bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the material basis and mechanism of action of clinacanthus nutans in treating renal cell carcinoma based on metabolomics and network pharmacology
Authors: Ye Zhandong , Fang Zhiqiang , Li Dan , Lin Xiaogang , Huang Song 
Published: October 2023

Background:

Clinacanthus nutans (for abbreviation thereafter) is often used as medicine in the form of fresh juice in the folk to treat many kinds of cancers, including renal cell carcinoma (RCC). It is speculated that its active ingredient may have heat sensitivity, but there are currently no reports on this aspect. Therefore, based on the folk application for fresh juice of C nutans, this study used metabonomics and network pharmacology to explore the material basis and mechanism of action of C nutans against RCC.

Methods:
Firstly, untargeted metabolomics profiling was performed by Liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry to screen the metabolites down-regulated by heat in the extract of C nutans. Secondly, we collected the targets of metabolites in the Swiss Target Prediction platform. In addition, the targets of RCC were obtained in the GeneCards database. The “component-target-disease” network was established by Cytoscape3.9.0 software. Then we constructed a protein-protein interaction network in the STRING network platform to screen core targets. The gene ontology and kyoto encyclopedia of genes and genomes enrichment analysis of core targets were carried out to predict the relevant pathway of C nutans in the treatment of RCC. Finally, the molecular docking verification of the core targets were carried out.

Results:
In this study, 35 potential active ingredients and 125 potential targets were obtained. And the core targets were Cellular tumor antigen p53, Signal transducer and activator of transcription 3, and so on. Then, 48 biological processes, 30 cell components, and 36 molecular functions were obtained by gene ontology enrichment analysis. Besides, 44 pathways were obtained by Kyoto encyclopedia of genes and genomes enrichment analysis, including Pathway in cancer, PI3K-Akt signal pathway, P53 signal pathway, and so on. The docking model between the core target and its corresponding components was stable.

Conclusion:
This research is based on the folk application of C nutans, showed its potential active ingredients by metabonomics, and predicted the potential mechanism of C nutans in the treatment of RCC by network pharmacology. It provides new references for follow-up research and new drug development.
A novel robot-assisted knee arthroplasty system (ROSA) and 1-year outcome: A single center experience
Authors: Demirtas Yunus , Emet Abdulsamet , Ayik Gokhan , Cakmak Gokhan , Aksahin Ertugrul , Celebi Levent 
Published: October 2023

Background:
Total knee arthroplasty is a successful procedure in the treatment of knee osteoarthritis. Searches in surgical technique have focused surgeons in particular on implant alignment. For this purpose, the use of robot-assisted total knee arthroplasty has become increasingly common in the last 10 years.

Methods:
A total of 46 patients (66 knees) who were operated for knee osteoarthritis with Robotic Surgical Assistant (ROSA, Zimmer-Biomet, Warshaw, Indiana, USA) between 2021 and 2023 were included in the study. Preoperative planning and intraoperative incision time, total surgical time, range of motion and follow-up time recorded. Oxford knee scores and knee society scores (KSS) of the patients were compared before and after surgery. At the last follow-up Forgotten Joint Score and the sagittal and coronal plane alignments were evaluated.

Results:
Preoperative mean Oxford score of the right knee of the patients was 18.5 ± 3.2, post-surgery mean Oxford score progressed to 43.5 ± 2.2. While the preoperative left knee Oxford score of the patients was 16.9 ± 2.3, the mean left knee Oxford score improved to 43.4 ± 2.2 postoperatively. The mean KSS score of the patients’ right knee preoperatively was 49.7 ± 3.5, and progressed to 89.2 ± 4.7 postoperatively. While the preoperative mean left knee KSS score of the patients was 46.5 ± 4.3, the mean KSS score improved to 89.8 ± 3.2 postoperatively. The mean Forgotten Joint Score of the left knee at the last follow-up of the patients was 77.4 ± 3.8, while the mean Forgotten Joint Score of the right knee was 75.4 ± 5.9.

Conclusion:
The results of ROSA-supported knee arthroplasty found to be functionally successful.
Highly active antiretroviral therapy-related effects on morphological connectivity in HIV
Authors: Wang Yiwen , Wu Guangyao , Wen Zhi , Lei Hao , Lin Fuchun 
Published: October 2023

Objective:
Suboptimal concentration of the antiretroviral drug is insufficient to inhibit HIV destruction on brain structure and function due to the resistance of blood brain barrier. We aimed to investigate highly active antiretroviral therapy (HAART)-related effects on the morphological connectivity in people with HIV (PWH).

