bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bias and representativeness in digitized newspaper collections: Introducing the environmental scan
Authors: Beelen Kaspar , Lawrence Jon , Wilson Daniel C S , Beavan David 
Published: July 2022

AbstractThis article introduces the ‘Environmental Scan’ as answer to the question of hidden biases in digital heritage collections. Its substantive focus is digitized nineteenth-century British provincial newspapers, and in particular the JISC corpus, a popular, publicly-funded resource for scholars. While multiple papers have meticulously investigated the genesis of such newspaper collections, in the process highlighting the often unacknowledged politics of collection, preservation and dissemination via microfilm and now digitization, our aim is to explore questions of representativeness and bias in new ways by enriching computational analysis of digital corpora with the historical insights that can be derived from a contemporaneous reference source: namely, the Victorian newspaper press directories.
Use of MEDEVAC Resources in Austere Settings: Paget–Schroetter in the Deployed Environment
Authors: O’Donnell Mary T , Huang Michelle L , Gerling Kimberely A , Rasmussen Todd E , White Joseph M , Koelling Erin E 
Published: July 2022

ABSTRACT
Medical evacuation (MEDEVAC) from a combat zone requires complex decision-making and coordination of assets. A MEDEVAC helicopter team transports not only battle-injured patients but also patients with urgent non-battle-related medical diagnoses from extremely remote locations and are at the mercy of terrain, weather, and enemy contact. The military represents a young population particularly susceptible to venous thoracic outlet syndrome (vTOS) given the rigorous physical activity demands. Current literature supports immediate anticoagulation and surgical decompression within 14 days of diagnosis of vTOS to prevent long-term morbidity. Presented is a case of service member with vTOS presenting at an extremely remote military clinic who underwent a prompt evacuation ∼7,000 miles utilizing rotary-wing transport, followed by three to four more fixed-wing flights to a military treatment facility in the United States. Immediate recognition and ultrasound of this patient to confirm vTOS upon presentation and effective communication to non-medical military commanders and the receiving medical personnel at each Echelon was necessary to ensure an expedited evacuation. The surgeons treating this patient recommend prompt evacuation of deployed service members with suspected vTOS, venogram at the Role 3 if ultrasound is inconclusive, anticoagulation, and return to a Role 4 CONUS facility for definitive surgical management within 14 days. This case is an example of the efficiency of the military MEDEVAC system on a global scale, ensuring optimum medical care for all service members deployed.
Madurella mycetomatis grains within a eumycetoma lesion are clonal
Authors: Nyuykonge Bertrand , Siddig Emmanuel Edwar , Konings Mickey , Bakhiet Sahar , Verbon Annelies , Klaassen Corné H W , Fahal Ahmed Hassan , van de Sande Wendy W J 
Published: July 2022

Abstract

Eumycetoma is a neglected tropical infection of the subcutaneous tissue, characterized by tumor-like lesions and most commonly caused by the fungus Madurella mycetomatis. In the tissue, M. mycetomatis organizes itself in grains, and within a single lesion, thousands of grains can be present. The current hypothesis is that all these grains originate from a single causative agent, however, this hypothesis was never proven. Here, we used our recently developed MmySTR assay, a highly discriminative typing method, to determine the genotypes of multiple grains within a single lesion. Multiple grains from surgical lesions obtained from 11 patients were isolated and genotyped using the MmySTR panel. Within a single lesion, all tested grains shared the same genotype. Only in one single grain from one patient, a difference of one repeat unit in one MmySTR marker was noted relative to the other grains from that patient. We conclude that within these lesions the grains originate from a single clone and that the inherent unstable nature of the microsatellite markers may lead to small genotypic differences.

