bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ detection of individual classical MHC-I gene products in cancer
Authors: Gonzalez-Ericsson Paula I. , Opalenik Susan R. , Sanchez Violeta , Palubinsky Amy , Hanna Ann , Sun Xiaopeng , Ocampo Andres A. , Garcia Guadalupe , Maldonado Leonel , Morante Zaida , Vidaurre Tatiana , Valencia Guillermo , Gomez Henry L. , Sanders Melinda E. , Kennedy Laura C. , Phillips Elizabeth , Balko Justin M. 
Published: January 2025

Abstract
Tumor-specific HLA class I expression is required for cytotoxic T-cell elimination of cancer cells expressing tumor-associated or neo-antigens. Cancers downregulate antigen presentation to avoid adaptive immunity. The highly polymorphic nature of the genes encoding these proteins, coupled with quaternary-structure changes after formalin fixation, complicate detection by immunohistochemistry. In this study we determined recognition of 16 specific HLA-A, B and C alleles by 15 antibodies commercially available for immunohistochemical use, identifying and validating pan and specific HLA-A, B, and C antibodies, providing a validated method that can be applied to investigate HLA-A, B and C molecule–specific loss in cancer. We applied this approach to a series of breast cancers as a proof of utility, identifying differential HLA-A, B and C loss, with a higher incidence of HLA-A and B loss in hormone-driven breast cancers, HLA-B loss in HER2+ cancers, and an equal loss of all three molecules in triple-negative disease. Additionally, we found that at the protein level, HLA-A and B loss were early events prevalent in premalignant lesions, while HLA-C loss was less common throughout tumor evolution. Effective response to immunotherapies such as checkpoint inhibitors and MHC-I–targeted cancer vaccines, which hinge on the carriage of specific allele groups, require MHC-I expression on tumor cells. These findings have implications for the success of checkpoint inhibitors and vaccine strategies.
The Impact of Contemporary Glucagon-like Peptide-1 Receptor Agonists on the Onset, Severity, and Conversion to Arthroplasty in Hip and Knee Osteoarthritis
Authors: Porto Joshua R. , Lavu Monish S. , Hecht Christian J. , Kaelber David C. , Sculco Peter K. , Heckmann Nathanael D. , Kamath Atul F. 
Published: January 2025

Background: The growing popularity of glucagon-like peptide-1 receptor agonists (GLP-1-RAs) for weight loss could significantly impact joint preservation and arthroplasty. While this will in part be driven by the association between obesity, osteoarthritis (OA), and total joint arthroplasty (TJA), recent evidence also indicates that GLP-1-RAs may have direct joint-protective, anti-inflammatory effects. Purpose: To evaluate the association between GLP-1-RA use and the onset and progression of hip and knee OA in an obese population. Study Design: Cohort study; Level of evidence, 3. Methods: A national health network was queried for patients with an index visit between June 1, 2021, and January 1, 2023, and a body mass index (BMI) ≥30. Patients were stratified into groups without (n = 1,092,225) and with(n = 237,043) preexisting hip and/or knee OA. One-to-one propensity score matching was used to balance GLP-1-RA use based on age, sex, race, BMI, and comorbid type 2 diabetes mellitus. Primary outcomes were incidence of hip OA, knee OA, major joint injections, total hip arthroplasty (THA), and total knee arthroplasty (TKA) within 1 year. Cox proportional hazards models were used to estimate hazard ratios (HRs) between cohorts prescribed and not prescribed GLP-1-RAs. Results: In patients with preexisting OA, GLP-1-RA use correlated with reduced odds of conversion to THA (1.1% vs 2.2%; HR, 0.6; 95% CI, 0.5 to 0.8) and TKA (1.4% vs 2.1%; HR, 0.8; 95% CI, 0.6 to 0.9) within 1 year. In patients without preexisting OA, GLP-1-RA use was associated with an increased incidence of hip OA (0.9% vs 0.7%; HR, 1.4; 95% CI, 1.2 to 1.6), knee OA (2.1% vs 1.9%; HR, 1.3; 95% CI, 1.2 to 3.1), major joint injections (2.2% vs 1.8%; HR, 1.4; 95% CI, 1.3 to 1.5), and TKA (0.09% vs 0.04%; HR, 2.6; 95% CI, 1.6 to 4.3). Comparing cohorts without prior OA, patients who were prescribed a GLP-1-RA demonstrated slightly greater decreases in BMI (–1.00; 95% CI, –1.06 to −0.96) at 1-year after the index visit compared with patients not prescribed a GLP-1-RA (–0.90; 95% CI, –0.94 to −0.84). However, in patients with a prior diagnosis of hip or knee OA, there was no difference noted in BMI change. Conclusion: GLP-1-RAs may provide direct disease-modifying behaviors in patients with preexisting OA diagnosis, per a reduced risk of conversion to TJA not attributable to weight loss. Further investigation is also needed to elucidate the association between GLP-1-RA use and the increased incidence of OA diagnosis and conversion to TKA in patients with no preexisting OA diagnosis.
Trochleoplasty Utilization in the Management of Patellofemoral Instability: Results From an International Survey of Surgeons
Authors: Williams Brendan A. , Batley Morgan G. , Schlechter John A. , Redler Lauren H. , Yaniv Moshe , Friel Nicole A. , Parikh Shital N. , Pace J. Lee , Shubin Stein Beth E. , Waldron Sean , Logterman Stephanie L. , Shea Kevin , Bradley Kendall E. , Crawford Eileen A. , Greenberg Elliot , Hannon Joseph , Kerrigan Alicia , Kuba Megan H.M. , Albaugh Jeffrey 
Published: January 2025

