bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relative Perioperative Analgesic Efficacy of Superficial Versus Deep Approach of Serratus Anterior Plane Block for Anterior Chest Wall Surgery
Authors: Singh Narinder P. , Makkar Jeetinder Kaur , Dhawan Ira , Singh Neha , Singh Preet M. , Siddiqui Naveed 
Published: September 2024

Objectives:
Both superficial and deep serratus anterior plane (SAP) blocks are effective for anterior chest wall surgeries, but there is little clarity on which is more effective. Hence, we conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to evaluate the comparative efficacy of the 2 approaches for SAP block after anterior chest wall surgery.

Materials and Methods:
A systematic literature search was performed using PubMed, Embase, Scopus, and Cochrane Central Registers of Controlled Trials for eligible RCTs from inception until August 2023. The primary outcome was opioid consumption during the first 24 hours of the postoperative period. The secondary outcomes included pain scores at various intervals, intraoperative opioid consumption, time to first analgesic request, block-related complications, opioid-related side effects, and patient satisfaction scores. Statistical analysis of the pooled data was performed using Review Manager Version 5.3.

Results:
We identified 7 RCTs published between 2020 and 2022, enrolling 371 patients (186 in the superficial SAP block and 187 in the deep SAP block). Moderate certainty of evidence suggests that both the approaches (deep and superficial) of SAP block were comparable for 24-hour oral morphine equivalent consumption with a mean difference (MD) of 3.78 mg (95% CI: −1.70 to 9.29; P = 0.18; I
2 = 87%). The results of other secondary outcomes were comparable, including resting pain scores with an MD of 0.08 (95% CI: −0.27 to 0.43; P = 0.67; I
2 = 87%) for early pain and MD of 0.63 (95% CI: −1.28 to 0.01; P = 0.05; I
2 = 95%) for late pain scores, time to first analgesic request with MD of −0.41 hour (95% CI: −1.40 to 0.59; P = 0.42; I
2 = 90%), and incidence of postoperative nausea and vomiting (odds ratio: 1.45 (95% CI: 0.72 to 2.90; P = 0.30; I
2 = 0%).

Conclusion:
Current evidence does not support the preference for one approach of SAP block over the other for postoperative pain. Based on the available data, we recommend further future trials to determine any differences between these interventions.
INCIDENCE OF STEROID-RELATED OCULAR HYPERTENSION AND CATARACT FORMATION AFTER SUB-TENON TRIAMCINOLONE IN NONUVEITIC PEDIATRIC PATIENTS
Authors: Patel Nimesh A. , Hoyek Sandra , López-Font Francisco J. , Shah Serena , Ha Sierra , da Cruz Natasha F. S. , Vu Daniel M. , Chang Ta Chen , Berrocal Audina M. 
Published: September 2024

Purpose:
To describe intraocular pressure changes after injection of sub-Tenon triamcinolone during examination under anesthesia for pediatric patients.

Methods:
Multicenter, retrospective case series of pediatric patients who received sub-Tenon triamcinolone from three tertiary care ophthalmic services between November 2018 and October 2023.

Results:
Of 392 patients identified, 59 eyes (10.5%) of 41 patients were included. Laser was administered in 95.1% of the cases. Sub-Tenon triamcinolone dose ranged from 4 to 20 mg. The most common diagnosis was retinopathy of prematurity (43.9%). Two eyes (3.4%) of two patients (4.9%) were mild steroid responders. One eye (1.7%) of 1 patient (2.4%) was a moderate responder. There were no high steroid responders, and all eyes with steroid response showed a return of intraocular pressure to normal range at next visit without needing any intraocular pressure-lowering medications. No patients were diagnosed with glaucoma or required glaucoma surgery. Only 1 eye (1.7%) developed trace posterior subcapsular cataract, whereas no optic disk cupping or inflammation were noted.

