bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the relative effectiveness of various ultrasound-guided ablation techniques for treating benign thyroid nodules: A systematic review and network meta-analysis
Authors: Sun Xiangmei , Chen Jiaojiao , Zou Yan , Lei Jiahao , Liu Weizong 
Published: May 2024

Background:
Benign thyroid nodules (BTNs) represent a prevalent clinical challenge globally, with various ultrasound-guided ablation techniques developed for their management. Despite the availability of these methods, a comprehensive evaluation to identify the most effective technique remains absent. This study endeavors to bridge this knowledge gap through a network meta-analysis (NMA), aiming to enhance the understanding of the comparative effectiveness of different ultrasound-guided ablation methods in treating BTNs.

Methods:
We comprehensively searched PubMed, Embase, Cochrane, Web of Science, Ovid, SCOPUS, and ProQuest for studies involving 16 ablation methods, control groups, and head-to-head trials. NMA was utilized to evaluate methods based on the percentage change in nodule volume, symptom score, and cosmetic score. This study is registered in INPLASY (registration number 202260061).

Results:
Among 35 eligible studies involving 5655 patients, NMA indicated that RFA2 (radiofrequency ablation, 2 sessions) exhibited the best outcomes at 6 months for percentage change in BTN volume (SUCRA value 74.6), closely followed by RFA (SUCRA value 73.7). At 12 months, RFA was identified as the most effective (SUCRA value 81.3). Subgroup analysis showed RFA2 as the most effective for solid nodule volume reduction at 6 months (SUCRA value 75.6), and polidocanol ablation for cystic nodules (SUCRA value 66.5).

Conclusion:
Various ablation methods are effective in treating BTNs, with RFA showing notable advantages. RFA with 2 sessions is particularly optimal for solid BTNs, while polidocanol ablation stands out for cystic nodules.
Ultrasound-guided subcostal approach of transversus abdominis plane block compared with wound infiltration for postoperative analgesia following laparoscopic cholecystectomy: A systematic review and meta-analysis
Authors: Park Sukhee , Park Ji-Hoon , Park Soyoon , Jang Jae Ni , Kim Chaeeun , Choi Young-Soon 
Published: May 2024

Background:
Despite laparoscopic cholecystectomy (LC) is a commonly performed operation under ambulatory setting, significant postoperative pain is still a major concern. The ultrasound-guided subcostal approach of transversus abdominis plane (sTAP) blocks and wound infiltration (WI) are both widely practiced techniques to reduce postoperative pain in patients undergoing LC. Although these methods have been shown to relieve postoperative pain effectively, the relative analgesic efficacy between ultrasound-guided sTAP blocks and WI is not well known.

Methods:
We searched PubMed, EMBASE, and CENTRAL to identify all randomized controlled trials (RCTs) comparing ultrasound-guided sTAP block versus WI for postoperative pain control in adult patients undergone LC. The search was performed until May 2023. Primary outcome was defined as 24-hour cumulative opioid consumption. Secondary outcomes were postoperative pain scores and the incidence of postoperative nausea and vomiting (PONV).

Results:
Finally, 6 RCTs were included, and data from 314 participants were retrieved. Postoperative 24-hour opioid consumption was significantly lower in ultrasound-guided sTAP group than in the WI group with a mean difference of −6.67 (95% confidence interval: −9.39 to − 3.95). The ultrasound-guided sTAP group also showed significantly lower pain scores. Incidence of PONV did not significantly differ between the 2 groups.

Conclusions:
We conclude that there is low to moderate evidence to advocate that ultrasound-guided sTAP block has better analgesic effects than WI in patients undergoing LC. Further trials are needed with robust methodology and clearly defined outcomes.
Arthroscopic rotator cuff repair combined with platelet-rich plasma products can reduce the rate of retearing and improve clinical outcomes: A meta-analysis of randomized controlled trials
Authors: Shen Zhe , Ye Xiaoang , He Yawen , Shen Gaobo , Xu Kuangying , Zhang Bingbing , Wu Lianguo 
Published: May 2024

