bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Changes of CT-radiomic and Systemic Inflammatory Features Predict Survival in Advanced Non–Small Cell Lung Cancer Patients Treated With Immune Checkpoint Inhibitors
Authors: Balbi Maurizio , Mazzaschi Giulia , Leo Ludovica , Moron Dalla Tor Lucas , Milanese Gianluca , Marrocchio Cristina , Silva Mario , Mura Rebecca , Favia Pasquale , Bocchialini Giovanni , Trentini Francesca , Minari Roberta , Ampollini Luca , Quaini Federico , Roti Giovanni , Tiseo Marcello , Sverzellati Nicola 
Published: August 2024

Purpose:
This study aims to determine whether longitudinal changes in CT radiomic features (RFs) and systemic inflammatory indices outperform single-time-point assessment in predicting survival in advanced non–small cell lung cancer (NSCLC) treated with immune checkpoint inhibitors (ICIs).

Materials and Methods:
We retrospectively acquired pretreatment (T0) and first disease assessment (T1) RFs and systemic inflammatory indices from a single-center cohort of stage IV NSCLC patients and computed their delta (Δ) variation as [(T1-T0)/T0]. RFs from the primary tumor were selected for building baseline-radiomic (RAD) and Δ-RAD scores using the linear combination of standardized predictors detected by LASSO Cox regression models. Cox models were generated using clinical features alone or combined with baseline and Δ blood parameters and integrated with baseline-RAD and Δ-RAD. All models were 3-fold cross-validated. A prognostic index (PI) of each model was tested to stratify overall survival (OS) through Kaplan-Meier analysis.

Results:
We included 90 ICI-treated NSCLC patients (median age 70 y [IQR=42 to 85], 63 males). Δ-RAD outperformed baseline-RAD for predicting OS [c-index: 0.632 (95%CI: 0.628 to 0.636) vs. 0.605 (95%CI: 0.601 to 0.608) in the test splits]. Integrating longitudinal changes of systemic inflammatory indices and Δ-RAD with clinical data led to the best model performance [Integrated-Δ model, c-index: 0.750 (95% CI: 0.749 to 0.751) in training and 0.718 (95% CI: 0.715 to 0.721) in testing splits]. PI enabled significant OS stratification within all the models (P-value <0.01), reaching the greatest discriminative ability in Δ models (high-risk group HR up to 7.37, 95% CI: 3.9 to 13.94, P<0.01).

Conclusion:
Δ-RAD improved OS prediction compared with single-time-point radiomic in advanced ICI-treated NSCLC. Integrating Δ-RAD with a longitudinal assessment of clinical and laboratory data further improved the prognostic performance.
Objective Analysis of Predictive Value of Ultrasound Quantitative Scoring System for Treatment Method Selection in Cesarean Scar Pregnancy
Authors: Zhang Jieying , Liu Yingying , Wan Hui , Lu Yue , Xin Yanli , Du Jianwen , Wang Hong 
Published: August 2024

Abstract
This study aimed to explore the feasibility of using the ultrasound quantitative scoring system to guide the selection of surgical methods for a cesarean scar ectopic pregnancy (CSEP). A retrospective analysis was conducted of the medical records of 117 cases of patients with a CSEP. All patients underwent transvaginal ultrasound examination before treatment, and the ultrasound results were compared with the results of surgical exploration. The treatment methods that were delivered for the 2 patient groups with CSEP were analyzed, and agreement between the predicted and actual treatment protocols was tested using the kappa consistency test. Residual myometrial thickness at the scar site was mainly concentrated above 3 mm in the low-risk group, with 70 cases accounting for 76.9%, while in the high-risk group, this was primarily in the range of 1–3 mm with 18 cases accounting for 69.2%. The grading of nourishing blood supply to the gestational sac showed that 96.7% of patients in the low-risk group had Grade I and Grade II blood flow, while 84.6% of the high-risk group had Grade I and Grade II blood flow; Grade II blood flow was predominant in the high-risk group. The majority of patients in both the low- and high-risk groups experienced intraoperative blood loss of ≤50 mL (93.9% vs 80.6%, respectively). The consistency test between the actual and predicted treatment methods yielded a kappa coefficient of 0.644, indicating consistency between the two. For patients with CSEP in the low-risk group (score <4), the ultrasound quantitative scoring system could provide individualized assessment and offer clinically valuable treatment protocols.
Presurgical Maxillary Segmented Orthodontics Associated With 3-Piece Le Fort 1 Osteotomy for Palatal Expansion
Authors: Ricard Daniel , Ferri Joël , Schlund Matthias 
Published: August 2024

Objective:
The aim of this study is to assess maxillary transverse dimension following presurgical maxillary segmented orthodontics associated with 3-piece Le Fort 1 osteotomy in a cohort of “long face syndrome” patients with palatal constriction.

