bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomedical evidence engineering for data-driven discovery
Authors: Zhao Sendong , Wang Aobo , Qin Bing , Wang Fei 
Published: October 2022

Abstract

Motivation
With the rapid development of precision medicine, a large amount of health data (such as electronic health records, gene sequencing, medical images, etc.) has been produced. It encourages more and more interest in data-driven insight discovery from these data. A reasonable way to verify the derived insights is by checking evidence from biomedical literature. However, manual verification is inefficient and not scalable. Therefore, an intelligent technique is necessary to solve this problem.

Results
This article introduces a framework for biomedical evidence engineering, addressing this problem more effectively. The framework consists of a biomedical literature retrieval module and an evidence extraction module. The retrieval module ensembles several methods and achieves state-of-the-art performance in biomedical literature retrieval. A BERT-based evidence extraction model is proposed to extract evidence from literature in response to queries. Moreover, we create a dataset with 1 million examples of biomedical evidence, 10 000 of which are manually annotated.

Availability and implementation
Datasets are available at https://github.com/SendongZhao.
P-043 A RETROSPECTIVE OUTCOME REVIEW OF THE USE OF EGIS ACELLULAR DERMAL MATRIX DURING ABDOMINAL WALL RECONSTRUCTION
Authors: Shaw A , Avrova A , Ramesh A , Mann T , Venkatasubramanian A , Moinuddin Z , Van Dellen D 
Published: October 2022

Abstract

Aim
We aimed to demonstrate the relative safety profile of an established non-crosslinked porcine acellular dermal matrix (ADM) during abdominal wall reconstruction.

Material & Methods
Individual real-world safety data on specific mesh products are often lacking. With recent media scrutiny over the use of mesh, we sought to quantify outcomes and demonstrate the safety of a specific ADM (reference 1). A retrospective casenote-based outcome analysis was performed on patients who underwent mesh augmentation during abdominal wall reconstruction from two NHS institutions. Both elective and emergency patients were included from January 2018 to December 2021.

Results
Fifty-five patients were included in the study across two NHS specialist hernia centres. We identified a mean wound infection rate of 14.2% (range 2–22%) with a median follow up of 9 months (range 3–18 months). Hernia recurrence rate was 10.4% (range 5–22%). We found 7 patients (12%) developed a seroma, 1 of whom required seroma aspiration. Only 4 patients (7%) had post-operative dehiscence requiring further intervention, all of whom had Ventral Hernia Working Group (VHWG) Grade 3 or 4 wounds pre-operatively.

Conclusions
Our data supports the continued use of a widely available ADM for abdominal wall reconstruction in both elective and emergency cases, highlighting its positive relative safety profile.
P-073 THE MODIFIED SUBLAY TECHNIQUE FOR THE MANAGEMENT OF MAJOR SUBCOSTAL INCISIONAL HERNIA: LONG-TERM FOLLOW-UP RESULTS OF 41 CONSECUTIVE PATIENTS
Authors: Zuvela M , Galun D , Bogdanovic A , Bidzic N , Zivanovic M , Zuvela M , Zuvela M 
Published: October 2022

Abstract

Aim
To present the concept of original technique in the management of major incisional subcostal hernias bassed on sublay position of large haevy-weight polypropylene mesh between the two myofascial layers in the anterolateral abdominal wall.

Material and methods
Between January 2010 and May 2022, 41 consecutive patients underwent the modified sublay technique for major incisional subcostal hernia (minimal defect surface100 cm2 or minimal defect width or height 10 cm). The operative technique is: a) hernia sac dissetion and reposition into the abdominal cavity; b) rectus muscle and rectus muscle stump dissection from posterior rectus sheath, rectus muscle atachement dissection from thoracic wall and external oblique muscle dissection from internal oblique muscle around hernia defect at the side of the hernia defect; c) separate posterior and anterior rectus sheaths reconstruction at the midline; d) reconstruction of the posterior miofascial layer suturing internal oblique/transversal muscle and posterior rectus sheaths; e) large haevy-weight polypropilene mesh placement between posterior and anterior miofascial layer; e) reconstruction of the anterior miofascial layer by suturing external oblique muscle and anterior rectus sheaths.

