bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implications of resampling data to address the class imbalance problem (IRCIP): an evaluation of impact on performance between classification algorithms in medical data
Authors: Welvaars Koen , Oosterhoff Jacobien H F , van den Bekerom Michel P J , Doornberg Job N , van Haarst Ernst P ,   OLVG Urology Consortium, and the Machine Learning Consortium, van der Zee J A , van Andel G A , Lagerveld B W , Hovius M C , Kauer P C , Boevé L M S , van der Kuit A , Mallee W , Poolman R 
Published: June 2023

Abstract

Objective
When correcting for the “class imbalance” problem in medical data, the effects of resampling applied on classifier algorithms remain unclear. We examined the effect on performance over several combinations of classifiers and resampling ratios.

Materials and Methods
Multiple classification algorithms were trained on 7 resampled datasets: no correction, random undersampling, 4 ratios of Synthetic Minority Oversampling Technique (SMOTE), and random oversampling with the Adaptive Synthetic algorithm (ADASYN). Performance was evaluated in Area Under the Curve (AUC), precision, recall, Brier score, and calibration metrics. A case study on prediction modeling for 30-day unplanned readmissions in previously admitted Urology patients was presented.

Results
For most algorithms, using resampled data showed a significant increase in AUC and precision, ranging from 0.74 (CI: 0.69–0.79) to 0.93 (CI: 0.92–0.94), and 0.35 (CI: 0.12–0.58) to 0.86 (CI: 0.81–0.92) respectively. All classification algorithms showed significant increases in recall, and significant decreases in Brier score with distorted calibration overestimating positives.

Discussion
Imbalance correction resulted in an overall improved performance, yet poorly calibrated models. There can still be clinical utility due to a strong discriminating performance, specifically when predicting only low and high risk cases is clinically more relevant.

Conclusion
Resampling data resulted in increased performances in classification algorithms, yet produced an overestimation of positive predictions. Based on the findings from our case study, a thoughtful predefinition of the clinical prediction task may guide the use of resampling techniques in future studies aiming to improve clinical decision support tools.
The 2023 Impact of Inflammatory Bowel Disease in Canada: Executive Summary
Authors: Windsor Joseph W , Kuenzig M Ellen , Murthy Sanjay K , Bitton Alain , Bernstein Charles N , Jones Jennifer L , Lee Kate , Targownik Laura E , Peña-Sánchez Juan-Nicolás , Rohatinsky Noelle , Ghandeharian Sara , Im James H B , Davis Tal , Weinstein Jake , Goddard Quinn , Gorospe Julia , Benchimol Eric I , Kaplan Gilaad G 
Published: June 2023

Abstract
The burden of inflammatory bowel disease (IBD) (i.e., associated direct and indirect costs, prevalence of disease, personal impact to the individual and to caregivers) continues to increase in Canada. The prevalence of IBD has increased since Crohn’s and Colitis Canada’s 2018 Impact of IBD report from an estimated 270,000 Canadians living with IBD in 2018 to an estimated 322,600 Canadians living with IBD today in 2023. Consequently, associated costs of IBD have also dramatically increased from an estimated $2.57 billion in 2018 to an estimated $5.38 billion in 2023; this increase is due to multiple factors including increased prevalence of disease, inflation, and additional identified factors (e.g., presenteeism, costs of childcare). Beyond the economic impact of IBD, these diseases have a significant impact on people living with the disease and their caregivers, including different presentations of disease, different commonly associated extra-intestinal manifestations or comorbid conditions, and different barriers to accessing care. In this supplementary issue, we review: Evolving trends in the epidemiology of IBD; updated estimates of indirect and direct costs (including out-of-pocket costs) associated with IBD; information specific to IBD in children, adolescents, and seniors; issues related to IBD pertaining to sex and gender; information specific to risks associated with COVID-19 and cancer related to IBD; an overview of current treatments for IBD; and evolving care models, including access to care.
Prolonging genetic circuit stability through adaptive evolution of overlapping genes
Authors: Chlebek Jennifer L , Leonard Sean P , Kang-Yun Christina , Yung Mimi C , Ricci Dante P , Jiao Yongqin , Park Dan M 
Published: June 2023