Conclusion:
Sub-Tenon triamcinolone injection is commonly used to prevent inflammation at the time of retinal photocoagulation treatment in pediatric patients. It has a favorable safety profile in relation to intraocular pressure elevation and cataract formation. There was no requirement for intraocular pressure–lowering medications or surgical interventions.
The fetal specific geneLIN28Bis essential for human fetal B-lymphopoiesis and initiation of KMT2A::AFF1 infant leukemia
Authors: Ling Rebecca , Jackson Thomas , Elliott Natalina , Cross Joe , Hamer Lucy , Wuppalapati Arundhati , Smith Alastair , Chahrour Catherine , Sevim Okan , Iskander Deena , Wang Guanlin , Rice Siobhan , O’Byrne Sorcha , Harman Joe , Psaila Bethan , Morgan Rhys , Roberts Irene , Milne Thomas A. , Roy Anindita 
Published: September 2024

ABSTRACTInfant ALL (iALL) is initiatedin utero, most often by rearrangement of theKMT2Agene (KMT2Ar). It carries a very poor prognosis despite a lack of additional oncogenic driver mutations common in childhood ALL. Here, we aimed to identify specific properties of human fetal hematopoietic stem/progenitor cells (HSPC) that promote leukemic transformation inKMT2AriALL using molecular, functional andin vivoassays. First, by comparing transcriptomes of human fetal HSPC to adult HSPC we derived a fetal-specific gene signature and identified the fetal oncogeneLIN28Band its downstream effectors among the top hits. These genes were also expressed in iALL. Functional assays revealed thatLIN28Bwas essential in human fetal liver (FL) CD34+ cells to maintain proliferation and stemness, and support B- and NK-lymphopoiesis. To interrogate the role ofLIN28Bin iALL, we utilised a human FL-derived CRISPR-Cas9 KMT2A::AFF1 model. In this model,LIN28B-expressing leukemias were more proliferativein vitroandin vivo, with this advantage being lost uponLIN28Bknockdown. Mechanistic studies showed that LIN28B acts by stabilizing key early B-lymphoid genes, epigenetic regulators, and cell cycle and anti-apoptotic genes. Finally, In the absence ofLIN28B, human FL CD34+ cells fail to transform upon induction of KMT2A::AFF1 translocation. Thus,LIN28Bhas an essential role in normal human fetal B-lymphopoiesis, and is necessary for the initiation ofKMT2A::AFF1iALL in fetal cells in the absence of co-operating mutations. It has a role in making leukemias more aggressive, suggesting it is a potential target inLIN28B-expressing leukemias.
The TMRCA of general genealogies in populations of variable size
Authors: Wences Alejandro H. , Peñaloza Lizbeth , Steinrücken Matthias , Siri-Jégousse Arno 
Published: September 2024

AbstractWe study the time to the most recent common ancestor of a sample of finite size in a wide class of genealogical models for populations with variable size. This is made possible by recently developed results on inhomogeneous phase-type random variables, allowing us to obtain the density and the moments of the TMRCA of time-dependent coalescent processes in terms of matrix formulas. We also provide matrix simplifications permitting a more straightforward calculation. With these results, the TMRCA provides an explicative variable to distinguish different evolutionary scenarios.
Liberality is More Explainable than PCA of Transcriptome for Vertebrate Embryo Development
Authors: Ogata Norichika 
Published: September 2024

AbstractDimensional reduction approaches of genome scale data are widely used. Liberality is one of the approaches which is a quantitative index of cellular differentiation and dedifferentiation. Here, we analyzed a trend of liberality of time course transcriptome data on vertebrate embryo development. Historically annotated embryo developmental stages matched changes in the trend of liberality. Analyzing liberality of various biological phenomena would be beneficial.
In Situ UNIversal Orthogonal Network (UNION) Bioink Deposition for Direct Delivery of Corneal Stromal Stem Cells to Corneal Wounds
Authors: Brunel Lucia G. , Cai Betty , Hull Sarah M. , Han Uiyoung , Wungcharoen Thitima , Fernandes-Cunha Gabriella Maria , Seo Youngyoon Amy , Johansson Patrik K. , Heilshorn Sarah C. , Myung David 
Published: September 2024

ABSTRACTThe scarcity of human donor corneal graft tissue worldwide available for corneal transplantation necessitates the development of alternative therapeutic strategies for treating patients with corneal blindness. Corneal stromal stem cells (CSSCs) have the potential to address this global shortage by allowing a single donor cornea to treat multiple patients. To directly deliver CSSCs to corneal defects within an engineered biomatrix, we developed a UNIversal Orthogonal Network (UNION) collagen bioink that crosslinksin situwith a bioorthogonal, covalent chemistry. This cell-gel therapy is optically transparent, stable against contraction forces exerted by CSSCs, and permissive to the efficient growth of corneal epithelial cells. Furthermore, CSSCs remain viable within the UNION collagen gel precursor solution under standard storage and transportation conditions. This approach promoted corneal transparency and re-epithelialization in a rabbit anterior lamellar keratoplasty model, indicating that the UNION collagen bioink serves effectively as anin situ-forming, suture-free therapy for delivering CSSCs to corneal wounds.TEASER.Corneal stem cells are delivered within chemically crosslinked collagen as a transparent, regenerative biomaterial therapy.
Mechanistic insights into Rho/MRTF inhibition-induced apoptotic events and prevention of drug resistance in melanoma: Implications for the involvement of pirin
Authors: Foda Bardees M. , Baker Annika E. , Joachimiak Łukasz , Mazur Marzena , Neubig Richard R. 
Published: September 2024

