bluuebunny/crossref_metadata_2025_split huggingface dataset:
SESAME - Self-supervised framework for Extractive queStion Answering over docuMent collEctions
Authors: Batista Vitor Alcantara , Gomes Diogo Silva Magalhães , Evsukoff Alexandre Gonçalves 
Published: March 2024

Abstract
Question Answering is one of the most relevant areas in the field of Natural Language Processing, rapidly evolving with promising results due to the increasing availability of suitable datasets and the advent of new technologies, such as Generative Models. This article introduces SESAME, a Self-supervised framework for Extractive queStion Answering over docuMent collEctions. SESAME aims to enhance open-domain question answering systems (ODQA) by leveraging domain adaptation with synthetic datasets, enabling efficient question answering over private document collections with low resource usage. The framework incorporates recent advances with large language models, and an efficient hybrid method for context retrieval. We conducted several sets of experiments with Machine Reading for Question Answering (MRQA) 2019 Shared Task datasets, FAQuAD - a Brazilian Portuguese reading comprehension dataset, Wikipedia, and Retrieval-Augmented Generation Benchmark, to demonstrate SESAME's effectiveness. The results indicate that SESAME's domain adaptation using synthetic data significantly improves QA performance, generalizes across different domains and languages, and competes with or surpasses state-of-the-art systems in ODQA.Finally, SESAME is an open-source tool, and all code, datasets and experimental data is available for public use in our repository.
Therapeutic inhibition of glycolysis preferentially targets pathogenic monocyte subsets and attenuates CNS inflammation in flavivirus encephalitis
Authors: King Nicholas , Wishart Claire , Spiteri Alanna , Tan Jian , Macia Laurence 
Published: March 2024

Abstract

Infiltrating monocytes play a dual role in central nervous system (CNS) diseases, both driving and attenuating inflammation. However, it is unclear how metabolic pathways preferentially fuel protective or pathogenic processes and whether these can be therapeutically targeted to enhance or inhibit these opposing functions. Here, we employed single-cell RNA-sequencing and metabolic protein flow analysis of brain and bone marrow (BM) to map the metabolic signatures of monocyte-derived cells (MCs) to their functions during lethal West Nile virus encephalitis. Using trajectory analysis, we showed progression of BM monocytes through 3 metabolic profiles before their migration to the brain where they differentiated into metabolically distinct MC populations. These included a single pro-inflammatory HIF1-α MC cluster that diverged into two disparate populations: an inducible nitric oxide synthase-positive (iNOS+) M1-like MC, with high glycolysis and amino acid metabolic scores, and a glycolytically quiescent, MHC-II+ antigen-presenting MC. Daily in vivo glycolysis inhibition with 2-deoxy-D-glucose significantly reduced CNS leukocyte numbers, reducing neuroinflammation and disease signs without increasing viral load. Reduced leukocyte numbers were not due to decreased myelopoiesis, but a preferential decrease in iNOS+, compared to antigen-presenting MC, highlighting different glycolytic dependencies between these subsets. Importantly, HIF1-a was independent of glycolysis, enabling continued antigen-presenting MC differentiation, while glycolysis inhibition did not impair generation of an effective antiviral response by cervical node T cells. Together, this integrative approach unveils the tight coupling of MC function and metabolism in viral CNS disease, highlighting novel metabolic therapeutic intervention points, potentially with anti-viral therapy, during severe or uncontrolled inflammation.
Detecting atypical sentinel lymph nodes in early-stage cervical cancer using a standardized technique with a hybrid tracer
Authors: Vila Joana Amengual , Colomer Anna Torrent , Bas Catalina Sampol , Duarte Adriana Quintero , Coll Mario Ruiz , Merlo Jorge Rioja , Cordoba Octavi 
Published: March 2024

