bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn’s Disease
Authors: Maddipatla Sushma Chowdary , Kolachala Vasantha L , Venkateswaran Suresh , Dodd Anne F , Pelia Ranjit Singh , Geem Duke , Yin Hong , Sun Yutong , Xu Congmin , Mo Angela , Kosters Astrid , Yang Junkai , Matthews Jason D , Ghosn Eliver , Kugathasan Subra , Qiu Peng 
Published: October 2022

Abstract

Background
Crohn’s disease is a lifelong disease characterized by chronic inflammation of the gastrointestinal tract. Defining the cellular and transcriptional composition of the mucosa at different stages of disease progression is needed for personalized therapy in Crohn’s.

Methods
Ileal biopsies were obtained from (1) control subjects (n = 6), (2) treatment-naïve patients (n = 7), and (3) established (n = 14) Crohn’s patients along with remission (n = 3) and refractory (n = 11) treatment groups. The biopsies processed using 10x Genomics single cell 5' yielded 139 906 cells. Gene expression count matrices of all samples were analyzed by reciprocal principal component integration, followed by clustering analysis. Manual annotations of the clusters were performed using canonical gene markers. Cell type proportions, differential expression analysis, and gene ontology enrichment were carried out for each cell type.

Results
We identified 3 cellular compartments with 9 epithelial, 1 stromal, and 5 immune cell subtypes. We observed differences in the cellular composition between control, treatment-naïve, and established groups, with the significant changes in the epithelial subtypes of the treatment-naïve patients, including microfold, tuft, goblet, enterocyte,s and BEST4+ cells. Surprisingly, fewer changes in the composition of the immune compartment were observed; however, gene expression in the epithelial and immune compartment was different between Crohn’s phenotypes, indicating changes in cellular activity.

Conclusions
Our study identified cellular and transcriptional signatures associated with treatment-naïve Crohn’s disease that collectively point to dysfunction of the intestinal barrier with an increase in inflammatory cellular activity. Our analysis also highlights the heterogeneity among patients within the same disease phenotype, shining a new light on personalized treatment responses and strategies.
Use of virtual reality for procedural planning of transcatheter aortic valve replacement
Authors: Ruyra Xavier , Permanyer Eduard , Huguet Marina , Maldonado Giuliana 
Published: October 2022

Abstract
This study sought to evaluate the impact of virtual reality (VR) tools in procedural planning of transcatheter aortic valve replacement. A prospective study involving 11 patients referred for transcatheter aortic valve replacement was conducted. A multidetector computed tomography was used to acquire and segment the anatomy of the access route and landing zone. From the information obtained with the multidetector computed tomography in DICOM format, we built a virtual platform (VisuaMed, Techer Team, Valencia, Spain) that contains all the clinical information of the patients and a virtualized model of their anatomy. Wearing VR devices, the professional was able to ‘walk inside’ the anatomy in an interactive and immersive way. Decisions after the evaluation of routine clinical images were compared with those after experience with VR models and intraprocedural findings.
Stressed Hyperplanes and Kazhdan–Lusztig Gamma-Positivity for Matroids
Authors: Ferroni Luis , Nasr George D , Vecchi Lorenzo 
Published: October 2022

Abstract
In this article, we make several contributions of independent interest. First, we introduce the notion of stressed hyperplane of a matroid, essentially a type of cyclic flat that permits to transition from a given matroid into another with more bases. Second, we prove that the framework provided by the stressed hyperplanes allows one to write very concise closed formulas for the Kazhdan–Lusztig, inverse Kazhdan–Lusztig, and $Z$-polynomials of all paving matroids, a class that is conjectured to predominate among matroids. Third, noticing the palindromicity of the $Z$-polynomial, we address its $\gamma $-positivity, a midpoint between unimodality and real-rootedness. To this end, we introduce the $\gamma $-polynomial associated to it, we study some of its basic properties, and we find closed expressions for it in the case of paving matroids. Also, we prove that it has positive coefficients in many interesting cases, particularly in the large family of sparse paving matroids, and other smaller classes such as projective geometries, thagomizer matroids, and other particular graphs. Our last contribution consists of providing explicit combinatorial interpretations for the coefficients of many of the polynomials addressed in this article by enumerating fillings in certain Young tableaux and skew Young tableaux.
Whole Genome Sequencing Reveals the Structure of Environment-Associated Divergence in a Broadly Distributed Montane Bumble Bee, Bombus vancouverensis
Authors: Heraghty Sam D , Rahman Sarthok Rasique , Jackson Jason M , Lozier Jeffrey D 
Published: October 2022

