bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting Depression and Posttraumatic Stress Symptoms Following Burn Injury: A Risk Scoring System
Authors: Stockly Olivia R , Wolfe Audrey E , Goldstein Richard , Roaten Kimberly , Wiechman Shelley , Trinh Nhi-Ha , Goverman Jeremy , Stoddard Frederick J , Zafonte Ross , Ryan Colleen M , Schneider Jeffrey C
Published: November 2021

Depression and posttraumatic stress (DPTS) are common psychiatric comorbidities following burn injury. The purpose of this study was to develop an admission scoring system that assesses the risk of development of depression or posttraumatic symptoms in the burn population. This study is a retrospective review of the prospectively collected Burn Model System National Database. Adult burn survivors enrolled from 2014 to 2018 (n = 486) were included. The primary outcome was the presence of DPTS symptoms at 6, 12, or 24 months postinjury. Logistic regression analysis was used to identify demographic and clinical predictors of DPTS symptoms. A risk scoring system was then created based on assigning point values to relevant predictor factors. The study population had a mean age of 46.5 ± 15.8 years, mean burn size of 18.3 ± 19.7%, and was 68.3% male. Prior to injury, 71.3% of the population was working, 47.9% were married, and 50.8% had completed more than a high school education. An 8-point risk scoring system was developed using the following predictors of DPTS symptom development: gender, psychiatric treatment in the past year, graft size, head/neck graft, etiology of injury, and education level. This study is the first to develop a DPTS symptom risk scoring system for burn injury. This scoring system will aid in identifying burn survivors at high risk of long-term psychiatric symptoms that may be used to improve screening, monitoring, timely diagnosis, and interventions.
The Complex History of Genome Duplication and Hybridization in North American Gray Treefrogs
Authors: Booker William W , Gerhardt H Carl , Lemmon Alan R , Ptacek Margaret B , Hassinger Alyssa T B , Schul Johannes , Lemmon Emily Moriarty
Published: November 2021

Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. Although systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid H. versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with approximate Bayesian computation, to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole-genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.
Impact of concomitant chronic kidney disease on hospitalised infections and remission in patients with rheumatoid arthritis: results from the IORRA cohort
Authors: Higuchi Tomoaki , Tanaka Eiichi , Inoue Eisuke , Abe Mai , Saka Kumiko , Sugano Eri , Sugitani Naohiro , Higuchi Yoko , Ochiai Moeko , Yamaguchi Rei , Sugimoto Naoki , Ikari Katsunori , Yamanaka Hisashi , Harigai Masayoshi
Published: November 2021

Objectives

To investigate the impact of concomitant chronic kidney disease (CKD) on unfavourable clinical events and remission in Japanese patients with rheumatoid arthritis (RA).

Methods

We included 5103 patients with RA and CKD from the Institute of Rheumatology Rheumatoid Arthritis (IORRA) cohort in 2012. CKD stages were classified into four groups: CKD with normal eGFR ≥60 ml/min/1.73 m2 and proteinuria; mild CKD, eGFR ≥45 to < 60; moderate CKD, eGFR ≥30 to < 45; and severe CKD, eGFR <30. We assessed the association between concomitant CKD and the occurrence of unfavourable clinical events or achieving remission during a 5-year observational period.

Results

Of the 5103 patients with RA, 686 (86.6%) had CKD. Concomitant CKD was associated with hospitalised infections [adjusted hazard ratio (aHR) 1.52, 95% confidence interval (CI) 1.07–2.13, p = .02], especially in the moderate to severe CKD group (aHR 1.93, 95% CI 1.12–3.13, p = .02). Of all subjects, 2407 (47.2%) had active RA at baseline and 401 (16.7%) had CKD. Concomitant CKD was also associated with the failure of achieving remission (aHR 0.82, 95% CI 0.68–0.99, p = .04).

Conclusions

Concomitant CKD was a risk factor for hospitalised infections in Japanese patients with RA and failure of achieving remission in patients with active RA.
Decade-long disease, secondary malignancy, and brainstem injury outcomes in pediatric and young adult medulloblastoma patients treated with proton radiotherapy
Authors: Baliga Sujith , Gallotto Sara , Bajaj Benjamin , Lewy Jacqueline , Weyman Elizabeth , Lawell Miranda P , Yeap Beow Y , Ebb David E , Huang Mary , Caruso Paul , Perry Alisa , Jones Robin M , MacDonald Shannon M , Tarbell Nancy J , Yock Torunn I
Published: November 2021

Background

Survivors of pediatric medulloblastoma experience long-term morbidity associated with the toxic effects of postoperative radiotherapy (RT). Proton RT limits radiation dose to normal tissues thereby reducing side effects of treatment while maintaining high cure rates. However, long-term data on disease outcomes and long-term effects of proton RT remain limited.

Methods

One hundred seventy-eight pediatric medulloblastoma patients treated with proton RT between 2002 and 2016 at the Massachusetts General Hospital comprise the cohort of patients who were treated with surgery, radiation therapy, and chemotherapy. We evaluated event-free survival (EFS), overall survival (OS), and local control using the Kaplan-Meier method. The cumulative incidence of brainstem injury and secondary malignancies was assessed.