Results
A median (range) hernia defect surface was 160 (100–500) cm2. A median operative time was 120 (90–330) minutes. The morbidity rate was 19.5%. A median (range) postoperative hospital stay was 7 (2–24) days. After the median follow-up of 50 (1–124) months, two patients (4,9%) developed recurrent hernia.

Conclusions
The modified sublay technique using large heavyweight polypropylene mesh provides good results in the management of major subcostal abdominal wall defects.
Successful visualization of pulmonary embolism using fluoroscopic video analysis in a patient with iodine contrast allergy: a case report
Authors: Hijikata Sadahiro , Sakurai Kaoru , Takahashi Yoshihide , Azegami Koji 
Published: October 2022

Abstract

Background
Contrast-enhanced computed tomography (CT) is commonly used to diagnose pulmonary embolism (PE). However, a history of iodine contrast allergy presents a dilemma in the management of patients with PE. As an alternative approach, X-ray fluoroscopic video analysis has been recently reported to be useful in diagnosing PE.

Case summary
A 78-year-old man with dyspnoea of 1-month duration visited our hospital. His oxygen saturation was 89%, and echocardiography demonstrated right heart strain. We could not perform contrast-enhanced CT because the patient had a history of contrast allergy and refused to undergo premedicated contrast CT with anti-histamine and/or corticosteroid. Therefore, a video analysis of pulmonary circulation using dynamic chest X-ray (DCR) was performed. The reconstructed pseudo-colour video showed defects of pulmonary circulation in both lung areas. We diagnosed PE and started anticoagulant therapy. Multiple segmental defects were also observed in pulmonary perfusion scintigraphy on Day 3, which confirmed the diagnosis of PE. He was discharged on Day 9, and an improvement of the pulmonary circulation as assessed with DCR was observed. He had no symptoms at the last follow-up visit at 1 year after discharge.

Discussion
We describe the successful visualization of PE using DCR in a patient with iodine contrast allergy.
Discovery and characterization of a new class of O-linking oligosaccharyltransferases from the Moraxellaceae family
Authors: Knoot Cory J , Wantuch Paeton L , Robinson Lloyd S , Rosen David A , Scott Nichollas E , Harding Christian M 
Published: October 2022

Abstract
Bacterial protein glycosylation is commonly mediated by oligosaccharyltransferases (OTases) that transfer oligosaccharides en bloc from preassembled lipid-linked precursors to acceptor proteins. Natively, O-linking OTases usually transfer a single repeat unit of the O-antigen or capsular polysaccharide to the side chains of serine or threonine on acceptor proteins. Three major families of bacterial O-linking OTases have been described: PglL, PglS, and TfpO. TfpO is limited to transferring short oligosaccharides both in its native context and when heterologously expressed in glycoengineered Escherichia coli. On the other hand, PglL and PglS can transfer long-chain polysaccharides when expressed in glycoengineered E. coli. Herein, we describe the discovery and functional characterization of a novel family of bacterial O-linking OTases termed TfpM from Moraxellaceae bacteria. TfpM proteins are similar in size and sequence to TfpO enzymes but can transfer long-chain polysaccharides to acceptor proteins. Phylogenetic analyses demonstrate that TfpM proteins cluster in distinct clades from known bacterial OTases. Using a representative TfpM enzyme from Moraxella osloensis, we determined that TfpM glycosylates a C-terminal threonine of its cognate pilin-like protein and identified the minimal sequon required for glycosylation. We further demonstrated that TfpM has broad substrate tolerance and can transfer diverse glycans including those with glucose, galactose, or 2-N-acetyl sugars at the reducing end. Last, we find that a TfpM-derived bioconjugate is immunogenic and elicits serotype-specific polysaccharide IgG responses in mice. The glycan substrate promiscuity of TfpM and identification of the minimal TfpM sequon renders this enzyme a valuable additional tool for expanding the glycoengineering toolbox.
Anatomy of Traditional Specialities Guaranteed: Analysis of the Functioning, Limitations and (Possible) Future of the Forgotten EU Quality Scheme
Authors: Zappalaglio Andrea 
Published: October 2022