Background:Although several studies on the potential benefits of protein-rich plasma (PRP) therapy for rotator cuff injuries have been published, the results have been conflicting. Therefore, this study aimed to determine whether PRP is beneficial for the prevention of retears after arthroscopic rotator cuff repair (ARCR).Methods:Two reviewers conducted independent literature searches based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Randomized controlled trials (RCTs) comparing a PRP treatment group with a control group were included. The quality of evidence was assessed using the Cochrane Collaboration Risk of Bias Tool. Clinical outcomes were compared using the risk ratio (RR) for dichotomous variables and weighted mean difference (WMD) for continuous variables. Statistical significance was set atP < .05.Results:This review included 21 RCTs (1359 patients). Significant results were noted in favor of PRP treatment compared with controls based on retearing rates (16.5% vs 23.6%, respectively;P = .002) and the Constant score in the short term (WMD: 1.98; 95% confidence interval [CI], 0.27–3.70; I2 = 0%;P = .02), medium term and long term (WMD: 2.56 [95% CI: 1.57–3.55]; I2 = 2%;P < .001); the University of California, Los Angeles score in the short term (WMD: 1.14 [95% CI: 0.43–1.85]; I2 = 25%;P = .002) but not in the medium and long term (WMD: 0.66 [95% CI: –0.16 to 1.48]; I2 = 57%;P = .11); and the visual analog scale score in the short term (WMD: –0.63 [95% CI: –0.83 to–0.43]; I2 = 41%;P < .001), medium and long term (WMD: –0.12 [95% CI: –0.19 to–0.05]; I2 = 0%;P = .008). There was no significant difference in American Shoulder and Elbow Surgeons scores between the treatment and control groups in the short term (WMD: –0.48 [95% CI: –2.80 to 1.85]; I2 = 22%;P = .69) or medium and long term (WMD: 0.92 [95% CI: –1.56 to 3.39]; I2 = 40%;P = .47).Conclusion:Intraoperative use of PRP reduces the risk of rotator cuff repair failure, improves clinical outcomes, and reduces recurrence rates.
Mindfulness and Interoceptive Awareness
Authors: Sala Margaret , Schanzer Sophie , Morris Claudia 
Published: May 2024

Abstract
Higher trait mindfulness is correlated with higher interoceptive awareness. However, there is a gap in understanding which mindfulness dimensions connect to which interoceptive awareness dimensions. This study (N = 1005) used network analysis to identify central and bridge nodes driving the linkage between mindfulness and interoceptive awareness. Central nodes included trusting body sensations, feeling a sense of calm when bringing awareness to the body, the ability to refocus one's attention from thinking to sensing the body, and the ability to accept all emotions. Bridge nodes included noticing how food and drink affect thoughts, bodily sensations, and emotions; staying alert to the sensations of the body when taking a shower; and noticing and letting go of distressing thoughts and feelings. Future research studies should explore whether mindfulness-based interventions may be more effective by targeting observations of sensations related to eating and the body as well as noticing and letting go of distressing thoughts and feelings.
Association between tight junction proteins and cognitive performance in untreated persons with HIV
Authors: Bai Francesca , Bono Valeria , Borghi Lidia , Bonazza Federica , Falcinella Camilla , Vitaletti Virginia , Miraglia Federica , Trunfio Mattia , Calcagno Andrea , Cusato Jessica , Vegni Elena , d’Arminio Monforte Antonella , Marchetti Giulia 
Published: May 2024

Background:HIV-associated neurocognitive disorders (HAND) still affects persons with HIV (PWH) and their pathogenesis is not completely understood. We aimed to explore the association between plasma and cerebrospinal fluid (CSF) markers of blood–brain barrier (BBB) impairment and HAND in untreated PWH.Design:Cross-sectional study.Methods:We enrolled untreated PWH, who underwent blood examinations and lumbar puncture to measure inflammation (IL-15, TNF-α), BBB damage (zonulin and tight junction proteins, tight junction proteins: occludin, claudin-5) and endothelial adhesion molecules (VCAM-1, ICAM-1). A comprehensive neurocognitive battery was used to diagnose HAND (Frascati criteria).Results:Twenty-one patients (21/78, 26.9%) patients presented HAND (100% ANI). HAND patients displayed more frequently non-CNS AIDS-defining conditions, lower nadir CD4+T cells and increased CD4+T-cell exhaustion (lower CD4+CD127+and CD4+CD45RA+T-cell percentages), in comparison to individuals without cognitive impairment. Furthermore, HAND was characterized by higher plasma inflammation (IL-15) but lower CSF levels of biomarkers of BBB impairment (zonulin and occludin). The association between BBB damage with HAND was confirmed by fitting a multivariable logistic regression. CSF/plasma endothelial adhesion molecules were not associated with HAND but with a poor performance in different cognitive domains.Conclusion:By showing heightened inflammation and BBB impairment, our study suggests loss of BBB integrity as a possible factor contributing to the development of HAND in untreated PWH.
Association between antioxidant metabolites and N-terminal fragment brain natriuretic peptides in insulin-resistant individuals
Authors: Anwardeen Najeha , Naja Khaled , Elrayess Mohamed A. 
Published: May 2024