Results

Median follow-up was 9.3 years. One hundred fifty-nine patients (89.3%) underwent a gross total resection (GTR). The 10-year OS for the entire cohort, standard-risk (SR), and intermediate/high-risk (IR/HR) patients was 79.3%, 86.9%, and 68.9%, respectively. The 10-year EFS for the entire cohort, SR, and IR/HR cohorts was 73.8%, 79.5%, and 66.2%. The 10-year EFS and OS for patients with GTR/NTR were 75.3% and 81.0% vs 57.7% and 61.0% for subtotal resection (STR). On univariate analysis, IR/HR status was associated with inferior EFS, while both anaplastic histology and IR/HR status were associated with worse OS. The 10-year cumulative incidence of secondary tumors and brainstem injury was 5.6% and 2.1%, respectively.

Conclusions

In this cohort study of pediatric medulloblastoma, proton RT was effective, and disease outcomes were comparable to historically treated photon cohorts. The incidence of secondary malignancies and brainstem injury was low in this cohort with mature follow-up.
Psychometric Evaluation of the Short-Form Vaping Consequences Questionnaire for Use With High School Adolescents Who Use and Do Not Use E-cigarettes
Authors: Morean Meghan E , Davis Danielle R , Bold Krysten W , Kong Grace , Jackson Asti , Lee Juhan , Rajesh Kumar Lavanya , Krishnan-Sarin Suchitra
Published: November 2021

Introduction

Assessing youth vaping expectancies using a psychometrically sound measure can improve understanding of e-cigarette susceptibility and use.

Aims and Methods

We evaluated the psychometric properties of the Short-Form Vaping Consequences Questionnaire (SF-VCQ), an expectancy measure previously validated with adults, within a sample of 1753 high school adolescents who completed an online, school-based survey in Fall 2020 (51.6% female; 15.56 [1.22] years old; 46.6% non-Hispanic white; 26.9% reported lifetime but no past-30-day vaping; 12.6% reported past-30-day vaping). Analyses included confirmatory factor analysis, internal consistency, measurement invariance, between-group differences, and test-criterion relationships.

Results

The four-factor structure was confirmed and was scalar invariant by lifetime and past-month vaping status, sex, and race. All subscales were internally reliable (mean α = 0.94). The subscales were sensitive to differences based on sex, race, vaping susceptibility among never users, and lifetime and past-month vaping status. For example, students who vaped in the past-month held weaker expectancies for negative consequences but stronger expectancies for positive reinforcement, negative reinforcement, and appetite/weight control compared to lifetime vapers. Unadjusted relationships within the subsamples of lifetime and past-month vapers provided evidence of convergent validity. Evidence for concurrent validity was observed for all samples after accounting for covariates. For example, expectancies for positive reinforcement, negative reinforcement, and appetite/weight control remained significantly associated with past-month vaping frequency.

Conclusions

The SF-VCQ evidenced excellent internal reliability, scalar measurement invariance, and construct, convergent, and concurrent validity in samples of never, lifetime, and past-month adolescent e-cigarette users. Findings support using the SF-VCQ for assessing youths’ vaping-related expectancies.

Implications

The current study established the psychometric properties of the SF-VCQ for use among adolescents with and without vaping experience, including measurement invariance that permits direct comparisons of expectancies across these two groups. When considered in concert with previously published research in adults, the SF-VCQ provides researchers with a measure that can be used with both youth and adult samples. Observed relationships between positive expectancies and vaping susceptibility in vaping naïve youth and indices of vaping frequency in youth with vaping experience suggest that challenging positive expectancies may be a valuable addition to prevention and intervention efforts to reduce youth vaping.
Assessing the Accuracy of Director of Clinical Education Roles/Responsibilities Taxonomy and Matrix: A Delphi Study
Authors: Engelhard Chalee , McCallum Christine , Murray Leigh K.
Published: November 2021

Introduction.

There is not a taxonomy that has been fully vetted for traditional positions in physical therapy programs and it is not known what efficiencies could be afforded by employing a taxonomy and matrix for the Director of Clinical Education (DCE) position, specifically. This study provides a pathway to greater understanding of the DCE competing roles and responsibilities both as a traditional faculty member and those that pertain specifically to the DCE through determining the accuracy of the DCE Taxonomy and Matrix. The study addressed the following questions: (1) Within the Taxonomy, do each of the levels' responsibilities and sample tasks accurately match the levels’ definition, as duties performed by a DCE at that level? (2) Within the Matrix, do the characteristics serve as a common descriptor across all taxonomy levels? and (3) Within the Matrix, do each of the characteristics and ranges align with the Taxonomy levels? We hypothesized that the DCE Taxonomy and Matrix would require minor revisions to refine the tools to confirm accurate descriptions of the DCE roles and responsibilities.

Directors of Clinical Education have an integral role with multiple responsibilities to fulfill as a bridge between the clinic and the academy as well as performing the traditional duties of a faculty member. Work completed by McCallum et al provided a foundational understanding of the DCE's work. Engelhard et al expanded on the foundational DCE study using Watts Taxonomy as a basis to develop the DCE Roles and Responsibilities Taxonomy and Matrix.