Design:
Case–control study.

Methods:
Fifty-five HAART-treated for more than 3 months and 54 untreated PWH, as well as 66 demographically matched healthy controls underwent a high-resolution 3D T1-weighted MRI. Individual-level morphological brain network based on gray matter volume of 90 brain regions was constructed and network topological properties were analyzed. Network-based statistics (NBS) was performed to identify sub-networks showing significant differences in morphological connectivity. Correlation and mediation analyses were employed to evaluate associations between the morphological properties and clinical variables of PWH.

Results:
Although PWH exhibited small-world architecture in their morphological brain networks, untreated PWH demonstrated altered network properties while HAART-treated PWH showed relatively similar network properties compared to healthy controls. Furthermore, HAART-related effects were mainly involved the bilateral putamen and left thalamus. The findings of NBS further indicated the cortico-striatum-thalamic-cortical loop was involved in the therapeutic-associated morphological network. The positive correlations between the HAART treatment and nodal degree and efficiency of the putamen were mediated by the number of CD4+ T lymphocytes.

Conclusions:
The topological properties are recovered to normal in PWH after HAART and the effects induced by HAART are mostly within the cortical-subcortical circuit.
Association of urine biomarkers of kidney health with subclinical cardiovascular disease among men with and without HIV
Authors: Lai Mason , Madden Erin , Shlipak Michael G. , Scherzer Rebecca , Post Wendy S. , Vittinghoff Eric , Haberlen Sabina , Brown Todd T. , Wolinsky Steven M. , Witt Mallory D. , Ho Ken , Abraham Alison G. , Parikh Chirag R. , Budoff Matthew , Estrella Michelle M. 
Published: October 2023

Objective:
The aim of this study was to determine whether urine biomarkers of kidney health are associated with subclinical cardiovascular disease among men with and without HIV.

Design:
A cross-sectional study within the Multicenter AIDS Cohort Study (MACS) among 504 men with and without HIV infection who underwent cardiac computed tomography scans and had urine biomarkers measured within the preceding 2 years.

Methods:
Our primary predictors were four urine biomarkers of endothelial (albuminuria), proximal tubule dysfunction (alpha-1-microglobulin [A1 M] and injury (kidney injury molecule-1 [KIM-1]) and tubulointerstitial fibrosis (pro-collagen-III N-terminal peptide [PIIINP]). These were evaluated for association with coronary artery calcium (CAC) prevalence, CAC extent, total plaque score, and total segment stenosis using multivariable regression.

Results:
Of the 504 participants, 384 were men with HIV (MWH) and 120 were men without HIV. In models adjusted for sociodemographic factors, cardiovascular disease risk factors, eGFR, and HIV-related factors, each two-fold higher concentration of albuminuria was associated with a greater extent of CAC (1.35-fold higher, 95% confidence interval 1.11–1.65), and segment stenosis (1.08-fold greater, 95% confidence interval 1.01–1.16). Associations were similar between MWH and men without HIV in stratified analyses. The third quartile of A1 M showed an association with greater CAC extent, total plaque score, and total segment stenosis, compared with the lowest quartile.

Conclusion:
Worse endothelial and proximal tubule dysfunction, as reflected by higher urine albumin and A1 M, were associated with greater CAC extent and coronary artery stenosis.
Association of tenofovir diphosphate and lamivudine triphosphate concentrations with HIV and hepatitis B virus viral suppression
Authors: Lartey Margaret , Ganu Vincent J. , Tachi Kenneth , Yang Hongmei , Anderson Peter L. , Langaee Taimour , Ojewale Oluwayemisi , Boamah Isaac , Obo-Akwa Adjoa , Antwi Kenneth , Bushman Lane R. , Ellison Lucas , Kwara Awewura 
Published: October 2023

Objective:
Concentrations of tenofovir diphosphate (TFV-DP) and lamivudine triphosphate (3TC-TP) in cells are correlates of medication adherence and antiviral activity. However, studies have yet to characterize the simultaneous relationship between TFV-DP and 3TC-TP concentrations with HIV and hepatitis B virus (HBV) suppression.

