bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innovative suture technique for robotic hepaticojejunostomy: double-layer interrupted sutures
Authors: Takagi Kosei , Umeda Yuzo , Yoshida Ryuichi , Fuji Tomokazu , Yasui Kazuya , Yagi Takahito , Fujiwara Toshiyoshi 
Published: July 2023

Abstract
Purpose
Biliary reconstruction remains a technically demanding and complicated procedure in minimally invasive hepatopancreatobiliary surgeries. No optimal hepaticojejunostomy (HJ) technique has been demonstrated to be superior for preventing biliary complications. This study aimed to investigate the feasibility of our unique technique of posterior double-layer interrupted sutures in robotic HJ.

Methods
We performed a retrospective analysis of a prospectively collected database. Forty-two patients who underwent robotic pancreatoduodenectomy using this technique between September 2020 and November 2022 at our center were reviewed. In the posterior double-layer interrupted technique, sutures were placed to bite the bile duct, posterior seromuscular layer of the jejunum, and full thickness of the jejunum.

Results
The median operative time was 410 (interquartile range [IQR], 388–478) min, and the median HJ time was 30 (IQR, 28–39) min. The median bile duct diameter was 7 (IQR, 6–10) mm. Of the 42 patients, one patient (2.4%) had grade B bile leakage. During the median follow-up of 12.6 months, one patient (2.4%) with bile leakage developed anastomotic stenosis. Perioperative mortality was not observed. A surgical video showing the posterior double-layer interrupted sutures in the robotic HJ is included.

Conclusions
Posterior double-layer interrupted sutures in robotic HJ provided a simple and feasible method for biliary reconstruction with a low risk of biliary complications.
Meta-analysis of second language research with complex research designs
Authors: Norouzian Reza , Bui Gavin 
Published: July 2023

AbstractMeta-analyses play an instrumental role in informing second language (L2) theory and practice. However, current (i.e., classic) approaches to meta-analysis are limited in their ability to do so because they often fail to capture the complexity inherent in primary studies’ research designs. As we argue in this article, when complex L2 studies are represented by simplistic meta-analyses, the latter cannot reach its potential to contribute to the development of cumulative knowledge. To mitigate this issue, we first discuss the fundamental problems of the classic approaches to meta-analysis of complex L2 research. Second, we introduce an alternative meta-analytic framework that will address those problems. Third, we apply the meta-analytic framework discussed to a complex L2 domain. Fourth, we offer free software to facilitate the conduct of the alternative meta-analytic approach described. Finally, we discuss the implications of this alternative framework for making evidence-based recommendations to the relevant stakeholders.
High‐Resolution Mantle Flow Models Reveal Importance of Plate Boundary Geometry and Slab Pull Forces on Generating Tectonic Plate Motions
Authors: Saxena Arushi , Dannberg Juliane , Gassmöller Rene , Fraters Menno , Heister Timo , Styron Richard 
Published: July 2023

AbstractMantle convection models based on geophysical constraints have provided us with a basic understanding of the forces driving and resisting plate motions on Earth. However, existing studies computing the balance of underlying forces are contradicting, and the impact of plate boundary geometry on surface deformation remains unknown. We address these issues by developing global instantaneous 3‐D mantle convection models with a heterogeneous density and viscosity distribution and weak plate boundaries prescribed using different geometries. We find that the plate boundary geometry of the Global Earthquake Model (GEM, Pagani et al., 2018, https://doi.org/10.1177/8755293020931866), featuring open plate boundaries with discrete lithospheric‐depth weak zones in the oceans and distributed crustal faults within continents, achieves the best fit to the observed GPS data with a directional correlation of 95.1% and a global point‐wise velocity residual of 1.87 cm/year. A good fit also requires plate boundaries being 3 to 4 orders of magnitude weaker than the surrounding lithosphere and low asthenospheric viscosities between 5 × 1017 and 5 × 1018 Pa s. Models without asthenospheric and lower mantle heterogeneities retain on average 30% and 70% of the plate speeds, respectively. Our results show that Earth's plate boundaries are not uniform and better described by more discrete plate boundaries within the oceans and distributed faults within continents. Furthermore, they emphasize the impact of plate boundary geometry on the direction and speed of plate motions and reaffirm the importance of slab pull in the uppermost mantle as a major plate driving force.
Risk factors in acquiring multidrug-resistant Klebsiella pneumoniae infections in a hospital setting in Saudi Arabia
Authors: Ibrahim Mutasim E. 
Published: July 2023

