bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serologic and urinary characteristics of laboratory-confirmed genitourinary tuberculosis at a tertiary hospital in the Philippines
Authors: So Paolo Nikolai H. , Villanueva Anthony Russell T. 
Published: September 2021

Abstract
Background
Genitourinary tuberculosis (GUTB) is known to cause high rates of structural organ damage, however, literature on its biochemical manifestations is limited. Additionally, local studies in the Philippine setting, where cases are rampant, are few and dated. This study aimed to determine the serologic and urinary profile of patients with GUTB admitted at a tertiary hospital within January 2009 to March 2020 and their association with short-term outcomes.

Methods
This retrospective study included 112 patients with laboratory-confirmed GUTB (i.e., positivity in acid-fast smear, polymerase chain reaction, culture, or histology). Demographic data, clinical characteristics, laboratory and radiologic findings, histopathology reports, treatment, and short-term outcomes were recorded.

Results
Bladder (54.5%) and kidney (36.4%) were the most affected organs. The male:female ratio was 1:1.15, and the mean age was 35.79 ± 18.29 years. Weakness (14.29%) was the most common chief complaint. A majority presented with anemia (83.04%), while several had leukocytosis (41.96%) and thrombocytosis (26.79%). Hypoalbuminemia (58.10%), impairment of renal function (36.94%), and electrolyte abnormalities such as hyponatremia (50.93%), hypercalcemia (20.19%), and hypokalemia (21.82%) were common. Proteinuria (67.96%) and pyuria (67.96%) were the most frequent abnormal findings, followed by hematuria (51.46%), acidic urine (45.63%) and low specific gravity (31.07%). Age, leukocytosis, and the need for pressors were all significantly associated with mortality (p values of <0.001, 0.010, and <0.001, respectively).

Conclusions
The young age at presentation with severe clinical and laboratory manifestations may reflect local epidemiology as TB continues to be widespread in the country. Apart from the more commonly cited abnormalities in literature, multiple electrolyte imbalances and urinary concentration defects were also observed in many cases, possibly indicating tubulointerstitial involvement—a complication increasingly mentioned in case reports. As several patient characteristics were found to be associated with the high mortality rates observed in the study, further research is recommended to explore predictive modeling.
The increasing impact of length of stay “outliers” on length of stay at an urban academic hospital
Authors: Hughes Andrew H. , Horrocks David , Leung Curtis , Richardson Melissa B. , Sheehy Ann M. , Locke Charles F. S. 
Published: September 2021

Abstract
Background
As healthcare systems strive for efficiency, hospital “length of stay outliers” have the potential to significantly impact a hospital’s overall utilization. There is a tendency to exclude such “outlier” stays in local quality improvement and data reporting due to their assumed rare occurrence and disproportionate ability to skew mean and other summary data. This study sought to assess the influence of length of stay (LOS) outliers on inpatient length of stay and hospital capacity over a 5-year period at a large urban academic medical center.

Methods
From January 2014 through December 2019, 169,645 consecutive inpatient cases were analyzed and assigned an expected LOS based on national academic center benchmarks. Cases in the top 1% of national sample LOS by diagnosis were flagged as length of stay outliers.

Results
From 2014 to 2019, mean outlier LOS increased (40.98 to 45.11 days), as did inpatient LOS with outliers excluded (5.63 to 6.19 days). Outlier cases increased both in number (from 297 to 412) and as a percent of total discharges (0.98 to 1.56%), and outlier patient days increased from 6.7 to 9.8% of total inpatient plus observation days over the study period.

Conclusions
Outlier cases utilize a disproportionate and increasing share of hospital resources and available beds. The current tendency to exclude such outlier stays in data reporting due to assumed rare occurrence may need to be revisited. Outlier stays require distinct and targeted interventions to appropriately reduce length of stay to both improve patient care and maintain hospital capacity.
An increase of phosphatidylcholines in follicular fluid implies attenuation of embryo quality on day 3 post-fertilization
Authors: Wang Ju , Zheng Wei , Zhang Shuoping , Yan Keqiang , Jin Miao , Hu Huiling , Ma Zhen , Gong Fei , Lu Guangxiu , Ren Yan , Lin Liang , Lin Ge , Hu Liang , Liu Siqi 
Published: September 2021

Abstract
Background
Although oocyte quality is the dominant factor determining embryo quality, few studies have been conducted to evaluate embryo quality based on the metabolites related to the oocyte. With quantification of the follicular fluid (FF) metabolites, in assisted reproductive technology (ART), this study sought to evaluate the embryo or oocyte quality through an informative approach.