Objectives
Oxidative stress plays a pivotal role in the development of metabolic syndrome, including heart failure and insulin resistance. The N-terminal fragment of brain natriuretic peptide (NT-proBNP) has been associated with heightened oxidative stress in heart failure patients. Yet, its correlation with insulin resistance remains poorly understood. Our objective is to investigate the association between oxidative stress markers and NT-proBNP levels in insulin-resistant individuals.

Methods
In this cross-sectional study involving 393 participants from the Qatar Biobank, clinical and metabolic data were collected, and the association between NT-proBNP and 72 oxidative stress metabolites was compared between insulin-sensitive and insulin-resistant individuals.

Results
Our results showed significantly lower NT-proBNP levels in insulin-resistant individuals (median = 17 pg/ml; interquartile range = 10.3–29) when compared to their insulin-sensitive counterparts (median = 31 pg/ml; interquartile range = 19–57). Moreover, we revealed notable associations between NT-proBNP levels and antioxidant metabolic pathways, particularly those related to glutathione metabolism, in insulin-resistant, but not insulin-sensitive individuals.

Conclusion
The significant decrease in NT-proBNP observed in individuals with insulin resistance may be attributed to a direct or indirect enhancement in glutathione production, which is regarded as a compensatory mechanism against oxidative stress. This study could advance our understanding of the interplay between oxidative stress during insulin resistance and cardiovascular risk, which could lead to novel therapeutic approaches for managing cardiovascular diseases. Further investigations are needed to assess the practical utility of these potential metabolites and understand the causal nature of their association with NT-proBNP in the etiology of insulin resistance.
Phase II study of nivolumab and ipilimumab for treatment of metastatic/recurrent adenoid cystic carcinoma (ACC) of all anatomic sites of origin and other malignant salivary gland tumors
Authors: Chae Young Kwang , Duan Richard , Chung Liam Il-Young , Oh Youjin , Alexiev Borislav , Shin Sangwon , Kim Sukjun , Helenowski Irene , Matsangou Maria , Villaflor Victoria , Mahalingam Devalingam 
Published: May 2024

AbstractObjectiveDual checkpoint inhibitor therapy with nivolumab and ipilimumab has been FDA-approved for a number of cancer sites. However, their role in the treatment of ACC and other salivary gland carcinomas is not well established.Methods and analysisWe performed a Simon’s two-stage prospective single-institution phase II clinical trial of nivolumab with ipilimumab. Two cohorts were analyzed: patients with metastatic/recurrent ACC and patients with other salivary gland cancers. The primary endpoint was median progression-free survival (PFS); secondary endpoints were overall response rate (ORR), overall survival (OS), and toxicity.ResultsPatients with ACC (n=19) and other salivary gland carcinomas (total n=5) were enrolled. The patients with ACC had median OS 30.0 months (95% CI 15.3-NR months), median PFS 8.3 months (95% CI 5.5-30.0 months), and disease control rate (DCR) 53% (10/19). The ORR in the ACC group was 5% (CR 0%, n=0; confirmed PR 5%, n=1), with one patient having continued stable disease at the time of trial conclusion. The patients with other salivary gland cancers had median OS 10.4 months (95% CI 6.21-NR months), median PFS 6.21 months (95% CI 2.83-NR months), and DCR 40% (2/5). The ORR in this cohort was 0%.ConclusionIn patients with recurrent or metastatic ACC and other salivary gland neoplasms, combination nivolumab with ipilimumab resulted in moderate disease control. Further studies are warranted to validate our findings.Trial number:NCT03146650
An allometric study of the contribution of prostrate stems to belowground development of juvenileFagus crenata
Authors: Shimizu Yutaro , Tondokoro Yudai , Ida Hideyuki 
Published: May 2024