Lay Abstract
In lesions of the implantation mycosis mycetoma many Madurella mycetomatis grains are noted. It was unknown if grains arose after implantation of a single isolate or a mixture of genetically diverse isolates. By typing the mycetoma grains we showed that all grains within a single lesion were clonal and originated from a single isolate.
Investigating the X-ray polarization of lamp-post coronae in BHXRBs
Authors: Zhang Wenda , Dovčiak Michal , Bursa Michal , Karas Vladimír , Matt Giorgio , Ursini Francesco 
Published: July 2022

ABSTRACT
High-sensitivity X-ray polarimetric observations of black hole X-ray binaries, which will soon become available with the launches of space-borne X-ray observatories with sensitive X-ray polarimeters, will be able to put independent constraints on the black hole as well as the accretion flow, and possibly break degeneracies that cannot be resolved by spectral/timing observations alone. In this work, we perform a series of general relativistic Monte Carlo radiative transfer simulations to study the expected polarization properties of X-ray radiation emerging from lamp-post coronae in black hole X-ray binaries. We find that the polarization degree of the coronal emission of black hole X-ray binaries is sensitive to the spin of the black hole, the height of the corona, and the dynamics of the corona.
High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing
Authors: Steiert Tim Alexander , Fuß Janina , Juzenas Simonas , Wittig Michael , Hoeppner Marc Patrick , Vollstedt Melanie , Varkalaite Greta , ElAbd Hesham , Brockmann Christian , Görg Siegfried , Gassner Christoph , Forster Michael , Franke Andre 
Published: July 2022

Abstract
Hybridisation-based targeted enrichment is a widely used and well-established technique in high-throughput second-generation short-read sequencing. Despite the high potential to genetically resolve highly repetitive and variable genomic sequences by, for example PacBio third-generation sequencing, targeted enrichment for long fragments has not yet established the same high-throughput due to currently existing complex workflows and technological dependencies. We here describe a scalable targeted enrichment protocol for fragment sizes of &gt;7 kb. For demonstration purposes we developed a custom blood group panel of challenging loci. Test results achieved &gt; 65% on-target rate, good coverage (142.7×) and sufficient coverage evenness for both non-paralogous and paralogous targets, and sufficient non-duplicate read counts (83.5%) per sample for a highly multiplexed enrichment pool of 16 samples. We genotyped the blood groups of nine patients employing highly accurate phased assemblies at an allelic resolution that match reference blood group allele calls determined by SNP array and NGS genotyping. Seven Genome-in-a-Bottle reference samples achieved high recall (96%) and precision (99%) rates. Mendelian error rates were 0.04% and 0.13% for the included Ashkenazim and Han Chinese trios, respectively. In summary, we provide a protocol and first example for accurate targeted long-read sequencing that can be used in a high-throughput fashion.
Impact of the 21-Gene Recurrence Score Assay on Treatment Decisions and Cost in Patients with Node-Positive Breast Cancer: A Multicenter Study in Quebec
Authors: Hassan Saima , Younan Rami , Patocskai Erica , Provencher Louise , Poirier Brigitte , Sideris Luca , Dubé Pierre , Mihalcioiu Catalin , Chabot-Blanchet Malorie , Guertin Marie-Claude , Boileau Jean-François , Robidoux André 
Published: July 2022

Abstract

Background
The 21-gene Breast Recurrence Score (RS) assay, “the assay”, has led to a paradigm shift for patients with hormone receptor-positive, node-negative early breast cancer and is emerging as an important tool to assist physician-patient decisions in foregoing chemotherapy in node-positive patients. We wanted to better understand the impact of the RS assay in node-positive patients upon physician treatment decisions and treatment cost in Quebec, Canada.

Patients and Methods
We conducted a multicenter, prospective observational trial for Estrogen/Progesterone Receptor (ER/PR)- positive, Human Epidermal Growth Factor Receptor 2 (HER2)-negative breast cancer patients with 1-3 positive lymph nodes. Physicians completed a questionnaire indicating treatment choice prior to and post availability of RS results. The primary endpoint was change in the physician’s recommendation for chemotherapy prior to and post assay results. Secondary endpoints included change in physician’s expressed level of confidence, and changes in estimated cost of recommended treatments prior to and post assay results.

Results
For the entire cohort, physician recommendation for chemotherapy was reduced by an absolute 67.1% by knowledge of the RS assay result (P &lt; .0001). Physician recommendation of chemotherapy was decreased by 75.9% for patients RS result &lt;14 (P &lt; .0001); and 67.5% for patients with RS result 14-25 (P &lt; .0001). Changes in treatment recommendations were associated with an overall reduction in cost by 73.7% per patient, and after incorporating the cost of the RS test, a cost benefit of $823 CAN at 6-month follow-up.

