bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aging modifies endometrial dendritic cell function and unconventional double negative T cells in the human genital mucosa
Authors: Parthasarathy Siddharth , Shen Zheng , Carrillo-Salinas Francisco J. , Iyer Vidya , Vogell Alison , Illanes Diego , Wira Charles R. , Rodriguez-Garcia Marta 
Published: July 2023

Abstract
Background
Immune function in the genital mucosa balances reproduction with protection against pathogens. As women age, genital infections, and gynecological cancer risk increase, however, the mechanisms that regulate cell-mediated immune protection in the female genital tract and how they change with aging remain poorly understood. Unconventional double negative (DN) T cells (TCRαβ + CD4-CD8-) are thought to play important roles in reproduction in mice but have yet to be characterized in the human female genital tract. Using genital tissues from women (27–77 years old), here we investigated the impact of aging on the induction, distribution, and function of DN T cells throughout the female genital tract.

Results
We discovered a novel site-specific regulation of dendritic cells (DCs) and unconventional DN T cells in the genital tract that changes with age. Human genital DCs, particularly CD1a + DCs, induced proliferation of DN T cells in a TFGβ dependent manner. Importantly, induction of DN T cell proliferation, as well as specific changes in cytokine production, was enhanced in DCs from older women, indicating subset-specific regulation of DC function with increasing age. In human genital tissues, DN T cells represented a discrete T cell subset with distinct phenotypical and transcriptional profiles compared to CD4 + and CD8 + T cells. Single-cell RNA and oligo-tag antibody sequencing studies revealed that DN T cells represented a heterogeneous population with unique homeostatic, regulatory, cytotoxic, and antiviral functions. DN T cells showed relative to CD4 + and CD8 + T cells, enhanced expression of inhibitory checkpoint molecules and genes related to immune regulatory as well as innate-like anti-viral pathways. Flow cytometry analysis demonstrated that DN T cells express tissue residency markers and intracellular content of cytotoxic molecules. Interestingly, we demonstrate age-dependent and site-dependent redistribution and functional changes of genital DN T cells, with increased cytotoxic potential of endometrial DN T cells, but decreased cytotoxicity in the ectocervix as women age, with implications for reproductive failure and enhanced susceptibility to infections respectively.

Conclusions
Our deep characterization of DN T cell induction and function in the female genital tract provides novel mechanistic avenues to improve reproductive outcomes, protection against infections and gynecological cancers as women age.
A quadruple fluorescence quantitative PCR method for the identification of wild strains of african swine fever and gene-deficient strains
Authors: Zuo Xuezhi , Peng Guorui , Xia Yingju , Xu Lu , Zhao Qizu , Zhu Yuanyuan , Wang Cheng , Liu Yebing , Zhao Junjie , Wang Haidong , Zou Xingqi 
Published: July 2023

Abstract
Background
Originating in Africa, African swine fever (ASF) was introduced to China in 2018. This acute and highly virulent infectious disease affects domestic pigs. The World Organization for Animal Health has listed it as a statutory reportable disease, and China has listed it as a category A infectious disease.

Methods
Primers and probes were designed for four ASFV genes (B646L, EP402R, MGF505-3R, and A137R). The primers/probes were highly conserved compared with the gene sequences of 21 ASFV strains.

Results
After optimization, the calibration curve showed good linearity (R2 > 0.99), the minimum concentration of positive plasmids that could be detected was 50 copies/µL, and the minimum viral load detection limit was 102 HAD50/mL. Furthermore, quadruple quantitative polymerase chain reaction (qPCR) with nucleic acids from three porcine-derived DNA viruses and cDNAs from eight RNA viruses did not show amplification curves, indicating that the method was specific. In addition, 1 × 106, 1 × 105, and 1 × 104 copies/µL of mixed plasmids were used for the quadruple qPCR; the coefficient of variation for triplicate determination between groups was < 2%, indicating the method was reproducible.