AbstractOver the last decades, the prevalence of multidrug-resistant (MDR) Klebsiella pneumoniae in clinical settings has increased progressively. This study determined the prevalence and risk factors associated with MDR K. pneumoniae infection among hospitalized patients in a referral hospital located in southern Saudi Arabia. A prospective cross-sectional study was conducted in King Abdullah Hospital from April 2021 to March 2022. K. pneumoniae (n = 211) bacteria were recovered from clinical samples of adult patients and examined for antibiotic susceptibility. Univariate and multivariate logistic regressions were applied to determine the factors associated with MDR K. pneumoniae infection. MDR K. pneumoniae strains was found in 66.8% (142/211) of the patients. Among MDR K. pneumoniae, the highest resistance rate was determined for ampicillin (100%), cefuroxime (97.9%), ceftriaxone (94.3%), and aztreonam (92.2%). The lowest resistance rate was determined for colistin (16.3%), and tigecycline (6.4%). Further, the patients’ gender, age group, intensive care unit (ICU) admission, invasive medical devices, and chronic illness were found to be significantly associated with MDR K. pneumoniae infection. The independent risk factors associated with MDR K. pneumoniae infection were the male gender (adjusted odds ratio [AOR] 2.107, 95% confidence interval CI 1.125‒3.945, p = 0.02), patients ≥ 65 years of age (AOR 1.905; CI 1.003‒3.616, p = 0.049), ICU admission (AOR 1.963; CI 1.033‒3.732, p = 0.04), diabetes (AOR 1.95; CI 1.02‒3.727, p = 0.043) and chronic obstructive pulmonary disease (AOR 7.172; CI 1.557‒33.032, p = 0.011). The study offered a vision of MDR K. pneumoniae infection in our setting and provided essential indications for further studies that may lead to the prevention and reduction of MDR bacteria.
Status of Patient Safety Culture in Community Pharmacy Settings: A Systematic Review
Authors: Kwon Kyoung-Eun , Nam Dal Ri , Lee Mo-Se , Kim Su-Jin , Lee Jae-Eun , Jung Sun-Young 
Published: July 2023

Objectives
This systematic aimed to understand the global status using the results of survey studies based on the Community Pharmacy Survey on Patient Safety Culture and set the directions of development in terms of the patient safety culture of community pharmacies.

Methods
Electronic searches were performed in EMBASE, MEDLINE, PubMed, and CINAHL databases by using the words “patient safety,” “culture,” and “community pharmacy” with synonyms or associated words in the original English language research articles published between January 1, 2012, and March 2, 2023. This systematic review was conducted based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

Results
Eleven surveys from 10 countries were selected. Five studies were conducted on pharmacists, whereas 6 studies were carried out on all pharmacy staff members such as pharmacists, technicians, clerks, and pharmacy students on apprenticeship. There was a considerable variation in the positive response rates across the dimensions of all the surveys. The highest positive response score was demonstrated for “teamwork” and “patient counseling,” whereas the “staffing, work pressure, and pace” dimension was essential for improving patient safety culture in community pharmacy settings. For overall rating of the pharmacy on patient safety, 84.8% of pharmacy staff members gave good, very good, or excellent as their responses.

