bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of gastric microbiota and Helicobacter pylori infection in gastroesophageal reflux disease
Authors: Sugihartono Titong , Fauzia Kartika Afrida , Miftahussurur Muhammad , Waskito Langgeng Agung , Rejeki Purwo Sri , I’tishom Reny , Alfaray Ricky Indra , Doohan Dalla , Amalia Rizki , Savitri Camilia Metadea Aji , Rezkitha Yudith Annisa Ayu , Akada Junko , Matsumoto Takashi , Yamaoka Yoshio 
Published: September 2022

Abstract
Background
We evaluated the microbiota in the stomach of Gastroesophageal Reflux Disease (GERD) patients. We compared Erosive Reflux Disease (ERD) to gastritis and Non-erosive Reflux Disease (NERD) subjects by 16S rRNA approach on gastric biopsy specimens. A total of 197 subjects were included consisting of gastritis (68; 34.52%), ERD (55; 27.92%), and NERD (74; 37.56%). After quality filtering, 187 samples were included for OTU analysis using Qiime2.

Results
We observed a significant difference in alpha diversity (Shannon and Simpson indexes were P = 0.0016 and P = 0.017, respectively). A significant decrease in alpha diversity index was observed in NERD with Helicobacter pylori (H. pylori)-positive subjects than in gastritis (Simpson index P = 0.022; Shannon index P = 0.029), indicating a significant influence of H. pylori on the diversity in the stomach despite the diseases. In H. pylori-negative samples, alpha diversity measurement by the abundance coverage estimates (ACE) and Fisher Test revealed that ERD had significantly lower richness than gastritis and NERD groups (P = 0.00012 and P = 0.00043, respectively). Anaerobacillus sp. could only be found in ERD patients by LEFse analysis.

Conclusions
The presence of ERD could alter microbiome diversity. A negative correlation between H. pylori and ERD is shown in this microbiome study but not in NERD.
Immortalised canine buccal epithelial cells’ CXCL8 secretion is affected by allergen extracts, Toll-like receptor ligands, IL-17A and calcitriol
Authors: Pelst Michael , Höbart Clara , de Rooster Hilde , Devriendt Bert , Cox Eric 
Published: September 2022

AbstractEpithelial cells are known to produce mediators which can influence the behaviour of neighbouring immune cells. Although the oral mucosa has gained increased interest as a route to induce allergy desensitisation and mucosal pathogen immunisation in dogs, there is only limited knowledge on the factors which impact mediator secretion by canine oral epithelial cells. The study’s objective was to enlarge the knowledge on the stimuli that can influence the secretion of some pro- and anti-inflammatory cytokines and the chemokine CXCL8 by canine buccal epithelial cells. To investigate this, buccal epithelial cells were isolated from a biopsy of a dog and immortalised by lentiviral transduction of the SV40 large T antigen. The cells were stained with a CD49f and cytokeratin 3 antibody to confirm their epithelial origin. Cells were incubated with allergen extracts, Toll-like receptor ligands (TLRL), recombinant cytokines and vitamin A and D metabolites. Subsequently, the secretion of the cytokines interleukin (IL)-4, IL-6, IL-10, IL-17A, IFN-γ, TGF-β1 and the chemokine CXCL8 was assayed by ELISA. Immortalised canine buccal epithelial cells stained positive for CD49f but not for cytokeratin 3. The cells produced detectable amounts of CXCL8 and TGF-β1. ADermatophagoides farinaeextract, anAlternaria alternataextract, Pam3CSK4, heat-killedListeria monocytogenes, FSL-1, flagellin and canine recombinant IL-17A significantly increased CXCL8 secretion, while the vitamin D metabolite calcitriol significantly suppressed the production of this chemokine. This study showed that certain allergens, TLRL, IL-17A and calcitriol modulate CXCL8 secretion in a cell line of canine buccal epithelial cells.
The impact of maternal health insurance coverage and adequate healthcare services utilisation on the risk of under-five mortality in Nigeria: a cross-sectional study
Authors: Imo Chukwuechefulam Kingsley , De Wet-Billings Nicole , Isiugo-Abanihe Uche Charlie 
Published: September 2022