Subjects.

Through purposive sampling, 86 faculty, including DCEs, ADCEs (Associate Directors of Clinical Education), and Program Directors, participated in the study.

Methods.

This Delphi, mixed methods study used 2 web-based survey rounds to achieve consensus, defined agreement as ≥80% of respondents. Round 1 sought agreement for DCE roles, responsibilities, and sample tasks in the Taxonomy. Matrix agreement was sought for each of the 4 characteristics. Round 2 involved refinement of the Taxonomy to improve clarity.

Results.

The Matrix achieved consensus after Round 1. Consensus was achieved at the conclusion of the Round 2 for the Taxonomy, which resulted in a concise description of the categories of Processor, Coordinator, and Director level roles and responsibilities.

Discussion and Conclusion.

Findings suggest a clear and concise classification of work-related elements that can contribute to success in the DCE position and ultimately the physical therapy program. As the profession goes forward, understanding of the impact of where we spend time in our programs must occur as we balance student matriculation and success with organizational knowledge of key program positions. By establishing the accuracy of the DCE Taxonomy and Matrix, insights to workload implications are gained.
Traits and Attributes of a Successful Physical Therapy Resident: A Delphi Study
Authors: Shepard Rebecca , Haines Lauren , Abraham Karen , Lievre A. J.
Published: November 2021

Introduction.

Given the limited number of positions in physical therapy (PT) residency programs, it is important to select individuals who are most likely to succeed. The purpose of the study is to obtain consensus from residency program directors regarding 1) the traits and/or characteristics that are likely to result in a successful residency experience, 2) how success in residency education is defined, and 3) what do programs aspire their residency graduates to accomplish professionally.

Review of the Literature:

Limited evidence exists that explores the qualities, skills, traits, or experiences that contribute to a successful PT resident or whether the current application process is able to identify these traits.

Subjects:

The residency directors of 246 American Board of Physical Therapy Residency and Fellowship Education-accredited programs were invited via email. One hundred nine (44.67%) residency program directors participated.

Methods:

Using the Delphi study design, consensus was reached after round 3 of the survey.

Results:

Five traits/characteristics, 9 characteristics/achievements of a successful residency graduate, and 4 postresidency aspirations reached consensus as “absolutely essential,” and 1 outcome measure reached consensus as “very useful.”

Discussion/Conclusion:

Residency programs may look to modify 1) their application/selection processes to identify applicants who possess desirable traits/characteristics and 2) their criteria for successful completion. Entry-level PT programs may use this information to guide what skills/traits are needed to prepare graduates for postprofessional experiences.
Using Virtual Reality for Movement System Examination in a Doctor of Physical Therapy Curriculum
Authors: Judd Dana L. , Kelly Brian , Corral Janet
Published: November 2021

Background and Purpose:

Examining and treating movement dysfunction is a cornerstone of physical therapist practice. Consequently, physical therapist education programs should prepare students to effectively analyze movement to inform clinical decision making. Current practice methods fall short due to variability in demonstration and realistic portrayal of movement disorders. Virtual reality (VR) is an alternative modality for high-fidelity simulation for learning movement system examination. The purpose of this study was to describe the development of a VR module to be used as part of a Doctor of Physical Therapy (DPT) curriculum, and to evaluate student reaction and attitudes regarding utilizing VR for practicing movement analysis skills.

Method/Model Description and Evaluation:

An original VR module consisting of 3 virtual patients performing a sit-to-stand transfer was created for students to practice movement observation and analysis. Fifteen first-year DPT students volunteered to experience the VR module and provide feedback. Students observed 3 different patients performing sit-to-stand transfers and performed a movement analysis on each. Students’ performance was assessed using a checklist developed from current physical therapy literature and curricular content. Participants also completed pre- and post-VR surveys to capture their opinions and attitudes regarding VR.

Outcomes:

After the VR module, all participations strongly agreed that they enjoyed using the VR module. All participants agreed that the animations were realistic enough to practice movement analysis skills. The average checklist score was 87.7%, indicating most benchmark behaviors for movement analysis were met. Most students disagreed that VR could replace face-to-face training opportunities.

Discussions and Conclusion:

The VR module was received favorably by DPT students; however, they felt strongly that VR should not replace traditional face-to-face laboratory opportunities. Notably, the VR environment provided a reliable space to practice movement examination skills. Utilizing this innovation would advance current concepts in simulation-based learning in DPT curricula and provide a unique platform for practicing movement examination.
Prone position in COVID 19-associated acute respiratory failure
Authors: Kharat Aileen , Simon Marie , Guérin Claude
Published: November 2021

Purpose of review

Prone position has been widely used in the COVID-19 pandemic, with an extension of its use in patients with spontaneous breathing (’awake prone’). We herein propose a review of the current literature on prone position in mechanical ventilation and while spontaneous breathing in patients with COVID-19 pneumonia or COVID-19 ARDS.

Recent findings

A literature search retrieved 70 studies separating whether patient was intubated (24 studies) or nonintubated (46 studies). The outcomes analyzed were intubation rate, mortality and respiratory response to prone. In nonintubated patient receiving prone position, the main finding was mortality reduction in ICU and outside ICU setting.