Abstract
This article focuses on traditional specialities guaranteed (TSGs), the least researched of the EU quality schemes that also include the better known protected designation of origin (PDO) and protected geographical indication (PGI). Firstly, this contribution presents a historical account of the evolution of this quality label. Secondly, it illustrates the results of the first empirical analysis of the contents of the Single Documents for all the TSGs registered, thus providing an unprecedented view of their nature. Thirdly, it divides TSGs into six categories, which will be called ‘profiles’, in order to provide a nuanced picture of what is protected by this quality scheme and how. Finally, this work reflects on why this label has always been essentially unsuccessful in terms of number of registrations, and what could be done to revive it. It concludes that, because of the residual nature of TSGs compared with PDOs/PGIs, it is highly unlikely that TSGs will acquire more importance as market-related labels. Hence, from this point of view, discontinuing them might lead to a simplification and clarification of the EU quality schemes. However, the fact that they are residual does not mean that they are superfluous. They may nonetheless play a meaningful role as tools aimed at connecting the names of traditional products with their original recipes, thus contributing to the preservation of relevant pieces of European gastronomic heritage that would otherwise be denied any form of recognition and protection.
How does the artificial intelligence-based image-assisted technique help physicians in diagnosis of pulmonary adenocarcinoma? A randomized controlled experiment of multicenter physicians in China
Authors: Li Jiaoyang , Zhou Lingxiao , Zhan Yi , Xu Haifeng , Zhang Cheng , Shan Fei , Liu Lei 
Published: October 2022

Abstract

Objective
Although artificial intelligence (AI) has achieved high levels of accuracy in the diagnosis of various diseases, its impact on physicians’ decision-making performance in clinical practice is uncertain. This study aims to assess the impact of AI on the diagnostic performance of physicians with differing levels of self-efficacy under working conditions involving different time pressures.

Materials and methods
A 2 (independent diagnosis vs AI-assisted diagnosis) × 2 (no time pressure vs 2-minute time limit) randomized controlled experiment of multicenter physicians was conducted. Participants diagnosed 10 pulmonary adenocarcinoma cases and their diagnostic accuracy, sensitivity, and specificity were evaluated. Data analysis was performed using multilevel logistic regression.

Results
One hundred and four radiologists from 102 hospitals completed the experiment. The results reveal (1) AI greatly increases physicians’ diagnostic accuracy, either with or without time pressure; (2) when no time pressure, AI significantly improves physicians’ diagnostic sensitivity but no significant change in specificity, while under time pressure, physicians’ diagnostic sensitivity and specificity are both improved with the aid of AI; (3) when no time pressure, physicians with low self-efficacy benefit from AI assistance thus improving diagnostic accuracy but those with high self-efficacy do not, whereas physicians with low and high levels of self-efficacy both benefit from AI under time pressure.

Discussion
This study is one of the first to provide real-world evidence regarding the impact of AI on physicians’ decision-making performance, taking into account 2 boundary factors: clinical time pressure and physicians’ self-efficacy.

Conclusion
AI-assisted diagnosis should be prioritized for physicians working under time pressure or with low self-efficacy.
Impact of Clinical Data Veracity on Cancer Genomic Research
Authors: Mehta Sunali , Wright Deborah , Black Michael A , Merrie Arend , Anjomshoaa Ahmad , Munro Fran , Reeve Anthony , McCall John , Print Cristin 
Published: October 2022

Abstract
Genomic analysis of tumors is transforming our understanding of cancer. However, although a great deal of attention is paid to the accuracy of the cancer genomic data itself, less attention has been paid to the accuracy of the associated clinical information that renders the genomic data useful for research. In this brief communication, we suggest that omissions and errors in clinical annotations have a major impact on the interpretation of cancer genomic data. We describe our discovery of annotation omissions and errors when reviewing an already carefully annotated colorectal cancer gene expression dataset from our laboratory. The potential importance of clinical annotation omissions and errors was then explored using simulation analyses with an independent genomic dataset. We suggest that the completeness and veracity of clinical annotations accompanying cancer genomic data require renewed focus by the oncology research community, when planning new collections and when interpreting existing cancer genomic data.
The Subcapital Femoral Neck Stress Fracture: A Novel Subtype of Compression-sided Stress Fracture—A Report of Three Cases
Authors: Biolzi Francesco , Dinnen Ryan , Jacobs Bonamico , Doty Tyler , Barkley Colleen , Jackson Keith Lynn , Shaw K Aaron 
Published: October 2022

