bluuebunny/crossref_metadata_2025 huggingface dataset:
Frontoparietal Anatomical Connectivity Predicts Second Language Learning Success
Authors: Sander Kaija , Barbeau Elise B , Chai Xiaoqian , Kousaie Shanna , Petrides Michael , Baum Shari , Klein Denise
Published: September 2021

There is considerable individual variability in second language (L2) learning abilities in adulthood. The inferior parietal lobule, important in L2 learning success, is anatomically connected to language areas in the frontal lobe via the superior longitudinal fasciculus (SLF). The second and third branches of the SLF (SLF II and III) have not been examined separately in the context of language, yet they are known to have dissociable frontoparietal connections. Studying these pathways and their functional contributions to L2 learning is thus of great interest. Using diffusion MRI tractography, we investigated individuals undergoing language training to explore brain structural predictors of L2 learning success. We dissected SLF II and III using gold-standard anatomical definitions and related prelearning white matter integrity to language improvements corresponding with hypothesized tract functions. SLF II properties predicted improvement in lexical retrieval, while SLF III properties predicted improvement in articulation rate. Finer grained separation of these pathways enables better understanding of their distinct roles in language, which is essential for studying how anatomical connectivity relates to L2 learning abilities.
Overcoming Data Bottlenecks in Genomic Pathogen Surveillance
Authors: Afolayan Ayorinde O , Bernal Johan Fabian , Gayeta June M , Masim Melissa L , Shamanna Varun , Abrudan Monica , Abudahab Khalil , Argimón Silvia , Carlos Celia C , Sia Sonia , Ravikumar Kadahalli L , Okeke Iruka N , Donado-Godoy Pilar , Aanensen David M , Underwood Anthony ,   NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance, Harste Harry , Kekre Mihir , Muddyman Dawn , Taylor Ben , Wheeler Nicole , David Sophia , Arevalo Alejandra , Fernanda Valencia Maria , Osma Castro Erik C D , Nagaraj Geetha , Govindan Vandana , Prabhu Akshata , Sravani D , Shincy M R , Rose Steffimole , Ravishankar Kundur N , Oaikhena Anderson O , Ajiboye Jolaade J , Ewomazino Odih Erkison , Lagrada Marietta L , Macaranas Polle Krystle V , Olorosa Agnettah M , Herrera Elmer M , Molloy Ali , Stelling John , Vegvari Carolin
Published: September 2021

Performing whole genome sequencing (WGS) for the surveillance of antimicrobial resistance offers the ability to determine not only the antimicrobials to which rates of resistance are increasing, but also the evolutionary mechanisms and transmission routes responsible for the increase at local, national, and global scales. To derive WGS-based outputs, a series of processes are required, beginning with sample and metadata collection, followed by nucleic acid extraction, library preparation, sequencing, and analysis. Throughout this pathway there are many data-related operations required (informatics) combined with more biologically focused procedures (bioinformatics). For a laboratory aiming to implement pathogen genomics, the informatics and bioinformatics activities can be a barrier to starting on the journey; for a laboratory that has already started, these activities may become overwhelming. Here we describe these data bottlenecks and how they have been addressed in laboratories in India, Colombia, Nigeria, and the Philippines, as part of the National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance. The approaches taken include the use of reproducible data parsing pipelines and genome sequence analysis workflows, using technologies such as Data-flo, the Nextflow workflow manager, and containerization of software dependencies. By overcoming barriers to WGS implementation in countries where genome sampling for some species may be underrepresented, a body of evidence can be built to determine the concordance of antimicrobial sensitivity testing and genome-derived resistance, and novel high-risk clones and unknown mechanisms of resistance can be discovered.
Assessment of the Urinary Microbiota of MSM Using Urine Culturomics Reveals a Diverse Microbial Environment
Authors: Sawhney Sanjam S , Johnson Caitlin , Shupe Angela , Fine Jeremy , Dantas Gautam , Burnham Carey-Ann D , Yarbrough Melanie L
Published: September 2021

Background

The urinary tract is not sterile and is populated by microbial communities that influence urinary health. Men who have sex with men (MSM) are understudied yet have increased risk factors for genitourinary infections. Our objective was to interrogate the composition of MSM urinary microbiota.

Methods

Midstream urine specimens (n = 129) were collected from MSM (n = 63) and men seen for routine care (clinical cohort, n = 30). Demographics and sexual/medical history were documented. Specimens underwent culture using standard-of-care and enhanced methods designed to isolate fastidious and anaerobic microorganisms. Isolates were identified by MALDI-TOF mass spectrometry or 16S rRNA gene sequencing.