The final results of the several randomized control trials completed or ongoing are needed to confirm the trend of these results. In intubated patients, observational studies showed that responders to prone in terms of oxygenation had a better survival than nonresponders.
Transbronchial biopsy vs. bronchoalveolar lavage in interstitial lung disease
Authors: Chugh Karan , Jatwani Shraddha
Published: November 2021

Purpose of review

Interstitial lung diseases (ILDs) are heterogeneous disorders characterized by varying degrees of inflammation and fibrosis in the lung parenchyma. The use of bronchoalveolar lavage (BAL) cellular analysis and transbronchial biopsy with forceps (TBLB) in ILD is often a matter of debate. ILDs have been a diagnostic challenge and require multidisciplinary discussion (MDD) to develop a consensus diagnosis based on clinical, radiologic, laboratory, BAL cellular analysis, and histologic information.

Recent findings

The BAL cellular analysis is a commonly performed tool, and some ILDs have distinctive cellular findings. Its use alone is seldom diagnostic and almost always requires clinical, radiologic findings, and or histologic information interpretation. The minimally invasive procedures, such as TBLB, transbronchial cryo-biopsy (TBCB), and invasive procedures, such as surgical lung biopsy (SLB) help obtain a histologic diagnosis.

This review serves as a resource to assist clinicians to develop effective communication and close collaboration through MDD for accurate selection of diagnostic tools to reach the correct and final diagnosis.
Reconciling Systolic Blood Pressure Intervention Trial with Eighth Joint National Commission: a nuanced view of optimal hypertension control in the chronic kidney disease population
Authors: Tantisattamo Ekamol , Hamiduzzaman Anum , Sohn Peter , Ahdoot Rebecca , Hanna Ramy M.
Published: November 2021

Purpose of review

Universally lowering blood pressure (BP) may adversely affect some populations especially in the older population. Recent landmark trials revealed cardiovascular benefits of tight controlling systolic BP (SBP) more than several recent BP targets. Implementing the evidence from the studies and guidelines in some populations is reviewed.

Recent findings

Eighth Joint National Commission (JNC-8) on hypertension issued conservative guidelines that provided an evolutionary change to BPcontrol in the elderly. However, intensive BP control with SBP < 120 mmHg in Systolic Blood Pressure Intervention Trial (SPRINT) focuses on the improvement of cardiovascular and cerebrovascular outcomes. Although increasingly guidelines are trending toward the SPRINT results, it is noteworthy that not all populations show a favorable outcome with intensive BP control given hypotensive risks to memory, kidney function, orthostasis, and morbidity risks.

Some populations may benefit from implementing the more intensive SBP target, whereas others such as elderly hypertensive patients may benefit from a more liberal SBP target. In the spirit of ‘Primum non Nocere’, we call for and suggest that a marriage of both SPRINT and JNC-8 recommendations be undertaken to champion the most cardiovascular protections for the greatest number of patients possible whereas preventing complications in vulnerable populations such as the elderly. Among the chronic kidney disease (CKD) population, SBP < 120 mmHg may not necessarily lead to favorable CKD outcomes.
Severe acute respiratory syndrome coronavirus 2 infection in the stem cell transplant recipient − clinical spectrum and outcome
Authors: Fernández-Ruiz Mario , Aguado José María
Published: November 2021

Purpose of review

Focusing on large multicenter cohorts reported over the last months, this review aims at summarizing the available evidence by July 2021 on the impact of coronavirus disease 2019 (COVID-19) on hematopoietic stem cell transplant (HSCT) recipients in terms of epidemiology, clinical features, and outcome.

Recent findings

The incidence of COVID-19 in institutional cohorts varied according to different regions and study periods from 0.4% to 8.3%. Clinical presentation was overall comparable to other immunocompromised hosts and the general population. Microbiologically confirmed superinfection occurred in 13–25% of recipients, with most episodes due to hospital-acquired bacteria and few reported cases of COVID-19-associated aspergillosis. Prolonged nasopharyngeal severe acute respiratory syndrome coronavirus 2 shedding has been demonstrated for as long as 210 days. Mortality rates were similar across studies (14.8–28.4%) and did not markedly differ from those observed in nontransplant hematological patients during the first wave. Older age and shorter time from transplantation were associated with mortality, as well as underlying disease status and amount of immunosuppression. No outcome differences were found in most studies between allogeneic and autologous procedures.

Considerable advances have been achieved in the characterization of COVID-19 in the HSCT population, although uncertainties remain in the optimal therapeutic management.
Public Opinions About Surgery in Older Adults
Authors: Dharmasukrit Charlie , Ramaiyer Malini , Dillon Ellis C. , Russell Marcia M. , Dutt Meghan , Colley Alexis , Tang Victoria L.
Published: November 2021

Objective:

To examine public opinions of surgery in older adults.

Background:

Increasing numbers of older adults are undergoing surgery. National healthcare organizations recognize the increased risks of postoperative complications and mortality in the older surgical population and have made efforts to improve the care of older adults undergoing surgery through hospital-level programs. However, limited research has explored the opinions and responses of the wider U.S. public regarding surgery in older adults.