Abstract

Background
Since October 2018, lymph node (LN) status has become part of the International Federation of Gynaecology and Obstetrics (FIGO) staging, given that it is one of the most important prognostic factors among women with cervical cancer (CC).
The aim of this study was to determine the rate of atypical lymphatic drainage in patients with clinical early-stage CC using a hybrid tracer (ICG-99mTc nanocolloid).
Methodology
A prospective, observational, descriptive, single-centre study conducted at Son Espases University Hospital between January 2019 and October 2023. Patients with clinical early-stage CC who underwent SLN mapping during surgical staging were included. External iliac and obturator nodes were defined as common SLN locations. Para-aortic, common iliac, presacral, internal iliac, and parametrial nodes were defined as uncommon (atypical) locations.
Results
Thirty-nine cases of CC were included. Overall SLN detection rate was 97.4%, with 89.5% bilaterally. Positive SLNs were found in 21.1% of patients. Atypical lymphatic drainage was present in 8 out of 38 (21.1%). Of the total SLNs (146), 10.3% corresponded to an atypical zone (the most frequent, common iliac vessels). SLNs in the atypical area had a higher proportion of metastasis than the usual area (37.5% vs. 16.7%; p=0.327).
Parametrial nodes were detected in 17.9% of patients; two of these (5.2%) with the presence of metastases. In all cases where a parametrial SLN was detected, drainage was also observed to a SLN in a common location. There was no involvement of parametrial lymphatic channels or parametrial nodes in any patient (7/8, 87.5%) with metastatic pelvic SLNs.
Conclusion
SLN biopsy can detect unusual drainage in a significant proportion of patients with CC. SLNs in atypical locations have a higher percentage of metastatic involvement, which consequently improves staging and tailoring therapy. Our series suggests that lymphatic drainage from the cervical tumour to the pelvic nodes could be a direct route that bypasses parametrial nodes.
We suggest that SLN mapping performed by a standardized surgical technique using a hybrid tracer (ICG-99mTc) could help in the identification of the "true sentinel lymph node" and ensure no empty node packet is obtained.
BCAP29/31 as a Poor Prognostic Biomarker for Head and Neck Squamous Carcinoma: Impacting the TGFβ1/Smad- EMT Pathway
Authors: Zhang Shurong , Gao Lihua , Gao Wen , Zhu Xiaoyu , Liao Yuxuan , Ma Xinyu , Wang Hongyi , Zhou Dawei , Zhang Bo , Chen Liangjian 
Published: March 2024

Abstract

Objectives This study aimed to investigate the possible mechanism of action of BCAP29/31 in head and neck squamous cell carcinoma (HNSC) and to provide clues for finding new therapeutic targets for HNSC.
Materials and methods We performed several data analyses including Kyoto Encyclopedia of the Genome (KEGG) and Gene Ontology (GO) analyses, immune infiltration, and single-cell analyses using databases such as TIMER2.0, TISIDB, STRING, Metascape, and GRNdb. The possible mechanism of action of BCAP29/31 in HNSC was investigated and validated using Q-PCR real-time fluorescence quantitative analysis.
Results BCAP29/31 manifested a trend of overexpression and a certain mutation rate in HNSC. BCAP29/31 are each other's members of the protein interactions network and are associated with calcineurin binding and vesicle transport function. BCAP29/31 demonstrated the same trend correlating with CD8+ T and B cells, and abnormal associations with endothelial cell and macrophage infiltration levels.
Conclusion The overexpression of BCAP29/31 is correlated with poor prognosis in HNSC and may affect the TGFβ1/Smad epithelial-mesenchymal transition (EMT) process. Overexpression of BCAP29/31 may be a factor causing the aberrant level of immune infiltration in HNSC. In conjunction with existing clinical treatment options, knockdown of BACP29/31 or targeted elimination of tumor-associated macrophage M2 tumor-associated macrophages (TAM M2) may help improve anti-PD-1/PD-L1 efficacy.
Clinical Relevance Our study elucidated the mechanism of action in which BCAP29/31 may be involved in HNSC. The results supported the use of BCAP29/31 as a poor prognostic biomarker for HNSC and offered new insights to improve the efficacy of anti-PD-1/PD-L1 therapies in HNSC in the future.
Likelihood of a novel pathogenic LDLR mutant allele inherited preferentially within an Indian family with familial hypercholesterolemia
Authors: Reddy Lakshmi Lavanya , Shah Swarup A. V , Paradkar Minal , Ponde Chandrashekhar K , Rajani Rajesh , Pillai Sudhir , Pradhan Dibyabhaba , Singh Harpreet Singh , Ashavaid Tester F 
Published: March 2024