AbstractBackgroundDespite the progress in reducing under-five mortality (U-5 M) in recent years, these deaths remain considerably high in Nigeria. This could be attributed to poor health policies including inequality of health insurance coverage and access to adequate healthcare services utilisations which has remained inimical to achieving sustainable development goals (SDGs). Therefore, this study examined the impact of maternal health insurance coverage and adequate healthcare services utilisation on the risk of U-5 M in Nigeria.MethodsThe data for the study were derived from the 2018 Nigeria Demographic and Health Survey and comprised a weighted sample of 127,545 birth histories of childbearing women. Descriptive and analytical analyses were carried out, including frequency tables and multivariate using Cox proportional regression. The results were presented as hazard ratios (HR) with 95% confidence intervals (CIs). Data were analyzed using Stata software version 15.1.ResultsThe results showed that 14.3% of the sampled birth histories of the childbearing women were children who died before age 5. The results further showed that 97.7% of the children were of mothers who have health insurance and over one-half (56.5%) were children whose mothers had adequate healthcare services utilisation. The risk of under-five death was significantly lower among the children of mothers who were covered by health insurance (HR: 0.66, CI: 0.42–1.02) and those whose mothers utilised adequate healthcare services (HR: 0.78, CI: 0.68–0.90). A similar result was observed among children whose mothers reported that distance to the health facility was not a problem (HR: 0.81, CI: 0.72–0.86). Some mothers’ characteristics including educational attainment, wealth quintile and region of residence significantly influenced the risk of U-5 M.ConclusionsThe study established that maternal health insurance coverage and adequate healthcare services utilisation were found to be protective factors against the risk of U-5 M. Also, the revealed low health insurance coverage of mothers calls for more pragmatic policy and intervention programmes through health insurance to achieve SDGs targets of ending preventable deaths of children under 5 years of age and ensuring quality, as well as universal access to maternal and child healthcare services.
Reading comprehension test fairness across gender and mode of learning: insights from IRT-based differential item functioning analysis
Authors: Moradi Elahe , Ghabanchi Zargham , Pishghadam Reza 
Published: September 2022

AbstractGiven the significance of the test fairness, this study aimed to investigate a reading comprehension test for evidence of differential item functioning (DIF) based on English as a Foreign Language (EFL) learners’ gender and their mode of learning (conventional vs. distance learning). To this end, 514 EFL learners were asked to take a 30-item multiple-choice reading comprehension test. After establishing the unidimensionality and local independence of the data as prerequisites to DIF analyses, Rasch model-based DIF analysis was conducted across learners’ gender and their mode of learning. The results showed that there were two gender-DIF items which functioned differentially in favor of female respondents. Also, DIF analysis in terms of EFL learners’ mode of learning revealed that there were no DIF items across the two target groups indicating that the reading comprehension test functioned the same way for learners who enjoyed conventional learning compared to those who experienced distance and self-directed learning. In the end, the findings were discussed and implications were provided.
Azimuthal differences and changes in strain rate and stress of the Japanese Islands deduced from geophysical data
Authors: Kosugi Issei , Mitsui Yuta 
Published: September 2022

AbstractGeodetic and seismological observations have shown discrepancies between azimuths of maximum contraction (strain rate) and maximum compression (stress). These discrepancies can be the results of the superposition of localized or transient mechanical processes such as fault coupling during seismic cycles. Rich sets of recent geophysical data allow us to conduct spatiotemporal imaging of the discrepancies. Here, we estimate the spatiotemporal evolution in the strain-rate fields of the Japanese Islands with optimized smoothing distances from 1997 to 2021 using Global Navigation Satellite System (GNSS) data, and investigate how the maximum contraction axes of horizontal strain rates differ from those of horizontal stress based on earthquake focal mechanisms. Several characteristic results are observed for each region within the Japanese Islands. Both azimuths of the strain rates and stress differ by more than 60° over hundreds of kilometers from the Kanto region to along the Nankai Trough, related to seismotectonics due to the dual subduction of the Philippine Sea plate and the Pacific plate beneath the Japanese Islands. The differences in the azimuths imply the effect of the very long-term stable subduction of the Pacific plate. We find that the azimuthal differences tend to be small along tectonic zones with active inland earthquakes and high strain rates on the back-arc sides. We also find that the 2011 off the Pacific coast of Tohoku earthquake caused notable azimuthal differences in the strain rates and the stress in the Tohoku region. The strength of fault may cause lower response sensitivity of seismological stress to major earthquakes than geodetic strain rate. Our dataset has wide spatiotemporal coverage and can serve as a basis for further research, for example, to estimate the current fault conditions during seismic cycles.Graphical Abstract
Added value of delayed post-contrast FLAIR in diagnosis of metastatic brain lesions
Authors: Ibrahim Rafik Mohamed , Rahman Shaimaa Ali Abdel , Elnekeidy Abd El Aziz Mohamed 
Published: September 2022