Abstract
Broadly distributed species experience divergent abiotic conditions across their ranges that may drive local adaptation. Montane systems where populations are distributed across both latitudinal and elevational gradients are especially likely to produce local adaptation due to spatial variation in multiple abiotic factors, including temperature, oxygen availability, and air density. We use whole-genome resequencing to evaluate the landscape genomics of Bombus vancouverensis Cresson (Hymenoptera: Apidae), a common montane bumble bee that is distributed throughout the western part of North America. Combined statistical approaches revealed several large windows of outlier SNPs with unusual levels of differentiation across the region and indicated that isothermality and elevation were the environmental features most strongly associated with these variants. Genes found within these regions had diverse biological functions, but included neuromuscular function, ion homeostasis, oxidative stress, and hypoxia that could be associated with tolerance of temperature, desiccation, or high elevation conditions. The whole-genome sequencing approach revealed outliers occurred in genome regions with elevated linkage disequilibrium, elevated mean FST, and low intrapopulation nucleotide diversity. Other kinds of structural variations were not widely associated with environmental predictors but did broadly match geographic separation. Results are consistent with other studies suggesting that regions of low recombination may harbor adaptive variation in bumble bees within as well as between species and refine our understanding of candidate genes that could be further investigated as possible targets of selection across the B. vancouverensis range.
Acquisition of genomic elements were pivotal for the success of Escherichia coli ST410
Authors: Chen Liang , Peirano Gisele , Kreiswirth Barry N , Devinney Rebekah , Pitout Johann D D 
Published: October 2022

Abstract

Background
Escherichia coli ST410 is an emerging MDR clone linked to blaCTX-M-15 and blaOXA-181. Limited comprehensive data about the global distribution of ST410 clades and mobile genetic elements associated with different β-lactamases are available.

Methods
Short- and long-read WGS were performed on a collection of ST410 producing carbapenemases (n = 45) obtained from 11 countries. The evolutionary history of global E. coli ST410 was also investigated.

Results
OXA-181 and NDM-5 were the most frequent carbapenemases and used different underlying strategies to ensure their successful association with ST410 clades. Our phylogenetic analysis of publicly available ST410 genomes amended the previously published ST410 B subclades: ST410-B1 is identical to B1/H24, ST410-B2 includes B2/H24R and B3/H24Rx, while ST410-B3 corresponds to B4/H24RxC. Long-read WGS identified the following genomic events that likely shaped the evolution of ST410-B3: (i) gyrA and parC mutations were acquired via homologous recombination events; (ii) chromosomal integration of blaCMY-2 among ST410-B3; (iii) the emergence of ST410-B3 from ST410-B2 was accompanied by the replacement of IncFII plasmids harbouring blaCTX-M-15 (i.e. F36:31:A4:B1 in ST410-B2 with F1:A1:B49 plasmids in ST410-B3); and (iv) the NDM-5 gene was integrated within F1:A1:B49 plasmids over time.