Background: Considerable variability exists in the described clinical and radiographic indications for use, surgical techniques, postoperative management, and risk profile after trochleoplasty for the management of patellofemoral instability (PFI). In areas of clinical uncertainty, a cohesive summary of expert opinion and identification of areas of variation in current practice can be useful in guiding current practice and future research efforts. Purpose: To assess the current indications for use, surgical techniques, postoperative rehabilitation practices, and observed complication profile for trochleoplasty in the management of PFI among surgeons who perform this procedure. Study Design: Cross-sectional study. Methods: A 21-item cross-sectional survey was developed to evaluate trochleoplasty in its current practice among surgeons around the world. The survey was distributed between December 2021 and April 2022 to the orthopaedic surgeon membership of multiple national and international knee, arthroscopy, and sports medicine societies to identify any surgeon with experience performing the trochleoplasty procedure in practice for the management of PFI. Descriptive statistics of survey responses were performed to address study aims, and univariate analyses were performed to compare differences between high- and low-volume trochleoplasty surgeons. Results: Survey distribution identified 32 orthopaedic surgeons with experience performing the trochleoplasty procedure. Procedural indications were most commonly felt to be met with Dejour classification of B or D on magnetic resonance imaging. Trochleoplasty was felt by most to be appropriate as a primary surgical intervention for PFI. A majority of surgeons utilized a Bereiter (thin-flap) trochleoplasty technique with suture-based fixation and performed concurrent medial patellofemoral ligament reconstruction, but other concomitant procedures varied. Range-of-motion precautions and bracing practices varied among respondents, and arthrofibrosis was the most frequently cited observed complication. High- and low-volume trochleoplasty surgeons differed in their radiographic and age-based indications for the procedure. Conclusion: Study findings indicated that variation exists in the surgical indicators, technique, and postoperative rehabilitation practices of trochleoplasty surgeons, with specific differences noted between high- and low-volume trochleoplasty surgeons. The results of this survey identified areas of equipoise and treatment variation that should direct future research efforts in the study of the trochleoplasty procedure.
A high-resolution global time series of street-network sprawl
Authors: Barrington-Leigh Christopher , Millard-Ball Adam 
Published: January 2025

Systems of street networks form a backbone for many aspects of human life and, once laid down, urban streets represent a nearly immutable influence on future urban form and concomitant travel, energy, and social outcomes. Moreover, as humanity is currently passing through its peak urbanization rate, decisions about how to design such networks at the local scale are being made faster than ever before. In this work, we quantify local street connectivity and provide a global, high-resolution time series of our Street Network Disconnectedness Index (SNDi) as an open data set. We derive a stylized version of the actual geographic road network from the 2023 vintage of OpenStreetMap by simplifying complex intersections, divided roads, and offset intersections. Using this functional representation of the network corrects systematic biases in derived properties of the network. We couple this simplified network with a newly available time series of urbanization in order to compute SNDi and provide a dynamic analysis to the year 2019 and a cross-sectional analysis for 2023. We release our data as the raw network of edges and nodes and as aggregates to a 1 km grid, to countries, and to five subnational administrative levels. We also provide interactive visualizations at sprawlmap.org . Overall, our findings present a picture of rapidly worsening street-network connectivity in many regions of the world.
Unravelling the transcriptomic symphony of muscle ageing: key pathways and hub genes altered by ageing and caloric restriction in rat muscle revealed by RNA sequencing
Authors: Altab Gulam , Merry Brian J. , Beckett Charles W. , Raina Priyanka , Lopes Inês , Goljanek-Whysall Katarzyna , de Magalhães João Pedro 
Published: January 2025