Conclusions
The results obtained by testing clinical samples containing detectable EP402R, MGF505-3R, and A137R strains with different combinations of gene deletions were as expected. Therefore, the established quadruple qPCR method was validated for the molecular diagnosis of ASF using gene-deleted ASFV strains.
Temporal dynamics of ecosystem, inherent, and underlying water use efficiencies of forests, grasslands, and croplands and their responses to climate change
Authors: Chen Wei , Liu Shuguang , Zhao Shuqing , Zhu Yu , Feng Shuailong , Wang Zhao , Wu Yiping , Xiao Jingfeng , Yuan Wenping , Yan Wende , Ju Hui , Wang Qinyi 
Published: July 2023

Abstract
Background
Understanding temporal trends and varying responses of water use efficiency (WUE) to environmental changes of diverse ecosystems is key to predicting vegetation growth. WUE dynamics of major ecosystem types (e.g., forest, grassland and cropland) have been studied using various WUE definitions/metrics, but a comparative study on WUE dynamics and their driving forces among different ecosystem types using multiple WUE metrics is lacking. We used eddy covariance measurements for 42 FLUXNET2015 sites (396 site years) from 1997 to 2014, as well as three commonly used WUE metrics (i.e., ecosystem, inherent, and underlying WUE) to investigate the commonalities and differences in WUE trends and driving factors among deciduous broadleaf forests (DBFs), evergreen needleleaf forests (ENFs), grasslands, and croplands.

Results
Our results showed that the temporal trends of WUE were not statistically significant at 73.8% of the forest, grassland and cropland sites, and none of the three WUE metrics exhibited better performance than the others in quantifying WUE. Meanwhile, the trends observed for the three WUE metrics were not significantly different among forest, grassland and cropland ecosystems. In addition, WUE was mainly driven by atmospheric carbon dioxide concentration at sites with significant WUE trends, and by vapor pressure deficit (VPD) at sites without significant trends (except cropland).

Conclusions
Our findings revealed the commonalities and differences in the application of three WUE metrics in disparate ecosystems, and further highlighted the important effect of VPD on WUE change.
Asymmetries of foot strike patterns during running in high-level female and male soccer players
Authors: Siegel Stanislav Dimitri , Mason Joel , Hamacher Daniel , Rahlf Anna Lina , Zech Astrid 
Published: July 2023

Abstract
Backround
Foot strike pattern (FSP) is defined by the way the foot makes initial ground contact and is influenced by intrinsic and extrinsic factors. This study investigated the effect of running speed on asymmetries of FSP.

Methods
Seventeen female and nineteen male soccer players performed an incremental running test on an instrumented treadmill starting at 2.0 m/s until complete exhaustion. Force plate data were used to categorize foot strikes into rearfoot (RFS) and non-rearfoot strikes. Additionally, peak vertical ground reaction force (peakGRF) and stride time were calculated. The symmetry index (SI) was used to quantify lateral asymmetries between legs.

Results
The SI indicated asymmetries of the rate of RFS (%RFS) of approximately 30% at slow running speed which decreased to 4.4% during faster running speed (p = 0.001). There were minor asymmetries in peakGRF and stride time at each running stage. Running speed influenced %RFS (p < 0.001), peakGRF (p < 0.001) and stride time (p < 0.001). Significant interaction effects between running speed and sex were shown for %RFS (p = 0.033), peakGRF (p < 0.001) and stride time (p = 0.041).