Abstract
Background
One of the drawbacks in contrast-enhanced T1-weighted imaging (CE-T1WI) is the enhancing cortical vessels which can be confused with meningeal enhancement. Previous studies reported that post-contrast FLAIR could be better for diagnosing the superficial brain abnormalities. So the purpose of this study was to evaluate the role of delayed post-contrast FLAIR, in comparison with post-contrast T1, in the detection and evaluation of brain metastases.

Results
The study was conducted on 40 patients with suspected/known brain metastases scanned in order to detect and evaluate brain metastases. All patients were subjected to the following: full history taking, review of clinical examination reports, and other imaging modalities whenever available, followed by brain MRI examination using 1.5 T closed magnet including pre-contrast series, axial and sagittal T1-weighted spin echo (SE), axial and coronal T2-weighted turbo spin echo (TSE) and axial FLAIR, while post-contrast series included axial, coronal and sagittal T1-weighted spin echo (SE) and lastly DPC-FLAIR sequence 10 min after contrast administration. This study included 18 males and 22 females, ranging in age from 26 to 75 years. Six out of a total of 40 patients had brain metastases of unknown origin, while 34 of them were presented with different types of known primary tumors. The detected lesions were subdivided into five groups according to their detectability by DPC-FLAIR and contrast-enhanced T1WI: Group (I): lesions detected only by DPC-FLAIR: 16 lesions; Group (II): lesions detected only by CE-T1WI: 1 lesion; Group (III): lesions detected by both DPC-FLAIR and CE-T1WI with equal conspicuity by both: 28 lesions; Group (IV): lesions detected by both, showing more obvious enhancement with DPC-FLAIR: 43 lesions; and Group (V): lesions detected by both, showing more obvious enhancement with CE-T1WI: 11 lesions. DPC-FLAIR had a sensitivity of 98.98% and a specificity of 100% for the detection of metastatic brain lesions and for CE-T1WI; sensitivity of 83.83%; and a specificity of 50%.

Conclusions
Delayed post-contrast FLAIR is a reliable sequence for the detection of metastatic brain lesions as it can detect more metastatic brain lesions compared to contrast-enhanced T1WI.
Building a healthy mouse model ecosystem to interrogate cancer biology
Authors: Devlin Ryan , Roberts Ed 
Published: September 2022

ABSTRACT
In a recent study, Sargent et al. characterise several novel Rag1−/− mouse strains and demonstrate that genetic background strongly influences xenograft development and phenotype. Here, we discuss this work within the broader context of cancer mouse modelling. We argue that new technologies will enable insights into how specific models align with human disease states and that this knowledge can be used to develop a diverse ecosystem of complementary mouse models of cancer. By utilising these diverse, well-characterised models to provide multiple perspectives on specific cancers, it should be possible to reduce the inappropriate attrition of sound hypotheses while protecting against false positives. Furthermore, careful re-introduction of biological variation, be that through outbred populations, environmental diversity or including animals of both sexes, can ensure that results are more broadly applicable and are less impacted by particular traits of homogeneous experimental populations. Thus, careful characterisation and judicious use of an array of mouse models provides an opportunity to address some of the issues surrounding both the reproducibility and translatability crises often referenced in pre-clinical cancer research.
ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data
Authors: Gupta Vikas , Paupério Joana , Burgin Josephine , Jayathilaka Suran , Cochrane Guy 
Published: September 2022