Conclusion
Altogether, we established that the assay led to a two-third reduction in the use of chemotherapy, and was a cost-effective approach for hormone receptor-positive, node-positive breast cancer.
Characteristics and outcomes of a Hispanic lupus nephritis cohort from Mexico
Authors: Zavala-Miranda María Fernanda , Perez-Arias Abril Alicia , Márquez-Macedo Sofía E , Comunidad-Bonilla Roque A , Romero-Diaz Juanita , Morales-Buenrostro Luis E , Mejía-Vilet Juan M 
Published: July 2022

AbstractObjectivesTo characterize the clinical presentation and outcomes of LN in a Hispanic cohort from Mexico.MethodsWe studied 440 subjects with systemic lupus erythematosus and biopsy-proven LN followed for &gt;36 months. We obtained demographic, clinical, laboratory, histopathological and treatment variables. All outcomes were analysed by survival analysis and included response to therapy, renal relapses, progression of kidney disease (decline in eGFR ≥ 30%, doubling of serum creatinine, end-stage kidney disease) and patient survival.ResultsThe median age of the study cohort was 29 years (IQR 23–37) and 96% were female. The median eGFR at inclusion was 81 mL/min/1.73m2 (IQR 48–118) and 24 h-uPCR was 3.4 g/g (IQR 1.9–5.6). Mixed class LN (III/IV+V) was the most frequently observed (69%). Over a median follow-up of 79 months, complete response rates were 22.3%, 40.5% and 51.6%, at 6, 12 and 24 months, respectively. Renal relapse rates were 32.3% and 50.6% at 3 and 5 years. By 3 and 5 years, 20.7% and 31.4% had decline in eGFR ≥30%, 14.4% and 22.5% doubled their serum creatinine, and 9.1% and 17.7% progressed to ESKD. The factors associated with loss of kidney function were age, eGFR at presentation, the histologic chronicity index in the kidney biopsy, and the type of response to therapy. Patient survival was 98.2% and 97.1% at 3 and 5 years.ConclusionAlthough the response to treatment and patient survival in this Latin American cohort is comparable to that observed in other regions, there is still a high rate of renal relapses and progression to decline in kidney function.
Telemedicine compared to standard face-to-face care for continuous positive airway pressure treatment: real-world Australian experience
Authors: Kosky Christopher , Madeira Neill , Boulton Kate , Hunter Marie-Therese , Ling Ivan , Reynor Ayesha , Sturdy Gavin , Walsh Jennifer , Dhaliwal Satvinder , Singh Bhajan , Eastwood Peter R , McArdle Nigel 
Published: July 2022

Abstract

Study Objectives
We tested a telemedicine model of care to initiate continuous positive airway pressure (CPAP) for patients with obstructive sleep apnea (OSA) living in remote Western Australia.

Methods
A prospective study comparing telemedicine for CPAP initiation in a remote population versus standard face-to-face CPAP initiation in a metropolitan population. The primary outcome was average nightly CPAP use in the final week of a CPAP trial.

Results
A total of 186 participants were allocated to either telemedicine (n = 56) or standard care (n = 130). The average distance from the study center for the telemedicine group was 979 km (±792 km) compared to 19 km (±14 km) for the standard care group. The CPAP trial duration in the standard care group was less than the telemedicine group (37.6 vs 69.9 days, p &lt; .001). CPAP adherence in the telemedicine group was not inferior to standard care (Standard 4.7 ± 0.2 h, Telemedicine 4.7 ± 0.3 h, p = 0.86). No differences were found between groups in residual apnea-hypopnea index, symptom response, sleep specific quality of life at the end of the trial, and continued CPAP use (3–6 months). Participant satisfaction was high in both groups. Total health care costs of the telemedicine model were less than the standard model of care. An estimated A$4538 per participant in travel costs was saved within the telemedicine group by reducing the need to travel to the sleep center for in-person management.