Methods:
Individuals with HIV/HBV coinfection on tenofovir disoproxil fumarate (TDF)-containing antiretroviral therapy (ART) were enrolled. Peripheral blood mononuclear cells (PBMCs) and dried blood spots (DBS) samples were collected and steady-state TFV-DP and 3TC-TP concentrations quantified using validated methods. The relationship between patient factors, TFV-DP, and 3TC-TP concentrations in PBMCs and DBS with HBV and HIV viral suppression were examined.

Results:
Of 138 participants on TDF-containing ART for a median duration (range) of 6 (0.75–15) years, the median age was 43 years and 64% were women. Overall, 128 (92.8%) and 129 (93.5%) had suppressed HIV and HBV viral loads, respectively. Of the 128 participants with suppressed HIV, 122 (95.3%) had suppressed HBV. Self-reported ART adherence, recent change to dolutegravir-based ART, TFV-DP, and 3TC-TP concentrations in PBMCs and DBS were associated with HIV RNA suppression, while HBe antigen positivity, HIV suppression, and TFV-DP concentrations in DBS were associated with HBV DNA suppression (including six persons with HBV nonsuppression and HIV suppression).

Conclusion:
Long-term TDF/3TC-conatining ART was highly efficacious in individuals with HIV/HBV coinfection. Higher TFV-DP concentrations were predictive of suppression for both viruses. Persistent HBV viremia on TDF/3TC-containg ART requires additional research, but may represent poor adherence and the need for adherence interventions or novel antivirals.
An APRI+ALBI Based Multivariable Model as Preoperative Predictor for Posthepatectomy Liver Failure
Authors: Santol Jonas , Kim Sarang , Gregory Lindsey A. , Baumgartner Ruth , Murtha-Lemekhova Anastasia , Birgin Emrullah , Gloor Severin , Braunwarth Eva , Ammann Markus , Starlinger Johannes , Pereyra David , Ammon Daphni , Ninkovic Marijana , Kern Anna E. , Rumpf Benedikt , Ortmayr Gregor , Herrmann Yannic , Dong Yawen , Huber Felix X. , Weninger Jeremias , Thiels Cornelius A. , Warner Susanne G. , Smoot Rory L. , Truty Mark J. , Kendrick Michael L. , Nagorney David N. , Cleary Sean P. , Beldi Guido , Rahbari Nuh N. , Hoffmann Katrin , Gilg Stefan , Assinger Alice , Gruenberger Thomas , Hackl Hubert , Starlinger Patrick 
Published: October 2023

Objective and Background:
Clinically significant posthepatectomy liver failure (PHLF B+C) remains the main cause of mortality after major hepatic resection. This study aimed to establish an APRI+ALBI, aspartate aminotransferase to platelet ratio (APRI) combined with albumin-bilirubin grade (ALBI), based multivariable model (MVM) to predict PHLF and compare its performance to indocyanine green clearance (ICG-R15 or ICG-PDR) and albumin-ICG evaluation (ALICE).

Methods:
12,056 patients from the National Surgical Quality Improvement Program (NSQIP) database were used to generate a MVM to predict PHLF B+C. The model was determined using stepwise backwards elimination. Performance of the model was tested using receiver operating characteristic curve analysis and validated in an international cohort of 2,525 patients. In 620 patients, the APRI+ALBI MVM, trained in the NSQIP cohort, was compared with MVM’s based on other liver function tests (ICG clearance, ALICE) by comparing the areas under the curve (AUC).

Results:
A MVM including APRI+ALBI, age, sex, tumor type and extent of resection was found to predict PHLF B+C with an AUC of 0.77, with comparable performance in the validation cohort (AUC 0.74). In direct comparison with other MVM’s based on more expensive and time-consuming liver function tests (ICG clearance, ALICE), the APRI+ALBI MVM demonstrated equal predictive potential for PHLF B+C. A smartphone application for calculation of the APRI+ALBI MVM was designed.