Methods:

We performed a qualitative, thematic analysis of reader comments posted in response to online newspaper articles relating to surgery in older adults. Articles were published in 2019-2020 and targeted for a popular press audience.

Results:

Nine hundred eight reader comments posted in response to 6 articles relating to surgery in older adults were identified. Articles were published in online editions of print newspapers with a digital circulation between 1.3 and 5.7 million subscribers. Three themes were identified: (1) wariness/distrust towards healthcare: including general distrust of medicine and distrust of surgery, (2) problems experienced: ineffective communication and unrealistic expectations, and (3) recommended solutions: the need for multidisciplinary teams and patient-centered communication.

Conclusions:

Overall, the public viewed surgery in older adults with wariness/distrust due to ineffective communication and unrealistic expectations. Specialized surgical care tailored to the unique needs of older adults is needed. The public perspective suggests that U.S. health systems should strongly consider adopting programs that provide care to meet the unique needs of older adults undergoing surgery and ultimately improve both patient outcomes and their surgical experience.
Chemical and microbiological properties of exudates with sugaring
of sea tangle, onion, aloe, maesil, and kale
Authors: Choi Mi-Young , Jhon Deok-Young
Published: November 2021

Exudates were prepared using sucrose from the edible parts of sea tangle, aloe,
onion, maesil (Prunus mume fruit) and kale. Changes in the
amount of sugar and organic acid were investigated during 12-month storage of
the exudates in hangari (a traditional Korean jar) and stainless-steel
containers. Dominant lactic acid-producing bacteria were isolated and
identified. Lactic acid was the major organic acid in the exudates of sea
tangle, onion, and aloe, whereas citric acid and acetic acid were the major
organic acids in maesil and kale exudates, respectively. In addition, it was
confirmed that container type affected the composition of each exudate. Overall,
the pH of these exudates decreased without any significant changes in acidity.
As the storage time increased, viable bacterial counts decreased, and the number
of acid-producing bacteria also decreased or disappeared. A total of 18 dominant
species of lactic acid-producing bacteria were screened and classified into
Lactobacillus homohiochii, Lactobacillus
plantarum, and Bacillus megaterium based on 16S
rRNA gene sequencing. Lactobacillus spp. showed high sugar
tolerance and multiplied even at sucrose concentrations of 20-50%. Depending on
the strain, these dominant bacteria hydrolyze sucrose to glucose and fructose,
with lactic acid as the final product. The dominant type of lactic
acid-producing bacteria differed depending on the type of sugaring exudate.
Further research on the role of these microorganisms in the food industry, such
as preparing exudates using bacterium as a starter material, is required.
Compassionate Use of REGEN-COV® in Patients with COVID-19 and Immunodeficiency-Associated Antibody Disorders
Authors: Stein David , Oviedo-Orta Ernesto , Kampman Wendy A , McGinniss Jennifer , Betts George , McDermott Margaret , Holly Beth , Lancaster Johnathan M , Braunstein Ned , Yancopoulos George D , Weinreich David M
Published: November 2021

Background

Patients with immunodeficiency-associated antibody disorders are at a higher risk of prolonged/persistent COVID-19 infection, having no viable treatment options.

Methods

This is a retrospective analysis of patients with primary and/or secondary immunodeficiency-associated antibody disorders who received casirivimab and imdevimab (REGEN-COV®) under emergency compassionate use. The objectives were to describe safety and response to REGEN-COV, with a focus on the subset of patients who had COVID-19 duration ≥21 days prior to treatment. Quantitative (change in oxygenation status and/or viral load) and/or qualitative (physician-reported clinical status) patient outcomes data are reported.

Results

Outcome data are available from 64 patients who received REGEN-COV. Improvement in ≥1 outcome measure was observed in 90.6% of the overall patient group. Thirty-seven of these patients had COVID-19 duration ≥21 days prior to treatment, with a median time from RT-PCR diagnosis to REGEN-COV administration of 60.5 days. Of the 29 patients with COVID-19 duration ≥21 days prior to treatment who had available outcome data, 96.6% showed improvement in ≥1 outcome measure evaluated following use of REGEN-COV. In the 14 patients who had post-treatment RT-PCR results available, 11 (78.6%) reported a negative RT-PCR following treatment with REGEN-COV, with 5 patients (45.5%) reporting a negative RT-PCR within 5 days of treatment and 8 (72.7%) reporting a negative RT-PCR within 21 days of treatment.

Conclusions

In this retrospective analysis of immunodeficient patients who were granted REGEN-COV under the compassionate use program, REGEN-COV treatment was associated with rapid viral clearance and clinical improvement in the evaluable patients with long-standing COVID-19.

