bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective clinical trial of EUS–guided choledochoduodenostomy without fistula dilation for malignant distal biliary obstruction
Authors: Koga Takehiko , Hijioka Susumu , Nagashio Yoshikuni , Maruki Yuta , Maehara Kosuke , Murashima Yumi , Kawasaki Yuki , Takeshita Kotaro , Yamada Natsumi , Yoshinari Motohiro , Hisada Yuya , Harai Shota , Kitamura Hidetoshi , Kawahara Shun , Ohba Akihiro , Morizane Chigusa , Ishida Yusuke , Hirai Fumihito , Okusaka Takuji 
Published: October 2023

ABSTRACT

Background and Objectives
During EUS–guided choledochoduodenostomy (EUS-CDS), fistula dilation before stent insertion is associated with adverse events (AEs), such as bile leakage and peritonitis. We hypothesized that EUS-CDS without fistula dilation using a novel self-expandable metal stent (SEMS) with a thin delivery system could overcome this problem, and we conducted this study to evaluate its feasibility and safety.

Methods
This was an open-label, single-arm, phase II study at a single institution. We planned EUS-CDS without fistula dilation using a fully covered SEMS with a 5.9-Fr delivery system for unresectable malignant distal biliary obstruction. The primary outcome was overall technical success. Secondary outcomes were technical success without fistula dilation, procedure time, functional success, time to recurrent biliary obstruction, and AEs. The planned sample size was 25 patients.

Results
In total, 24 patients were included in this study. In 21 patients, EUS-CDS was performed as primary drainage. The overall technical success rate was 100% (24 of 24 patients). The technical success rate without fistula dilation was 96% (23 of 24). The median procedure time was 16 min (range, 10–66 min). The functional success rate was 96% (23 of 24). The median time to recurrent biliary obstruction was 148 days (95% confidence interval, 29–266 days). There were no procedure-related AEs. Furthermore, computed tomography immediately after the procedure showed no leakage of contrast medium into the abdominal cavity in any patient.

Conclusions
EUS–guided choledochoduodenostomy without fistula dilation using a fully covered SEMS with a 5.9-Fr delivery system is feasible with a high probability and can be achieved quickly while effectively preventing bile leakage and peritonitis.
Comparison of Magnetic Resonance Imaging and Endoscopic Ultrasound in the Sizing of Intraductal Papillary Mucinous Neoplasia of the Pancreas
Authors: Hesse Felix , Ritter Jessica , Hapfelmeier Alexander , Braren Rickmer , Phillip Veit 
Published: October 2023

Objectives
Because IPMNs are potentially malignant, surveillance of IPMN is recommended by magnetic resonance imaging (MRI) and endoscopic ultrasound (EUS). The aim of the study was the evaluation of the concordance between EUS and MRI regarding cyst size.

Methods
Retrospective data analysis was done for patients with IPMN in whom EUS and MRI were performed simultaneously (≤60 days). The measured cyst size of both procedures was compared by Bland-Altman plots. Agreement of cyst localization and dilation of main pancreatic duct was assessed using kappa statistics.

Results
Fifty-nine cases were evaluated (median age, 71 years; 65% female; median time interval between both investigations, 17 days). The mean difference of IPMN maximal diameter between EUS and MRI was 0.55 mm with a prediction interval of −9.20 to +10.29 mm for 95% of the expected differences. There was strong interobserver agreement regarding cyst localization (κ = 0.669, P = 1.06e−13) and the width of main pancreatic duct (<5, 5–9, and ≥10 mm; κ = 0.676 caput, κ = 0.823 corpus).