Abstract
The development of synthetic biological circuits that maintain functionality over application-relevant time scales remains a significant challenge. Here, we employed synthetic overlapping sequences in which one gene is encoded or ‘entangled’ entirely within an alternative reading frame of another gene. In this design, the toxin-encoding relE was entangled within ilvA, which encodes threonine deaminase, an enzyme essential for isoleucine biosynthesis. A functional entanglement construct was obtained upon modification of the ribosome-binding site of the internal relE gene. Using this optimized design, we found that the selection pressure to maintain functional IlvA stabilized the production of burdensome RelE for &gt;130 generations, which compares favorably with the most stable kill-switch circuits developed to date. This stabilizing effect was achieved through a complete alteration of the allowable landscape of mutations such that mutations inactivating the entangled genes were disfavored. Instead, the majority of lineages accumulated mutations within the regulatory region of ilvA. By reducing baseline relE expression, these more ‘benign’ mutations lowered circuit burden, which suppressed the accumulation of relE-inactivating mutations, thereby prolonging kill-switch function. Overall, this work demonstrates the utility of sequence entanglement paired with an adaptive laboratory evolution campaign to increase the evolutionary stability of burdensome synthetic circuits.
Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)
Authors: Okeke Damasus C , Lidman Jens , Matečko-Burmann Irena , Burmann Björn M 
Published: June 2023

Abstract
In order to cope with the risk of stress-induced mutagenesis, cells in all kingdoms of life employ Y-family DNA polymerases to resolve resulting DNA lesions and thus maintaining the integrity of the genome. In Escherichia coli, the DNA polymerase IV, or DinB, plays this crucial role in coping with these type of mutations via the so-called translesion DNA synthesis. Despite the availability of several high-resolution crystal structures, important aspects of the functional repertoire of DinB remain elusive. In this study, we use advanced solution NMR spectroscopy methods in combination with biophysical characterization to elucidate the crucial role of the Thumb domain within DinB’s functional cycle. We find that the inherent dynamics of this domain guide the recognition of double-stranded (ds) DNA buried within the interior of the DinB domain arrangement and trigger allosteric signals through the DinB protein. Subsequently, we characterized the RNA polymerase interaction with DinB, revealing an extended outside surface of DinB and thus not mutually excluding the DNA interaction. Altogether the obtained results lead to a refined model of the functional repertoire of DinB within the translesion DNA synthesis pathway.
You are fired! Exclusion words induce corticospinal modulations associated with vicarious pain
Authors: Vitale Francesca , Urrutia Mabel , Avenanti Alessio , de Vega Manuel 
Published: June 2023

Abstract
Self- and vicarious experience of physical pain induces inhibition of the motor cortex (M1). Experience of social rejections recruits the same neural network as physical pain; however, whether social pain modulates M1 corticospinal excitability remains unclear. This study examines for the first time whether social exclusion words, rather than simulated social exclusion tasks, modulate embodied sensorimotor networks during the vicarious experience of others’ pain. Participants observed visual sequences of painful and functional events ending with a superimposed word with social exclusion, social inclusion or non-social meaning. Motor-evoked potentials (MEPs) to single-pulse transcranial magnetic stimulation of the left M1 were recorded at 400 or 550 ms from word onset. MEPs tended to inhibit during the observation of pain, relative to functional events. Moreover, MEPs recorded at 400 ms from word onset, during pain movies, decreased following the presentation of exclusion, relative to inclusion/neutral words. The magnitude of these two modulations marginally correlated with participants’ interindividual differences in personal distress and self-esteem. These findings provide evidence of vicarious responses to others’ pain in the M1 corticospinal system and enhancement of such vicarious response in the earlier phases of semantic processing of exclusion words—supporting activation of social pain–embodied representations.
The Sights and Sounds of State Violence: Encounters with the Archive of David Oluwale
Authors: Perry Kennetta Hammond 
Published: June 2023

Abstract
This article dwells in the archive documenting the existence of David Oluwale, a Nigerian-born British citizen whose life is captured historically by way of his encounters with the state. Working within and against the dynamics of violation, racialization, and dispossession structuring his archival presence, this article looks to the visual and sonic registers of an archive of Black dispossession to excavate histories of anti-Black state violence in Britain during the second half of the twentieth century. Likewise, it considers the extent to which an archive steeped in Black dispossession might offer possibilities for imagining Black emotive lives and constructing histories of Black sentience and affect even as they are produced in the context of racialized violence and duress.
Clinical utility of inflammatory and genetic biomarkers for cardiovascular disease prevention, categorization, and treatment
Authors: Mewborn Emily K. , Wright David B. , Wicks Mona N. 
Published: June 2023