Patients with immunodeficiency-associated antibody disorders are at a higher risk of prolonged/persistent COVID-19 infection. In this retrospective analysis, compassionate use of REGEN-COV in such patients was associated with rapid viral clearance and/or clinical improvement in the evaluable patients.
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing
Authors: Rozhoňová Hana , Danciu Daniel , Stark Stefan , Rätsch Gunnar , Kahles André , Lehmann Kjong-Van
Published: November 2021

Motivation

Several recently developed single-cell DNA sequencing technologies enable whole-genome sequencing of thousands of cells. However, the ultra-low coverage of the sequenced data (< 0.05x per cell) mostly limits their usage to the identification of copy number alterations in multi-megabase segments. Many tumors are not copy number-driven, and thus single-nucleotide variant (SNV)-based subclone detection may contribute to a more comprehensive view on intra-tumor heterogeneity. Due to the low coverage of the data, the identification of SNVs is only possible when superimposing the sequenced genomes of hundreds of genetically similar cells. Thus, we have developed a new approach to efficiently cluster tumor cells based on a Bayesian filtering approach of relevant loci and exploiting read overlap and phasing.

Results

We developed Single Cell Data Tumor Clusterer (SECEDO, lat. ‘to separate’), a new method to cluster tumor cells based solely on SNVs, inferred on ultra-low coverage single-cell DNA sequencing data. We applied SECEDO to a synthetic dataset simulating 7,250 cells and eight tumor subclones from a single patient, and were able to accurately reconstruct the clonal composition, detecting 92.11% of the somatic SNVs, with the smallest clusters representing only 6.9% of the total population. When applied to four real single-cell sequencing datasets from a breast cancer patient, each consisting of ≈2,000 cells, SECEDO was able to recover the major clonal composition in each dataset at the original coverage of 0.03x, achieving an ARI score of ≈0.6. The current state-of-the-art SNV-based clustering method achieved an ARI score of ≈0, even after increasing the coverage in silico by a factor of 10, and was only able to match SECEDO’s performance when pooling data from all four datasets, in addition to artificially increasing the sequencing coverage by a factor of 7. Variant calling on the resulting clusters recovered more than twice as many SNVs as would have been detected if calling on all cells together. Further, the allelic ratio of the called SNVs on each subcluster was more than double relative to the allelic ratio of the SNVs called without clustering, thus demonstrating that calling variants on subclones, in addition to both increasing sensitivity of SNV detection and attaching SNVs to subclones, significantly increases the confidence of the called variants.

Availability

SECEDO is implemented in C++ and is publicly available at https://github.com/ratschlab/secedo.
Crystal structure and Hirshfeld surface analysis of 2-{[(E)-(3-cyclobutyl-1H-1,2,4-triazol-5-yl)imino]methyl}phenol
Authors: Gumus Mustafa Kemal , Sen Fatih , Kansiz Sevgi , Dege Necmi , Saif Eiad
Published: November 2021

The title compound, C13H14N4O, was developed using the reaction of salicylaldehyde and 3-amino-5-cyclobutyl-1,2,4-triazole in ethanol under microwave irradiation. This eco-friendly microwave-promoted method proved to be efficient in the synthesis of 2-{[(E)-(3-cyclobutyl-1H-1,2,4-triazol-5-yl)imino]methyl}phenol in good yields and purity. The title compound is a Schiff base that exists in the phenol–imine tautomeric form and adopts an E configuration. The three independent molecules in the asymmetric unit (A, B and C) are not planar, the cyclobutyl and the phenol-imine rings are twisted to each other making a dihedral angle of 67.8 (4)° in molecule A, 69.1 (2)° in molecule B and 89.1 (2)° in molecule C. In each molecule an intramolecular O—H...N hydrogen bond is present, forming an S(6) ring motif. A Hirshfeld surface analysis was performed to investigate the contributions of the different intermolecular contacts within the supramolecular structure. The major interactions are H...H (53%), C...H (19%) and N...H (17%) for molecule A, H...H (50%), N...H (20%) and C...H (20%) for molecule B and H...H (57%), C...H (14%) and N...H (13%) for molecule C.
Managing the resource allocation for the COVID-19 pandemic in healthcare institutions: a pluralistic perspective
Authors: Arunmozhi Manimuthu , Persis Jinil , Sreedharan V. Raja , Chakraborty Ayon , Zouadi Tarik , Khamlichi Hanane
Published: November 2021

Purpose

As COVID-19 outbreak has created a global crisis, treating patients with minimum resources and traditional methods has become a hectic task. In this technological era, the rapid growth of coronavirus has affected the countries in lightspeed manner. Therefore, the present study proposes a model to analyse the resource allocation for the COVID-19 pandemic from a pluralistic perspective.

Design/methodology/approach

The present study has combined data analytics with theK-mean clustering and probability queueing theory (PQT) and analysed the evolution of COVID-19 all over the world from the data obtained from public repositories. By usingK-mean clustering, partitioning of patients’ records along with their status of hospitalization can be mapped and clustered. AfterK-mean analysis, cluster functions are trained and modelled along with eigen vectors and eigen functions.

Findings

After successful iterative training, the model is programmed usingRfunctions and given as input to Bayesian filter for predictive model analysis. Through the proposed model, disposal rate; PPE (personal protective equipment) utilization and recycle rate for different countries were calculated.

Research limitations/implications

Using probabilistic queueing theory and clustering, the study was able to predict the resource allocation for patients. Also, the study has tried to model the failure quotient ratio upon unsuccessful delivery rate in crisis condition.