Abstract
Background & Aims:
Familial hypercholesterolemia (FH) is an autosomal dominant disorder characterized by increased levels of low-density lipoprotein cholesterol (LDL-C). LDL receptor (LDLR) gene mutations is the primary genetic cause thereby necessitating the screening of family members for early detection and management. We aim to report an Indian family with FH harboring a novel pathogenic nonsense mutation in LDLR gene with a strong likelihood of preferential transmission.
Methods
EDTA blood samples were collected from the available family members upon obtaining written informed consent. Genotyping for LDLR mutation was performed by PCR amplification and Sanger sequencing. 11 of the 16 family members were clinically affected and identified as having dyslipidemia. A novel mutation (c.743_744delinsAA) in exon 5 of LDLR gene was identified in the proband and 05 of the investigated family members that were dyslipidemic. In silico tools predicted, the novel mutation to be pathogenic and deleterious.
Conclusions
The present case study of an Indian family with FH identifies a novel pathogenic LDLR mutation (c.743_744delinsAA), which is predicted to induce non-decay mediated mRNA decay (NMD). Based on the inheritance pattern of the mutant LDLR allele, across the 3 generations, there seem to be a strong likelihood of preferential transmission of mutant allele indicating genetically-biased fertilization over the wild-type allele. This case report for a first time suggests a strong likelihood of preferential transmission in FH and underscores the importance of genetic testing for FH diagnosis as well as cascade screening for early detection, risk stratification and implementation of preventive strategies.
Declining number of general practitioners can impair influenza vaccination uptake in Italy
Authors: Domnich Alexander , Lapi Francesco , Orsi Andrea , Grattagliano Ignazio , Rossi Alessandro , Cricelli Claudio , Icardi Giancarlo 
Published: March 2024

Abstract
Background
As in many other countries, seasonal influenza vaccination coverage in Italian older adults is insufficient. In Italy, most influenza vaccine doses are administered by general practitioners (GPs), whose number has been declining in recent years. In parallel, the number of patients per GP and consequent GP workload increased dramatically. In this longitudinal study, we aimed to test whether influenza vaccination coverage may be affected by the increased GP workload.
Methods
The study outcome was the influenza vaccination coverage rate in adults aged ≥ 65 years and registered in 20 Italian regions over the last 23 years. The independent variable of interest was GP workload, proxied as the proportion of GPs with more than 1,500 patients, which is an imposed normative ceiling. By adopting an econometric approach, different specifications of fixed- and random-effects panel regression models were run to assess the association of interest, when adjusted for potential confounders.
Results
Over the last two decades, most regions showed a negative association between influenza vaccination coverage rates and the density of GPs with a high number of patients. This latter negative association was confirmed (P < 0.05) in different panel model specifications. In particular, in the fully adjusted two-way fixed-effects model, which explained 72.6% of the variance, each 10% increase in the number of GPs with more than 1,500 patients was associated with a 1.7% decrease in influenza vaccination coverage. However, this association was present only in region-years where at least 18% of GPs were deemed overloaded.
Conclusions
In the upcoming years, the number of Italian GPs is projected to decline further. At the same time, the aging Italian population will determine an even greater workload for GPs. This study demonstrated that increased GP workload may partially explain the spatiotemporal variation in influenza vaccination uptake in the Italian elderly. With the imperative of increasing or at least maintaining influenza vaccination coverage rates, several short- and mid-term initiatives should be implemented in order to optimize GP workload during seasonal immunization campaigns.
Disease pattern and mortality rate among patients admitted to the Intensive Care Unit in Arbaminch General Hospital, Southern Ethiopia
Authors: Daniel Tigabu , Abera Yonas , Yihune Menaye 
Published: March 2024

Abstract

Background: Disease patterns in intensive care Unit is differ from place to place. Cardiac disease, septic shock, trauma, and acute abdomen are the common causes of admission. The mortality rate in the Intensive Care Unit (ICU) was higher than that in the other hospital units. Our aim was to assess the common admission diagnosis and mortality rate among Intensive Care Unit (ICU) patients in the Arbaminch General Hospital.
Methods: A retrospective cross-sectional study was conducted based on a review of the records and charts of patients admitted from January 1, 2019, to January 1, 2021. Descriptive statistics were also calculated. An independent variable effect on the mortality rate was observed.
Result: The most common admission diagnoses were cardiac and other medical diseases, septic shock and ARDS followed by acute abdomen and other surgical diseases. The overall mortality rate was 40.7%. On multivariate logistic regression analysis, no significant mortality rate affecting factors were identified.
Conclusion: Cardiac and other medical diseases were the most common admissions diagnoses, with an overall mortality rate of 40.7%. No significant association was found between the mortality rate and independent variables in the multivariate logistic regression.
Nanopore direct RNA sequencing provides additional insight into transcriptome differentiation during transition to the aquatic environment of amphibious liverwort Riccia fluitans L. (Marchantiales)
Authors: Maździarz Mateusz , Krawczyk Katarzyna , Kurzyński Mateusz , Paukszto Łukasz , Szablińska-Piernik Joanna , Szczecińska Monika , Sulima Paweł , Sawicki Jakub 
Published: March 2024