Conclusion
FSP of soccer players are asymmetric at slower running speed, but symmetry increases with increasing speed. Future studies should consider that FSP are non-stationary and influenced by running speed but also differ between legs.
Breathing cessation events that compose the apnea–hypopnea index are distinctively associated with the adverse outcomes in Alzheimer’s disease
Authors: Targa Adriano D. S. , Benítez Iván D. , Moncusí-Moix Anna , Dakterzada Farida , Minguez Olga , Vaca Rafaela , Dalmases Mireia , Sanchez-de-la-Torre Manuel , Barbé Ferran , Piñol-Ripoll Gerard 
Published: July 2023

Abstract
Background
Previous studies challenge the impact of obstructive sleep apnea (OSA) once patients are diagnosed with Alzheimer’s disease (AD). Nevertheless, OSA recognizably disrupts sleep, and relevant associations between sleep, AD pathological markers, and cognition have been demonstrated. We aimed to further explore this, evaluating the associations between each breathing cessation event that compose the apnea–hypopnea index (AHI) and the sleep structure to finally investigate whether this was related to increased levels of AD markers and higher cognitive decline.

Methods
Observational, prospective study, including consecutive patients diagnosed with mild-moderate AD. The participants were submitted to overnight polysomnography followed by a cerebrospinal fluid collection for AD pathological markers levels determination. Neuropsychological assessment was performed at baseline and after 12 months of follow-up.

Results
The cohort was composed of 116 patients (55.2% females) with a median [p25;p75] age of 76.0 [72.0;80.0] years and an AHI of 25.9 [15.1;48.5], which was mainly defined by the presence of hypopneas and obstructive apneas. These were distinctively associated with the sleep structure, with obstructive apneas being related to arousals and sleep lightening and hypopneas being related to an increased number of arousals only. Despite having a lower frequency, mixed and central apneas also presented associations with the sleep structure, particularly increasing the time spent in the lighter sleep stages. In relation to AD pathological markers, obstructive and mixed apneas were related to an augment in neurofilament light levels while hypopneas were associated with a higher phosphorylated-tau/amyloid-beta protein ratio. Hypopneas were the most important event for an increased cognitive decline at the 12-month follow-up.

Conclusions
Our findings highlight the importance of a patient-centered approach, with a comprehensive and detailed analysis of the AHI to effectively predict the different outcomes and tailor the appropriate therapeutic strategies.
Infection prevention and control in the medical imaging environment: a scoping review
Authors: Jimenez Yobelli A. , Lewis Sarah J. 
Published: July 2023

Abstract
Infection prevention and control (IPC) practices are key to preventing and controlling the spread of pathogens in medical imaging departments (MIDs). The objective of this scoping review was to synthesise information about current research in MID regarding IPC and to use the Systems Engineering Initiative for Patient Safety (SEIPS) model to identify the work system factors (‘persons’, ‘organisation’, ‘tools and technology’, ‘tasks’ and ‘environment’) influencing the practice of IPC, in order to better understand challenges and facilitators that affect IPC in MID. Predefined search terms and medical subject headings relating to IPC in the medical imaging setting were used to search 3 databases. A total of 46 publications met the inclusion criteria, which combined, encompassed all five SEIPS domains influencing IPC. The literature supports the interrelated nature of the five SEIPS domains, and influence to one another. Hand hygiene was a major focus of publications. Mechanisms of infection in contrast-enhanced computed tomography were most reported, with human error, lack of education, and issues associated with devices and processes mechanisms found to influence IPC breaches. A systems approach, such as the SEIPS model, is useful for understanding barriers and hence opportunities for improvement of IPC in the medical imaging setting. Future studies should address individuals’ decision-making processes in the medical imaging setting, and a greater focus should be placed into the procedural steps, education and tools used for contrast media administration.

Critical relevance statement
A systems approach, such as the Systems Engineering Initiative for Patient Safety model, is useful for understanding barriers and hence opportunities for improvement of IPC in the medical imaging setting.

Graphical Abstract

Key points

IPC in the medical imaging setting would benefit from a systems approach.

The role of education and monitoring of IPC compliance requires further research.