Practical implications

The study has gathered epidemiological and clinical data from various government websites and research laboratories. Using these data, the study has identified the COVID-19 impact in various countries. Further, effective decision-making for resource allocation in pluralistic setting has being evaluated for the practitioner's reference.

Originality/value

Further, the proposed model is a two-stage approach for vulnerability mapping in a pandemic situation in a healthcare setting for resource allocation and utilization.
Seven information practices for alleviating information vulnerability
Authors: Potnis Devendra Dilip , Winberry Joseph
Published: November 2021

Purpose

This literature review aims to identify conscious, intentional, repetitive and transferrable information-related decisions and activities (i.e. information practices) for individuals to alleviate their information vulnerability. Information vulnerability refers to the lack of access to accurate, affordable, complete, relevant and timely information or the inability to use such information, which can place individuals, communities or society at disadvantage or hurt them.

Design/methodology/approach

Conceptual literature review.

Findings

This review presents seven conscious, intentional, repetitive and transferrable information practices to alleviate information vulnerability.

Practical implications

Due to the transferability potential of the seven information practices, diverse populations in varied contexts could refer to, adapt and benefit from appropriate combinations of information practices and their manifestations. The framework can be used by individuals for alleviating information vulnerability. Thus, this paper responds to the call for conducting action-driven research in information science for addressing real-world problems. Information professionals can help individuals select and implement appropriate combinations of seven information practices for alleviating information vulnerability.

Originality/value

We propose (1) a parsimonious, episodic framework for alleviating information vulnerability, which depicts the inter-relationship among the seven information practices and (2) a three-dimensional plot with information access, use and value as three axes to map the manifestation and outcome of alleviating information vulnerability.
Lung cancer risk following previous abnormal chest radiographs: A 27‐year follow‐up study of a Chinese lung screening cohort
Authors: Fan Yaguang , Su Zheng , Wei Mengna , Liang Hao , Jiang Yong , Li Xuebing , Meng Zhaowei , Wang Ying , Wu Heng , Song Jinzhao , Qiao Youlin , Zhou Qinghua
Published: November 2021

Background

Chest radiograph (CXR) is still one of the most commonly used diagnostic tools for chest diseases. In this cohort study, we attempted to investigate the magnitude and temporal pattern of lung cancer risk following abnormal CXR findings.

Methods

We conducted an extended follow‐up of an occupational screening cohort in Yunnan, China. The associations between abnormal CXR results from baseline screening, the first four consecutive rounds of CXR screening, all previous rounds of screening and lung cancer risk were analyzed using time‐varying coefficient Cox regression model. The associations of lung cancer risk and previous CXR‐screening results according to histology were also considered. Sensitivity analyses were conducted to assess the robustness of the previous abnormal CXR findings on subsequent lung cancer risk.

Results

Abnormal CXR findings were associated with a significantly increased lung cancer risk. This relative hazard significantly decreased over time. Compared to negative screening results, the adjusted hazard ratios (HR) of baseline abnormal CXR results, and at least one abnormal result in the first four consecutive screening rounds during the first 5 years of follow‐up were 17.06 (95% CI: 11.74–24.79) and 13.77 (95%: 9.58–17.79), respectively. This significantly increased lung cancer risk continued over the next 5 years. These associations were stronger for persistent abnormal findings, and abnormal findings identified in recent screening rounds.

Conclusions

The increased risk was significant for both squamous cell carcinoma and adenocarcinoma. Although decreased over time, an increased lung cancer risk relative to abnormal CXR findings can continue for 10 years.
Suspensory ligament or interosseous muscle? Histology of the interosseous muscle of South American Camelids
Authors: Schraml Susanne , Barrios Santos William Arthur , Bässler Claus , Mülling Christoph
Published: November 2021

The interosseous muscles (IOM) have evolved to largely collagenized structures in many large grazers, including South American Camelids (SACs). SACs include lama (Lama glama), alpaca (Vicugna pacos), guanaco (Lama guanicoe) and vicuna (Vicugna vicugna). This study reports on a comparative histomorphological evaluation of the IOM in these four species. First, a descriptive qualitative analysis of the tissue composition within the physiological IOM clearly demonstrates that the IOM of all SAC species is predominantly tendinous. However, we can always find a small amount of striated muscle fibres supporting the claim that the term “interosseous muscle” should be preferred over the denomination “suspensory ligament”. Second, we quantify the ratio of muscle tissue (MTr) occupying the cross‐sectional area (CSA) of 80 limbs at three levels and examine it in relation to limb, sample localization and species. Values for MTr are highest at the middle level, ranging from 0.4% to 15.2% with a mean of 3.4% ± 3.2%. We also detect notable amounts of muscle tissue at the distal sample level in the area of the branches of the IOM. Of all SACs, alpacas present the highest MTr. Lamas have a significantly larger MTr than guanacos. These results suggest the influence of domestication and/or physical activity on the muscle tissue content of the IOM of SACs. Amounts and distribution of muscle, adipose and lose connective tissue vary greatly for each sample localization and within individuals of one species. This may complicate the interpretation of MRI images of SACs’ IOM for diagnostic purposes.
Cutaneous squamous cell carcinoma metastatic to the axilla and groin: Outcomes and prognostic factors
Authors: Bucknell Nicholas W , Gyorki David E , Bressel Mathias , Estall Vanessa , Webb Angela , Henderson Michael , Chua Margaret S‐T , Rischin Danny , Tiong Albert
Published: November 2021

Purpose

This study examined the clinical outcomes and prognostic factors of patients with metastatic cutaneous SCC metastatic to the axilla and groin when managed with curative‐intent lymphadenectomy and received (neo)adjuvant treatment.