Methods:
Patients with maxillary transverse insufficiency were retrospectively included. They all underwent maxillary segmented orthodontics followed by a 3-piece Le Fort 1 osteotomy with palatal expansion. Palatal width dimensions were collected preoperatively, postoperatively, and at the time of the final follow-up, the stability of the expansion was analyzed.

Results:
Nineteen patients were included. There was no complication. The mean postoperative expansion was 6 mm (range: 3.1–8.7 mm) in the canine region and 4.3 mm (range: 0–9.1 mm) in the second molar region. The mean relapse was 0.36 mm (range: 0–1.4 mm) or 6% (range: 0%–16.1%) in the canine region and 0.17 mm (range: 0–1.3 mm) or 4% (range: 0%–14%) in the second molar region.

Conclusion:
Presurgical maxillary segmented orthodontics with 3-piece Le Fort 1 osteotomy has shown high stability of the maxillary transverse dimension in a 1-step surgery without dental tipping. It should be considered as an alternative to rapid palatal expansion.
Planning for implementation success: insights from conducting an implementation needs assessment
Authors: Graham Nicole D. , Graham Ian D. , Vanderspank-Wright Brandi , Nadalin-Penno Letitia , Fergusson Dean A. , Squires Janet E. 
Published: August 2024

ABSTRACT

Aim:
The aim of this paper is to provide insights into conducting an implementation needs assessment using a case example in a less-research-intensive setting.

Design and methods:
In the case example, an implementation needs assessment was conducted, including (1) an environmental scan of the organization's website and preliminary discussions with key informants to learn about the implementation context, and (2) a formal analysis of the evidence–practice gap (use of sedation interruptions) deploying a chart audit methodology using legal electronic reports.

Results:
Our needs assessment was conducted over 5 months and demonstrated how environmental scans reveal valuable information that can inform the evidence–practice gap analysis. A well-designed gap analysis, using suitable indicators of best practice, can reveal compliance rates with local protocol recommendations, even with a small sample size. In our case, compliance with the prescribed practices for sedation interruptions ranged from 65% (n=53) to as high as 84% (n=69).

Conclusions:
Implementation needs assessments provide valuable information that can inform implementation planning. Such assessments should include an environmental scan to understand the local context and identify both current recommended best practices and local best practices for the intervention of interest. When addressing an evidence–practice gap, analyses should quantify the difference between local practice and desired best practice.

Impact:
The insights gained from the case example presented in this paper are likely transferrable to implementation research or studies conducted in similar, less-research-intensive settings.

Spanish abstract:

http://links.lww.com/IJEBH/A257
Mycovorax composti gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from button mushroom compost
Authors: Thai Meghann , Bell Tina L. , Kertesz Michael A. 
Published: August 2024

Two Gram-stain-negative, aerobic, rod-shaped, orange-coloured bacterial strains, designated strain C216T and strain M2295, were isolated from mature mushroom compost from composting facilities in Victoria and South Australia, Australia, respectively. External structures such as flagella or pili were not observed on the cells under scanning electron microscopy. Optimal growth was found to occur at 45 °C, at pH 7.25 and in the absence of NaCl on Emerson’s 350 YpSs medium. The genome sequence of strain C216T was 3 342 126 bp long with a G+C content of 40.5 mol%. Functional analysis of the genome of strain C216T revealed genes encoding chitinolytic and hemi-cellulolytic functions, with 166 predicted genes associated with carbohydrate metabolism (8.9% of the predicted genes). These functions are important for survival in the mushroom compost environment, which is rich in hemicelluloses. No antibiotic resistance genes were found in the genome sequence. The major fatty acids of strain C216T were iso-C15 : 0 (56.7%), iso-C17 : 0 3-OH (15.6%), C16 : 1
ω7c/iso-C15 : 0 2-OH (7.3%) and iso-C15 : 1 G (6.1%). The only respiratory quinone was MK-7. The major polar lipid of strain C216T was phosphatidylethanolamine, but three unidentified phospholipids, four unidentified aminophospholipids/aminolipids and one unidentified glycolipid were also detected. Phylogenetic analysis based on proteins encoded by the core genome (bac120, 120 conserved bacterial genes) showed that strain C216T forms a distinct lineage in the family Chitinophagaceae and that the closest identified relative is Niabella soli (69.69% ANI). These data demonstrate that strain C216T represents a novel genus and novel species within the family Chitinophagaceae, for which we propose the name Mycovorax composti. The type strain is C216T (=DSM 114558T=LMG 32998T).
Cyclic Electromagnetic DNA Simulation (CEDS) can enhance the Functions of Anticancer miR-26a-5p and miR-126-5p in RAW 264.7 cells
Authors: Kim Yeon Sook , Lee Suk Keun 
Published: August 2024