Conclusions
Despite the differences among studies, findings of this study are expected to be used as valuable evidence to develop patient safety improvement strategies after reflecting each country’s health care setting or community pharmacy practice. Furthermore, the results would offer meaningful assistance to achieve the goals of global campaigns such as the World Health Organization Patient Safety Challenge.
Socioeconomic and Demographic Barriers Associated with Delays in Pancreatic Cancer Germline Genetic Testing
Authors: Zou Xianghui , Sidiqi Baho , Patruni Sunita , Rezak Leora , Hollweg Christopher , Kauff Noah , King Daniel 
Published: July 2023

AbstractBackgroundGermline genetic testing is recommended for patients with pancreatic ductal adenocarcinoma (PDAC) and pre-diagnostic testing is offered to patients with a significant family history. However, only 41% of patients in our institution obtained genetic testing. We identified associations between patient social profiles and delays in obtaining germline genetic testing from New York’s largest healthcare system.MethodsPatients with PDAC were identified using our EMR between Mar 2016 and Feb 2022 with an IRB-approved protocol. Median income was extrapolated using zip code. Date of diagnosis (DOD) was recorded as the date of biopsy. Delays of testing was calculated as the difference between DOD and the date of germline test. Social work needs and insurance were captured by EMR review of social work notes.Results329 patients with PDAC were identified, with 135 (41%) having reports found. Availability of germline testing did not vary by median income. Pearson analysis between income and delays showed a negative correlation (r=-0.258, p=0.0025). Patients who received social security and were unemployed/disabled had significant delays (167d) in testing compared to patients receiving social security (13d) and retired or patients receiving salaries (30d).African Americans and Hispanics, classified as underserved minority, had significant delays in testing (66d) compared to not underserved patients (22.5d, p=0.021). In addition, African American patients had significant delays in testing (66d) compared to White patients (20d, p=0.0076).Patients with social work needs had significant delays in testing (104d) compared to patients without SW needs (20.5d, p=0.0002). Of the twelve patients who required SW, six required home care, three required transportation, and two required financial assistance. In addition, patients with Medicare and supplementary insurances had significant decreases in delays (10d) of germline testing compared with patients with Medicare alone (32d, p=0.0077), Medicaid (57d, p=0.020), or commercial insurances (21d, p=0.021).We identified 12 patients who had germline mutation reports before PDAC diagnosis. For patients with pre-diagnostic testing, 5 had Medicare with supplementary insurances. For the rest of patients with germline testing after the diagnosis of PDAC, 10 had supplementary insurances (p=0.0043).ConclusionThe analysis of our 329-patient cohort showed a striking and concerning negative correlation between patient income and delays in germline testing. Under-represented minority patients had significant delays in germline testing and did not obtain any pre-diagnostic testing. Social work needs and insurance may be barriers as well. Interprofessional collaborations may be required to prompt germline testing.
Microenvironment of metastasis reveals key predictors of PD-1 blockade response in renal cell carcinoma
Authors: Jeanneret Florian , Bazelle Pauline , Schoch Sarah , Pillet Catherine , Um In Hwa , Bouzit Assilah , Evrard Bertrand , Seffar Evan , Chalmel Frédéric , Alfaro Javier A , Pesquita Catia , Zanzotto Fabio Massimo , Stares Mark , Symeonides Stefan N , Laird Alexander , Long Jean-Alexandre , Descotes Jean Luc , Pflieger Delphine , Harrison David J , Filhol Odile , Axelson Håkan , Battail Christophe 
Published: July 2023