ABSTRACT
The complex interplay of increased atherogenic lipoproteins, inflammation, and immune activation hallmarks the pathogenesis of atherosclerotic cardiovascular disease (ASCVD). Atherosclerotic cardiovascular disease remains a leading cause of death, yet risk estimator tools lack comprehensiveness for genetic/inflammatory biomarkers associated with ASCVD. Unexplained ASCVD risk necessitates a better understanding of primary, secondary, and tertiary prevention variables. This article discusses the clinical utility of genetic and inflammatory biomarkers for ASCVD risk prediction, management, treatment, and recategorization into primary, secondary, and tertiary prevention. Furthermore, nurse practitioners (NPs) should use a ternary prevention classification system instead of the current binary system to mitigate risk in the large group of patients with subclinical ASCVD. High-sensitivity C-reactive protein (hs-CRP)—linearly associated with ASCVD—and lipoprotein-associated phospholipase-A2 (Lp-PLA2) and myeloperoxidase (MPO), both associated with plaque vulnerability/rupture, are inflammatory biomarkers. Elevated hs-CRP, MPO, and Lp-PLA2 treatment requires addressing root causes of elevation (e.g., obesity, insulin resistance, tobacco use, gingival disease, and chronic autoimmune/infectious conditions). In addition, haptoglobin (Hp) phenotype determines the antioxidant potential of Hp. Haptoglobin phenotype, a root cause of ASCVD, is a one-time test. Individuals with Hp 2-2 should adopt a gluten-free diet to reduce endothelial and intestinal inflammation. Nurse practitioners should use stricter glycemic goals (hemoglobin A1c ≤6.5%) and add daily vitamin E if this group has type 2 diabetes. Genetic/inflammatory biomarkers should be used to better predict ASCVD risk and tailor primary, secondary, and tertiary prevention treatment. Clinical use of these biomarkers reaches beyond the standard of care to reduce residual ASCVD risk.
A case of endocervical adenocarcinoma of the gastric type that was repeatedly misdiagnosed: A case report and literature review
Authors: Zhang Shurong , Jin Guoyu , Ding Feier , Zhang Junlei , Li Qiuju , Wang Guoyun , Li Changzhong , Yang Chunrun 
Published: June 2023

Rationale:
Gastric-type endocervical adenocarcinoma (GAS) is non-human papillomavirus-associated cervical cancer and the location of the lesions is in the cervical canal mostly.

Patient concerns:
Vaginal discharge is mistakenly thought to be caused by uterine fibroids. Misdiagnosis leads to disease progression.

Diagnoses:
Magnetic resonance imaging is an auxiliary tool and pathology is the gold standard for the diagnosis.

Interventions:
Surgery and supplementary radiotherapy and chemotherapy ± targeted therapy are the main treatment methods.

Outcomes:
GAS with high malignant degree poor prognosis and insidious development, tends to develop toward the cervical canal and is lack of specific tumor markers, so it is easy to misdiagnosis and missed diagnosis.

Lessons:
This case highlights the importance of improving the understanding of GAS. And when patients perform vaginal discharge, cervical canal hypertrophy, and cervical cancer screening negative, clinicians ought to be highly alert to GAS.
A case of collagenous gastritis and literature review: A case report
Authors: Wu Channi , Wang Lin , Zhang Lan , Ni Yangdan , Wang Zhiyong , Qu Yichen 
Published: June 2023

Rational:
Collagenous gastritis (CG) is rarely encountered in clinical practice. Here, we reported a case of CG with iron-deficiency anemia as the main symptom.

Patient concerns:
The patient was a 26-year-old woman who sought medical advice with a chief complaint of recurrent upper abdominal distention and anemia since the last 3 years.

Diagnoses:
Gastroscopy at admission showed diffuse nodular mucosa. The pathology showed the formation of a belt hyperplasia of collagen in the superficial mucosa along with the infiltration of inflammatory cells. The subepithelial collagen band was 17.68 to 35.73-μm thick and tested positive for Masson staining, thereby confirming the diagnosis of CG.

Interventions:
A polysaccharide iron complex capsule was given in a dosage of 0.3 t.i.d., p.o. in combination with an omeprazole capsule (20 mg q.d. p.o).