Conclusions
In remote dwelling adults starting CPAP for the treatment of OSA, outcomes using telemedicine were comparable to in-person management in a metropolitan setting,
Management Reasoning: Empirical Determination of Key Features and a Conceptual Model
Authors: Cook David A. , Stephenson Christopher R. , Gruppen Larry D. , Durning Steven J. 
Published: July 2022

Purpose
Management reasoning is a critical yet understudied phenomenon in clinical practice and medical education. The authors sought to empirically identify key features of management reasoning and construct a model describing the management reasoning process.

Method
In November 2020, 4 investigators each reviewed 10 video clips of simulated outpatient physician–patient encounters and used a coding form to document key features and insights related to management reasoning. The team used a constant comparative approach to distill 120 pages of raw observations into an 18-page list of management tasks, processes, and insights. The team then had a series of discussions to iteratively refine these findings into a parsimonious model of management reasoning.

Results
The investigators empirically identified 12 distinct features of management reasoning: contrasting and selection among multiple solutions; prioritization of patient, clinician, and system preferences and constraints; communication and shared decision making; ongoing monitoring and adjustment of the management plan; dynamic interplay among people, systems, and competing priorities; illness-specific knowledge; process knowledge; management scripts; clinician roles as patient teacher and salesperson; clinician–patient relationship; prognostication; and organization of the clinical encounter (sequencing and time management). Management scripts seemed to play a prominent and critical role. The model of management reasoning comprised 4 steps: instantiation of a management script, identifying (multiple) options and beginning to teach the patient, shared decision making, and ongoing monitoring and adjustment. This model also conceives 2 overarching features: that management reasoning is personalized to the patient and that it occurs between individuals rather than exclusively within the clinician’s mind.

Conclusions
Management scripts constitute a key feature of management reasoning, along with teaching patients about viable options, shared decision making, ongoing monitoring and adjustment, and personalization. Management reasoning seems to be constructed and negotiated between individuals rather than exclusively within the clinician.
Improving 10-year atherosclerotic cardiovascular disease estimation management using a Smartphrase for automated risk screening
Authors: Chappell Anna L. 
Published: July 2022

ABSTRACT

Background:
Cardiovascular disease (CVD) is the most common cause of death in the United States, and 90% of cardiovascular events are preventable. The 2020 American College of Cardiology/American Heart Association Guidelines on the Primary Prevention of Cardiovascular Disease recommends 10-year atherosclerotic cardiovascular disease (ASCVD) risk estimates for 40- to 75-year-old adults with CVD risk indications to decrease the likelihood of cardiovascular events.

Local Problem:
At the project site, the 10-year ASCVD risk estimates were rarely completed by providers. The purpose of this project was to increase 10-year ASCVD risk estimation screening and improve pharmacological therapy for 40- to 75-year-old patients with CVD risk indications.

Methods:
To increase 10-year ASCVD risk estimation screening and improve pharmacological therapy, a multifaceted bundle was created for providers.

Interventions:
Three interventions were initiated: an electronic health record Smartphrase was created to produce automatic 10-year risk scores; laminated paper reminders for the Smartphrase were visible on providers' desks; educational in-services were performed to promote risk score adherence.

Results:
The project aims were achieved with an increase from a 14% completion rate for 10-year ASCVD risk estimation during the preintervention phase to a 98% completion rate at the end of the postintervention phase. Appropriate pharmacological therapy improved from a 64% rate during the preintervention phase to a maximum rate of 79% during postintervention.

Conclusion:
The project was effective at increasing risk estimate completion and improving appropriate pharmacological therapy. There was an increase in provider–patient discussions toward primary prevention for cardiovascular events.
99mTc-Sestamibi Thyroid Scintigraphy in Amiodarone-Induced Thyrotoxicosis
Authors: Wang Ray , Better Nathan , Sivaratnam Dinesh , Westcott James , Forehan Simon , Christie Michael , Pattison David A. , Fourlanos Spiros 
Published: July 2022