AbstractAimOvercoming therapy resistance is critical for effective melanoma control. Upregulation of Rho/MRTF signaling in human and mouse melanomas causes resistance to targeted therapies. Inhibition of this pathway by MRTFi, CCG-257081 resensitized resistant melanomas to BRAF and MEK inhibitors. It also prevented the development of resistance to vemurafenib (Vem). Here, we investigate the role of apoptosis and the protein pirin in CCG-257081-mediated suppression of drug resistance.MethodsUsing naïve and resistant mouse YUMMER melanoma cells, we studied the effect of the BRAF inhibitor Vem with or without CCG-257081 on real-time growth and apoptosis (activation of caspase, Propidium iodide (PI) staining, and PARP cleavage). The effects of CCG-257081 on proliferation (Ki67) and caspase-3 activation were assessed in resistant YUMMER_R tumorsin vivo. Finally, two CCG-257081 enantiomers were tested for pirin binding, inhibition of the Rho/MRTF-mediated activation of ACTA2 gene expression in fibroblasts, and the prevention of Vem resistance development by YUMMER_P cells.ResultsVem reduced growth of parental but not resistant cells, while CCG-257081 inhibited both. The combination was more effective than Vem alone. CCG-257081, but not Vem, induced activation of caspase-3 and -7 in resistant cells and increased PARP cleavage and PI staining. CCG-257081 reduced proliferation and activated caspase-3 in YUMMER_R melanoma tumors. Both CCG-257081 enantiomers robustly suppressed development of Vem-resistant colonies with the S isomer being more potent (1 μM IC50).ConclusionCCG-257081 appears to target pre-resistant cells and Vem-induced resistant cells through enhanced apoptosis. Inhibition of pirin or the Rho/MRTF pathway can be employed to prevent melanoma resistance.
Innate immune epigenomic landscape following controlled human influenza virus infection
Authors: Thistlethwaite William , Vangeti Sindhu , Cheng Wan-Sze , Agarwal Pankaj , Cappuccio Antonio , Wang Wenliang , Wei Bei , Myers Rachel , Rubenstein Aliza B. , Chawla Daniel , Hariharan Manoj , McClain Micah T. , Burke Thomas W. , Kleinstein Steven H. , Ecker Joseph R. , Woods Christopher W. , Greenleaf William J. , Chen Xi , Ramos Irene , Zaslavsky Elena , Evans Thomas G. , Troyanskaya Olga G. , Sealfon Stuart C. 
Published: September 2024

SummaryViral infections can induce changes in innate immunity that persist after virus clearance. Here, we used blood samples from a human influenza H3N2 challenge study to perform comprehensive multi-omic analyses. We detected remodeling of immune programs in innate immune cells after resolution of the infection that was proportional in magnitude to the level of prior viral load. We found changes associated with suppressed inflammation including decreased cytokine and AP-1 gene expression as well as decreased accessibility at AP-1 targets and interleukin-related gene promoter regions. We also found decreased histone deacetylase gene expression, increased MAP kinase gene expression, and increased accessibility at interferon-related gene promoter regions. Genes involved in inflammation and epigenetic-remodeling showed modulation of gene-chromatin site regulatory circuit activity. These results reveal a coordinated rewiring of the epigenetic landscape in innate immune cells induced by mild influenza virus infection.
CAR Treg synergy with anti-CD154 mediates infectious tolerance to dictate heart transplant outcomes
Authors: Durgam Samarth S , Rosado-Sánchez Isaac , Yin Dengping , Speck Madeleine , Mojibian Majid , Sayin Ismail , Hynes Grace E , Alegre Maria Luisa , Levings Megan K , Chong Anita S 
Published: September 2024

