bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for recurrence of colorectal conventional adenoma and serrated polyp
Authors: Chi Zengjie , Lin Yanyun , Huang Juanni , Lv Min-Yi , Chen Junguo , Chen Xijie , Zhang Bin , Chen Yufeng , Hu Jiancong , He Xiaosheng , Lan Ping 
Published: September 2021

Abstract

Background
Removal of colorectal polyps during screening could reduce the incidence of colorectal cancer (CRC). However, there is a lack of data on risk factors associated with recurrence of polyps, including conventional adenomas and serrated polyps (SPs). This study aimed to determine risk factors for recurrence of colorectal polyps and their subtypes based on the characteristics of the patients and polyps.

Methods
A total of 1,165 patients diagnosed with conventional adenoma or SP in the Sixth Affiliated Hospital of Sun Yat-sen University between January 2013 and December 2019 were enrolled in this study, including 668 cases with conventional adenomas, 385 with SPs, and 112 with coexistence of adenomas and SPs. Univariate analysis and multivariate logistic regression were used to identify potential risk factors for polyp recurrence. A nomogram was established according to risk factors and the performance was evaluated using calibration plots.

Results
During a median follow-up of 24 months, recurrent polyps were observed in 531 (45.6%) cases. Male, age ≥50 years, body mass index (BMI) ≥24 kg/m2, at least three polyps, smoking, alcohol consumption, family history of polyps, and family history of CRC were independent risk factors for polyp recurrence. The Harrell’s C-index of the nomogram developed with these parameters was 0.69 and the calibration plots showed good agreement between actual polyp recurrence and nomogram-predicted recurrence probability. In the subtype analyses, conventional adenomas had the same risk factors for recurrence as all polyps, while smoking, alcohol consumption, family history of polyps, and family history of CRC were not risk factors for SP recurrence.

Conclusions
We identified several risk factors for recurrence of colorectal polyps and found that some of them could increase the risk of adenoma recurrence but not SP recurrence, including smoking, alcohol consumption, and family history of polyps/CRC, which might help us to understand different etiology and biology between conventional adenomas and SPs.
The gateway reflex: breaking through the blood barriers
Authors: Murakami Kaoru , Tanaka Yuki , Murakami Masaaki 
Published: September 2021

Abstract
We have been studying inflammatory diseases, with a special focus on IL-6, and discovered two concepts related to inflammation development. One is the gateway reflex, which is induced by the activation of specific neural circuits followed by establishing gateways for autoreactive CD4+ T cells to pass through blood barriers toward the central nervous system (CNS) and retina during tissue-specific inflammatory diseases. We found that the formation of these gateways is dependent on the IL-6 amplifier, which is machinery for enhanced NF-κB activation in endothelial cells at specific sites. We have found five gateway reflexes in total. Here, we introduce the gateway reflex and the IL-6 amplifier.
Characteristics of mucosal-associated invariant T cells and their roles in immune diseases
Authors: Chiba Asako , Murayama Goh , Miyake Sachiko 
Published: September 2021

Abstract
Mucosal-associated invariant T (MAIT) cells are a subset of innate-like T cells that express a semi-invariant T-cell receptor and are restricted by the major histocompatibility complex class I-related molecule 1 (MR1). MAIT cells recognize biosynthetic derivatives of the riboflavin synthesis pathway present in microbes. MAIT cells have attracted increased interest related to various immune responses because of their unique features including their abundance in humans, non-peptidic antigens and ability to respond to antigenic and non-antigenic stimuli. The numbers of circulating MAIT cells are decreased in many immune diseases such as multiple sclerosis, systemic lupus erythematosus and inflammatory bowel diseases. However, the remaining MAIT cells have an increased cytokine-producing capacity and activated status, which are related to disease activity. Additionally, MAIT cells have been observed at sites of inflammation including the kidneys, synovial fluid and intestinal mucosa. These findings suggest their involvement in the pathogenesis of immune diseases. In this mini-review, we summarize the recent findings of MAIT cells in human immune diseases and animal models, and discuss their role and potential as a therapeutic target.
The intersection of big data and epidemiology for epidemiologic research: The impact of the COVID-19 pandemic
Authors: Tang Chunlei , Plasek Joseph M , Zhang Suhua , Xiong Yun , Zhu Yangyong , Ma Jing , Zhou L I , Bates David W 
Published: September 2021

Abstract
Big data epidemiology facilitates pandemic response by providing data-driven insights by utilizing big data tools that differ from traditional methods. Aspects regarding ‘garbage in, garbage out’, such as insufficient data, inaccessibility of data, missing data, uncertainty in handling data and bias in analysis or common findings are addressable by combining techniques across disciplines.
Adopting systems models for multiple incident analysis: utility and usability
Authors: Wheway Jayne L , Jun Gyuchan Thomas 
Published: September 2021

Abstract

Background
This study aims to present two system models widely used in Human Factors and Ergonomics (HF/E) and evaluate whether the models are adoptable to England’s national patient safety team in improving the exploration and understanding of multiple incident reports of an active patient safety issue and the development of the remedial actions for a potential National Patient Safety Alert. The existing process of examining multiple incidents is based on inductive thematic analysis and forming the remedial actions is based on barrier analysis of intelligence on potential solutions. However, no formal systems models evaluated in this study have been used.