Outcomes:
The symptoms (upper abdominal distention and anemia) were ameliorated after 8-week treatment. Blood routine showed that the hemoglobin level rose to 91 g/L.

Lessons:
It is difficult to diagnose CG. Hence, a comprehensive examination based on clinical manifestations, endoscopic findings, and pathological features is required.
Plateau Pressure and Driving Pressure in Volume- and Pressure-Controlled Ventilation: Comparison of Frictional and Viscoelastic Resistive Components in Pediatric Acute Respiratory Distress Syndrome
Authors: Cruces Pablo , Moreno Diego , Reveco Sonia , Ramirez Yenny , Díaz Franco 
Published: June 2023

OBJECTIVES:To examine frictional, viscoelastic, and elastic resistive components, as well threshold pressures, during volume-controlled ventilation (VCV) and pressure-controlled ventilation (PCV) in pediatric patients with acute respiratory distress syndrome (ARDS).DESIGN:Prospective cohort study.SETTING:Seven-bed PICU, Hospital El Carmen de Maipú, Chile.PATIENTS:Eighteen mechanically ventilated patients less than or equal to 15 years old undergoing neuromuscular blockade as part of management for ARDS.INTERVENTIONS:None.MEASUREMENTS AND MAIN RESULTS:All patients were in VCV mode during measurement of pulmonary mechanics, including: the first pressure drop (P1) upon reaching zero flow during the inspiratory hold, peak inspiratory pressure (PIP), plateau pressure (PPLAT), and total positive end-expiratory pressure (tPEEP). We calculated the components of the working pressure, as defined by the following: frictional resistive = PIP–P1; viscoelastic resistive = P1–PPLAT; purely elastic = driving pressure (ΔP) = PPLAT–tPEEP; and threshold = intrinsic PEEP. The procedures and calculations were repeated on PCV, keeping the same tidal volume and inspiratory time. Measurements in VCV were considered the gold standard. We performed Spearman correlation and Bland-Altman analysis. The median (interquartile range [IQR]) for patient age was 5 months (2–17 mo). Tidal volume was 5.7 mL/kg (5.3–6.1 mL/kg), PIP cm H2O 26 (23–27 cm H2O), P1 23 cm H2O (21–26 cm H2O), PPLAT19 cm H2O (17–22 cm H2O), tPEEP 9 cm H2O (8–9 cm H2O), and ΔP 11 cm H2O (9–13 cm H2O) in VCV mode at baseline. There was a robust correlation (rho > 0.8) and agreement between frictional resistive, elastic, and threshold components of working pressure in both modes but not for the viscoelastic resistive component. The purely frictional resistive component was negligible. Median peak inspiratory flow with decelerating-flow was 21 (IQR, 15–26) and squared-shaped flow was 7 L/min (IQR, 6–10 L/min) (p< 0.001).CONCLUSIONS:PPLAT, ΔP, and tPEEP can guide clinical decisions independent of the ventilatory mode. The modest purely frictional resistive component emphasizes the relevance of maintaining the same safety limits, regardless of the selected ventilatory mode. Therefore, peak inspiratory flow should be studied as a mechanism of ventilator-induced lung injury in pediatric ARDS.
A Lens on Caregiver Stress in Cancer: Longitudinal Investigation of Cancer-Related Stress and Telomere Length Among Family Caregivers of Adult Patients With Cancer
Authors: Kim Youngmee , Lin Jue , Epel Elissa S. , Carver Charles S. 
Published: June 2023

ABSTRACT

Objective
Family members are typically the primary caregivers of patients with chronic illnesses. Family caregivers of adult relatives with cancer are a fast-growing population, yet the physical consequences of their stress due to the cancer in the family have been poorly understood. This study examined the bidirectional relations of the perceived stress of family caregivers of individuals recently diagnosed with cancer and leukocyte cellular aging indexed by telomere length for 2 years.

Methods
Family caregivers (N = 168; mean age = 51 years, 70% female, 46% Hispanic, 36% spouse to the patient) of patients with colorectal cancer provided psychological data and peripheral blood samples approximately 4 (T1), 12 (T2), and 21 months (T3) after diagnosis. Time-lagged cross-panel modeling was used to test the associations of perceived cancer-related stress and telomere length, controlling for age, sex, and body mass index.

Results
Cancer-related stress was highest at T1 and decreased by 1 year. Greater cancer-related stress predicted longer telomere length at subsequent assessments for 2 years (β ≥ 0.911, p ≤ .019). However, telomere length did not change significantly for 2 years overall and did not prospectively predict cancer-related stress over this period.