AbstractProstrate stems represent an important morphological component ofFagus crenata(Siebold’s beech). This unique stem-bending growth strategy has led to the dominance of this tree species in regions with heavy snowfall along the Sea of Japan. We investigated the early-stage aboveground–belowground dynamics ofF. crenataby applying allometric scaling theory to analyze morphological development in saplings (aged 3–20 years). Samples were collected from 25 trees in three forests in Nagano, central Japan. The scaling exponent (b) demonstrated an increase in the fraction of aboveground biomass (i.e., dry mass) in relation to the overall surface area (aboveground,b= 0.748; belowground,b= 0.626) and biomass (aboveground,b= 1.087; belowground,b= 0.983). These values are highly consistent with recent field observations by other researchers. Aboveground biomass growth was supported by the increasing role of prostrate stems in belowground development (b= 1.114). Despite its extension belowground, the growth properties of the prostrate stem may be identical to those of shoots, as both are directly influenced by nutrient sources above the germination point. Our findings highlight the significance of the prostrate stem in supporting beech survival in areas with heavy snowfall.
Hydrogel-embedded precision-cut lung slices supportex vivoculture ofin vivo-induced premalignant lung lesions
Authors: Hauer Caroline , Blomberg Rachel , Sompel Kayla , Magin Chelsea M. , Tennis Meredith A. 
Published: May 2024

AbstractLung cancer is the leading cause of global cancer death and prevention strategies are key to reducing mortality. Medical prevention may have a larger impact than treatment on mortality by targeting high-risk populations and reducing their lung cancer risk. Premalignant lesions (PMLs) that can be intercepted by prevention agents are difficult to study in humans but easily accessible in murine preclinical carcinogenesis studies. Precision-cut lung slices (PCLS) are underutilized as anex vivomodel for lung cancer studies due to limited culture time. Embedding PCLS within bioengineered hydrogels extends PCLS viability and functionality for up to six weeks. Here, we embedded PCLS generated from urethane-induced murine PMLs in cell-degradable and non-degradable hydrogels to study viability and activity of the tissues over six weeks. PMLs in hydrogel-embedded PCLS maintained viability, gene expression, and proliferation. Treatment of hydrogel-embedded PCLS containing urethane-induced PMLs with iloprost, a known lung cancer prevention agent, recapitulatedin vivogene expression and activity. These studies also showed that iloprost reduced proliferation and PML size in hydrogel-embedded PCLS, with some differences based on hydrogel formulation and suggested that hydrogel-embedded PCLS models may support long-term culture ofin vivogenerated PMLs to improve preclinical studies of lung cancer and prevention agents.
Reproducible differentiation of pure ovarian support cells from clinical-grade hiPSCs as a novel infertility treatment
Authors: Paulsen Bruna , Barrachina Ferran , Noblett Alexander D. , Johnson Mark , Kats Simone , Piechota Sabrina , Marchante Maria , Figueroa Alexandra B. , Potts Kathryn S , Rockwell Graham , Giovannini Alexa , Kramme Christian C. 
Published: May 2024

AbstractIn vitro maturation (IVM) is an infertility treatment used during in vitro fertilization (IVF) procedures in which immature oocytes are matured outside the body, limiting the excessive hormone doses required for retrieval of ready-to-fertilize oocytes. To overcome the historically low embryo formation rate associated with IVM, we have recently demonstrated that co-culture of hiPSC-derived ovarian support cells (OSCs) yielded higher rates of oocyte maturation and euploid embryo formation, by mimicking the complex ovarian environment in vitro, offering a novel solution to overcome the IVM main limitation. To translate this process into clinics, we sourced and engineered a compliant female clinical-grade (CG) hiPSC line to derive OSCs with similar quality attributes and clinical outcomes to results previously demonstrated with a research hiPSC line. We further optimized our manufacturing protocols to enable increased scale and substituted reagents with appropriate higher-quality alternatives. This strategic approach to product development has successfully met scalable manufacturing needs and ultimately resulted in a product of improved reproducibility, purity, and efficacy. Our findings support the use of a similar strategy to fine-tune hiPSC-derived products facilitating translation to clinical applications.
Natural Killer Cell Dysfunction In Human Bladder Cancer Is Caused By Tissue-Specific Suppression of SLAMF6 Signaling
Authors: Farkas Adam M. , Youssef Dina , Tran Michelle A. , Balan Sreekumar , Newman Jenna H. , Audenet François , Anastos Harry , Velazquez Leandra G. , Peros Ante , Ananthanarayanan Aparna , Daza Jorge , Gonzalez-Gugel Elena , Sadanala Keerthi , Theorell Jakob , Galsky Matthew D. , Horowitz Amir , Sfakianos John P. , Bhardwaj Nina 
Published: May 2024