AbstractImmune checkpoint blockade (ICB) therapies have improved the overall survival (OS) of many patients with advanced cancers. However, the response rate to ICB varies widely among patients, exposing non-responders to potentially severe immune-related adverse events. The discovery of new biomarkers to identify patients responding to ICB is now a critical need in the clinic. We therefore investigated the tumor microenvironment (TME) of advanced clear cell renal cell carcinoma (ccRCC) samples from primary and metastatic sites to identify molecular and cellular markers of response to ICB. We revealed a significant discrepancy in treatment response between subgroups based on cell fractions inferred from metastatic sites. One of the subgroups was enriched in non-responders and harbored a lower fraction of CD8+ T cells and plasma cells, as well as a decreased expression of immunoglobulin genes. In addition, we developed the Tumor-Immunity Differential (TID) score which combines features from tumor cells and the TME to accurately predict response to anti-PD-1 immunotherapy (AUC-ROC=0.88, log-rank tests for PFS P < 0.0001, OS P = 0.01). Finally, we also defined TID-related genes (YWHAE,CXCR6andBTF3), among whichYWHAEwas validated as a robust predictive marker of ICB response in independent cohorts of pre- or on-treatment biopsies of melanoma and lung cancers. Overall, these results provide a rationale to further explore variations in the cell composition of metastatic sites, and underlying gene signatures, to predict patient response to ICB treatments.One Sentence SummaryTumor microenvironment balance of metastasis and associated genes are key predictors of immunotherapy patient response in kidney cancer.
Effect of sample preprocessing and extraction methods on the physical and molecular profiles of extracellular vesicles
Authors: Alexandre Lucile , Shen Molly L. , de Araujo Lorenna Oliveira Fernandes , Renault Johan , DeCorwin-Martin Philippe , Martel Rosalie , Ng Andy , Juncker David 
Published: July 2023

ABSTRACTExtracellular vesicles (EVs) are nanometric lipid vesicles that shuttle cargo between cells. Their analysis could shed light on health and disease conditions, but EVs must first be preserved, extracted and often pre-concentrated. Here we firstly compare plasma preservation agents, and secondly, using both plasma and cell supernatant, four EV-extraction methods including (i) ultracen-trifugation (UC), (ii) size exclusion chromatography (SEC), (iii) centrifugal filtration (LoDF), and (iv) accousto-sorting (AcS). We benchmarked them by characterizing integrity, size-distribution, concentration, purity and the expression profiles for nine proteins of EVs, as well as overall throughput, time-to-result and cost. We found that the difference between EDTA and citrate anticoagulants vary with the extraction method. In our hands, ultracentrifugation produced a high yield of EVs with low contamination; SEC is low-cost, fast, and easy to implement, but the purity of EVs is lower; LoDF and AcS are both compatible with process automation, small volume requirement, and rapid processing times. When using plasma, the LoDF was susceptible to clogging and sample contamination, while the AcS featured high purity but a lower yield of extraction. Analysis of protein profiles suggest that extraction methods extract different sub-population of EVs. Our study highlights the strength and weakness of sample preprocessing methods, and the variability in concentration, purity, and EV expression profiles of the extracted EVs. Pre-analytical parameters such as collection or pre-processing protocols must be considered as part of the entire process in order to address EV diversity and their use as clinically actionable indicators.
Optical Control of G-Actin with a Photoswitchable Latrunculin
Authors: Vepřek Nynke A. , Cooper Madeline H. , Laprell Laura , Yang Emily Jie-Ning , Folkerts Sander , Bao Ruiyang , Oertner Thomas G. , Pon Liza A. , Zuchero J. Bradley , Trauner Dirk H. 
Published: July 2023

ABSTRACTActin is one of the most abundant proteins in eukaryotic cells and a key component of the cytoskeleton. A range of small molecules have emerged that interfere with actin dynamics by either binding to polymeric F-actin or monomeric G-actin to stabilize or destabilize filaments or prevent their formation and growth, respectively. Amongst these, the latrunculins, which bind to G-actin and affect polymerization, are widely used as tools to investigate actin-dependent cellular processes. Here, we report a photoswitchable version of latrunculin, termed opto-latrunculin (OptoLat), which binds to G-actin in a light-dependent fashion and affords optical control over actin polymerization.OptoLatcan be activated with 390 – 490 nm pulsed light and rapidly relaxes to the inactive form in the dark. Light activatedOptoLatinduced depolymerization of F-actin networks in oligodendrocytes and budding yeast, as shown by fluorescence microscopy. Subcellular control of actin dynamics in human cancer cell lines was demonstrated by live cell imaging. Light-activatedOptoLatalso reduced microglia surveillance in organotypic mouse brain slices while ramification was not affected. Incubation in the dark did not alter the structural and functional integrity of microglia. Together, our data demonstrate thatOptoLatis a useful tool for the elucidation of G-actin dependent dynamic processes in cells and tissues.
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
Authors: Vakirlis Nikolaos , Kupczok Anne 
Published: July 2023