ABSTRACT
Femoral neck stress fractures (FNSFs) are increasingly common, particularly in military training. The usual mode of classifying these injuries is based on the involvement of the compression or tension side of the femoral neck; however, this may oversimplify and fail to address factors such as the orientation of the fracture line. We present a novel subtype of a compression-sided FNSF affecting the subcapital femoral neck and report the treatment outcomes in a military trainee population. A retrospective analysis of patients with a subcapital, compression-sided FNSF was identified from a single U.S. Army basic trainee installation. Radiographic evaluation as well as treatment outcomes associated with the ability to complete military training were reported. A total of three patients with a subcapital compression-sided FNSF were identified in a military trainee population, accounting for 10% of all FNSFs that developed over a 3-month period. Of these individuals, one was treated operatively while the other two were treated non-operatively. Overall, one patient was able to return to and successfully complete military training.
Patterns of Population Structure and Introgression Among Recently Differentiated Drosophila melanogaster Populations
Authors: Coughlan Jenn M , Dagilis Andrius J , Serrato-Capuchina Antonio , Elias Hope , Peede David , Isbell Kristin , Castillo Dean M , Cooper Brandon S , Matute Daniel R 
Published: October 2022

Abstract
Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how genetic variation is partitioned within its putative ancestral range in Southern Africa remains unresolved. Here, we study patterns of population genetic structure, admixture, and the spatial structuring of candidate incompatibility alleles across a global sample, including 223 new accessions, predominantly from remote regions in Southern Africa. We identify nine major ancestries, six that primarily occur in Africa and one that has not been previously described. We find evidence for both contemporary and historical admixture between ancestries, with admixture rates varying both within and between continents. For example, while previous work has highlighted an admixture zone between broadly defined African and European ancestries in the Caribbean and southeastern USA, we identify West African ancestry as the most likely African contributor. Moreover, loci showing the strongest signal of introgression between West Africa and the Caribbean/southeastern USA include several genes relating to neurological development and male courtship behavior, in line with previous work showing shared mating behaviors between these regions. Finally, while we hypothesized that potential incompatibility loci may contribute to population genetic structure across the range of D. melanogaster; these loci are, on average, not highly differentiated between ancestries. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the partitioning of diversity across its range.
Evaluation of activation criteria in paediatric multi-trauma
Authors: Cohen Neta , Davis Adrienne L , Test Gidon , Singer–Harel Dana , Pasternak Yehonatan , Beno Suzanne , Scolnik Dennis 
Published: October 2022

AbstractObjectiveTo explore the optimal set of trauma activation criteria predicting paediatric patients’ need for acute care following multi-trauma, with particular attention to Glasgow Coma Scale (GCS) cut-off value.MethodsA retrospective cohort study of paediatric multi-trauma patients aged 0 to 16 years, performed at a Level 1 paediatric trauma centre. Trauma activation criteria and GCS levels were examined with respect to patients’ need for acute care, defined as: direct to operating room disposition, intensive care unit admission, need for acute interventions in the trauma room, or in-hospital death.ResultsWe enrolled 436 patients (median age 8.0 years). The following predicted need for acute care: GCS &lt;14 (adjusted odds ratio [aOR] 23.0, 95% confidence interval [CI]: 11.5 to 45.9, P &lt; 0.001), hemodynamic instability: (aOR 3.7, 95% CI: 1.2-8.1, P = 0.01), open pneumothorax/flail chest (aOR: 20.0, 95% CI: 4.0 to 98.7, P &lt; 0.001), spinal cord injury (aOR 15.4, 95% CI; 2.4 to 97.1, P = 0.003), blood transfusion at the referring hospital (aOR: 7.7, 95% CI: 1.3 to 44.2, P = 0.02) and GSW to the chest, abdomen, neck, or proximal extremities (aOR 11.0, 95% CI; 1.7 to 70.8, P = 0.01). Using these activation criteria would have decreased over- triage by 10.7%, from 49.1% to 37.2% and under-triage by 1.3%, from 4.7% to 3.5%, in our cohort of patients.ConclusionsUsing GCS&lt;14, hemodynamic instability, open pneumothorax/flail chest, spinal cord injury, blood transfusion at the referring hospital, and GSW to the chest, abdomen, neck of proximal extremities, as T1 activation criteria could decrease over- and under-triage rates. Prospective studies are needed to validate the optimal set of activation criteria in paediatric patients.
Implementation fidelity of the Promoting First Relationships intervention program in a Native community
Authors: Booth-LaForce Cathryn , Oxford Monica L , O’Leary Rae , Rees Jennifer , Petras Anthippy , Buchwald Dedra S 
Published: October 2022