AbstractSince cyclic electromagnetic DNA simulation (CEDS) was found to increase the hybridization potential of double-stranded DNA (dsDNA) and affect the functions of plasmid DNA (1), in this study, Dodecagonal CEDS was applied to RAW 264.7 cells to target anticancer miRNAs, miR-26a-5p and miR-126-5p, at 20-25 Gauss for 20 min during cell culture, followed by cytological observation, quantitative polymerase chain reaction (qPCR), and immunoprecipitation-based high-performance liquid chromatography (IP-HPLC). Both of miR-26a-5p*-CEDS and miR-126-5p*-CEDS induced significant decrease in cell number, and strong immunoreaction of c-caspase 3 in the remaining cells compared to oncogenic miR-21-5p*-CEDS and untreated control. In qPCR results, miR-26a-5p*-CEDS and miR-126-5p*-CEDS markedly increased the expression of target primary and mature miRNAs. IP-HPLC analysis showed that both miR-26a-5p*-CEDS and miR-126-5p*-CEDS induced potent anticancer effect on RAW 264.7 cells by suppressing RAS signaling, proliferation-growth-cytodifferentiation signaling axis, and angiogenesis-survival-oncogenesis-chronic inflammation axis compared to the untreated control and the positive control performed with non-specific poly-A 12A*-CEDS. MiR-26a-5p*-CEDS increased miRNA biogenesis and ER stress signaling more than miR-126-5p*-CEDS, while miR-126-5p*-CEDS increased NFkB signaling-immunity-apoptosis signaling axis more than miR-26a-5p*-CEDS. Therefore, it is proposed that the sequential treatment of miR-26a-5p*-CEDS and miR-126-5p*-CEDS may give a synergistic anticancer effect on RAW 264.7 cells. It is postulated that CEDS using a miRNA sequence can stimulate hybridization between miRNA and target mRNA and also increase the expression of target miRNA, and subsequently decrease the expression of miRNA target proteins, resulting in the alteration of protein signaling pathways in cells.
Cyclic Electromagnetic DNA Simulation (CEDS) targeting Telomere Repeat Sequence can enhance Anticancer Effect, while CEDS targeting Canonical E-box Sequence induce Oncogenic Effect in Cells
Authors: Kim Yeon Sook , Lee Suk Keun 
Published: August 2024

AbstractCyclic electromagnetic DNA simulation (CEDS) was used in the previous study (1) to stimulate the base pair polarities of oligo-dsDNAs, plasmid DNAs, and miRNAs. This study applied dodecagonal CEDS to target telomere repeat sequence (TTAGGG*-CEDS), canonical E-box sequence (CACGTG*-CEDS) in genomic DNA of RAW 264.7 cells and KB cells. During cell culture, CEDS was performed at 20-25 Gauss for 20 min, and followed by cytological observation and immunoprecipitation high-performance liquid chromatography (IP-HPLC) using 350 antisera. KB cells treated with TTAGGG*-CEDS showed a significant decrease in cell density and metachromasia in toluidine blue staining compared to untreated control, while only a slight decrease in cell density and metachromasia was observed by telomere mutation sequence, TTTGGG*-CEDS. Conversely, CACGTG*-CEDS induced almost no change in cell density, cell number, metachromasia in toluidine blue staining compared to random sequence*-CEDS (2(ACGT)*-CEDS) and untreated control. IP-HPLC results showed that TTAGGG*-CEDS induced a potent anticancer effect by downregulating RAS, oncogenesis, and telomere signaling, and activating NFkB signaling-p53-and FAS-mediated apoptosis-innate and cellular immunity signaling axis compared to untreated control and positive control performed with nonspecific poly-A 12A*-CEDS. In contrast, CACGTG*-CEDS exhibited a significant oncogenic effect by enhancing of RAS and NFkB signaling and resulting oncogenesis-glycolysis-chronic inflammation signaling axis. Therefore, it is suggested that CEDS is able to target DNA motif sequences in genomic DNA, and that TTAGGG*-CEDS and CACGTG*-CEDS are favorable candidates to regulate important genes involved in oncogenesis, inflammation, apoptosis, etc.
pyVIPER: A fast and scalable Python package for rank-based enrichment analysis of single-cell RNASeq data
Authors: Wang Alexander L.E. , Lin Zizhao , Zanella Luca , Vlahos Lukas , Anglada Girotto Miquel , Zafar Aziz , Noh Heeju , Califano Andrea , Vasciaveo Alessandro 
Published: August 2024