AbstractSpecies-specific genes, also known as orphans, are ubiquitous across life’s domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses, followed by horizontal gene transfer, while the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4,644 human gut microbiome species and identified over 600,000 unique SSOGs, representing an average of 2.6% of a given species’ pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most SSOGs. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.
Natural disaster alters the adaptive benefits of sociality in a primate
Authors: Testard C. , Shergold C. , Acevedo-Ithier A. , Hart J. , Bernau A. , Negron-Del Valle JE. , Phillips D. , Watowich MM. , Sanguinetti-Scheck JI. , Montague MJ. , Snyder-Mackler N. , Higham JP. , Platt ML. , Brent LJN. 
Published: July 2023

AbstractWeather-related disasters can radically alter ecosystems. When disaster-driven ecological damage persists, the selective pressures exerted on individuals can change, eventually leading to phenotypic adjustments. For group-living animals, social relationships are believed to help individuals cope with environmental challenges and may be a critical mechanism enabling adaptation to ecosystems degraded by disasters. Yet, whether natural disasters alter selective pressures on patterns of social interactions and whether group-living animals can, as a result, adaptively change their social relationships remains untested. Here, we leveraged unique data collected on rhesus macaques from 5 years before to 5 years after a category 4 hurricane, leading to persistent deforestation which exacerbated monkeys’ exposure to intense heat. In response, macaques increased tolerance for and decreased aggression toward other monkeys, facilitating access to scarce shade critical for thermoregulation. Social tolerance predicted individual survival for 5 years after the hurricane, but not before it, revealing a clear shift in the adaptive function of social relationships in this population. We demonstrate that an extreme climatic event altered selection on sociality and triggered substantial and persistent changes in the social structure of a primate species. Our findings unveil the function and adaptive flexibility of social relationships in degraded ecosystems and identify natural disasters as potential evolutionary drivers of sociality.One-Sentence SummaryTestard et al.show that a natural disaster altered selection on sociality in group-living primates triggering persistent changes in their social structure.
Effects of sex and gonadal hormones on manually segmented hypothalamic and pituitary gland volumes in young healthy adults
Authors: Jones Sherri Lee , Anastassiadis Chloe , Dupuis Matthieu , Pruessner Jens 
Published: July 2023

AbstractThe hypothalamus and pituitary regulate, amongst other functions, third order endocrine systems, and their volumes have been associated with normal and pathological outcomes. Yet, there are very few studies that examine their combined structural variationsin vivo. This is due, in part, to their small size and a lack of comprehensive image segmentation protocols. In the current project we acquired high-resolution T1- (1mm isotropic) and T2-weighted (0.4mm in plane resolution) 3T magnetic resonance images (MRI) of the hypothalamus and pituitary gland, as well as salivary estradiol and testosterone from 31 (17M, 14F) young healthy adults. Women reported oral contraceptive use. Image preprocessing included non-uniformity correction, signal intensity normalization and standard stereotaxic space registration. We applied a comprehensive manual segmentation protocol of the whole hypothalamus, with detailed segmentation of the pituitary stalk, the anterior and posterior pituitary gland, and the posterior bright spot. We also propose a novel medial-lateral hypothalamic parcellation into medial preoptic, periventricular (PVN), and lateral hypothalamic regions. The protocol yielded good inter- (range: 0.78-0.92) and intra-rater (range: 0.79-0.94) Dice kappa overlap coefficients. We detected sex differences of the whole hypothalamus and each hemisphere, and a trend for the right preoptic region to be larger in males than in females, with a moderate effect size. Sex differences were maintained or enhanced when covarying for estradiol, but not when covarying for testosterone. In addition, testosterone was associated with the volume of the PVN, but only in women. In summary, these results suggest that there are morphometric differences at the level of the pituitary and hypothalamus that are likely driven by central regulation of gonadal hormones. The here described protocol allows the structural investigation of neuroendocrine effects in the central nervous system.