Results

The MSM cohort was younger (mean (SD), 35.4 (11.26) years) compared to the clinical cohort (62.7 (15.95) years). Organism recovery was significantly increased using enhanced vs standard culture for the MSM (mean of 9.1 vs 0.6 species/sample [P < 0.001]) and clinical (7.8 vs 0.9 species/sample [P < 0.001]) cohorts. The microbial composition of MSM urine specimens was dominated by Gram-positive and anaerobic microbes and clustered distinctly from that of clinical urine specimens. Composition of microbial species recovered within the same subject was dynamic between urine specimens but more similar relative to inter-individual comparisons. Principal coordinate analysis showed no correlation between urinary microbiota composition and age, recent antibiotic use, sexually transmitted infection/HIV status, or sexual practices.

Conclusions

Enhanced culture recovered a large diversity of microbial species from MSM urine specimens, especially taxa typically associated with mucosal surfaces. These findings may increase understanding of urologic disease in MSM and improve diagnostic methods for detection of genitourinary infections.
Youtube Trending Videos: Boosting Machine Learning Results Using Exploratory Data Analysis
Authors: Khanam Sana , Tanweer Safdar , Khalid Syed Sibtain
Published: September 2021

With the emergence of social media and the Internet, bulks of data are generated every day in different fields. However, filtering out useful information, which can be turned into knowledge, requires significant effort. This can be achieved using various Big Data Technologies, statistics, data mining and a variety of machine learning algorithms that corporates and businesses are using to improve their performance every day for a long time now. In this paper, we analyze YouTube trending video data that analyses the target that grabs the user’s attention over a relatively short time. We present our analysis by measuring, mining, analyzing and comparing key aspects of time-series YouTube data with respect to its view and audience response statistics from 40 000 trending YouTube videos collected over 205 days. We have performed an exploratory data analysis (EDA) on all of it's aspect to get data insights and used statistics to find similarities between them to understand viewing pattern of different video categories. We also compare and observe the variation of activity over time with the nature of the event that affects the quality of our analysis. We make the viewership pattern clear belonging to each category separately by direct analysis. The results and findings can help us predict the category of the video that could probably be trending next in the upcoming days and help individuals get boosted views and performance when they upload video as per the predictions and analysis.
The Relationship Between Endoscopic and Clinical Recurrence in Postoperative Crohn’s Disease: A Systematic Review and Meta-analysis
Authors: Ble Alessandro , Renzulli Cecilia , Cenci Fabio , Grimaldi Maria , Barone Michelangelo , Sedano Rocio , Chang Joshua , Nguyen Tran M , Hogan Malcolm , Zou Guangyong , MacDonald John K , Ma Christopher , Sandborn William J , Feagan Brian G , Merlo Pich Emilio , Jairath Vipul
Published: September 2021

Background and Aims

We aimed to quantify the magnitude of the association between endoscopic recurrence and clinical recurrence [symptom relapse] in patients with postoperative Crohn’s disease.

Methods

Databases were searched to October 2, 2020, for randomised controlled trials [RCTs] and cohort studies of adult patients with Crohn’s disease with ileocolonic resection and anastomosis. Summary effect estimates for the association between clinical recurrence and endoscopic recurrence were quantified by risk ratios [RR] and 95% confidence intervals [95% CI]. Mixed-effects meta-regression evaluated the role of confounders. Spearman correlation coefficients were calculated to assess the relationship between these outcomes as endpoints in RCTs. An exploratory mixed-effects meta-regression model with the logit of the rate of clinical recurrence as the outcome and the rate of endoscopic recurrence as a predictor was also evaluated.

Results

In all, 37 studies [N = 4053] were included. For eight RCTs with available data, the RR for clinical recurrence for patients who experienced endoscopic recurrence was 10.77 [95% CI 4.08 to 28.40; GRADE moderate certainty evidence]; the corresponding estimate from 11 cohort studies was 21.33 [95% CI 9.55 to 47.66; GRADE low certainty evidence]. A single cohort study showed a linear relationship between Rutgeerts score and clinical recurrence risk. There was a strong correlation between endoscopic recurrence and clinical recurrence treatment effect estimates as trial outcomes [weighted Spearman correlation coefficient 0.51].