Abstract

99mTc-sestamibi thyroid scintigraphy (STS) can aid in differentiating between types 1 and 2 amiodarone-induced thyrotoxicosis (AIT). We present a consecutive case series of 4 men (aged 56–75 years) in whom both 99mTc-STS and thyroid histology were consistent with a diagnosis of type 2 AIT, representing the first reported histopathologic correlation for this diagnostic test. Median amiodarone treatment duration was 26 months (range, 10–39 months), and amiodarone was discontinued a median of 3 months preoperatively (range, 2–4 months) in all 4 cases. 99mTc-STS is a promising functional imaging modality, which has the potential to aid clinicians in the diagnostic workup and treatment of AIT.
Effect of an Artificial Intelligence Chest X-Ray Disease Prediction System on the Radiological Education of Medical Students: A Pilot Study
Authors: Dao Lan , Harmouch Sabrina Sofia , Chin Anne , Dao Tien , Thian Zhe , Chartrand-Lefebvre Carl , Cohen Joseph Paul 
Published: July 2022

BACKGROUNDWe aimed to evaluate the feasibility of implementing Chester, a novel web-based chest X-ray (CXR) interpretation artificial intelligence (AI) tool, in the medical education curriculum and explore its effect on the diagnostic performance of undergraduate medical students.METHODSThird-year trainees were randomized in experimental (N=16) and control (N=16) groups and stratified for age, gender, confidence in CXR interpretation, and prior experience. Participants filled a pre-intervention survey, a test exam (Exam1), a final exam (Exam2), and a post-intervention survey. The experimental group was allowed to use Chester during Exam1 while the control group could not. All participants were forbidden from using any resources during Exam2. The diagnostic interpretation of a fellowship-trained chest radiologist was used as the standard of reference. Chester’s performance on Exam1 was 60%. A five-point Likert scale was used to assess students’ perceived confidence before/after the exams as well as Chester’s perceived usefulness.RESULTSUsing a mixed model for repeated measures (MMRM), it was found that Chester did not have a statistically significant impact on the experimental group’s diagnostic performance nor confidence level when compared to the control group. The experimental group rated Chester’s usefulness at 3.7/5, its convenience at 4.25/5, and their likelihood to reuse it at 4.1/5.CONCLUSIONOur experience highlights the interest of medical students in using AI tools as educational resources. While the results of the pilot project are inconclusive for now, they demonstrate proof of concept for a repeat experiment with a larger sample and establish a robust methodology to evaluate AI tools in radiological education. Finally, we believe that additional research should be focused on the applications of AI in medical education so students understand this new technology for themselves and given the growing trend of remote learning.
Integrated single-cell sequencing analysis reveals peripheral immune landscape across the human lifespan
Authors: Tong Renyang , Li Ronghong , Zhao Yichao , Luo Lingjie , Zhong Jianmei , Li Zheng , Wei Lin , Chen Yifan , Shi Jianfeng , Gao Yu , Sun Mingze , Lyu Yuyan , Yuan Ancai , Sun Lingyue , Guo Yuping , Wang Honglin , Chen Haoyan , Chen Lei , Li Bin , Lin Wei , Wang Feng , Wang Li , Pu Jun 
Published: July 2022

SUMMARYSystematic understanding of immune dynamics across the entire human lifespan at single-cell resolution is currently lacking. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor (TCR)/B cell receptor (BCR) sequencing (scTCR/BCR-seq) on over 380,000 peripheral blood mononuclear cells collected from 45 healthy participants aged 0 to over 90 years. We revealed that the functions of T cell subsets were most susceptible to senescence among all PBMCs, featured by increased NF-κB signaling and IFN-γ responses pathways, while reduced telomere maintenance and energy metabolism. We subsequently explored the rewiring of cell-cell interactions among different immune cells across the lifespan and revealed the major alteration of immune checkpoints in T cells within the cellular interaction networks. By combined analysis of scRNA-seq and scTCR-seq, we revealed that 1) GNLY+CD8 Effector T cells exhibited a high clonal expansion with distinct functional signatures in children and the elderly; 2) Naïve CD4+T and naïve CD8+T cells displayed different aging patterns in both transcriptomes and immune repertoires; and 3) CD8+MAIT cells showed a higher cell abundance and clonal diversity in adolescents. Furthermore, we identified a unique cytotoxic B cell subset enriched in children by scRNA-seq and scBCR-seq analysis and experimental validations. In summary, our work provided valuable insights and rich resources for understanding the development and aging of the human immune system across the lifespan.