Conclusions
We found a clinically relevant difference in cyst size comparing EUS and MRI. Therefore, alternating EUS and MRI for follow-up of the “worrisome feature” size growth is not reasonable.
Association of Longitudinal Mobility Levels in the Hospital and Injurious Inpatient Falls
Authors: Hoyer Erik , Young Daniel , Ke Victor , Zhang Jia Yi , Colantuoni Elizabeth , Farley Holley , Dahbura Anton , Ghobadi Kimia 
Published: October 2023

Abstract
Falls are one of the most common adverse events in hospitals, and patient mobility is a key risk factor. In hospitals risk assessment tools are used to identify patient-centered fall risk factors and guide care plans, but these tools have limitations. To address these issues, we examined daily patient mobility levels prior to injurious falls using the Johns Hopkins Highest Level of Mobility (JH-HLM), which quantifies key patient mobility milestones from low-level to community distances of walking. We aimed to identify longitudinal characteristics of patient mobility prior to a fall to help identify fallers before the event. Conducting a retrospective matched case-control analysis, we compared mobility levels in the days leading up to an injurious fall between fallers and non-fallers. We observed that patients who suffered an injurious fall, on average, spent 28% of their time pre-fall at a low mobility level (JH-HLM levels 1 to 4), compared to non-fallers who spent 19% of their time at a low mobility level (Mean Absolute Difference: 9%; 95% CI 1% to 16%, p = 0.026; Relative Difference: 44%). This suggests that assessing a patient’s mobility levels over time can help identify those at an increased risk for falls and enable hospitals to manage mobility problems more effectively.
Artificial Intelligence–based Quantification of Pleural Plaque Volume and Association With Lung Function in Asbestos-exposed Patients
Authors: Groot Lipman Kevin B.W. , Boellaard Thierry N. , de Gooijer Cornedine J. , Bogveradze Nino , Hong Eun Kyoung , Landolfi Federica , Castagnoli Francesca , Vakhidova Nargiza , Smesseim Illaa , van der Heijden Ferdi , Beets-Tan Regina G.H. , Wittenberg Rianne , Bodalal Zuhir , Burgers Jacobus A. , Trebeschi Stefano 
Published: October 2023

Purpose:
Pleural plaques (PPs) are morphologic manifestations of long-term asbestos exposure. The relationship between PP and lung function is not well understood, whereas the time-consuming nature of PP delineation to obtain volume impedes research. To automate the laborious task of delineation, we aimed to develop automatic artificial intelligence (AI)–driven segmentation of PP. Moreover, we aimed to explore the relationship between pleural plaque volume (PPV) and pulmonary function tests.

Materials and Methods:
Radiologists manually delineated PPs retrospectively in computed tomography (CT) images of patients with occupational exposure to asbestos (May 2014 to November 2019). We trained an AI model with a no-new-UNet architecture. The Dice Similarity Coefficient quantified the overlap between AI and radiologists. The Spearman correlation coefficient (r) was used for the correlation between PPV and pulmonary function test metrics. When recorded, these were vital capacity (VC), forced vital capacity (FVC), and diffusing capacity for carbon monoxide (DLCO).

Results:
We trained the AI system on 422 CT scans in 5 folds, each time with a different fold (n = 84 to 85) as a test set. On these independent test sets combined, the correlation between the predicted volumes and the ground truth was r = 0.90, and the median overlap was 0.71 Dice Similarity Coefficient. We found weak to moderate correlations with PPV for VC (n = 80, r = −0.40) and FVC (n = 82, r = −0.38), but no correlation for DLCO (n = 84, r = −0.09). When the cohort was split on the median PPV, we observed statistically significantly lower VC (P = 0.001) and FVC (P = 0.04) values for the higher PPV patients, but not for DLCO (P = 0.19).

Conclusion:
We successfully developed an AI algorithm to automatically segment PP in CT images to enable fast volume extraction. Moreover, we have observed that PPV is associated with loss in VC and FVC.
A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues
Authors: Yan Ze , Yang Ji , Wei Wen-Tian , Zhou Ming-Liang , Mo Dong-Xin , Wan Xing , Ma Rui , Wu Mei-Ming , Huang Jia-Hui , Liu Ya-Jing , Lv Feng-Hua , Li Meng-Hua 
Published: October 2023

AbstractHigh-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we used sheep as an animal model for plain-to-plateau transplantation. We generated multi-omics data including time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterized transcriptional changes of all genes in each tissue, and examined multi-tissue temporal dynamics and transcriptional interactions among genes. In particular, we identified critical functional genes regulating the short response to hypoxia in each tissue (e.g.,PARGin the cerebellum andHMOX1in the colon). We further identified TAD-constrainedcis-regulatory elements, which suppressed the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicated that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provided time-series expression data of candidate genes associated with human mountain sickness (e.g.,BMPR2) and high-altitude adaptation (e.g.,HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
COMPARATIVE PHYTOCHEMICAL ANALYSIS OF TWO ALPINIA SPECIES FROM ZINGEBERACEAE FAMILY
Authors: Rabita N. , Palanisamy K. 
Published: October 2023