Conclusions

The associations between endoscopic recurrence and subsequent clinical recurrence lend support to the choice of endoscopic recurrence to monitor postoperative disease activity and as a primary endpoint in clinical trials of postoperative Crohn’s disease.
Cardiovascular magnetic resonance imaging in suspected cardiac tumour: a multicentre outcomes study
Authors: Shenoy Chetan , Grizzard John D , Shah Dipan J , Kassi Mahwash , Reardon Michael J , Zagurovskaya Marianna , Kim Han W , Parker Michele A , Kim Raymond J
Published: September 2021

Aims

Cardiovascular magnetic resonance (CMR) imaging is a key diagnostic tool for the evaluation of patients with suspected cardiac tumours. Patient management is guided by the CMR diagnosis, including no further testing if a mass is excluded or if only a pseudomass is found. However, there are no outcomes studies validating this approach.

Methods and results

In this multicentre study of patients undergoing clinical CMR for suspected cardiac tumour, CMR diagnoses were assigned as no mass, pseudomass, thrombus, benign tumour, or malignant tumour. A final diagnosis was determined after follow-up using all available data. The primary endpoint was all-cause mortality. Among 903 patients, the CMR diagnosis was no mass in 25%, pseudomass in 16%, thrombus in 16%, benign tumour in 17%, and malignant tumour in 23%. Over a median of 4.9 years, 376 patients died. Compared with the final diagnosis, the CMR diagnosis was accurate in 98.4% of patients. Patients with CMR diagnoses of pseudomass and benign tumour had similar mortality to those with no mass, whereas those with malignant tumour [hazard ratio (HR) 3.31 (2.40–4.57)] and thrombus [HR 1.46 (1.00–2.11)] had greater mortality. The CMR diagnosis provided incremental prognostic value over clinical factors including left ventricular ejection fraction, coronary artery disease, and history of extracardiac malignancy (P < 0.001).

Conclusion

In patients with suspected cardiac tumour, CMR has high diagnostic accuracy. Patients with CMR diagnoses of no mass, pseudomass, and benign tumour have similar long-term mortality. The CMR diagnosis is a powerful independent predictor of mortality incremental to clinical risk factors.
New evidence: Cryoballoon ablation vs. antiarrhythmic drugs for first-line therapy of atrial fibrillation
Authors: Andrade Jason G , Chierchia Gian-Battista , Kuniss Malte , Wazni Oussama M
Published: September 2021

Atrial fibrillation (AF) is a commonly encountered chronic and progressive heart rhythm disorder, characterized by exacerbations and remissions. Contemporary clinical practice guidelines recommend a trial of antiarrhythmic drugs (AADs) as the initial therapy for sinus rhythm maintenance; however, these medications have modest efficacy and are associated with significant adverse effects. Recently, several trials have demonstrated that an initial treatment strategy of cryoballoon catheter ablation significantly improves arrhythmia outcomes (e.g. freedom atrial tachyarrhythmia and reduction in arrhythmia burden), produces clinically meaningful improvements in patient-reported outcomes (e.g. symptoms and quality of life), and significantly reduces subsequent healthcare resource utilization (e.g. hospitalization), without increasing the risk of serious or any adverse events. These findings are relevant to patients, providers, and healthcare systems, helping inform the decision regarding the initial choice of rhythm-control therapy in patients with treatment-naïve AF.
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

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

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

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

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

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

Background

Bloodstream 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.

Objectives

To 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.

Methods

Consecutive 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.

Results

Among 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.

Conclusions

These 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

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

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

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

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

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.
Responsible travel to and within India during the COVID-19 pandemic
Authors: Mandal Sandip , Arinaminpathy Nimalan , Bhargava Balram , Panda Samiran
Published: September 2021

Following the ‘second wave’ of COVID-19 in India, there has been an upsurge of domestic travel to holiday destinations, particularly Himalayan mountain towns. Modelling suggests that such travel could enhance the peak of a third wave in these states by almost 50%. Principles of ‘responsible travel’ should be adhered to.
Visualizing second world war violence through an Atlas of Nazi–Fascist Repression
Authors: Vitali Giovanni Pietro
Published: September 2021

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

The 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.
Planetary nebulae with Wolf–Rayet-type central stars – II. Dissecting the compact planetary nebula M 2-31 with GTC MEGARA
Authors: Rechy-García J S , Toalá J A , Cazzoli S , Guerrero M A , Sabin L , Gómez-González V M A , Ramos-Larios G
Published: September 2021

