expressed genes were mainly enriched in metabolism-related functions and pathways. A decrease in conjunctival bacterial species diversity and abundance in diabetic mice compared to control mice. In contrast, fungal species richness and diversity were not affected by diabetes. The microbial colonies were mainly associated with cellular process pathways regulating carbohydrate and lipid metabolism, as well as cell growth and death. Additionally, some interactions between bacteria and fungi at different taxonomic levels were also observed.

Conclusion
The present study revealed significant differences in the abundance and composition of bacterial and fungal communities in the conjunctival tissue of diabetic mice compared to control mice. The study also highlighted interactions between bacteria and fungi at different taxonomic levels. These findings may have implications for the diagnosis and treatment of diabetes.
Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato
Authors: Mu Fangfang , Zheng Hao , Zhao Qiaorui , Zhu Mingku , Dong Tingting , Kai Lei , Li Zongyun 
Published: March 2024

AbstractSweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.
Effect of deep neuromuscular block on the quality of early recovery after sleeve gastrectomy in obese patients: a randomized controlled trial
Authors: Yang Wan-li , Wen Ya-ling , Xu Wen-mei , Xu Chi-liang , Yin Wen-qin , Lin Jing-yan 
Published: March 2024

Abstract
Background
Deep neuromuscular block (NMB) has been shown to improve surgical conditions and alleviate post-operative pain in bariatric surgery compared with moderate NMB. We hypothesized that deep NMB could also improve the quality of early recovery after laparoscopic sleeve gastrectomy (LSG).

Methods
Eighty patients were randomized to receive either deep (post-tetanic count 1–3) or moderate (train-of-four count 1–3) NMB. The QoR-15 questionnaire was used to evaluate the quality of early recovery at 1 day before surgery (T0), 24 and 48 h after surgery (T2, T3). Additionally, we recorded diaphragm excursion (DE), postoperative pain, surgical condition, cumulative dose of analgesics, time of first flatus and ambulation, post-operative nausea and vomiting, time of tracheal tube removal and hospitalization time.

Main results
The quality of recovery was significantly better 24 h after surgery in patients who received a deep versus moderate block (114.4 ± 12.9 versus 102.1 ± 18.1). Diaphragm excursion was significantly greater in the deep NMB group when patients performed maximal inspiration at T2 and T3 (P < 0.05). Patients who underwent deep NMB reported lower visceral pain scores 40 min after surgery; additionally, these patients experienced lower pain during movement at T3 (P < 0.05). Optimal surgical conditions were rated in 87.5% and 64.6% of all measurements during deep and moderate NMB respectively (P < 0.001). The time to tracheal tube removal was significantly longer in the deep NMB group (P = 0.001). There were no differences in other outcomes.

Conclusion
In obese patients receiving deep NMB during LSG, we observed improved QoR-15 scores, greater diaphragmatic excursions, improved surgical conditions, and visceral pain scores were lower. More evidence is needed to determine the effects of deep NMB on these outcomes.

Trial registration
ChiCTR2200065919. Date of retrospectively registered: 18/11/2022.
The relation between usage of an eHealth intervention for stress urinary incontinence and treatment outcomes: an observational study
Authors: Firet Lotte , Teunissen Theodora Alberta Maria , Kool Rudolf Bertijn , Akkermans Reinier Peter , Lagro-Janssen Antoinette Leonarda Maria , van der Vaart Huub , Assendelft Willem Jan Jozef 
Published: March 2024

Abstract
Background
Stress urinary incontinence (SUI), though a prevalent condition among women, is undertreated in primary care. EHealth with pelvic floor muscle training is an evidence-based alternative to care-as-usual. It is unknown, however, how eHealth usage is related to treatment outcome, and this knowledge is required for general practitioners to implement eHealth in their practice. This study examines the relation between usage of eHealth for SUI and treatment outcomes by examining log data. Baseline factors were also explored for associations with treatment success.

Method
In this pre-post study, women with SUI participated in “Baasoverjeblaas.nl”, a web-based intervention translated from the Swedish internet intervention "Tät®-treatment of stress urinary incontinence". Usage was based on log data and divided into three user groups (low, intermediate and high). Online questionnaires were sent before, after treatment and at six-months follow-up. The relation between usage and the primary outcome − treatment success (PGI-) − was studied with a binomial logistic regression analysis. Changes in the secondary outcomes − symptom severity (ICIQ-UI SF) and quality of life (ICIQ-LUTSqol) − were studied per user group with linear mixed model analysis.

Results
Included were 515 users with a mean age of 50.5 years (12.0 SD). The majority were low users (n = 295, 57.3%). Treatment success (PGI-I) was reached by one in four women and was more likely in high and intermediate users than in low users (OR 13.2, 95% CI 6.1–28.5, p < 0.001 and OR 2.92, 95% CI 1.35–6.34, p = 0.007, respectively). Symptom severity decreased and quality of life improved significantly over time, especially among high users. The women’s expected ability to train their pelvic floor muscles and the frequency of pelvic floor muscle exercises at baseline were associated with treatment success.

Conclusion
This study shows that usage of eHealth for SUI is related to all treatment outcomes. High users are more likely to have treatment success. Treatment success is more likely in women with higher expectations and pelvic floor muscle training at baseline. These findings indicate that general practitioners can select patients that would be more likely to benefit from eHealth treatment, and they can enhance treatment effect by stimulating eHealth usage.

Trial registration
Landelijk Trial Register NL6570; https://onderzoekmetmensen.nl/nl/trial/25463.