ABSTRACTThe traditional applications of the rhizomes of two Alpinia species,Alpinia galangaandAlpinia nigra, both of which belong to the Zingiberaceae family, are widely recognized. Alpinia has been concentrating on its biological defenses against terrible diseases including cancer and devastating viral infections. In order to develop the diagnostic keys for these significant medications based on the phytochemical analysis, the current research work was done to conduct a detailed comparative phytochemical investigation of the two species.Alpinia galangaandAlpinia nigrawere the focus of this study’s evaluation of their phytochemical components. Alkaloids, saponins, quinones, terpenoids, steroids, tannins, flavonoids, cardiac glycosides, and coumarins were all investigated in our experiments to see if they were present within the two species. The primary chemical compounds found inAlpinia galangaandAlpinia nigrathat may be significant from a pharmacological perspective are highlighted in this article. A qualitative phytochemical study of plant extracts revealed that most of the substances, such as quinones, terpenoids, tannins, steroids, flavonoids, cardiac glycosides, and coumarins, were present.
Metabolic and behavioral alterations associated with viral vector-mediated toxicity in the paraventricular hypothalamic nucleus
Authors: Savani Rohan , Park Erin , Busannagari Nidhi , Lu Yi , Kwon Hyokjoon , Wang Le , Pang Zhiping P. 
Published: October 2023

ABSTRACTObjectiveCombining adeno-associated virus (AAV)-mediated expression of Cre recombinase with genetically modified floxed animals is a powerful approach for assaying the functional role of genes in regulating behavior and metabolism. Extensive research in diverse cell types and tissues using AAV-Cre has shown it can save time and avoid developmental compensation as compared to using Cre driver mouse line crossings. We initially sought to study the impact of ablation of corticotropin-releasing hormone (CRH) in the paraventricular hypothalamic nucleus (PVN) using intracranial AAV-Cre injection in adult animals.MethodsIn this study, we stereotactically injected AAV8-hSyn-Cre or a control AAV8-hSyn-GFP both Crh-floxed and wild-type mouse PVN to assess behavioral and metabolic impacts. We then used immunohistochemical markers to systematically evaluate the density of hypothalamic peptidergic neurons and glial cells.ResultsWe found that delivery of one specific preparation of AAV8-hSyn-Cre in the PVN led to the development of obesity, hyperphagia, and anxiety-like behaviors. This effect occurred independent of sex and in both floxed and wild-type mice. We subsequently found that AAV8-hSyn-Cre led to neuronal cell death and gliosis at the site of viral vector injections. These behavioral and metabolic deficits were dependent on injection into the PVN. An alternatively sourced AAV-Cre did not reproduce the same results.ConclusionsOur findings reveal that delivery of a specific batch of AAV-Cre could lead to cellular toxicity and lesions in the PVN that cause robust metabolic and behavioral impacts. These alterations can complicate the interpretation of Cre-mediated gene knockout and highlight the need for rigorous controls.
Aggression: A gut reaction? The effects of the gut microbiome on aggression
Authors: Uzan-Yulzari Atara , Turjeman Sondra , Getselter Dmitriy , Rautava Samuli , Isolauri Erika , Khatib Soliman , Elliott Evan , Koren Omry 
Published: October 2023