We present a comprehensive analysis of the compact planetary nebula M 2-31 investigating its spectral properties, spatio-kinematical structure, and chemical composition using Gran Telescopio Canarias (GTC) Multi-Espectrógrafo en GTC de Alta Resolución para Astronomía (MEGARA) integral field spectroscopic observations and Nordic Optical Telescope(NOT) Alhambra Faint Object Spectrograph and Camera (ALFOSC) medium-resolution spectra and narrow-band images. The GTC MEGARA high-dispersion observations have remarkable tomographic capabilities, producing an unprecedented view of the morphology and kinematics of M 2-31 that discloses a fast spectroscopic bipolar outflow along position angles 50○ and 230○, an extended shell, and a toroidal structure or waist surrounding the central star perpendicularly aligned with the fast outflows. These observations also show that the C ii emission is confined in the central region and enclosed by the [N ii] emission. This is the first time that the spatial segregation revealed by a two-dimensional map of the C ii line implies the presence of multiple plasma components. The deep NOT ALFOSC observations allowed us to detect broad Wolf–Rayet (WR) features from the central star of M 2-31, including previously undetected broad O vi lines that suggest a reclassification as a [WO4]-type star.
Lensing magnification: gravitational waves from coalescing stellar-mass binary black holes
Authors: Shan Xikai , Wei Chengliang , Hu Bin
Published: September 2021

Gravitational waves (GWs) may be magnified or de-magnified due to lensing. This phenomenon will bias the distance estimation based on the matched filtering technique. Via the multi-sphere ray-tracing technique, we study the GW magnification effect and selection effect with particular attention to the stellar-mass binary black holes. We find that, for the observed luminosity distance $\lesssim 3\, \mathrm{Gpc}$, which is the aLIGO/Virgo observational horizon limit, the average magnification keeps as unity, namely unbiased estimation, with the relative distance uncertainty $\sigma (\hat{d})/\hat{d}\simeq 0.5{{\ \rm per\ cent}}\sim 1{{\ \rm per\ cent}}$. Beyond this observational horizon, the estimation bias can not be ignored, and with the scatters $\sigma (\hat{d})/\hat{d} = 1{{\ \rm per\ cent}}\sim 15{{\ \rm per\ cent}}$. Furthermore, we forecast these numbers for Einstein Telescope (ET). We find that the average magnification keeps closely as unity for the observed luminosity distance $\lesssim 90\, \mathrm{Gpc}$. The luminosity distance estimation error due to lensing for ET is about $\sigma (\hat{d})/\hat{d} \simeq 10{{\ \rm per\ cent}}$ for the luminosity distance $\gtrsim 25\, \mathrm{Gpc}$. Unlike the aLIGO/Virgo case, this sizable error is not due to the selection effect. It purely comes from the unavoidably accumulated lensing magnification. Moreover, we investigated the effects of the orientation angle and the BH mass distribution models. We found that the results are strongly dependent on these two components.
The cumulative star formation histories of dwarf galaxies with TNG50. I: environment-driven diversity and connection to quenching
Authors: Joshi Gandhali D , Pillepich Annalisa , Nelson Dylan , Zinger Elad , Marinacci Federico , Springel Volker , Vogelsberger Mark , Hernquist Lars
Published: September 2021

We present the cumulative star formation histories (SFHs) of >15 000 dwarf galaxies ($M_{\rm *}=10^{7-10}\, {\rm M}_{\odot }$) simulated with the TNG50 run of the IllustrisTNG suite across a vast range of environments. The key factors that determine the dwarfs’ SFHs are their central/satellite status and stellar mass, with centrals and more massive dwarfs assembling their stellar mass at later times, on average, compared to satellites and lower mass dwarfs. Satellites (in hosts of mass $M_{\rm 200c, host}=10^{12-14.3}\, {\rm M}_{\odot }$) assembled 90 per cent of their stellar mass ${\sim}7.0_{-5.5}^{+3.3}$ Gyr ago, on average and within the 10th to 90th percentiles, while the centrals did so only ${\sim}1.0_{-0.5}^{+4.0}$ Gyr ago. TNG50 predicts a large diversity in SFHs, so that individual dwarfs can have significantly different cumulative SFHs compared to the stacked median SFHs. Satellite dwarfs with the highest stellar mass to host cluster mass ratios have the latest stellar mass assembly. Conversely, satellites at fixed stellar and host halo mass found closer to the cluster centre or accreted at earlier times show significantly earlier stellar mass assembly. These trends and the shapes of the SFHs themselves are a manifestation of the varying proportions within a given subsample of quenched versus star-forming galaxies, which exhibit markedly distinct SFH shapes. Finally, satellite dwarfs in the most massive hosts have higher SFRs at early times, well before accretion into their z = 0 host, compared to a control sample of centrals mass-matched at the time of accretion. This is the result of the satellites being preprocessed in smaller hosts prior to accretion. Our findings are useful theoretical predictions for comparison to future resolved stellar population observations.
Formation of ring-like structures in flared α-discs with X-ray/FUV photoevaporation
Authors: Vallejo Juan C , Gómez de Castro Ana Inés
Published: September 2021