Abstract
Age-related muscle wasting, sarcopenia is an extensive loss of muscle mass and strength with age and a major cause of disability and accidents in the elderly. Mechanisms purported to be involved in muscle ageing and sarcopenia are numerous but poorly understood, necessitating deeper study. Hence, we employed high-throughput RNA sequencing to survey the global changes in protein-coding gene expression occurring in skeletal muscle with age. Caloric restriction (CR) is a known prophylactic intervention against sarcopenia. Therefore, total RNA was isolated from the muscle tissue of both rats fed ad libitum and CR rats. RNA-seq data were subjected to Gene Ontology, pathway, co-expression, and interaction network analyses. This revealed the functional pathways most activated by both ageing and CR, as well as the key “hub” proteins involved in their activation.
RNA-seq revealed 442 protein-coding genes to be upregulated and 377 to be downregulated in aged muscle, compared to young muscle. Upregulated genes were commonly involved in protein folding and immune responses; meanwhile, downregulated genes were often related to developmental biology. CR was found to suppress 69.7% and rescue 57.8% of the genes found to be upregulated and downregulated in aged muscle, respectively. In addition, CR uniquely upregulated 291 and downregulated 304 protein-coding genes. Hub genes implicated in both ageing and CR included Gc, Plg, Irf7, Ifit3, Usp18, Rsad2, Blm and RT1-A2, whilst those exclusively implicated in CR responses included Alb, Apoa1, Ambp, F2, Apoh, Orm1, Mx1, Oasl2 and Rtp4. Hub genes involved in ageing but unaffected by CR included Fgg, Fga, Fgb and Serpinc1. In conclusion, this comprehensive RNA sequencing study highlights gene expression patterns, hub genes and signalling pathways most affected by ageing in skeletal muscle. This data may provide the initial evidence for several targets for potential future therapeutic interventions against sarcopenia.
Improving natural red pigment production by Streptomyces phaeolivaceus strain GH27 for functionalization of textiles with in silico ADME prediction
Authors: Sayed Gehad H. El , Fadel Mohamed , Fouad Rasha , Ahmed Hend M. , Hamed Ahmed A. 
Published: January 2025

Abstract
The red pigment was recovered from the S. phaeolivaceus GH27 isolate, which was molecularly identified using 16S rRNA gene sequencing and submitted to GenBank as OQ145635.1. The ideal growth conditions included 1% (w/v) starch, diammonium citrate, dibasic sodium phosphate, 5% (v/v) inoculum, pH 8, a rotation speed of 150 rpm, a temperature of 37 °C, and an incubation period of 9 days. Using ethanol as a solvent, the red pigment was effectively recovered. Data indicates that pigment content remained steady at 40 and 50 °C. Heating the pigment extract to 60, 70, 80, 90, and 100 °C for one hour results in pigment retention of 98%, 96.5%, 95.5%, 94.6%, and 92.6% of its pigment density, respectively. Studies indicate that the pigment extracts exhibited optimal stability at alkaline pH levels. The findings demonstrate that the red pigment extract has a peak absorbance range of 280–340 nm, with a λmax of 300 nm. GC/MS analysis revealed that the primary components of the pigment extract were linolenic acid methyl ester and oleic acid methyl ester, constituting 26.41% and 25.25%, respectively. Fabrics dyed with extracted red pigment exhibit excellent fastness when using the comprehensive green method. In comparison to conventional and nanotechnological attributes, printed samples exhibit significant color strength without environmental repercussions. The treatment of cotton, wool, and polyester samples suppressed pathogen growth to differing extents. Polyester had the most important inhibitory effects on Staphylococcus aureus (50.03%) and Bacillus cereus (39.49%). The ADME physicochemical properties of the predominant medication were assessed, together with its bioavailability. The radar plot demonstrated ideal parameters for size, polarity, lipophilicity, solubility, and saturation, excluding flexibility. It exhibited intermediate synthetic accessibility, exceptional permeability and absorption, elevated gastrointestinal absorption, and blood–brain barrier penetration; nonetheless, it did not adhere to the medicinal chemistry rule of three.