Conclusions
The global ST410 population producing carbapenemases is dominated by the ST410-B2 and B3 subclades with varied geographical distribution that requires ongoing genomic surveillance. We provided an updated timeline of pivotal genomic events that have shaped the success of the ST410-B3 subclade.
Trading-off privacy and utility: the Washington State experience assessing the performance of a public health digital exposure notification system for coronavirus disease 2019
Authors: Segal Courtney D , Lober William B , Revere Debra , Lorigan Daniel , Karras Bryant T , Baseman Janet G 
Published: October 2022

AbstractObjectiveDigital exposure notifications (DEN) systems were an emergency response to the coronavirus disease 2019 (COVID-19) pandemic, harnessing smartphone-based technology to enhance conventional pandemic response strategies such as contact tracing. We identify and describe performance measurement constructs relevant to the implementation of DEN tools: (1) reach (number of users enrolled in the intervention); (2) engagement (utilization of the intervention); and (3) effectiveness in preventing transmissions of COVID-19 (impact of the intervention). We also describe WA State’s experience utilizing these constructs to design data-driven evaluation approaches.MethodsWe conducted an environmental scan of DEN documentation and relevant publications. Participation in multidisciplinary collaborative environments facilitated shared learning. Compilation of available data sources and their relevance to implementation and operation workflows were synthesized to develop implementation evaluation constructs.ResultsWe identified 8 useful performance indicators within reach, engagement, and effectiveness constructs.DiscussionWe use implementation science to frame the evaluation of DEN tools by linking the theoretical constructs with the metrics available in the underlying disparate, deidentified, and aggregate data infrastructure. Our challenges in developing meaningful metrics include limited data science competencies in public health, validation of analytic methodologies in the complex and evolving pandemic environment, and the lack of integration with the public health infrastructure.ConclusionContinued collaboration and multidisciplinary consensus activities can improve the utility of DEN tools for future public health emergencies.
Tōjisha Research and Narrative Medicine: Contribution of a Japanese Experiment in the Investigation of Patients’ Personal Experience
Authors: Gaillard Maxence 
Published: October 2022

Abstract
Tōjisha research is a methodology intended to help psychiatric patients through dialogue. It was introduced in the context of community care in Bethel House (Hokkaido, Japan) in the early 2000s and later spread to other parts of Japan as well as abroad because of its originality and apparent therapeutic success. It offers patients a framework to investigate their own problems, symptoms, and delusions and to build a discourse around them. In this paper, I present a short account of tōjisha research and I put it in the context of current debates over the benefits and drawbacks of narrative medicine. I argue that there is an original conception of the self and of empowerment of patients in tōjisha research compared to other models of narrative medicine. Finally, I mobilize these original aspects to address some rebuttals of narrative medicine.
Trimodality Therapy vs Definitive Chemoradiation in Older Adults With Locally Advanced Esophageal Cancer
Authors: Gaber Charles E , Shaheen Nicholas J , Edwards Jessie K , Sandler Robert S , Nichols Hazel B , Sanoff Hanna K , Lund Jennifer L 
Published: October 2022

Abstract

Background
The comparative effectiveness of trimodality therapy vs definitive chemoradiation for treating locally advanced esophageal cancer in older adults is uncertain. Existing trials lack generalizability to older adults, a population with heightened frailty. We sought to emulate a hypothetical trial comparing these treatments using real-world data.

Methods
A cohort of adults aged 66-79 years diagnosed with locally advanced esophageal cancer between 2004 and 2017 was identified in the Surveillance Epidemiology and End Results–Medicare database. The clone-censor-weight method was leveraged to eliminate time-related biases when comparing outcomes between treatments. Outcomes included overall mortality, esophageal cancer–specific mortality, functional adverse events, and healthy days at home.

Results
A total of 1240 individuals with adenocarcinomas and 661 with squamous cell carcinomas were identified. For adenocarcinomas, the standardized 5-year risk of mortality was 73.4% for trimodality therapy and 83.8% for definitive chemoradiation (relative risk [RR] = 0.88, 95% confidence interval [CI] = 0.82 to 0.95). Trimodality therapy was associated with mortality risk reduction for squamous cell carcinomas (RR = 0.87, 95% CI = 0.70 to 1.01). The 1-year incidence of functional adverse events was higher in the trimodality group (adenocarcinomas RR = 1.40, 95% CI = 1.22 to 1.65; squamous cell carcinomas RR = 1.21, 95% CI = 1.00 to 1.49). Over 5 years, trimodality therapy was associated with 160 (95% CI = 67 to 229) and 177 (95% CI = 51 to 313) additional home days in individuals with adenocarcinomas and squamous cell carcinomas, respectively.