AbstractSuccessful allograft specific tolerance induction would eliminate the need for daily immunosuppression and improve post-transplant quality of life. Adoptive cell therapy with regulatory T cells expressing donor-specific Chimeric Antigen Receptors (CAR-Tregs) is a promising strategy, but as monotherapy, cannot prolong the survival with allografts with multiple MHC mismatches. Using an HLA-A2-transgenic haplo-mismatched heart transplantation model in immunocompetent C57Bl/6 recipients, we show that HLA-A2-specific (A2) CAR Tregs was able to synergize with low dose of anti-CD154 to enhance graft survival. Using haplo-mismatched grafts expressing the 2W-OVA transgene and tetramer-based tracking of 2W- and OVA-specific T cells, we showed that in mice with accepted grafts, A2.CAR Tregs inhibited endogenous non-A2 donor- specific T cell, B cell and antibody responses, and promoted a significant increase in endogenous FoxP3+Tregs with indirect donor-specificity. By contrast, in mice where A2.CAR Tregs failed to prolong graft survival, FoxP3negA2.CAR T cells preferentially accumulated in rejecting allografts and endogenous donor-specific responses were not controlled. This study therefore provides the first evidence for synergy between A2.CAR Tregs and CD154 blockade to promote infectious tolerance in immunocompetent recipients of haplo-mismatched heart grafts and defines features of A2.CAR Tregs when they fail to reshape host immunity towards allograft tolerance.
Probing visual literacy skills reveals unexpected student conceptions of chromosomes
Authors: Uminski Crystal , Newman Dina L. , Wright L. Kate 
Published: September 2024

AbstractMolecular biology can be challenging for undergraduate students because it requires visual literacy skills to interpret abstract representations of submicroscopic concepts, structures and processes. The Conceptual-Reasoning-Mode framework suggests that visual literacy relies on applying conceptual knowledge to appropriately reason with the different ways of representing concepts in molecular biology. We used this framework to specifically explore visual literacy related to chromosomes. We conducted 35 semi-structured interviews with students who had taken at least a year of college-level biology courses, and we asked them to sketch chromosomes, interpret an abstract representation of chromosomes, and use the abstract representation to answer a multiple-choice question about meiosis. While many participants used the correct vocabulary to describe chromosome structure and function, probing their visual literacy skills revealed gaps in their understanding. Notably, 97% of participants (34 of 35) held conceptual errors related to chromosome structure and function, which were often only revealed in their sketches or explanations of their sketches. Our findings highlight the importance of scaffolding visual literacy skills into instruction by teaching with a variety of visual models and engaging students in using and interpreting the conventions of abstract representations of chromosomes.
Seasonality and inter-annual stability in the population genetic structure of Batrachospermum gelatinosum (Rhodophyta)
Authors: Shainker-Connelly Sarah , Stoeckel Solenn , Vis Morgan L. , Crowell Roseanna M. , Krueger-Hadfield Stacy 
Published: September 2024

AbstractTemporal population genetic studies have investigated evolutionary processes, but few have characterized the temporal patterns of reproductive system variation. Yet, temporal sampling may improve our understanding of reproductive system evolution through assessing the relative rates of selfing, outcrossing, and clonality. In this study, we focus on the monoicous, haploid-diploid freshwater red algaBatrachospermum gelatinosum.This species has a perennial, microscopic diploid phase (chantransia) that produces an ephemeral, macroscopic haploid phase (gametophyte). Recent work focusing on single time point genotyping suggested high rates of intragametophytic selfing, though there was variation among sites. We expand on this work by genotyping 191 gametophytes from four sites with reproductive system variation at multiple time points within and among years. Intra-annual data suggest shifts in gametophytic genotypes present throughout the gametophytic season. We hypothesize this pattern is likely due to the seasonality of the life cycle and the timing of meiosis among the chantransia. Inter-annual patterns were characterized by consistent genotypic and genetic composition, indicating stability in the prevailing reproductive system through time. Yet, our study identified limits to which available theoretical predictions and analytical tools can resolve reproductive system variation using haploid data. There is a need to develop better tools to understand the evolution of sex by expanding our ability to characterize the spatiotemporal variation in reproductive systems across diverse life cycles.
snCED-seq: High-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues
Authors: Guo Yunxia , Ma Junjie , Qi Ruicheng , Ma Xiaoying , Xu Jitao , Ye Kaiqiang , Huang Yan , Yang Xi , Wang Guang-zhong , Zhao Xiangwei 
Published: September 2024