Graphical Abstract
Associations between changes in the gut microbiota and liver cirrhosis: a systematic review and meta-analysis
Authors: Liu Ye , Chen Ziwei , Li Chang , Sun Tianhan , Luo Xuanmei , Jiang Boyue , Liu Meilan , Wang Qing , Li Tong , Cao Jianfu , Li Yayu , Chen Yuan , Kuai Lu , Xiao Fei , Xu Hongtao , Cui Hongyuan 
Published: January 2025

Abstract

Objective
Summaries of the relationships between the microbiota and liver cirrhosis and their conclusions are not consistent. This study describes microbial differences in patients with liver cirrhosis by performing a meta-analysis.

Methods
We searched PubMed, Embase, Web of Science, and the Cochrane Library and collected related articles published before March 10, 2024. Ratio of autochthonous to non-autochthonous taxa was calculated as the cirrhosis dysbiosis ratio (CDR). Using a random-effects model, the standard mean deviation (SMD) and 95% confidence interval (CI) were calculated. We subsequently performed subgroup, sensitivity, and publication bias analyses. cirrhosis dysbiosis ratio.

Results
A total of 53 eligible papers including 5076 participants were included. The pooled estimates revealed a moderately significant reduction in gut microbiome richness in patients with liver cirrhosis compared with controls, including the Shannon, Chao1, observed species, ACE, and PD indices, but no significant difference was observed for the Simpson index. Over 80% of the studies reported significant differences in β diversity. Families Enterobacteriaceae and Pasteurellaceae, belonging to the phylum Proteobacteria, along with the family Streptococcaceae and the genera Haemophilus, Streptococcus, and Veillonella, were significantly associated with liver cirrhosis compared to the control group. In contrast, the healthy group exhibited a higher abundance of the class Clostridia, particularly the families Lachnospiraceae and Ruminococcaceae, which are known for their diversity and role as common gut commensals. Furthermore, the class Bacilli, predominantly represented by the genus Streptococcus, was markedly enriched in the cirrhosis group.

Conclusions
The microbiota richness of liver cirrhosis patients was lower than that of healthy controls. Alterations in gut microbiota linked to liver cirrhosis were characterized by a decrease in Lachnospiraceae, Ruminococcaceae, and Clostridia and an enrichment of Enterobacteriaceae, Pasteurellaceae, Streptococcaceae, Bacilli, and Streptococcus.
Relationship between kidney function and healthy life expectancy: A historical cohort study
Authors: Ogura Hisayuki , Toyama Tadashi , Samuta Hikaru , Hirako Kohei , Itatani Tomoya , Nakagawa Shiori , Oshima Megumi , Kitajima Shinji , Hara Akinori , Sakai Norihiko , Shimizu Miho , Takura Tomoyuki , Wada Takashi , Iwata Yasunori 
Published: January 2025

Abstract

Background
The impact of chronic kidney disease (CKD) on healthy life expectancy and healthcare costs requires research. This study examined associations between CKD and healthy life expectancy, and its economic burden.

Methods
This study of community-dwelling adults residing in Hakui City, Ishikawa Prefecture, Japan used data from the National Health Insurance database between 2012 and 2022. Participants were grouped by baseline estimated glomerular filtration rate (eGFR) (< 45, ≥ 45 to < 60, ≥60 to < 75, ≥75 to < 90, and ≥ 90 mL/min/1.73 m²). The primary endpoint was a composite of becoming a care level ≥ 2 or death. Multivariable Cox proportional hazards models were used to calculate the risk regarding time to the primary endpoint. Secondary endpoints were the annual medical and long-term care costs.

Results
The 5,592 participants had a mean follow-up of 6.4 years. The hazard ratio was 1.86 (95% confidence interval [CI]: 1.35 to 2.55) for the eGFR < 45 group and 1.60 (95% CI: 1.13 to 2.25) for the eGFR ≥ 90 group, both compared with the eGFR ≥ 60 to < 75 group. Both annual costs were significantly higher in the lower eGFR groups than in the higher eGFR groups. For the eGFR < 45 group, the median medical care cost was 0.38 million yen/year in all participants and the median long-term care cost was 0.40 million yen/year in primary endpoint achievers. A lower eGFR was correlated with longer unhealthy years of life.