Conclusions
Compared with definitive chemoradiation, trimodality therapy was associated with reduced mortality but increased risk of function-related adverse events. Discussing these tradeoffs may help optimize care plans.
Drug-related problems identified at a Japanese community pharmacy: a cross-sectional study
Authors: Takaki Hiroko , Kaneko Erina , Sonoda Masanobu , Yamano Toru , Ieiri Ichiro 
Published: October 2022

Abstract

Objectives
This study aimed to identify drug-related problems (DRPs) using data regarding the communication of pharmacists with prescribers over the phone at a community pharmacy. Furthermore, we elucidated the frequency of the sources of information for detecting each DRP and evaluated the decisions made by the prescribers for each DRP.

Methods
This cross-sectional study was conducted at a community pharmacy in Fukuoka Prefecture, Japan. We anonymously collected data obtained by pharmacists through contacting prescribers over the phone relating to any problems or doubts found in prescriptions between April 2016 and March 2019. We classified the data and identified DRPs. We elucidated the frequency of sources of information for detecting each DRP using descriptive analyses and evaluated prescribers’ decisions regarding each DRP via multivariate Poisson regression analyses.

Key findings
Of the 95 023 prescriptions, 5073 DRPs were identified (5073/95 023 = 5.34%). The most frequent DRP was inappropriate dosage and administration (1349/5073 = 26.59%), followed by non-adherence (1272/5073 = 25.07%) and incorrect prescription periods (889/5073 = 17.52%). Patient interviews were the most frequent sources of information for detecting following DRPs: non-adherence (1057/1272 = 83.10%), untreated indication (590/631 = 93.50%) and adverse drug reactions (80/107 = 74.77%). Most of the DRPs were resolved by making changes to the prescriptions (4571/5073 = 90.10%).

Conclusions
Inappropriate dosage and administration and non-adherence issues were the most frequent DRPs in a Japanese community pharmacy. Patient interviews were an important source of information for detecting DRPs. Further research is warranted to address the impact of DRPs on patient safety.
Pharmacological and phytochemical potential of Rubus ellipticus: a wild edible with multiple health benefits
Authors: Kewlani Pushpa , Tiwari Deepti , Rawat Sandeep , Bhatt Indra D 
Published: October 2022

Abstract

Objectives
Rubus ellipticus (family Rosaceae) is used for its delicious edible fruits in the Himalayan region and other parts of the globe. However, the full potential of the species is yet to be harnessed. The current review focuses on the phytochemical, traditional uses, morphological, molecular and pharmacological potential of R. ellipticus.

Key findings
The review of the literature reveals that many health-promoting compounds of R. ellipticus have been reported from the species along with the different biological properties, such as nephroprotective, anti-inflammatory, analgesic, anti-pyretic, anti-proliferative, cytotoxicity, anti-cancer, wound healing, anti-fertility, anti-plasmodial, anti-microbial and antioxidant. Traditionally, it is used in many formulations, which are validated through primary pharmacological assays. However, several medicinal properties are still need to be validated through detailed pharmacological and clinical studies.

Summary
All the information is available in a scanty form, and the complete information is missing on a single platform. Such type of information will help researchers to better utilize the available data for initiating future research on the species as it has the potential to contribute to the food and pharmaceutical industry. The review highlights the need for further studies on the species to harness its potential in nutraceutical, functional food, energy supplement, and beneficial therapeutic drug development program.
Triterpenoid saponins of Ilex pubescens against TNF-α induced inflammation and apoptosis in human umbilical vein endothelial cells via autophagy pathway
Authors: Yan Xuemei , Shang Xueying , Feng Zhiqiang , Chen Bingying , Wu Yurong , Zhou Yuan , Li Yu , Zhang Lei 
Published: October 2022

Abstract

Objectives
Triterpenoid saponins of Ilex pubescens (IPTS), the main active components of Ilex pubescens, has a therapeutic effect on atherosclerosis (AS). The ingredients in IPTS that could be intracellularly transported by human umbilical vein endothelial cells (HUVECs) may play an essential role in AS. This study attempted to explore its mechanism from the perspectives of HUVECs’ inflammation, apoptosis, and autophagy.