Conclusion:
Risk assessment via the APRI+ALBI MVM for PHLF B+C increases preoperative predictive accuracy and represents an universally available and cost-effective risk assessment prior to hepatectomy, facilitated by a freely available smartphone app.
Would you be surprised? Prospective multicenter study of the Surprise Question as a screening tool to predict mortality in trauma patients
Authors: Hoffman Melissa Red , Slivinski Andrea , Shen Yan , Watts Dorraine D. , Wyse Ransom J. , Garland Jeneva M. , Fakhry Samir M. ,   the Surprise Question in Trauma Research Group
Published: October 2023

BACKGROUND
The Surprise Question (SQ) (“Would I be surprised if the patient died within the next year?”) is a validated tool used to identify patients with limited life expectancy. Because it may have potential to expedite palliative care interventions per American College of Surgeons Trauma Quality Improvement Program Palliative Care Best Practices Guidelines, we sought to determine if trauma team members could use the SQ to accurately predict 1-year mortality in trauma patients.

METHODS
A multicenter, prospective, cohort study collected data (August 2020 to February 2021) on trauma team members' responses to the SQ at 24 hours from admission. One-year mortality was obtained via social security death index records. Positive/negative predictive values and accuracy were calculated overall, by provider role and by patient age.

RESULTS
Ten Level I/II centers enrolled 1,172 patients (87.9% blunt). The median age was 57 years (interquartile range, 36–74 years), and the median Injury Severity Score was 10 (interquartile range, 5–14 years). Overall 1-year mortality was 13.3%. Positive predictive value was low (30.5%) regardless of role. Mortality prediction minimally improved as age increased (positive predictive value highest between 65 and 74 years old, 34.5%) but consistently trended to overprediction of death, even in younger patients.

CONCLUSION
Trauma team members' ability to forecast 1-year mortality using the SQ at 24 hours appears limited perhaps because of overestimation of injury effects, preinjury conditions, and/or team bias. This has implications for the Trauma Quality Improvement Program Guidelines and suggests that more research is needed to determine the optimal time to screen trauma patients with the SQ.

LEVEL OF EVIDENCE
Prognostic and Epidemiological; Level III.
Validity and Reliability of Virtually Obtained Functional Outcomes in Older Adults
Authors: Jasper Amie , Karim Rania , Uy Samuel John Montecalvo , Tayag Eleazar , Vitente Arvie C. , Baloy Rodiel Kirby , Lazaro Rolando 
Published: October 2023

Introduction:
The validity and reliability of tests and measures conducted virtually without the in-person presence of a physical therapist is a challenge in telehealth. This study evaluated the validity and reliability of telehealth administration of outcome measures.

Methods:
Six participants were examined by 3 independent raters. The outcome measures used were the 2-minute step test, 30-second chair stand test, and Timed Up and Go.

Results:
There was a high level of validity and reliability between the in-person and virtually conducted tests.

Discussion:
The preliminary findings demonstrated that outcome measures can be conducted virtually with validity of scoring and results.
Effects of Telemedicine for Postural Instability in Independent Patients With Parkinson's Disease
Authors: De Vitis Andrea , Battaglino Andrea , Sinatti Pierluigi , Sánchez Romero Eleuterio A. , Bissolotti Luciano , Cotella Diego , Villafañe Jorge Hugo 
Published: October 2023

Background:
The purpose of this study is to examine the evidence of the effectiveness of telemedicine in postural stability treatment in independent patients affected by Parkinson's disease (PD).

Methods:
This is a literature review of studies investigating the effect of telemedicine in postural stability treatment in independent patients affected by PD. PRISMA guidelines were followed during the design, search, and reporting stages of this review. The search was carried out in the MEDLINE databases.

Results:
A total of 1854 studies were detected and analyzed by performing the proposed searches in the detailed databases. After removing duplicates and analyzing the titles and abstracts of the remaining articles, 6 studies were ultimately selected for this review. At least 50% of the studies included in this review showed positive results in improving postural stability in patients with PD after a home-based intervention.