Methods
AcciMap and Systems Engineering Initiative for Patient Safety (SEIPS) were selected, applied and evaluated to the analysis of two different sets of patient safety incidents: (i) incidents concerning ingestion of superabsorbent polymer granules and (ii) incidents concerning the interruption in use of High Nasal Flow Oxygen. The first set was analysed by the first author and the utility and usability were reflected. The second set was analysed collectively by a purposeful sample of patient safety team members, who create the National Patient Safety Alerts from incident-level data and information. All of them attended a 30-min video-based training and a 1.5 h case-based online workshop. Post-workshop individual interviews were conducted to evaluate their perceived utility and usability of each model.

Results
The patient safety team showed overwhelming support for the utility of the system models as a ‘framework’ that provides a systematic, structured way of looking at an issue and examining the causes, whilst also sharing concerns regarding their usability. AcciMap was viewed useful particularly in providing a visual comprehensive overview of the issue but considered chaotic by some participants due to many arrows between factors. SEIPS was perceived easier to understand due to the familiarity of the structure (Donbedian’s model), but the non-hierarchical format of SEIPS was considered less useful.

Conclusions
The participants of the study agreed with the high level of utility of both models for their unique strengths, but shared some concern for the usability of them in terms of complexity and further training/coaching time would be required to adopt these models in their daily practices. It is recommended that the gap between HF/E practitioners and patient safety practitioners can be narrowed by strengthening education, and coaching and mentoring relationships between the two groups, led by the increasing number of healthcare practitioners who embrace their membership to HF/E practice.
AutoBend: An Automated Approach for Estimating Intervertebral Joint Function from Bone-Only Digital Models
Authors: Jones K E , Brocklehurst R J , Pierce S E 
Published: September 2021

Synopsis
Deciphering the biological function of rare or extinct species is key to understanding evolutionary patterns across the tree of life. While soft tissues are vital determinants of joint function, they are rarely available for study. Therefore, extracting functional signals from skeletons, which are more widely available via museum collections, has become a priority for the field of comparative biomechanics. While most work has focused on the limb skeleton, the axial skeleton plays a critical role in body support, respiration, and locomotion, and is therefore of central importance for understanding broad-scale functional evolution. Here, we describe and experimentally validate AutoBend, an automated approach to estimating intervertebral joint function from bony vertebral columns. AutoBend calculates osteological range of motion (oROM) by automatically manipulating digitally articulated vertebrae while incorporating multiple constraints on motion, including both bony intersection and the role of soft tissues by restricting excessive strain in both centrum and zygapophyseal articulations. Using AutoBend and biomechanical data from cadaveric experiments on cats and tegus, we validate important modeling parameters required for oROM estimation, including the degree of zygapophyseal disarticulation, and the location of the center of rotation. Based on our validation, we apply a model with the center of rotation located within the vertebral disk, no joint translation, around 50% strain permitted in both zygapophyses and disks, and a small amount of vertebral intersection permitted. Our approach successfully reconstructs magnitudes and craniocaudal patterns of motion obtained from ex vivo experiments, supporting its potential utility. It also performs better than more typical methods that rely solely on bony intersection, emphasizing the importance of accounting for soft tissues. We estimated the sensitivity of the analyses to vertebral model construction by varying joint spacing, degree of overlap, and the impact of landmark placement. The effect of these factors was small relative to biological variation craniocaudally and between bending directions. We also present a new approach for estimating joint stiffness directly from oROM and morphometric measurements that can successfully reconstruct the craniocaudal patterns, but not magnitudes, derived from experimental data. Together, this work represents a significant step forward for understanding vertebral function in difficult-to-study (e.g., rare or extinct) species, paving the way for a broader understanding of patterns of functional evolution in the axial skeleton.
Oxacillin plus ertapenem combination therapy leads to rapid blood culture clearance and positive outcomes among patients with persistent MSSA bacteraemia: a case series
Authors: El-Dalati Sami , Sridaran Sanjay , Uricchio Marissa , Kline Ellen G , Shields Ryan 
Published: September 2021