Background: Metadata attributes of sequences that accurately reference their biological sources, as specimens or other materials of origin, and link with natural history collections, are essential to facilitate the connections between different fields in life sciences and promote reusability of data. However, metadata used to reference the biological source of sequences available within the molecular data repositories are not always well structured or comprehensive. Methods: Within the scope of the Horizon 2020 project Biodiversity Community Integrated Knowledge Library (BiCIKL), we have developed a tool, the European Nucleotide Archive (ENA) Source Attribute Helper Application Programming Interface (API), to help users accurately report biological source-related sequence and sample attributes. This tool currently focuses on the attributes in which specimens, cultures or other materials are identified, from which the sequence data were derived, and uses curated data to obtain the unique codes for the institutions and collections holding the vouchers. The API's main functions include the presentation of metadata associated with queried institutions or collections, validation of institution and collection codes in the attribute strings provided by the user, and the construction of an attribute string based on user-entered data. The API does not however support the search of voucher specimen codes, as these need to be obtained directly from the voucher institutions. We describe the API and discuss use cases for its different endpoints. The API is available at https://www.ebi.ac.uk/ena/sah/api/. Conclusions: We expect the API to promote and support the initial submission and any subsequent curation of biological source attributes, and hereby contribute to better links between sequence data and natural history collections, and hence on to taxonomy and biodiversity research, towards increasing the discoverability, reusability and impact of data.
When Less Is More: How Statistical Discrimination Can Decrease Predictive Accuracy
Authors: Csaszar Felipe A. , Jue-Rajasingh Diana , Jensen Michael 
Published: September 2022

Discrimination is a pervasive aspect of modern society and human relations. Statistical discrimination theory suggests that profit-maximizing employers should use all the information about job candidates, including information about group membership (e.g., race or gender), to make accurate predictions. In contrast, research on heuristics in psychology suggests that using less information can be better. Drawing on research on heuristics, we show that even small amounts of inconsistency can make predictions using group membership less accurate than predictions that do not use this information. That is, whereas statistical discrimination theory implies that better predictions can be achieved by using all available information about an individual (including group characteristics that may be correlated with but do not cause performance), our model shows that using all available information only improves predictive accuracy under a very specific set of conditions, thus suggesting that statistical discrimination often results in worse predictions. By understanding when statistical discrimination improves or worsens predictions, our work cautions decision makers and uncovers paths toward reducing the occurrence of situations in which statistical discrimination benefits predictive accuracy, thus reducing its pervasiveness in society. Supplemental Material: The online appendix is available at https://doi.org/10.1287/orsc.2022.1626 .
Differential attainment, socioeconomic factors and surgical training
Authors: Vinnicombe Z , Little M , Super J , Anakwe R 
Published: September 2022

Introduction Differential attainment (DA) is the gap in levels of achievement between different groups; socioeconomic factors are thought to play a significant role in DA. The aim of this study was to review and assess the evidence for DA in early surgical training and to examine the potential influence of socioeconomic status. Methods Data were obtained from the General Medical Council GMC for those taking Membership of the Royal College of Surgeons (MRCS) examinations between 2016 and 2019 and core surgical training annual review of competency progression (ARCP) outcomes between 2017 and 2019. The index of multiple deprivation (IMD) was used as a measure of socioeconomic background. Trainees were then divided into deprivation quintiles (DQ1=most deprived, DQ5=least deprived). MRCS and ARCP outcomes were compared between DQ groups using 95% confidence intervals and chi-square tests. Results Those from lower socioeconomic backgrounds had significantly lower overall MRCS pass rates (DQ1=45.5%, DQ2=48.9% vs DQ4=59.6%, DQ5=61.5%, p<0.05) and 1st time pass rates (DQ1&2=46.6% vs DQ4&5=63.5%, p<0.001). Additionally, they had a significantly higher number of attempts required to pass MRCS (DQ 1&2=1.86 vs DQ 4&5=1.54, p<0.01). Those from lower socioeconomic backgrounds had a significantly greater proportion of unsatisfactory ARCP outcomes (DQ1&2=24.4% vs DQ 4&5=14.2%, p<0.05). Conclusions There is clear evidence of the influence of socioeconomic background on DA in early surgical training. However, the reasons for this are likely complex and more work is required to investigate this relationship.
The role of cholecystectomy following endoscopic sphincterotomy and bile duct stone removal
Authors: Toogood K , Pike T , Coe P , Everett S , Huggett M , Paranandi B , Bassi V , Toogood G , Smith A 
Published: September 2022