Methods
By using a tumour necrosis factor-α (TNF-α)-induced HUVECs injury model, cell viability and the expression of intercellular adhesion molecule 1 (ICAM1), matrix metalloproteinase 9 (MMP9), cleave-caspase-3 and cleave-caspase-9, in combination with the results of flow cytometry, JC-1 and Hoechst 33258 staining were investigated to evaluate the anti-inflammatory and anti-apoptotic impact effects of IPTS on HUVECs. Afterwards, the expression of microtubule-associated proteins light chain 3II (LC3II) and sequestosome 1 (p62) was determined to test the effect of IPTS on autophagy. Finally, by adding an autophagy inhibitor 3-methyladenine (3-MA), we investigated whether IPTS exerts anti-inflammatory and anti-apoptotic effects through the autophagy pathway.

Key findings
We firstly demonstrated that pretreatment with IPTS could increase the cell viability, maintain the cell morphology and reduce TNF-α-induced inflammation and apoptosis of HUVECs. Moreover, IPTS pretreatment was proved to raise the expression of LC3II /LC3I while decreasing the expression of p62, which indicated that IPTS could activate HUVECs’ autophagy. IPTS has been shown for the first time to exert anti-inflammatory and anti-apoptotic effects through autophagy and thereby resisting TNF-α-induced inflammatory injury of HUVECs.

Conclusions
This study preliminarily confirmed that IPTS ameliorated HUVECs’ inflammation and apoptosis by increasing autophagy.
Effects of artemether on pancreatic islet morphology, islet cell turnover and α-cell transdifferentiation in insulin-deficient Glu
CreERT2;ROSA26-eYFP diabetic mice
Authors: Sarnobat Dipak , Lafferty Ryan A , Charlotte Moffett R , Tarasov Andrei I , Flatt Peter R , Irwin Nigel 
Published: October 2022

Abstract

Objectives
The antimalarial drug artemether is suggested to effect pancreatic islet cell transdifferentiation, presumably through activation γ-aminobutyric acid receptors, but this biological action is contested.

Methods
We have investigated changes in α-cell lineage in response to 10-days treatment with artemether (100 mg/kg oral, once daily) on a background of β-cell stress induced by multiple low-dose streptozotocin (STZ) injection in GluCreERT2; ROSA26-eYFP transgenic mice.

Key findings
Artemether intervention did not affect the actions of STZ on body weight, food and fluid intake or blood glucose. Circulating insulin and glucagon were reduced by STZ treatment, with a corresponding decline in pancreatic insulin content, which were not altered by artemether. The detrimental changes to pancreatic islet morphology induced by STZ were also evident in artemether-treated mice. Tracing of α-cell lineage, through co-staining for glucagon and yellow fluorescent protein (YFP), revealed a significant decrease of the proportion of glucagon+YFP− cells in STZ-diabetic mice, which was reversed by artemether. However, artemether had no effect on transdifferentiation of α-cells into β-cells and failed to augment the number of bi-hormonal, insulin+glucagon+, islet cells.

Conclusions
Our observations confirm that artemisinin derivatives do not impart meaningful benefits on islet cell lineage transition events or pancreatic islet morphology.
Research on the psychology of fictional characters based on artificial intelligence—an example study on The Family
Authors: Yuan Ying 
Published: October 2022

Abstract
Using ecological recognition based on artificial intelligence technology and Chinese psychology analysis system, by comparing the characters’ dialogs in The Family, we got the main characters’ big-five personality scores. In order to confirm the validity of this method, we compared the predicted scores with documents related to characters’ psychological analysis and novel descriptions. The prediction results are supported by the literature and plot. This indicates that the analysis of characters’ personalities by literary intelligence is effective. This research method provides data support for literary critics and quantitatively reflects the personality differences of characters in novels.