Results
An evaluation model consisting of 17 features was generated to distinguish the embryo quality on day 3 post-fertilization, and phosphatidylcholines (PCs) were the key contributors to the evaluation. The model was extended to the patients under different ages and hyperstimulations, and the features were further enriched to facilitate the evaluation of the embryo quality. The metabolites were clustered through pathway analysis, leading to a hypothesis that accumulation of arachidonic acid induced by PCs might weaken embryo quality on day 3 post-fertilization.

Conclusions
A discriminating model with metabolic features elicited from follicular fluid was established, which enabled the evaluation of the embryo or oocyte quality even under certain clinical conditions, and the increase of PCs in follicular fluid implies the attenuation of embryo quality on day 3 post-fertilization.
Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis
Authors: Reddy Hemakumar M. , Bhattacharya Rupa , Tiwari Shrish , Mishra Kankadeb , Annapurna Pranatharthi , Jehan Zeenath , Praveena Nissankararao Mary , Alex Jomini Liza , Dhople Vishnu M. , Singh Lalji , Sivaramakrishnan Mahadevan , Chaturvedi Anurag , Rangaraj Nandini , Shiju Thomas Michael , Sreedevi Badanapuram , Kumar Sachin , Dereddi Ram Reddy , Rayabandla Sunayana M. , Jesudasan Rachel A. 
Published: September 2021

Abstract
Background
Deciphering the functions of Y chromosome in mammals has been slow owing to the presence of repeats. Some of these repeats transcribe coding RNAs, the roles of which have been studied. Functions of the noncoding transcripts from Y chromosomal repeats however, remain unclear. While a majority of the genes expressed during spermatogenesis are autosomal, mice with different deletions of the long arm of the Y chromosome (Yq) were previously also shown to be characterized by subfertility, sterility and sperm abnormalities, suggesting the presence of effectors of spermatogenesis at this location. Here we report a set of novel noncoding RNAs from mouse Yq and explore their connection to some of the autosomal genes expressed in testis.

Results
We describe a set of novel mouse male-specific Y long arm (MSYq)-derived long noncoding (lnc) transcripts, named Pirmy and Pirmy-like RNAs. Pirmy shows a large number of splice variants in testis. We also identified Pirmy-like RNAs present in multiple copies at different loci on mouse Y chromosome. Further, we identified eight differentially expressed autosome-encoded sperm proteins in a mutant mouse strain, XYRIIIqdel (2/3 Yq-deleted). Pirmy and Pirmy-like RNAs have homology to 5′/3′UTRs of these deregulated autosomal genes. Several lines of experiments show that these short homologous stretches correspond to piRNAs. Thus, Pirmy and Pirmy-like RNAs act as templates for several piRNAs. In vitro functional assays reveal putative roles for these piRNAs in regulating autosomal genes.

Conclusions
Our study elucidates a set of autosomal genes that are potentially regulated by MSYq-derived piRNAs in mouse testis. Sperm phenotypes from the Yq-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of MSYq-derived ncRNAs in male sterility and speciation.
Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep
Authors: Zhao Bingru , Luo Hanpeng , He Junmin , Huang Xixia , Chen Siqian , Fu Xuefeng , Zeng Weidan , Tian Yuezhen , Liu Shuli , Li Cong-jun , Liu George E. , Fang Lingzhao , Zhang Shengli , Tian Kechuan 
Published: September 2021

AbstractBackgroundCharacterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Merino is the most important breed of fine-wooled sheep in the world. In this study, we systematically investigated the complexity of sheep hair follicle development by integrating transcriptome and methylome datasets from Merino sheep skin.ResultsWe analysed 72 sequence datasets, including DNA methylome and the whole transcriptome of four gene types, i.e. protein-coding genes (PCGs), lncRNAs, circRNAs, and miRNAs, across four embryonic days (E65, E85, E105, and E135) and two postnatal days (P7 and P30) from the skin tissue of 18 Merino sheep. We revealed distinct expression profiles of these four gene types across six hair follicle developmental stages, and demonstrated their complex interactions with DNA methylation. PCGs with stage-specific expression or regulated by stage-specific lncRNAs, circRNAs, and miRNAs were significantly enriched in epithelial differentiation and hair follicle morphogenesis. Regulatory network and gene co-expression analyses identified key transcripts controlling hair follicle development. We further predicted transcriptional factors (e.g. KLF4, LEF1, HOXC13, RBPJ, VDR, RARA, and STAT3) with stage-specific involvement in hair follicle morphogenesis. Through integrating these stage-specific genomic features with results from genome-wide association studies (GWAS) of five wool-related traits in 7135 Merino sheep, we detected developmental stages and genes that were relevant with wool-related traits in sheep. For instance, genes that were specifically upregulated at E105 were significantly associated with most of wool-related traits. A phenome-wide association study (PheWAS) demonstrated that candidate genes of wool-related traits (e.g.SPHK1,GHR,PPP1R27,CSRP2,EEF1A2, andPTPN1) in sheep were also significantly associated with dermatological, metabolic, and immune traits in humans.ConclusionsOur study provides novel insights into the molecular basis of hair follicle morphogenesis and will serve as a foundation to improve breeding for wool traits in sheep. It also indicates the importance of studying gene expression in the normal development of organs in understanding the genetic architecture of economically important traits in livestock. The datasets generated here are useful resources for functionally annotating the sheep genome, and for elucidating early skin development in mammals, including humans.
Single-cell analysis at the protein level delineates intracellular signaling dynamic during hematopoiesis
Authors: Wang Jinheng , Tu Chenggong , Zhang Hui , Huo Yongliang , Menu Eline , Liu Jinbao 
Published: September 2021

Abstract
Background
Hematopoietic stem and progenitor cell (HSPC) subsets in mice have previously been studied using cell surface markers, and more recently single-cell technologies. The recent revolution of single-cell analysis is substantially transforming our understanding of hematopoiesis, confirming the substantial heterogeneity of cells composing the hematopoietic system. While dynamic molecular changes at the DNA/RNA level underlying hematopoiesis have been extensively explored, a broad understanding of single-cell heterogeneity in hematopoietic signaling programs and landscapes, studied at protein level and reflecting post-transcriptional processing, is still lacking. Here, we accurately quantified the intracellular levels of 9 phosphorylated and 2 functional proteins at the single-cell level to systemically capture the activation dynamics of 8 signaling pathways, including EGFR, Jak/Stat, NF-κB, MAPK/ERK1/2, MAPK/p38, PI3K/Akt, Wnt, and mTOR pathways, during mouse hematopoiesis using mass cytometry.

Results
With fine-grained analyses of 3.2 million of single hematopoietic stem and progenitor cells (HSPCs), and lineage cells in conjunction with multiparameter cellular phenotyping, we mapped trajectories of signaling programs during HSC differentiation and identified specific signaling biosignatures of cycling HSPC and multiple differentiation routes from stem cells to progenitor and lineage cells. We also investigated the recovery pattern of hematopoietic cell populations, as well as signaling regulation in these populations, during hematopoietic reconstruction. Overall, we found substantial heterogeneity of pathway activation within HSPC subsets, characterized by diverse patterns of signaling.

Conclusions
These comprehensive single-cell data provide a powerful insight into the intracellular signaling-regulated hematopoiesis and lay a solid foundation to dissect the nature of HSC fate decision. Future integration of transcriptomics and proteomics data, as well as functional validation, will be required to verify the heterogeneity in HSPC subsets during HSC differentiation and to identify robust markers to phenotype those HSPC subsets.
The cell adhesion molecule TMIGD1 binds to moesin and regulates tubulin acetylation and cell migration
Authors: Rahimi Nader , Ho Rachel X. Y. , Chandler Kevin Brown , De La Cena Kyle Oliver Corcino , Amraei Razie , Mitchel Ashley J. , Engblom Nels , Costello Catherine E. 
Published: September 2021

Abstract
Background
The cell adhesion molecule transmembrane and immunoglobulin (Ig) domain containing1 (TMIGD1) is a novel tumor suppressor that plays important roles in regulating cell–cell adhesion, cell proliferation and cell cycle. However, the mechanisms of TMIGD1 signaling are not yet fully elucidated.