Geographical location is a key variable in IPC research in medical imaging.
A simple scoring system for the prediction of early pregnancy loss developed by following 13,977 infertile patients after in vitro fertilization
Authors: Ouyang Yan , Peng Yangqin , Zhang Senmao , Gong Fei , Li Xihong 
Published: July 2023

AbstractA retrospective study was conducted to investigate a convenient simple scoring system for the prediction of early pregnancy loss (EPL) based on simple demographics. A total of 13,977 women undergoing transvaginal ultrasound scans on Days 27–29 after in vitro fertilization-embryo transfer (IVF-ET) from June 2016 and December 2017 were included. The first trimester pregnancy outcome was recorded at 12 weeks of gestation. The areas under the curve of this scoring system were 0.884 (95% confidence interval (CI) 0.870–0.899) and 0.890 (95% CI 0.878–0.903) in the training set and test set, respectively. The score totals ranged from -8 to 14 points. A score of 5 points, which offered the highest predictive accuracy (94.01%) and corresponded to a 30% miscarriage risk, was chosen as the cutoff value, with a sensitivity of 62.84%, specificity of 98.79%, positive predictive value (PPV) of 88.87% and negative predictive value (NPV) of 94.54% for the prediction of EPL in the training set. In the test set, a score of 5 points had a sensitivity of 64.69%, specificity of 98.78%, PPV of 89.87% and NPV of 93.62%, and 93.91% of the cases were correctly predicted. Therefore, the simple scoring system using conventionally collected data can be conveniently used to predict EPL after ET. However, considering the limitations, its predictive value needs to be further verified in future clinical practice.
Neotropical bee microbiomes point to a fragmented social core and strong species-level effects
Authors: Kueneman Jordan G. , Bonadies Ernesto , Thomas Devin , Roubik David W. , Wcislo William T. 
Published: July 2023

AbstractBackgroundIndividuals that band together create new ecological opportunities for microorganisms. In vertical transmission, theory predicts a conserved microbiota within lineages, especially social bees. Bees exhibit solitary to social behavior among and/or within species, while life cycles can be annual or perennial. Bee nests may be used over generations or only once, and foraging ecology varies widely. To assess which traits are associated with bee microbiomes, we analyzed microbial diversity within solitary and social bees of Apidae, Colletidae, and Halictidae, three bee families in Panama’s tropical forests. Our analysis considered the microbiome of adult gut contents replicated through time, localities, and seasons (wet and dry) and included bee morphology and comparison to abdominal (dissected) microbiota. Diversity and distribution of tropical bee microbes (TBM) within the corbiculate bee clade were emphasized.ResultsWe found the eusocial corbiculate bees tended to possess a more conserved gut microbiome, attributable to vertical transmission, but microbial composition varied among closely related species. Euglossine bees (or orchid bees), corbiculates with mainly solitary behavior, had more variable gut microbiomes. Their shorter-tongued and highly seasonal species displayed greater diversity, attributable to flower-visiting habits. Surprisingly, many stingless bees, the oldest corbiculate clade, lacked bacterial genera thought to predate eusociality, while several facultatively social, and solitary bee species possessed those bacterial taxa. Indeed, nearly all bee species displayed a range of affinities for single or multiple variants of the “socially associated” bacterial taxa, which unexpectedly demonstrated high sequence variation.ConclusionsTaken together, these results call into question whether specific bacterial associates facilitate eusocial behavior, or are subsequently adopted, or indicate frequent horizontal transmission between perennial eusocial colonies and other social, facultatively social, and solitary bees.
Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics
Authors: Tafazoli Alireza , Mikros John , Khaghani Faeze , Alimardani Maliheh , Rafigh Mahboobeh , Hemmati Mahboobeh , Siamoglou Stavroula , Golińska Agnieszka Kitlas , Kamiński Karol A. , Niemira Magdalena , Miltyk Wojciech , Patrinos George P. 
Published: July 2023

Abstract
Background
This pilot study aims to identify and functionally assess pharmacovariants in whole exome sequencing data. While detection of known variants has benefited from pharmacogenomic-dedicated bioinformatics tools before, in this paper we have tested novel deep computational analysis in addition to artificial intelligence as possible approaches for functional analysis of unknown markers within less studied drug-related genes.