AbstractBackgroundBloodstream infections caused by MSSA are associated with significant morbidity and mortality. Traditional treatment of MSSA bacteraemia includes an IV antistaphylococcal β-lactam and surgical source control when indicated.ObjectivesTo evaluate the time to blood culture clearance as well as in-hospital and 90 day mortality in patients with persistent MSSA bacteraemia treated with combination antistaphylococcal penicillin plus carbapenem therapy.MethodsConsecutive patients with persistent MSSA bacteraemia treated with combination therapy were identified by study investigators and reviewed by independent clinicians. The decision to initiate combination therapy was made by the consulting clinician or by the institution’s multidisciplinary endocarditis team.ResultsAmong 10 patients with a median of 5 days of persistent MSSA bacteraemia, treatment with an antistaphylococcal penicillin plus carbapenem led to sterilization of blood cultures in all patients. Blood culture clearance occurred in a median of 1 day and patients received a median of 6 days of combination treatment. Four of seven patients who underwent source control of their primary site of infection cleared their bacteraemia on combination therapy prior to the surgical intervention. All patients survived to hospital discharge and 90 days post-discharge.ConclusionsThese data extend prior findings and provide further evidence that suggests the potential benefits of combination therapy among patients with persistent MSSA bacteraemia.
An atomic approach to the design and implementation of a research data warehouse
Authors: Visweswaran Shyam , McLay Brian , Cappella Nickie , Morris Michele , Milnes John T , Reis Steven E , Silverstein Jonathan C , Becich Michael J 
Published: September 2021

Abstract

Objective
As a long-standing Clinical and Translational Science Awards (CTSA) Program hub, the University of Pittsburgh and the University of Pittsburgh Medical Center (UPMC) developed and implemented a modern research data warehouse (RDW) to efficiently provision electronic patient data for clinical and translational research.

Materials and Methods
We designed and implemented an RDW named Neptune to serve the specific needs of our CTSA. Neptune uses an atomic design where data are stored at a high level of granularity as represented in source systems. Neptune contains robust patient identity management tailored for research; integrates patient data from multiple sources, including electronic health records (EHRs), health plans, and research studies; and includes knowledge for mapping to standard terminologies.

Results
Neptune contains data for more than 5 million patients longitudinally organized as Health Insurance Portability and Accountability Act (HIPAA) Limited Data with dates and includes structured EHR data, clinical documents, health insurance claims, and research data. Neptune is used as a source for patient data for hundreds of institutional review board-approved research projects by local investigators and for national projects.

Discussion
The design of Neptune was heavily influenced by the large size of UPMC, the varied data sources, and the rich partnership between the University and the healthcare system. It includes several unique aspects, including the physical warehouse straddling the University and UPMC networks and management under an HIPAA Business Associates Agreement.

Conclusion
We describe the design and implementation of an RDW at a large academic healthcare system that uses a distinctive atomic design where data are stored at a high level of granularity.
Development of a computer-aided text message platform for user engagement with a digital Diabetes Prevention Program: a case study
Authors: Rodriguez Danissa V , Lawrence Katharine , Luu Son , Yu Jonathan L , Feldthouse Dawn M , Gonzalez Javier , Mann Devin 
Published: September 2021

Abstract
Digital Diabetes Prevention Programs (dDPP) are novel mHealth applications that leverage digital features such as tracking and messaging to support behavior change for diabetes prevention. Despite their clinical effectiveness, long-term engagement to these programs remains a challenge, creating barriers to adherence and meaningful health outcomes. We partnered with a dDPP vendor to develop a personalized automatic message system (PAMS) to promote user engagement to the dDPP platform by sending messages on behalf of their primary care provider. PAMS innovates by integrating into clinical workflows. User-centered design (UCD) methodologies in the form of iterative cycles of focus groups, user interviews, design workshops, and other core UCD activities were utilized to defined PAMS requirements. PAMS uses computational tools to deliver theory-based, automated, tailored messages, and content to support patient use of dDPP. In this article, we discuss the design and development of our system, including key requirements and features, the technical architecture and build, and preliminary user testing.
Transferability of neural network clinical deidentification systems
Authors: Lee Kahyun , Dobbins Nicholas J , McInnes Bridget , Yetisgen Meliha , Uzuner Özlem 
Published: September 2021

Abstract

Objective
Neural network deidentification studies have focused on individual datasets. These studies assume the availability of a sufficient amount of human-annotated data to train models that can generalize to corresponding test data. In real-world situations, however, researchers often have limited or no in-house training data. Existing systems and external data can help jump-start deidentification on in-house data; however, the most efficient way of utilizing existing systems and external data is unclear. This article investigates the transferability of a state-of-the-art neural clinical deidentification system, NeuroNER, across a variety of datasets, when it is modified architecturally for domain generalization and when it is trained strategically for domain transfer.