Results
TMIGD1 binds to the ERM family proteins moesin and ezrin, and an evolutionarily conserved RRKK motif on the carboxyl terminus of TMIGD1 mediates the interaction of TMIGD1 with the N-terminal ERM domains of moesin and ezrin. TMIGD1 governs the apical localization of moesin and ezrin, as the loss of TMIGD1 in mice altered apical localization of moesin and ezrin in epithelial cells. In cell culture, TMIGD1 inhibited moesin-induced filopodia-like protrusions and cell migration. More importantly, TMIGD1 stimulated the Lysine (K40) acetylation of α-tubulin and promoted mitotic spindle organization and CRISPR/Cas9-mediated knockout of moesin impaired the TMIGD1-mediated acetylation of α-tubulin and filamentous (F)-actin organization.

Conclusions
TMIGD1 binds to moesin and ezrin, and regulates their cellular localization. Moesin plays critical roles in TMIGD1-dependent acetylation of α-tubulin, mitotic spindle organization and cell migration. Our findings offer a molecular framework for understanding the complex functional interplay between TMIGD1 and the ERM family proteins in the regulation of cell adhesion and mitotic spindle assembly, and have wide-ranging implications in physiological and pathological processes such as cancer progression.
Design, synthesis, and preliminary evaluation of a potential synthetic opioid rescue agent
Authors: Hedrick Sidnee L. , Luo Dan , Kaska Sophia , Niloy Kumar Kulldeep , Jackson Karen , Sarma Rupam , Horn Jamie , Baynard Caroline , Leggas Markos , Butelman Eduardo R. , Kreek Mary Jeanne , Prisinzano Thomas E. 
Published: September 2021

Abstract
Background
One of the most prominent opioid analgesics in the United States is the high potency agonist fentanyl. It is used in the treatment of acute and chronic pain and as an anesthetic adjuvant. When used inappropriately, however, ingestion of just a few milligrams of fentanyl or other synthetic opioid can cause opioid-induced respiratory depression (OIRD), often leading to death. Currently, the treatment of choice for OIRD is the opioid receptor antagonist naloxone. Recent reports, however, suggest that higher doses or repeated dosing of naloxone (due to recurrence of respiratory depression) may be required to reverse fully fentanyl-induced respiratory depression, rendering this treatment inadequate. To combat this synthetic opioid overdose crisis, this research aims at identifying a novel opioid reversal agent with enhanced efficacy towards fentanyl and other synthetic opioids.

Methods
A series of naltrexone analogues were characterized for their ability to antagonize the effects of fentanyl in vitro utilizing a modified forskolin-induced cAMP accumulation assay. Lead analogue 29 was chosen to undergo further PK studies, followed by in vivo pharmacological analysis to determine its ability to antagonize opioid-induced antinociception in the hot plate assay.

Results
A series of potent MOR antagonists were identified, including the highly potent analogue 29 (IC50 = 2.06 nM). Follow-up PK studies revealed 29 to possess near 100% bioavailability following IP administration. Brain concentrations of 29 surpassed plasma concentrations, with an apparent terminal half-life of ~ 80 min in mice. In the hot plate assay, 29 dose-dependently (0.01–0.1 mg/kg; IP) and fully antagonized the antinociception induced by oxycodone (5.6 mg/kg; IP). Furthermore, the dose of 29 that is fully effective in preventing oxycodone-induced antinociception (0.1 mg/kg) was ineffective against locomotor deficits caused by the KOR agonist U50,488.

Conclusions
Methods have been developed that have utility to identify enhanced rescue agents for the treatment of OIRD. Analogue 29, possessing potent MOR antagonist activity in vitro and in vivo, provides a promising lead in our search for an enhanced synthetic opioid rescue agent.
Positive association between the ratio of triglycerides to high-density lipoprotein cholesterol and diabetes incidence in Korean adults
Authors: Kim Joungyoun , Shin Sang-Jun , Kim Ye-Seul , Kang Hee-Taik 
Published: September 2021

Abstract
Background
Insulin resistance is associated with the incidence of diabetes and cardiovascular diseases such as myocardial infarction. The ratio of triglycerides (TG) to high-density lipoprotein cholesterol (HDL-C) (TG/HDL-C ratio) is positively correlated with insulin resistance. This study aimed to investigate the relationship between the TG/HDL-C ratio and the incidence of diabetes in Korean adults.