Methods and Materials

We conducted a single institution retrospective review. Patients who had nodal disease without distant spread were 18 years or older with no non‐cutaneous primary identified.

Results

From January 2000 to July 2015, 78 patients were treated for axilla (64, 82%) or inguinal (14, 18%) involvement with cSCC. The median age was 75.5 years (range: 29–95), and 8 patients (11%) were immunosuppressed. The median size of the largest node was 45 mm (range: 8–135), and extracapsular extension was found in 63 (81%) cases. A majority of patients were treated with surgery alone (21, 26.9%) and surgery with adjuvant radiation therapy (54, 69%). The 2‐year OS and PFS were 50% (95% CI: 40%–63%) and 43% (95% CI: 33%–56%), and 5‐year OS and PFS were 33% (95% CI:23%–47%) and 32% (95% CI:22%–46%) respectively in the entire cohort. On univariable analysis, factors associated with longer OS were as follows: younger age (HR 1.1, 95% CI: 0.9–1.3 P = 0.021), improved performance status (HR 1.5, 95% CI:1.0–2.3 P = 0.026), lack of immunosuppression (HR 3.3, 95% CI: 1.5–7.3 P = 0.001), lower lymph node ratio (HR 1.2, 95% CI:1.0–1.3 P = 0.007), lower number of positive nodes (HR 1.1, 95% CI:1.0–1.2 P = 0.004) and the use of radiation therapy (HR 0.5, 95% CI:0.3–0.9 P = 0.012).

Conclusion

Metastasis to the axilla and groin with cSCC has poor outcomes with standard treatment. The addition of immunotherapy warrants investigation.
Academic freedom and intellectual dissent in post‐soviet Ukraine
Authors: Oleksiyenko Anatoly V.
Published: November 2021

This paper conceptualizes intellectual dissent as a galvanizer of academic freedom in a post‐totalitarian academia that is moving toward democratization. Drawing on the case of Ukraine, the analytical narrative describes difficulties in overcoming legacies in universities emerging from repressive rule that discouraged creativity, initiative, and critical inquiry, and having to envisage a transition to democratic governance in the context of neoliberal geopolitics. The case analysis suggests that intellectual dissent is essential but limited in its ability to establish the praxis of academic freedom under increasing control by oligarchic governments and a self‐serving bureaucracy. By exploring interdependencies between intellectual dissent and academic freedom, this paper lays ground for an analytical framework that can be helpful in rethinking the prospects of universities at the crossroads of authoritarianism and democracy.
Molecular genetic characterization of acute myeloid leukemia with isolated trisomy of chromosomes 4, 11, and 21
Authors: Zhou Feng , Shen Hongjie , Wang Zheng , Hua Haiying , Wu Pin , Han Wenmin , xia Jia Zhu , Cai Xiaohui , Chao Hongying , Lu Xuzhang
Published: November 2021

Background

Autosomal trisomy is a relatively rare abnormality observed in AML, occurring singly or as a secondary event in association with other karyotypic changes, and associated with prognosis. The molecular genetic and clinical characterizations of acute myeloid leukemia (AML) with isolated trisomy 4, 11, or 21 have been poorly investigated.

Materials and Methods

Interphase fluorescence in situ hybridization, reverse transcriptase‐quantitative polymerase chain reaction for 41 chromosomal gene translocations/fusion genes, and next‐generation sequencing (NGS) were performed on 29 AML patients with trisomy 4, 11, or 21 as the sole chromosomal anomaly.

Results

Of the 29 patients, one or more mutations were detected in 93.1% of patients. CEBPA had the highest mutation frequency, followed by TET2, NPM1, DNMT3A, and FLT3‐ITD. The sole +11 AML patients exhibited more mutations in FLT3‐ITD (P = .031) than the sole +21 AML patients, while CEBPA mutation was more frequently found in the sole +21 AML patients than that in the sole +11 AML patients(P = .07). The median overall survival (OS) and disease‐free survival (DFS) for patients with +11 were shorter than those with +4(P = .015, 0.046) or +21 (0.057, 0.064), but no difference was found between +4 patients and +21 patients. In the whole cohort, only the FLT3‐ITD mutation was significantly associated with inferior OS (18 vs. 35 months, P = .023) and DFS (12 months vs. NR, P = .046). There were no significant differences in OS and DFS according to the gene mutation status of CEBPA, TET2, NPM1, DNMT3A, and IDH1/2.

Conclusion

There was a significantly different mutation profile among the sole +4, +11, +21 AML patients. Our research provided new insight into the molecular characteristics of AML with isolated trisomy.