Conclusions
Findings suggest the need to better understand how the perceived stress of colorectal cancer caregivers, which tends to be intense for a relatively short period compared with dementia caregiving, may impact immune cell distributions and telomere length. These findings emphasize the need for further knowledge about psychobiological mechanisms of how cancer caregiving may impact cellular aging.
Diversity in the Plastic Surgery Match: The Effect of Program Chair, Program Director, and Faculties’ Race and Sex on Matched Applicants
Authors: Steiner Quinn , Edalatpour Armin , Seitz Allison J. , Bentz Michael L. , Afifi Ahmed M. 
Published: June 2023

Introduction:
Prior studies have identified the lack of diversity within the field of plastic surgery (PS) and associated residency matches. In this study, the authors aimed to examine the effect of PS program chairs (PCs), program directors (PD), and faculty members’ race and sex on PS applicants and matriculants within the same program.

Methods:
Deidentified applicant data from 2017 to 2021 submitted to the University of Wisconsin-Madison’s integrated PS program were analyzed. Applicants’ self-reported sex and race were collected. Integrated PS program websites were assessed to determine whether applicants matched the program. Race and sex of PCs, PDs, and faculty members were collected from each program’s website.

Results:
Overall, 79 integrated PS programs’ websites and 1470 applicants were reviewed. The majority of PCs, PDs, and faculty members were male (87.3%, 81.0%, and 69.6%, respectively) and white (74.7%, 70.9%, and 68.8%, respectively). Most applicants were male (54.0%) and white (60.8%). For a given program, white PCs and PDs have 5 and 6 times the odds of matching an applicant of the same race (P<0.001 for both). Having male PCs and PDs did not significantly increase the odds of matching an applicant of the same sex (P=0.198 and 0.905, respectively).

Conclusion:
Although the field of PS has made great strides to close the sex gap within the residency match process, this study highlights ongoing racial disparities among nonwhite applicants.
ECHOCARDIOGRAPHIC MANIFESTATIONS OF COVID 19 ILLNESS AND DEVELOPMENT OF PERSISTENT RV DYSFUNCTION AND PULMANARY HYPERTENSION AS A LONG TERM SEQUELAE OF COVID 19 ILLNESS: A STUDY AMONG PATIENTS OF SOUTH EAST ASIAN REGION
Authors: Kumar Lalit , Mahla Himanshu , Chaturvedi Neeraj , Sidhu Navdeep Singh , Keshav Manisha , Sharma Shashi Mohan , Bagarhatta Rajeev , Agrawal V.V. , Pathak Vijay , Meena Chandrabhan , Maheshwari Deepak , Meena Pradeep , Pachar Balbir Singh , Sharma Sohan Kumar , Gautam Dinesh , Chaudhary Sarita , Shekhawat Dhananjay 
Published: June 2023

AbstractObjectivesTo study the Echocardiographic manifestations of covid 19 illness among patients admitted in our facility, Correlate MAPSE, TAPSE, PASP, CRP levels and CTSI among covid 19 patients with their 28 day outcome as survivors and non survivors and to look for evidence of residual RV dysfunction and Pulmonary hypertension using TTE after 1 year of follow-up.Study designProspective observational study at various medical wards and ICUs in SMS medical college and associated hospitals.Methods258 patients with a Covid-19 RT-PCR positive report from a throat or a nasal swab within 72 hours of admission were included in the study. Each patient underwent a complete clinical assessment and routine blood investigations including CRP levels were done. A complete transthoracic echocardiogram was done within 48 hours of admission. Patients also underwent a HRCT chest and CTSI scores were estimated. All patients were followed for a period of 28 days. The MAPSE, TAPSE, PASP, CTSI and CRP levels were then correlated with the outcome of the patient. The survivors again underwent a TTE at 1 year after their recovery from covid-19 illness to look for residual RV dysfunction by TAPSE and the development of pulmonary hypertension as measured by PASP using Bernoulli’s equation.ResultsAmongst patient of covid 19 illness the MAPSE, TAPSE, PASP, CTSI and CRP levels all correlated well with outcome of patients. While most covid-19 survivors recovered from their illness yet some patients showed evidence of persistent RV dysfunction and pulmonary hypertension even after 1 year of follow up.