Conclusions:
The home-based intervention based upon technologically assisted telerehabilitation may support the aspects of an effective and efficient physical therapy allowing the physiotherapists to deliver functional rehabilitation in the home setting outside the hospital and supervise more than one patient simultaneously during rehabilitation sessions.
Recruitment limitation increases susceptibility to fishing-induced collapse in a spawning aggregation fishery
Authors: Mason Erica T. Jarvis , Riecke Thomas V. , Bellquist Lyall F. , Pondella Daniel J. , Semmens Brice X. 
Published: October 2023

ABSTRACTAggregation-based fisheries are notorious for booms and busts driven by aggregation discovery and subsequent fishing-induced collapse. However, environment-driven sporadic recruitment in some since-protected populations has delayed recovery, suggesting recruitment-limitation may be a key driver of their population dynamics and fishery recovery potential. To glean insight into this dynamic, we focused on an overexploited temperate aggregate spawner (Barred Sand Bass;Paralabrax nebulifer) and leveraged a long-term mark-recapture data set spanning different oceanographic and harvest histories in a custom Bayesian capture-mark-reencounter modeling framework. We coupled this demographic analysis with long-term trends in sea surface temperature, harvest, adult and juvenile densities, and historical accounts in the literature. Our results point to a history of multidecadal windows of fishing opportunity and fishing-induced collapse that were largely driven by sporadic, warm water recruitment events, which may be externally sourced. Nevertheless, we found that environment-driven sporadic recruitment was not a factor impeding recovery following the last collapse, as recruitment remained elevated due to novel, anomalously warm conditions. Despite signs of incipient population recovery, spawning aggregations remain absent, indicating other potential factors (e.g., continued fishing during spawning season, residual Allee effects) have delayed fishery recovery to date. Aggregate spawner populations that are dependent on sporadic recruitment, especially those at their geographic margins, are thus highly susceptible to sudden and potentially extended periods of collapse, making them ill-suited to high CPUE fishing that occurs on spawning grounds. If the goal is to balance the protection of spawning aggregations with long-term fishery sustainability, then limiting aggregation-based fishing during spawning season may be the best insurance policy against collapse and recovery failure.
GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT
Authors: Chen Yiqun , Zou James 
Published: October 2023

AbstractThere has been significant recent progress in leveraging large-scale gene expression data to develop foundation models for single-cell biology. Models such as Geneformer and scGPT implicitly learn gene and cellular functions from the gene expression profiles of millions of cells, which requires extensive data curation and resource-intensive training. Here we explore a much simpler alternative by leveraging ChatGPT embeddings of genes based on literature. Our proposal, GenePT, uses NCBI text descriptions of individual genes with GPT-3.5 to generate gene embeddings. From there, GenePT generates single-cell embeddings in two ways: (i) by averaging the gene embeddings, weighted by each gene’s expression level; or (ii) by creating a sentence embedding for each cell, using gene names ordered by the expression level. Without the need for dataset curation and additional pretraining, GenePT is efficient and easy to use. On many downstream tasks used to evaluate recent single-cell foundation models — e.g., classifying gene properties and cell types — GenePT achieves comparable, and often better, performance than Geneformer and other models. GenePT demonstrates that large language model embedding of literature is a simple and effective path for biological foundation models.
PBRM-1/PBAF-regulated genes in a multipotent progenitor
Authors: Mathies Laura D. , Kim Andrew C. , Soukup Evan M. , Thomas Alan’da E. , Bettinger Jill C. 
Published: October 2023

AbstractTheCaenorhabditis eleganssomatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The two SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates and the other dies by programmed cell death. The PBAF chromatin remodeling complex promotes the multipotent SGP fate. Complete loss of PBAF causes lethality, so we used a combination of Cre/lox recombination and GFP nanobody-directed protein degradation to eliminate PBRM-1, the signature subunit of the PBAF complex, from 83 mesodermal cells, including SGPs, body muscles, and the hmc. We used RNA sequencing to identify genes acting downstream of PBAF in these cells and identified 1955 transcripts that were significantly differentially expressed betweenpbrm-1(-)andpbrm-1(+)in the mesoderm of L1 larvae. We found that genes involved in muscle cell function were overrepresented; most of these genes had lower expression in the absence of PBRM-1, suggesting that PBAF promotes muscle differentiation. Among the differentially expressed genes were 125 genes that are normally expressed at higher levels in SGPvs. hmc and positively regulated bypbrm-1and 53 that are normally expressed at higher levels in hmcvs. SGP and are negatively regulated bypbrm-1;these are candidate regulators of the SGP/hmc fate decision. We validated one candidate gene using a fluorescent reporter; thehsp-12.3reporter was derepressed in SGPs inpbrm-1 mutants, suggesting thathsp-12.3expression is normally repressed bypbrm-1in SGPs.