Abstract
Background
Riccia fluitans, an amphibious liverwort, exhibits a fascinating adaptation mechanism to transition between terrestrial and aquatic environments. Utilizing nanopore direct RNA sequencing, we try to capture the complex epitranscriptomic changes undergo in response to land-water transition.
Results
A significant finding is the identification of 45 differentially expressed genes (DEGs), with a split of 33 downregulated in terrestrial forms and 12 upregulated in aquatic forms, indicating a robust transcriptional response to environmental changes. Analysis of N6-methyladenosine (m6A) modifications revealed 173 m6A sites in aquatic and only 27 sites in the terrestrial forms, indicating a significant increase in methylation in the former, which could facilitate rapid adaptation to changing environments. The aquatic form showed a global elongation bias in poly(A) tails, which is associated with increased mRNA stability and efficient translation, enhancing the plant's resilience to water stress. Significant differences in polyadenylation signals were observed between the two forms, with nine transcripts showing notable changes in tail length, suggesting an adaptive mechanism to modulate mRNA stability and translational efficiency in response to environmental conditions. This differential methylation and polyadenylation underline a sophisticated layer of post-transcriptional regulation, enabling Riccia fluitans to fine-tune gene expression in response to its living conditions.
Conclusions
These insights into transcriptome dynamics offer a deeper understanding of plant adaptation strategies at the molecular level, contributing to the broader knowledge of plant biology and evolution. These findings underscore the sophisticated post-transcriptional regulatory strategies Riccia fluitansemploys to navigate the challenges of aquatic versus terrestrial living, highlighting the plant's dynamic adaptation to environmental stresses and its utility as a model for studying adaptation mechanisms in amphibious plants.
Prognosis and management of chronic obstructive pulmonary disease in a real-world setting: A 5-year follow-up analysis of a multi-institutional registry
Authors: Takano Tomotsugu , Tsubouchi Kazuya , Hamada Naoki , Ichiki Katsuyuki , Torii Ryo , Takata Shohei , Kawakami Satoru , Nakagaki Noriaki , Yoshida Makoto , Kitasato Yasuhiko , Tobino Kazunori , Harada Eiji , Ishii Hiroshi , Wataya Hiroshi , Maeyama Takashige , Fujita Masaki , Yatera Kazuhiro , Okamoto Masaki , Yabuuchi Hidetake , Kiyomi Fumiaki , Tokunaga Shoji , Nakanishi Yoichi , Okamoto Isamu 
Published: March 2024

Abstract

Background
We conducted a prospective observational study to elucidate the long-term prognosis and management of chronic obstructive pulmonary disease (COPD) in Japan in the mid-2010s in clinical practice.
Methods
This prospective cohort study included 29 facilities. A total of 427 patients clinically diagnosed with COPD, enrolled between September 2013 and April 2016, were analysed. Interstitial pneumonia was excluded through a central multidisciplinary discussion. Follow-up data were collected for up to 5 years after patient registration.
Results
In total, 67 patients clinically diagnosed with COPD did not have airflow limitations (AFL) at the time of registration. In the cohort with AFL (n=370), 266 patients completed a 5-year follow-up, while 58 patients died during the 1556.7 person-years of observation. The overall 5-year survival rate was 85.2%. Stratified by % forced expiratory volume in one second (FEV1), survival rates were 93.4% in the 50 ≤ %FEV1 group, 82.5% in the 30 ≤ %FEV1 < 50 group, and 66.1% in the %FEV1 < 30 group. The prognosis of the subpopulation without AFL was poor with 5-year survival of 83.0%. This subpopulation exhibited respiratory symptoms, low vital capacity and total lung capacity, and emphysematous changes.
Conclusions
Our study presents the 5-year survival and real-world clinical practice scenario of a prospective cohort of patients clinically diagnosed with COPD in Japan in the mid-2010s. Overall, 13% of the patients in this cohort did not show AFL at registration with respiratory symptoms, distinct spirometric patterns, and poor prognosis.
Umbilical Artery Atherosclerosis as the Risk Factor for Anorectal Malformation
Authors: Diposarosa Rizki , Pamungkas Kurniawan Oki , Anita Melian , Wikanadi Sinung 
Published: March 2024