Conclusions
Higher and lower eGFRs were associated with increased risks of reduced healthy life expectancy. A lower eGFR was associated with higher medical and long-term care costs.
Visible and invisible cultural patterns influencing women’s use of maternal health services among Igala women in Nigeria: a focused ethnographic study
Authors: Opara Uchechi Clara , Iheanacho Peace Njideka , Petrucka Pammla 
Published: January 2025

Abstract

Background
Explicit and implicit cultural patterns are critical cultural norms, beliefs, and practices that determine women’s health-seeking behaviour. These cultural patterns could limit women’s use of maternal health services, resulting in maternal health complications. The study aims to provide an in-depth understanding of explicit and implicit cultural patterns, their meanings and how they influence women’s use of maternal health services among Igala women in Nigeria.

Methods
Roper and Shapira’s (2000) focused ethnography was employed with 43 women aged 18–43 years recruited using the purposive and snowballing technique. The study was conducted with 21 women for one-on-one interviews and two focus group discussions with six women in the rural area and seven women in the urban area. In addition, participant observation of nine women from the third trimester to birth was conducted, yielding 189 h of observation in two primary healthcare facilities in rural and urban areas. Data analysis was conducted using Roper and Shapira’s (2000) method.

Result
Three themes were generated using the PEN3 cultural model: perceptions, enabler, and nurturers. Subthemes generated under the theme of perception were, Belief in witchcraft, Pregnancy announces itself, I cannot tell people I am in labour, and Unspoken acquiescence to the culture. Under the theme of nurturer, Home birth was found to limit access to maternal health services. The theme of enabler yielded subthemes such as You are not woman enough; I want my placenta and Rising matriarchs.

Conclusion
Implicit and explicit cultural patterns significantly influence women’s use of maternal health services. Given the complexity of culture and its influence on women’s use of maternal health services, multifaceted strategies tailored to the cultural needs of communities are needed to enhance the realization of Sustainable Development Goal #3:1 in Nigeria.
Nurse worry as a trigger for rapid response team activation improving outcomes: a retrospective cohort study in non-critical units
Authors: Gentil Luana L.S. , Nascimento Milena S. , Jaures Michele , de Carvalho Leonardo P. , Laselva Claudia R. , Brandi Simone 
Published: January 2025

Abstract

Background
Patients hospitalized outside of monitored environments may experience sudden clinical worsening requiring transfer to the Intensive Care Unit. Early detection based on the clinical nurse’s identification of the risk of clinical deterioration represents an opportunity to prevent serious adverse events. Nurse worry is defined as the use of clinical reasoning combined with intuition that precedes the patient’s clinical deterioration.

Objective
The objective of this study was to evaluate nurse worry as a trigger for rapid response team activation in patients hospitalized in non-critical units and its association with the need in ICU admission.

Methods
This retrospective cohort study utilized data retrieved from an anonymized institutional database used to monitor the actions of the rapid response team. Data collected from January 2021 to December 2022 were analyzed, encompassing patients over 18 years old admitted to non-critical units and evaluated by the rapid response team. Analyzed variables included demographic characteristics, MEWS score, and causes for activating the rapid response team, such as changes in vital signs and nurse worry. Main outcomes assessed were transfer to the ICU, medical procedures, and drug administration. Patients were divided into three groups for analysis: those triggered for RRT assessment exclusively by changes in vital signs, those triggered exclusively by nurse worry and those triggered by the nurse worry combined with changes in vital signs.

Results
A total of 4634 rapid response team consultations were included, with 1574 triggered by changes in vital signs, 1263 triggered by nurse worry and 1797 triggered by the nurse worry associated with changes in vital signs. The group with nurse concern showed a lower need for transfers to the ICU (40%) compared to the group with changes in vital signs (50%) p < 0.001 although there was no difference in relation to the need for medical procedures,17% in both groups.

Conclusion
The NW emerges as a relevant factor in triggering RRT and may be associated with improved outcomes, such as reduced need for ICU transfers. However, the observational design of the study does not allow for establishing causal relationships.