Methods
This retrospective study used data from the National Health Insurance Service-National Health Screening Cohort. The TG/HDL-C ratio was divided into three tertiles, the T1, T2, and T3 groups, based on sex. We estimated the hazard ratios (HRs) and 95% confidence intervals (CIs) for diabetes using multivariate Cox proportional hazards regression analyses.

Results
A total of 80,693 subjects aged between 40 and 79 years were enrolled. The median follow-up period was 5.9 years. The estimated cumulative incidence of diabetes in the T1, T2, and T3 groups was 5.94%, 8.23%, and 13.50%, respectively, in men and 4.12%, 4.72%, and 6.85%, respectively, in women. Compared to T1, the fully adjusted HRs (95% CIs) of the T2 and T3 groups for new-onset diabetes were 1.17 (1.06–1.30) and 1.47 (1.34–1.62), respectively, in men and 1.20 (1.02–1.42) and 1.52 (1.30–1.78), respectively, in women.

Conclusions
Increased TG/HDL-C ratio was significantly associated with a higher risk of new-onset diabetes in both sexes.
TRIB3 regulates FSHR expression in human granulosa cells under high levels of free fatty acids
Authors: Wang Nan , Si Chenchen , Xia Lan , Wu Xian , Zhao Sheng , Xu Huihui , Ding Zhide , Niu Zhihong 
Published: September 2021

Abstract
Background
Granulosa cells (GCs) in cumulus oophorus highly express follicle stimulating hormone receptor (FSHR), which is the most important mediator of both estradiol synthesis and oocyte maturation. Obese women have elevated free fatty acids (FFAs) levels in their follicular fluids and decreased FSHR expression in GCs, which is related to an altered protein kinase B/glycogen synthase kinase 3β (Akt/GSK3β) signaling pathway. Such FFA increases accompany 3-fold rises in pseudokinase 3 (TRIB3) expression and reduce the Akt phosphorylation status in both the human liver and in insulinoma cell lines. Therefore, in a high FFA environment, we determined if TRIB3 mediates regulation of FSHR via the Akt/GSK3β signaling pathway in human GCs.

Methods
GCs from women undergoing in vitro fertilization were collected and designated as high and low FFAs cohorts based on their follicular fluid FFA content. GCs with low FFA levels and a human granulosa-like tumor (KGN) cell line were exposed to palmitic acid (PA), which is a dominate FFA follicular fluid constituent. The effects were assessed of this substitution on the Akt/GSK3β signaling pathway activity as well as the expressions of TRIB3 and FSHR at both the gene and protein levels by qPCR, Western blot and immunofluorescence staining analyses. Meanwhile, the individual effects of TRIB3 knockdown in KGN cells and p-AKT inhibitors were compared to determine the mechanisms of FFA-induced FSHR downregulation.

Results
The average FSH dose consuming per oocyte (FSH dose/oocyte) was elevated and Top embryo quality ratio was decreased in women with high levels of FFAs in their follicular fluid. In these women, the GC TRIB3 and ATF4 protein expression levels were upregulated which was accompanied by FSHR downregulation. Such upregulation was confirmed based on corresponding increases in their gene expression levels. On the other hand, the levels of p-Akt decreased while p-GSK3β increased in the GCs. Moreover, TRIB3 knockdown reversed declines in FSHR expression and estradiol (E2) production in KGN cells treated with PA, which also resulted in increased p-Akt levels and declines in the p-GSK3β level. In contrast, treatment of TRIB3-knockdown cells with an inhibitor of p-Akt (Ser473) resulted in rises in the levels of both p-GSK3β as well as FSHR expression whereas E2 synthesis fell.

Conclusions
During exposure to a high FFA content, TRIB3 can reduce FSHR expression through stimulation of the Akt/GSK3β pathway in human GCs. This response may contribute to inducing oocyte maturation.