AbstractSummarySingle-cell sequencing has revolutionized biomedical research by offering insights into cellular heterogeneity at unprecedented resolution. Yet, the low signal-to-noise ratio, characteristic of single-cell RNA sequencing (scRNASeq), challenges quantitative analyses. We have shown that gene regulatory network (GRN) analysis can help overcome this obstacle and support mechanistic elucidation of cellular state determinants, for example by using the VIPER algorithm to identify Master Regulator (MR) proteins from gene expression data. A key challenge, as the size and complexity of scRNASeq datasets grow, is the need for highly scalable tools supporting the analysis of large-scale datasets with up to hundreds of thousands of cells. To address it, we introduce pyVIPER, a fast, memory-efficient, and highly scalable Python toolkit for assessing protein activity in large-scale scRNASeq datasets. pyVIPER supports multiple enrichment analysis algorithms, data transformation/postprocessing modules, a novel data structure for GRNs manipulation, and seamless integration with AnnData, Scanpy and several widely adopted machine learning libraries. Compared to VIPER, benchmarking reveals orders of magnitude runtime reduction for large datasets—i.e., from hours to minutes— thus supporting VIPER-based analysis of virtually any large-scale single-cell dataset, as well as integration with other Python-based tools.Availability and ImplementationpyVIPER is available on GitHub (https://github.com/alevax/pyviper) and PyPI (https://pypi.org/project/viper-in-python/).Contactav2729@cumc.columbia.eduSupplementary informationSupplementary data are available at Bioinformatics online. Accompanying data for the tutorials are available on Zenodo (https://zenodo.org/records/10059791).
PCDHGC3silencing promotes clear cell renal cell carcinoma metastasis via mTOR/HIF2α and lipid metabolism reprogramming
Authors: Celada Lucía , Cubiella Tamara , Salerno Laura , San-Juan-Guardado Jaime , Murias Eduardo , Da Silva Torres Marina , Suárez-Priede Álvaro , Weiner Joshua A. , Herrada-Manchón Helena , Fernández M. Alejando , Chiara María-Dolores 
Published: August 2024

AbstractClustered protocadherins (cPCDH) are widely expressed in the nervous system with known functions, but their roles in cancer, particularly metastasis, are largely unexplored. Our previous research revealed that epigenetic silencing ofPCDHGC3is linked to decreased survival in neuroendocrine cancer patients. This study investigatesPCDHGC3’s role in clear cell renal cell carcinoma (ccRCC). We found that decreasedPCDHGC3expression is associated with lower survival and advanced disease stage in ccRCC patients. shRNA-mediatedPCDHGC3silencing in renal cancer cell lines significantly increased cell proliferation, invasion, and survival. In orthotopic mouse models,PCDHGC3silencing promoted metastasis. The mTOR and HIF2α pathways were identified as downstream targets activated byPCDHGC3loss. Inhibition of these pathways counteracted the effects ofPCDHGC3silencing, highlighting their importance in tumor progression. Proteomic and metabolomic analyses showed thatPCDHGC3silencing led to overexpression of proteins involved in fatty acid and cholesterol synthesis, increasing lipid droplets and shifting lipid metabolism. This metabolic reprogramming characterizes aggressive ccRCC. Our study emphasizesPCDHGC3’s impact on ccRCC metastasis and suggests mTOR or HIF2α inhibitors as potential therapies forPCDHGC3-deficient patients.
Effects of injury size on local and systemic immune cell dynamics in volumetric muscle loss
Authors: Whitaker Ricardo , Sung Samuel , Tylek Tina , Risser Gregory , O’Brien Erin , Chua Phoebe Ellin , Li Thomas , Petrie Ryan J. , Han Lin , Binder-Markey Benjamin , Spiller Kara L. 
Published: August 2024