Protoplanetary discs are complex dynamical systems where several processes may lead to the formation of ring-like structures and planets. These discs are flared following a profile where the vertical scale height increases with radius. In this work, we investigate the role of this disc flaring geometry on the formation of rings and holes. We combine a flattening law change with X-ray and FUV photoevaporative winds. We have used a semi-analytical 1D viscous α approach, presenting the evolution of the disc mass and mass rate in a grid of representative systems. Our results show that changing the profile of the flared disc may favour the formation of ring-like features resembling those observed in real systems at the proper evolutionary times, with proper disc masses and accretion rate values. However, these features seem to be short-lived and further enhancements are still needed for better matching all the features seen in real systems.
Birth of the ELMs: a ZTF survey for evolved cataclysmic variables turning into extremely low-mass white dwarfs
Authors: El-Badry Kareem , Rix Hans-Walter , Quataert Eliot , Kupfer Thomas , Shen Ken J
Published: September 2021

We present a systematic survey for mass-transferring and recently detached cataclysmic variables (CVs) with evolved secondaries, which are progenitors of extremely low mass white dwarfs (ELM WDs), AM CVn systems, and detached ultracompact binaries. We select targets below the main sequence in the Gaia colour–magnitude diagram with ZTF light curves showing large-amplitude ellipsoidal variability and orbital period Porb < 6 h. This yields 51 candidates brighter than G = 18, of which we have obtained many-epoch spectra for 21. We confirm all 21 to be completely or nearly Roche lobe filling close binaries. Thirteen show evidence of ongoing mass transfer, which has likely just ceased in the other eight. Most of the secondaries are hotter than any previously known CV donors, with temperatures 4700 < Teff/K < 8000. Remarkably, all secondaries with $T_{\rm eff} \gtrsim 7000\, \rm K$ appear to be detached, while all cooler secondaries are still mass-transferring. This transition likely marks the temperature where magnetic braking becomes inefficient due to loss of the donor’s convective envelope. Most of the proto-WD secondaries have masses near $0.15\, \rm M_{\odot }$; their companions have masses near $0.8\, \rm M_{\odot }$. We infer a space density of $\sim 60\, \rm kpc^{-3}$, roughly 80 times lower than that of normal CVs and three times lower than that of ELM WDs. The implied Galactic birth rate, $\mathcal {R}\sim 60\, \rm Myr^{-1}$, is half that of AM CVn binaries. Most systems are well-described by mesa models for CVs in which mass transfer begins only as the donor leaves the main sequence. All are predicted to reach minimum periods 5 ≲ Porb min−1 ≲ 30 within a Hubble time, where they will become AM CVn binaries or merge. This sample triples the known evolved CV population and offers broad opportunities for improving understanding of the compact binary population.
A Japanese patient with anti-PM/Scl and centromere antibody-positive scleroderma-amyopathic dermatomyositis overlap syndrome who developed renal crisis
Authors: Nishida Tomoya , Nakano Kazuhisa , Satoh Minoru , Fukuyo Shunsuke , Akashi Koichi , Tanaka Yoshiya
Published: September 2021

Anti-PM/Scl antibodies are associated with the overlap syndrome of systemic sclerosis and dermatomyositis/polymyositis (SSc-DM/PM), and are found in 50% of SSc-DM/PM cases in Europe and the USA, whereas they are rare in Japan. We report a case of an 80-year-old Japanese female with SSc-amyopathic dermatomyositis overlap syndrome, who developed scleroderma renal crisis, a complication of SSc. She had positive antinuclear antibodies in a discrete-speckled and nucleolar pattern and anti-centromere antibodies and anti-PM/Scl antibodies were confirmed by enzyme-linked immunosorbent assay and immunoprecipitation, respectively. The incidence rate of SRC in SSc patients varies significantly depending on the specificity of autoantibodies, with the highest incidence of ∼50% in anti-RNA polymerase III antibody positive patients, followed by ∼10% in anti-PM/Scl and lower incidence of 0.45% in anti-centromere antibody-positive cases. Anti-PM/Scl antibodies are uncommon in Japanese patients presumably due to its strong association with certain human leucocyte antigen haplotype that is rare in Japanese. Clinical significance of anti-PM/Scl antibodies in Japanese patients will need to be clarified with accumulation of cases in future studies.