Materials and Methods
We conducted a comparative study of the transferability of NeuroNER using 4 clinical note corpora with multiple note types from 2 institutions. We modified NeuroNER architecturally to integrate 2 types of domain generalization approaches. We evaluated each architecture using 3 training strategies. We measured transferability from external sources; transferability across note types; the contribution of external source data when in-domain training data are available; and transferability across institutions.

Results and Conclusions
Transferability from a single external source gave inconsistent results. Using additional external sources consistently yielded an F1-score of approximately 80%. Fine-tuning emerged as a dominant transfer strategy, with or without domain generalization. We also found that external sources were useful even in cases where in-domain training data were available. Transferability across institutions differed by note type and annotation label but resulted in improved performance.
Modelling Modular Living: Furniture and Life Magazine and Interior Design in 1980s China
Authors: Altehenger Jennifer 
Published: September 2021

Abstract
In 1981, Furniture and Life magazine commenced publication in the city of Xi'an in the People’s Republic of China. By the late 1980s, it had become a well-known furniture and home-making magazine, read for its DIY guides, advice columns, and home stories. Each issue discussed how to beautify homes and turn the Chinese Communist Party’s vision for a ‘socialist material civilization’ into practice and lived experience. This article uses the case of Furniture and Life to chart the role of modular furniture in urban interior design and the cultural imagination of the 1980s, the first decade of the CCP’s economic reforms following the end of the Cultural Revolution. It traces the context in which the magazine was established, illustrating why furniture had become a pressing concern for many people across the country. It then shows how editors, themselves often architects, furniture designers, and engineers, focused on modular, ‘board-style’ furniture to solve people’s concrete problems of small living spaces and a growing desire for personal space. In this process, the magazine editors connected modular furniture and interiors to the CCP’s vision of socialist material and spiritual civilization, thus trying to lend concrete shape to broad political concepts.
The Medicalization of the Transsexual: Patient-Physician Narratives in the First Half of the Twentieth Century
Authors: Vicente Marta V 
Published: September 2021

Abstract
This article explores the history of what the German-American endocrinologist Harry Benjamin labeled in 1966, “the transsexual phenomenon.” By mid-century, a growing number of individuals in both Europe and America were approaching physicians such as Benjamin searching for answers and means to change their bodies to match their gender. This phenomenon had started in Europe in the 1930s, when the Danish painter Einar Wegener underwent a series of operations that transformed a body defined at birth as male into the female body of Lili Elbe. The news of Elbe’s transformation ignited interest and discussion among physicians as well as the public on the capacity science had to alter bodies to fit their intended selves. The case of Elbe combines the three main aspects studied in this article—the medicalization of the homosexual, the birth of the transsexual, and the physician–patient relationship in transsexual narratives. The study of physician and patient narratives allow us to see how the transsexual phenomenon was in fact created out of the intersection of interests from both physicians and their transsexual patients.
Visualizing second world war violence through an Atlas of Nazi–Fascist Repression
Authors: Vitali Giovanni Pietro 
Published: September 2021

Abstract
In Italy’s complex political past, the memory of resistance against nationalism has always been at the centre of political clashes between the right and the left. Considering that the memory of the Second World War (WWII) is still alive in Italian society, an analysis of the violence perpetrated by the Fascists and Nazis on Italian territory in this period is a way to discuss the historical responsibilities of both. This article aims to oppose this instrumental use of history. The aim of this work is to show how violence was exerted against Italian civilians during WWII through a spatial and statistical inquiry. I created an Atlas of Nazi–Fascist Repression combining three different databases into a unique dataset.
Understanding of source code in language: Contribution of philosophical hermeneutics to the critical code studies
Authors: Bajer Anna 
Published: September 2021

AbstractThe article discusses the attempt to understand a source code under the conception of philosophical hermeneutics guided by language. Based on a confrontation between H.-G. Gadamer’s and Paul Ricoeur’s philosophy, our main goal would be searching for the essence of the source code in language. Thus, a closer look is taken into cultural symbols, natural language, and artificial languages. Especially, there would be discussed the problem of abstraction, linguistic community, self-forgetfulness, vitality of formal languages, and display of individuality. This is where the cultural layer of the code can be traced, hence we may find our world-view verbal in nature. In line with the Critical Code Studies approach, in this article, the source code is treated as text. Because of its complexity, the issue should be studied within philosophical inquiry and computer science knowledge. Hence, the perspective developed here goes back to origins and provides a philosophical foundation for Critical Code Studies thinking. The article presents academics with a philosophical challenge: how to understand the source code with an adaptation of a philosophy rejecting artificiality. With philosophical reflection, the source code gains additional meaning and experiences increase in being. Understanding happens in language, which realizes as discourse.