AbstractProfiling cellular heterogeneity in formalin-fixed paraffin-embedded (FFPE) tissues is key to characterizing clinical specimens for biomarkers, therapeutic targets, and drug responses. Recent advancements in single-nucleus RNA sequencing (snRNA-seq) techniques tailored for FFPE tissues have demonstrated their feasibility. However, isolation of high-quality nuclei from FFPE tissue with current methods remains challenging due to RNA cross-linking. We, therefore, proposed a novel strategy for the preparation of high-fidelity nuclei from FFPE samples, cryogenic enzymatic dissociation (CED) method, and performed snRandom-seq (snCED-seq) for polyformaldehyde (PFA)-fixed and FFPE brains to verify its applicability. The method is compatible with both PFA-based and FFPE brains or other organs with less hands-on time and lower reagent costs, and produced 10 times more nuclei than the homogenate method, without secondary degradation of RNA, and maximized the retention of RNA molecules within nuclei. snCED-seq shows 1.5-2 times gene and UMI numbers per nucleus, higher gene detection sensitivity and RNA coverage, and a minor rate of mitochondrial and ribosomal genes, compared with the nuclei from traditional method. The correlation gene expression of nucleus from the post-fixed and the frozen sample can be up to 94 %, and the gene expression of our nuclei was more abundant. Moreover, we applied snCED-seq to cellular heterogeneity study of the specimen on Alzheimer’s Disease (AD) to demonstrate a pilot application. Scarce Cajal Retzius cells in older mice were robustly detected in our data, and we successfully identified two subpopulations of disease-associated in astrocytes, microglia and oligodendrocytes, respectively. Meanwhile, we found that most cell types are affected at the transcriptional level by AD pathology, and there is a disease susceptibility gene set that affects these cell types similarly. Our method provides powerful nuclei for snRNA-seq studies for FFPE specimens, and even helps to reveal multi-omics information of clinical samples.
The efficacy and safety of Acupoint herbal patching in treating peptic ulcer: protocol for a systematic review and meta-analysis
Authors: Wang He , Jiang Yuxin , Sun Qiaoyue , Zhao Jinying , zhang Qi , Wang Fuchun 
Published: September 2024

ABSTRACTIntroductionPeptic ulcer (PU) is prone to recurrence and can have a prolonged course, significantly impacting patients’ quality of life. Clinical treatment commonly involves combating Helicobacter pylori(HP), reducing gastric acid secretion, and promoting gastric mucosal protection. Nevertheless, Western medicine often entails various adverse effects and long-term use. Consequently, numerous scholars have redirected their focus towards traditional Chinese medicine (TCM) for external treatments of PU due to its minimal toxicity, fewer side effects, and lower recurrence rates. This study aims to assess the efficacy and safety of Acupoint herbal patching (AHP) in treating PU, offering a foundation for future clinical investigations.Methods and analysisThe computer will conduct a comprehensive search for relevant studies on the utilization of AHP in the management of PU from the inception of the database in various scholarly platforms including China Journal Network, Wanfang Database, Chongqing Wipo Database, China Biomedical Literature Database, PubMed, and Cochrane Library. Eligible literature will undergo meticulous scrutiny based on predefined criteria, with data extraction and quality assessment executed independently by two researchers. Meta-analysis utilizing RevMan 5.4.1 software will be employed to synthesize the collected data. The study will focus on the TCM Symptom Score Scale as the primary outcome measure, while secondary outcomes will encompass serum inflammatory factors, endoscopic findings, quality of life, recurrence rate, and adverse events. Furthermore, assessments on effectiveness, cure rate, and potential publication bias will be carried out. This investigation aims to assess the efficacy of AHP in the treatment of PU and its impact on enhancing the well-being of patients.Ethics and disseminationSince the present work constitutes a literature review, it is important to note that ethical approval is deemed unnecessary. The outcomes of this investigation are intended for dissemination in a scholarly periodical subject to peer review.PROSPERO registration numberCRD42023456995STRENGTHS AND LIMITATIONS OF THIS STUDYA thorough examination of the literature will be undertaken across six electronic databases in both Chinese and English languages.The methodology will adhere to the guidelines outlined in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA).Evaluation of the studies’ quality will be conducted utilizing the updated Cochrane Risk of Bias 2.0 tool.Variations in patch locations and treatment protocols may introduce significant heterogeneity, posing challenges to the synthesis of data.