AbstractWe took a systems approach to the analysis of macrophage phenotype in regenerative and fibrotic volumetric muscle loss outcomes in mice together with analysis of systemic inflammation and of other leukocytes in the muscle, spleen, and bone marrow. Macrophage dysfunction in the fibrotic group occurred as early as day 1, persisted to at least day 28, and was associated with increased numbers of leukocytes in the muscle and bone marrow, increased pro-inflammatory marker expression in splenic macrophages, and changes in the levels of pro-inflammatory cytokines in the blood. The most prominent differences were in muscle neutrophils, which were much more abundant in fibrotic outcomes compared to regenerative outcomes at day 1 after injury. However, neutrophil depletion had little to no effect on macrophage phenotype or on muscle repair outcomes. Together, these results suggest that the entire system of immune cell interactions must be considered to improve muscle repair outcomes.
Invertebrate species distributions in urban ecosystems are driven by habitat availability, not by anthropogenic drivers
Authors: Morpurgo Joeri , Remme Roy P. , Mudde Quinten , Didaskalou Emilie A. , Serwatowska Kornelia J. , Trimbos Krijn , Hu Mingming , Van Bodegom Peter M. 
Published: August 2024

AbstractRapid urbanisation puts pressure on biodiversity by habitat fragmentation and habitat quality among others. These habitat changes are known to affect species dispersal and connectivity and ultimately species distribution in many ecosystems. However, little is known about the changing urban species distributions which in turn influence community assembly. New DNA-based sampling methods combined with species distribution modelling provide a way to quantitatively estimate urban community assembly through assessing many species distributions and their drivers simultaneously.We investigated species distributions of entire communities in the city of The Hague (the Netherlands) by sampling DNA with two distinct methods: collecting data on invertebrate occurrence with traditional trapping (bulk; n = 205) and a novel Environmental DNA method (eDNA; n = 207). After DNA sequencing, species were identified using Operational Taxonomic Units. Subsequently, individual species presence and absence were used in Species Distribution Models (SDMs), based on spatial information on vegetation and anthropogenic influences.The results show a difference in coverage of sampling methods (bulk vs. eDNA), indicating their complementary information. The models on species distributions were generally significantly better than random models (59.5%), and performed well during calibration (90.4%, AUC > 0.70). In contrast, during validation very few SDMs (1.3%, AUC > 0.70) performed adequately in predicting species distributions.Through this novel combination of DNA sampling with SDMs we show that density and structure of vegetation, as well as distance to water are more important for urban invertebrate distribution than direct anthropogenic pressures. This suggests that dispersal is not a limiting factor in The Hague’s urban environment. The availability of a variety of urban green infrastructures seems sufficient to attract many of the species observed. Hence, ensuring sufficient green infrastructure in the urban environment should be the first priority to enhance biodiversity in the urban environment.HighlightsVegetation and water indicators are the most important predictors for accurate assessment of species’ distributionAnthropogenic pressures have lower impact on urban species distributionsDNA-SDM combinations show potential in guiding urban planners in evidence-based decision making
Acetate enhances spatial memory in females via sex- and brain region-specific epigenetic and transcriptional remodeling
Authors: Periandri Erica M. , Dodson Kala M. , Vitorino Francisca N. , Garcia Benjamin A. , Glastad Karl M. , Egervari Gabor 
Published: August 2024

ABSTRACTMetabolic control of chromatin and gene expression is emerging as a key, but largely unexplored aspect of gene regulation. In the brain, metabolic-epigenetic interactions can influence critical neuronal functions. Here, we use a combination of behavioral, proteomic and genomic approaches to demonstrate that the intermediary metabolite acetate enhances memory in a brain region- and sex-specific manner. We show that acetate facilitates the formation of dorsal hippocampus-dependent spatial memories in female but not in male mice, while having no effect on cortex-dependent non-spatial memories in either sex. Acetate-enhanced spatial memory is driven by increased acetylation of histone variant H2A.Z, and upregulation of genes implicated in spatial learning in the dorsal hippocampus of female mice. In line with the sex-specific behavioral outcomes, the effect of acetate on dorsal hippocampal histone modifications and gene expression shows marked differences between the sexes during critical windows of memory formation (consolidation and recall). Overall, our findings elucidate a novel role for acetate, a ubiquitous and abundant metabolite, in regulating dorsal hippocampal chromatin, gene expression and learning, and outline acetate exposure as a promising new approach to enhance memory formation.