SummaryNK cells are innate lymphocytes critical for surveillance of viruses and tumors, however the mechanisms underlying NK cell dysfunction in cancer are incompletely understood. We assessed the effector function of NK cells from bladder cancer patients and found severe dysfunction in NK cells derived from tumors versus peripheral blood. While both peripheral and tumor-infiltrating NK cells exhibited conserved patterns of inhibitory receptor over-expression, this did not explain the observed defects in NK surveillance in bladder tumors. Rather, TME-specific TGF-β and metabolic perturbations such as hypoxia directly suppressed NK cell function. Specifically, an oxygen-dependent reduction in signaling through SLAMF6 was mechanistically responsible for poor NK cell function, as tumor-infiltrating NK cells culturedex vivounder normoxic conditions exhibited complete restoration of function, while deletion of SLAMF6 abrogated NK cell cytolytic function even under normoxic conditions. Collectively, this work highlights the role of tissue-specific factors in dictating NK cell function, and implicates SLAMF6 signaling as a rational target for immuno-modulation to improve NK cell function in bladder cancer.Graphical Abstract
ntEmbd: Deep learning embedding for nucleotide sequences
Authors: Hafezqorani Saber , Nip Ka Ming , Birol Inanc 
Published: May 2024

ABSTRACTEnabled by the explosion of data and substantial increase in computational power, deep learning has transformed fields such as computer vision and natural language processing (NLP) and it has become a successful method to be applied to many transcriptomic analysis tasks. A core advantage of deep learning is its inherent capability to incorporate feature computation within the machine learning models. This results in a comprehensive and machine-readable representation of sequences, facilitating the downstream classification and clustering tasks. Compared to machine translation problems in NLP, feature embedding is particularly challenging for transcriptomic studies as the sequences are string of thousands of nucleotides in length, which make the long-term dependencies between features from different parts of the sequence even more difficult to capture. This highlights the need for nucleotide sequence embedding methods that are capable of learning input sequence features implicitly. Here we introduce ntEmbd, a deep learning embedding tool that captures dependencies between different features of the sequences and learns a latent representation for given nucleotide sequences. We further provide two sample use cases, describing how learned RNA features can be used in downstream analysis. The first use case demonstrates ntEmbd’s utility in classifying coding and noncoding RNA benchmarked against existing tools, and the second one explores the utility of learned representations in identifying adapter sequences in nanopore RNA-seq reads. The tool as well as the trained models are freely available on GitHub athttps://github.com/bcgsc/ntEmbd
MicroRNA hsa-miR-203a-3p promotes H1N1 and NDV Virus Replication by suppressing the IFNA signaling
Authors: kumar Pramod , Kumar Ashish , Kumar Akhilesh , Kumar Himanshu 
Published: May 2024

AbstractMicroRNAs (miRNAs) are small non-coding molecules that act as essential post-transcriptional regulators in various biological processes. Many studies suggest that miRNAs may modulate the host’s immune response during virus infections. We analyzed publicly available transcriptomics data involving infection with different RNA viruses and selected the most prominent candidate, miR-203a-3p. miR-203a-3p is upregulated during H7N1, HCV, and HIV+HPV infections. Interestingly, pathway analysis of microRNA-targeted genes shows that miR-203a-3p targets the type–I interferon pathway. In this study, we report that the expression of miR-203a-3p is elevated in response to polyinosinic-polycytidylic acid [poly(I:C)] transfection and infection with RNA viruses like Newcastle Disease Virus (NDV) and H1N1 influenza virus. We found that overexpression of miR-203-3p promotes the replication of H1N1 virus by suppressing the host’s type-I interferons and interferon-stimulated genes. In addition, miR-203a-3p overexpression reduced the expression of ISGs, and is attributed to the binding of miR-203a-3p to 3’ UTRs of Janus-activated kinase 1 (JAK1), STAT1, SOCS3, and multiple IFNA transcripts, as shown by luciferase and Ago-2 pulldown assays. Altogether, these findings strongly suggest that miR-203a-3p acts as a pro-viral molecule during H1N1 and NDV infection by targeting the host’s IFN signaling pathways.