AbstractRecent research has unveiled conflicting evidence regarding the link between aggression and the gut microbiome. In our investigation, we meticulously examined the behavioral patterns of four groups of mice – wild-type, germ-free (GF), mice treated with antibiotics, and recolonized GF mice – to gain mechanistic insights into the impact of the gut microbiome on aggression. We discovered a significant correlation between diminished microbiome and increased aggression. Importantly, this behavioral shift could be restored when a WT microbiota was reinstated. Microbiota manipulation also significantly altered brain function, particularly in aggression-associated genes, and urine metabolite profiles. Notably, our study extends beyond the murine model, shedding light on clinical implications of early-life antibiotic exposure. We found that fecal microbiome transplants from 1mo old infants prescribed antibiotics during their first days of life led to a marked increase in aggression in recipient mice. This research demonstrates that the microbiota modulates aggression and underscores its importance in the realm of behavioral science.One-Sentence SummaryThe antibiotic-altered gut microbiome is implicated in increased aggression. It also leads to altered brain function, particularly in genes linked to aggression, and urine metabolite profiles showing a multi-system response to microbiota disruption.
High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly
Authors: Mann Ludwig , Balasch Kristin , Schmidt Nicola , Heitkam Tony 
Published: October 2023

AbstractBackgroundDespite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative full-length repeat consensuses be derived from unassembled genomes?ResultsHere, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplification setups, and (3) specific repeat-centred questions, such as the linked vs. unlinked arrangement of ribosomal genes. In all our use-cases, the derived consensuses are robust and representative. To evaluate overall performance, we compare our high-fidelity repeat consensuses to RepeatExplorer2-derived contigs and check, if they represent real transposable elements as found in long reads. Our results demonstrate that it is possible to generate useful, reliable and trustworthy consensuses from short reads by a combination from read cluster and genome assembly methods in an automatable way.ConclusionWe anticipate that our workflow opens the way towards more efficient and less manual repeat characterization and annotation, benefitting all genome studies, but especially those of non-model organisms.
Species Composition and Distribution of Anopheles gambiae Complex Circulating in Kinshasa
Authors: Zanga Josue , Metelo Emery , Mvuama Nono , Nsabatien Victoire , Mvudi Vanessa , Banzulu Degani , Mansiangi Osée , Bamba Maxwel , Basosila Narcisse , Agossa Rodrigue , Wumba Roger 
Published: October 2023

AbstractUnderstanding the distribution ofAnophelesspecies in a region is an important task in the planning and implementation of malaria control programmes. This study was proposed to evaluate the composition and distribution of cryptic species of the main malaria vector,Anopheles gambiaecomplex, circulating in different districts of Kinshasa.To study the distribution of members of theAn.gambiaecomplex,Anopheleswere sampled by CDC light trap and larva collection across the four districts of Kinshasa city between July 2021 and June 2022. After morphological identification, an equal proportion ofAnopheles gambiaes.l. sampled per site were subjected to polymerase chain reaction (PCR) for identification of crypticAn.gambiaecomplex species.TheAnopheles gambiaecomplex was widely identified in all sites across the city of Kinshasa, with a significant difference in mean density, captured by CDC light, inside and outside households in Kinshasa (p=0.002). Two species of this complex circulate in Kinshasa:Anopheles gambiae(82.1%) andAnopheles coluzzii(17.9%). In all study sites,Anopheles gambiaewas the most prevalent species.Anopheles coluzziiwas very prevalent in Tshangu district. No hybrids (Anopheles coluzzii/Anopheles gambiae) were identified.Two cryptic species of theAnopheles gambiaecomplex circulate in Kinshasa.Anopheles gambiaes.s., present in all districts andAnopheles coluzzii, with a limited distribution. Studies on the ecology of the larval sites are essential to better understand the factors influencing the distribution of members of theAn. gambiaecomplex in this megalopolis.
Marine protection enhances the resilience of biological communities on temperate rocky reefs
Authors: Sanabria-Fernandez Jose A. , Alday Josu G. 
Published: October 2023

AbstractConservation science faces the urgent challenge of halting the biodiversity loss caused by the biological crisis of the present era. To achieve this, conservation science requires cutting-edge tools to focus on vital properties of ecosystems, such as the resilience. Resilience informs about the cost of recovering biological communities. Here, we developed a metric to quantify the communities ecological recovery cost based on the multidimensional distance between unprotected and partially protected communities from totally protected communities in Cabo de Gata Marine Reserve. Our results show that the biological community composed of fish, macroinvertebrates and cryptic fish, and macroalgae species in unprotected zones requires a higher ecological recovery cost than in partially protected zones when moving towards a fully protected community. This research contributes to monitoring marine the effectiveness of marine protection from a resilience perspective, with the goal of promoting the use of the recovery cost metric for building resilient coastal ecosystems.
Influenza vaccine effectiveness against hospitalized SARS-CoV-2 infection
Authors: Lee Yung-Chun , Liu Lufeiya , Yuan Liyang , Risk Malcolm , Heinrich Kevin , Witteveen-Lane Martin , Hayek Salim , Malosh Ryan , Pop-Busui Rodica , Jiang Bian , Shen Chen , Chesla Dave , Kennedy Richard , Xu Shi , Sims Matthew , Homayouni Ramin , Zhao Lili 
Published: October 2023