Methods
Pharmacovariants from 1800 drug-related genes from 100 WES data files underwent (a) deep computational analysis by eight bioinformatic algorithms (overall containing 23 tools) and (b) random forest (RF) classifier as the machine learning (ML) approach separately. ML model efficiency was calculated by internal and external cross-validation during recursive feature elimination. Protein modelling was also performed for predicted highly damaging variants with lower frequencies. Genotype–phenotype correlations were implemented for top selected variants in terms of highest possibility of being damaging.

Results
Five deleterious pharmacovariants in the RYR1, POLG, ANXA11, CCNH, and CDH23 genes identified in step (a) and subsequent analysis displayed high impact on drug-related phenotypes. Also, the utilization of recursive feature elimination achieved a subset of 175 malfunction pharmacovariants in 135 drug-related genes that were used by the RF model with fivefold internal cross-validation, resulting in an area under the curve of 0.9736842 with an average accuracy of 0.9818 (95% CI: 0.89, 0.99) on predicting whether a carrying individuals will develop adverse drug reactions or not. However, the external cross-validation of the same model indicated a possible false positive result when dealing with a low number of observations, as only 60 important variants in 49 genes were displayed, giving an AUC of 0.5384848 with an average accuracy of 0.9512 (95% CI: 0.83, 0.99).

Conclusion
While there are some technologies for functionally assess not-interpreted pharmacovariants, there is still an essential need for the development of tools, methods, and algorithms which are able to provide a functional prediction for every single pharmacovariant in both large-scale datasets and small cohorts. Our approaches may bring new insights for choosing the right computational assessment algorithms out of high throughput DNA sequencing data from small cohorts to be used for personalized drug therapy implementation.
Differential characteristics of bipolar I and II disorders: a retrospective, cross-sectional evaluation of clinical features, illness course, and response to treatment
Authors: Brancati Giulio Emilio , Nunes Abraham , Scott Katie , O’Donovan Claire , Cervantes Pablo , Grof Paul , Alda Martin 
Published: July 2023

Abstract
Background
The distinction between bipolar I and bipolar II disorder and its treatment implications have been a matter of ongoing debate. The aim of this study was to examine differences between patients with bipolar I and II disorders with particular emphasis on the early phases of the disorders.

Methods
808 subjects diagnosed with bipolar I (N = 587) or bipolar II disorder (N = 221) according to DSM-IV criteria were recruited between April 1994 and March 2022 from tertiary-level mood disorder clinics. Sociodemographic and clinical variables concerning psychiatric and medical comorbidities, family history, illness course, suicidal behavior, and response to treatment were compared between the bipolar disorder types.

Results
Bipolar II disorder patients were more frequently women, older, married or widowed. Bipolar II disorder was associated with later “bipolar” presentation, higher age at first (hypo)mania and treatment, less frequent referral after a single episode, and more episodes before lithium treatment. A higher proportion of first-degree relatives of bipolar II patients were affected by major depression and anxiety disorders. The course of bipolar II disorder was typically characterized by depressive onset, early depressive episodes, multiple depressive recurrences, and depressive predominant polarity; less often by (hypo)mania or (hypo)mania-depression cycles at onset or during the early course. The lifetime clinical course was more frequently rated as chronic fluctuating than episodic. More patients with bipolar II disorder had a history of rapid cycling and/or high number of episodes. Mood stabilizers and antipsychotics were prescribed less frequently during the early course of bipolar II disorder, while antidepressants were more common. We found no differences in global functioning, lifetime suicide attempts, family history of suicide, age at onset of mood disorders and depressive episodes, and lithium response.

Conclusions
Differences between bipolar I and II disorders are not limited to the severity of (hypo)manic syndromes but include patterns of clinical course and family history. Caution in the use of potentially mood-destabilizing agents is warranted during the early course of bipolar II disorder.