Abstract
Background: Anorectal malformation (ARM) is a congenital anomaly in which the anus and rectum are not normally developed. The causes of this anomaly are thought to be multifactorial. Umbilical cord pathology is related to various congenital anomalies and atherosclerosis of the umbilical artery may induce negative effects on the fetus, therefore, this study analyzed the correlation between umbilical artery atherosclerosis and the incidence of ARM.
Method: This case-control study was conducted between November 2020 and March 2021. Umbilical cord samples were taken from neonates with/without ARM and evaluated for the presence of umbilical artery atherosclerosis. Spearman analysis was utilized to determine any correlations.
Result: Umbilical cord samples from 30 newborns without ARM and 30 newborns with ARM were analyzed revealing that 10 newborns with ARM had initial atherosclerotic lesions in their umbilical artery.
Conclusion: The incidence of an initial atherosclerotic lesion instead of an atherosclerotic lesion in the patients with ARM was significantly correlated with the incidence of ARM.
Onion Peel Extract/Copper Oxide Nanoparticles as Corrosion Inhibitors for Carbon Steel in Hydrochloric Acid; Extraction, Characterization, Electrochemical Study, and Theoretical Explorations
Authors: Darweesh Mona , Emam Sanaa M. , Wahba Adel , Ayad Mohamed I. , El-Nahass Marwa , Abdelhamied Amany , Hammad Wafaa 
Published: March 2024

Abstract

The effectiveness of onion peel extract, (OPE), for carbon steel in one molar (1 M) hydrochloric acid solution was illustrated utilizing weight loss (WL) techniques, potentiodynamic polarization (PDP), electrochemical impedance spectroscopy (EIS), and surface morphological examination. Also, this process was characterized using Fourier transform infrared (FT-IR), energy dispersive X-ray spectroscopy (EDX), thermogravimetric analysis (TGA), atomic force microscopy (AFM), and scanning electron microscope (SEM). The protective efficiency rises as OPE concentration rises and decreases with corrosive solution temperature, according to weight loss measurements. Polarization curves display that OPE behaves as a mixed-type inhibitor in hydrochloric acid. The adsorption process mechanism is supported by EIS, which demonstrates that charge-transfer resistance rises, and double-layer capacitance falls with inhibitor concentration. OPE adhering to carbon steel follows the Langmuir isotherm, through a physical adsorption process and the inhibitor molecules were shown to have spontaneously adsorbed onto the carbon steel based on the negative values of Gibb's free energy of adsorption. The synergistic effect of copper oxide nanoparticles, CuO-NPs in combination with OPE on the inhibition corrosion of carbon steel was evaluated. The results showed that the inhibition efficiency of OPE increases in the presence of CuO-NPs due to synergistic interactions of OPE extract molecules with CuO-NPs. The electron-donating capacity of the chemical component of the OPE has been shown in theoretical studies employing quantum chemistry methods.
Manifestations and Biomarkers to Predict Mortality Risk in Adults with Invasive Streptococcus dysgalactiae
Authors: Hanada Shigeo , Wajima Takeaki , Takata Misako , Morozumi Miyuki , Shoji Michi , Iwata Satoshi , Ubukata Kimiko 
Published: March 2024

Abstract
Purpose: The incidence of invasive Streptococcus dysgalactiae subsp. equisimilis (iSDSE) infections is increasing in developed countries, but studies on the risk factors for death in iSDSE infection are scant. Here, we aimed to clarify risk factors and predictors of mortality in adults with iSDSE infection.
Methods: A multicentre observational study of adults with iSDSE infection (n = 588) was conducted to investigate the effects of host factors, disease severity, biomarkers, and antibiotic regimens, and bacterial factors on 28-day mortality.
Results: The overall mortality rate was 10.4%, with a significant increase in those aged ≥60 years. Most of the patients (97.4%) had some underlying diseases. The mortality rate (70.4%) of patients with severe disease was significantly higher than that of patients with mild-to-moderate disease (4.3%). The risk factors for death identified using multivariate analysis were age ≥60 years (hazard ratio [HR], 3.4; 95% confidence interval [CI], 1.0–11.3, p = 0.042); severe disease (HR, 15.0; 95% CI 7.7–29.2, p < 0.001); bacteraemia without primary focus (HR, 20.5; 95% CI 2.8–152.3, p = 0.003); serum creatinine ≥2.0 mg/dL (HR, 2.2; 95% CI 1.2–4.0, p = 0.010); serum creatine kinase ≥300 IU/L (HR, 2.1; 95% CI 1.1–3.8, p = 0.019); and macrolide resistance (HR, 1.8; 95% CI 1.0–3.3, p = 0.048). Treatment regimens and emm types were not associated with poor outcomes.
Conclusion: Evaluation of clinical manifestations and biomarkers on admission is important to predict invasive SDSE infection prognosis.