AbstractBackgroundSome studies conducted before the Delta and Omicron variant-dominant periods have indicated that influenza vaccination provided protection against COVID-19 infection or hospitalization, but these results were limited by small study cohorts and a lack of comprehensive data on patient characteristics. No studies have examined this question during the Delta and Omicron periods (08/01/2021 to 2/22/2022).MethodsWe conducted a retrospective cohort study of influenza-vaccinated and unvaccinated patients in the Corewell Health East(CHE, formerly known as Beaumont Health), Corewell Health West(CHW, formerly known as Spectrum Health) and Michigan Medicine (MM) healthcare system during the Delta-dominant and Omicron-dominant periods. We used a test-negative, case-control analysis to assess the effectiveness of the influenza vaccine against hospitalized SARS-CoV-2 outcome in adults, while controlling for individual characteristics as well as pandameic severity and waning immunity of COVID-19 vaccine.ResultsThe influenza vaccination has shown to provided some protection against SARS-CoV-2 hospitalized outcome across three main healthcare systems. CHE site (odds ratio [OR]=0.73, vaccine effectiveness [VE]=27%, 95% confidence interval [CI]: [18-35], p<0.001), CHW site (OR=0.85, VE=15%, 95% CI: [6-24], p<0.001), MM (OR=0.50, VE=50%, 95% CI: [40-58], p <0.001) and overall (OR=0.75, VE=25%, 95% CI: [20-30], p <0.001).ConclusionThe influenza vaccine provides a small degree of protection against SARS-CoV-2 infection across our study sites.
Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls
Authors: Larsen Daniel Nyberg , Kaczmarek Jakub Zbigniew , Palarasah Yaseelan , Graversen Jonas Heilskov , Højrup Peter 
Published: October 2023

AbstractUnderstanding protein-protein interaction is essential when designing drugs or investigating biological processes. A variety of techniques can be employed in order to map the regions on proteins that are involved in binding eg., CryoEM, X-ray spectroscopy, linear epitope mapping, or mass spectrometry-based methods. The most commonly utilized mass spectrometry-based techniques are cross-linking and hydrogen-deuterium exchange (HDX). An alternative technique for identifying residues on the three-dimensional structure of proteins, that are involved in binding, can be hydroxyl radical protein footprinting (HRPF). However, this method is currently hampered by high initial cost and complex experimental setup. Here we set out to present a generally applicable method using Fenton chemistry for mapping of epitopes in a standard mass spectrometry laboratory. Furthermore, the described method illustrates the importance of controls on several levels when performing mass spectrometry-based epitope mapping. In particular, the inclusion of a negative antibody control has not previously been widely utilized in epitope mapping by HRPF analysis. In order to limit the number of false positives, we further introduced quantification by TMT labelling, thereby allowing for direct comparison between sample conditions and biological triplicates. Lastly, up to six technical replicates were incorporated in the experimental setup in order to achieve increased depth of the final analysis.Both binding and opening of regions on receptor-binding domain (RBD) from SARS-CoV-2 Spike Protein, Alpha, and Delta variants, were observed. The negative control antibody experiment combined with the high overlap between biological triplicates resulted in the exclusion of 40% of the significantly changed regions, including both binding and opening regions. The final identified binding region was mapped to a three-dimensional structure and agrees with the literature for neutralizing antibodies towards SARS-CoV-2 Spike Protein.The presented method is straightforward to implement for the analysis of HRPF in a generic MS-based laboratory. The high reliability of the data was achieved by increasing the number of technical and biological replicates combined with negative antibody controls.