Abstract
Promoting First Relationship (PFR) is an evidence-based intervention designed to promote positive, supportive relationships between primary caregivers and their young children. Implementing and testing the efficacy of PFR in a remote Native community is especially challenging and requires methods and tools for ensuring implementation fidelity. Tribal members of a Native community were successfully trained and certified to deliver PFR by university-based personnel. During PFR delivery, they achieved very high scores on adherence to intervention content (M = 0.99, SD = 0.02), and their quality of delivery uniformly exceeded established criteria. High attrition occurred before PFR was delivered. However, participants who remained in the study completed all 10 sessions of PFR content. Participants’ satisfaction with the program was very high (M = 3.90 [of 4 points], SD = 0.19). High implementation fidelity was attained in the face of many inherent challenges. The suite of methods and tools used for training, monitoring, and evaluating implementation fidelity in this study provides an example that may be useful in the evaluation of evidence-based programs more generally.
Illuminating Privacy and Security Concerns in Older Adults’ Technology Adoption
Authors: Knight Thora , Yuan Xiaojun , Bennett Gayle DeeDee 
Published: October 2022

Abstract
Privacy and security are among the salient factors that prevent older adults from adopting information communication technologies. Using the original APCO model (Antecedents, Privacy Concern, Outcomes), we conducted a PRISMA review on older adults’ perceptions of technology. This commentary draws upon findings from the PRISMA review and then proposes expansions to the APCO framework. More specifically, we advance that technology type is an antecedent to privacy concerns that contribute to older adults’ willingness to use or adopt technology. We also aggregate specific privacy and security concerns that older adults expressed are barriers to their technology use. Because these concerns vary according to technology type, we highlight methodological challenges for consideration in future research that investigates contextual relationships between technology and privacy-related factors.
Long-Term Efficacy and Safety of Fecal Microbiota Transplantation for C. difficile Infections Across Academic and Private Clinical Settings
Authors: Dogra Siddhant , Oneto Caterina , Sherman Alex , Varughese Resmi , Yuen Alexa , Sherman Isabel , Cohen Avi , Luo Yuying , Chen Lea Ann 
Published: October 2022

Purpose:
Fecal microbiota transplant (FMT) is increasingly performed for Clostridioides difficile infection (CDI), although long-term efficacy and safety data are limited and are focused on results from academic medical centers rather than private settings where most patients receive care.

Methods:
Medical records of 165 patients who received FMTs for CDI were reviewed from an academic medical center and an adjacent, unaffiliated private practice. Of these patients, 68 also completed a survey regarding their long-term disease course and interval health.

Results:
CDI resolution occurred in 81.3% (100/123) at the academic center and 95.2% (40/42) in the private setting. Private practice patients were more likely to present with recurrent, rather than refractory, CDI (92.9% vs. 66.7% P<0.001). Those from the academic center were more likely to have comorbid IBD, recent hospitalization, recent proton pump inhibitor use, ongoing immunosuppression, and inpatient FMT (all P values <0.05).
Among surveyed patients, 29.4% developed interval comorbidities or changes to pre-existing conditions after a median follow-up of 33.7 months (IQR 13.2 to 44.3 mo). Of 30 patients requiring subsequent antibiotics, 13.3% suffered CDI relapse. All subjects who had initially responded to FMT but had a subsequent CDI (17.9%, 10/56) responded to another FMT.

Conclusions:
In a real-world setting, patients who underwent FMT at academic centers differed significantly in clinical characteristics from those treated at a private practice. In both settings, FMT is an effective treatment for CDI not responding to standard therapies, even after subsequent antibiotic use. New diagnoses following FMT, however, are common and merit further exploration.