Introduction Choledocholithiasis is common, with patients usually treated with endoscopic retrograde cholangiopancreatography (ERCP) and subsequent cholecystectomy to remove the presumed source of common bile duct (CBD) stones. However, previous investigations into the management of patients following ERCP have focused on recurrent CBD stones, negating the risks of cholecystectomy. This article appraises the role of cholecystectomy following successful endoscopic clearance of bile duct stones. Methods Patients undergoing ERCP and CBD clearance for choledocholithiasis at St James’s University Hospital January 2015–December 2018 were included. Patients were divided into those who received cholecystectomy and those managed non-operatively. Readmissions, operative morbidity, mortality and treatment costs were investigated. Results Eight hundred and forty-four patients received ERCP and CBD clearance with 3.9 years follow-up. Two hundred and nine patients underwent cholecystectomy with 15% requiring complex surgery. Three hundred and seventy-three patients were non-operatively managed. Unplanned readmissions occurred in 15% following ERCP, mostly within two years. There was no difference in readmissions between the two groups. Accounting for the entire patient pathway, non-operative management was less expensive. Conclusions The majority of patients do not require readmission following ERCP for CBD stones, and cholecystectomy did not reduce the risk of readmission. Few patients have recurrent CBD stones, but complex biliary surgery is frequently required. Routine cholecystectomy following ERCP needs to be re-evaluated and a more stratified approach to future risk developed.
Consultant aspirations: a surgical trainee consensus process
Authors: Barlow E , Srikandarajah N , Burke J , Glasbey J , Mohan H , Bathla S , Humm G ,   on behalf of the ASiT Consultant Aspirations Consensus Collaborative Group, Ali W , Barclay J , Beamish A , Beaumont O , Chin Y , Clements J , Peckham-Cooper A , Das A , Deekonda P , Dovell G , Elanko A , Fleming C , Giwa L , Gonzi G , Hogg G , Hughes K , Hughes R , Kane E , King M , Man CB , Manook M , McLaughlin N , Mohamed W , Nally D , Naveed T , Nicholas R , Pucher P , Rajaretnam N , Rashid S , Rintoul-Hoad S , Sahnan K , Sarmah P , Stefanova I , Tanase A , Thaventhiran A , Wilkins A , Zhang C 
Published: September 2022

Understanding what the current generation of trainees want to achieve is the key to understanding the future of the workforce Introduction Reform to surgical training over the last three decades has significantly affected the surgical workforce, career planning and progression. Despite changes to consultant job plans, there are no published data on trainees' aspirations and priorities for their future practice. In order to inform the design and structure of consultant job plans, this study sought to produce a trainee consensus statement regarding essential and desirable aspirations for their future professional practice as consultant surgeons. Methods This study used qualitative methodology with an initial survey to define themes, followed by an open invitation to a consensus session held at the Association of Surgeons in Training annual conference in Belfast in 2019. Results Fourteen essential and eight desirable aspirations for consultant practice were voted in and ratified at a formal consensus session. Essential aspirations included: regular theatre lists of cases in the clinician's subspecialty area of interest; regular theatre lists for teaching; regular ward rounds of the clinician's own patients; regular involvement in multidisciplinary team meetings, and morbidity and mortality meetings; a fixed elective schedule; specialty specific procedural lists; flexible working; dedicated time for administration, teaching, education and continuing professional development; options for sabbatical leave; and working in a supportive department. Conclusions This is the first formal national consensus process used to identify what surgical trainees deem as essential and desirable aspirations for their future practice as consultants. Healthcare employers should consider these aspirations when creating job plans and posts to attract trainees, encourage job satisfaction, improve workforce retention, and ultimately improve service delivery and patient care.