bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pneumocystis pneumonia and rheumatic disease: diagnostic potential of circulating microbial cell-free DNA sequencing
Authors: Li Jia , Li Jun , Yu Yuetian , Wang Rongsheng , Zhou Mi , Lu Liangjing 
Published: December 2021

Abstract

Objectives
The aim of this study was to explore the clinical utility of circulating microbial cell-free DNA (cfDNA) sequencing as a non-invasive approach for diagnosis of Pneumocystis jirovecii pneumonia (PJP) in immunocompromised patients with rheumatic disease (RD).

Methods
The study included 72 RD patients with suspected lung infections admitted to Renji hospital. Eighteen individuals were diagnosed with PJP, and 54 patients without PJP were enrolled as the control group. All patients had undergone pulmonary CT scans, and blood and respiratory tract specimens had been subjected to metagenomic next-generation sequencing (mNGS) and conventional microbiological tests. The clinical and laboratory parameters were collected, and the efficacy of circulating microbial cfDNA of P. jirovecii was evaluated.

Results
Of the 18 patients with PJP, the average age was 53.0 years, and the median time between RD diagnosis and PJP presentation was 126.0 days (interquartile range 84.0–176.3 days). Low circulating CD4+ cell counts and a lack of PJP prophylaxis were observed in the patients. Metagenomic NGS of circulating microbial cfDNA was performed in 69 patients, including 15 cases with PJP and 54 controls. Twelve (80%) of 15 analysed blood samples contained P. jirovecii sequences in the PJP group, with P. jirovecii not detected among controls. There was a significant difference between PJP and non-PJP groups (P &lt; 0.001), with a sensitivity of 83.3% and specificity of 100% when using plasma cfDNA sequencing. Higher β-D-glucan levels were found in patients with positive results for P. jirovecii in plasma cfDNA sequencing.

Conclusion
Metagenomic NGS of circulating microbial cfDNA is a potential tool for diagnosis of PJP in RD patients.
Abnormal rapid eye movement sleep atonia control in chronic post-traumatic stress disorder
Authors: Feemster John C , Steele Tyler A , Palermo Kyle P , Ralston Christy L , Tao Yumeng , Bauer David A , Edgar Liam , Rivera Sonia , Walters-Smith Maxwell , Gossard Thomas R , Teigen Luke N , Timm Paul C , Richardson Jarrett W , Robert Auger R , Kolla Bhanuprakash , McCarter Stuart J , Boeve Bradley F , Silber Michael H , St. Louis Erik K 
Published: December 2021

Abstract

Study Objectives
Post-traumatic stress disorder (PTSD) and rapid eye movement (REM) sleep behavior disorder (RBD) share some common features including prominent nightmares and sleep disturbances. We aimed to comparatively analyze REM sleep without atonia (RSWA) between patients with chronic PTSD with and without dream enactment behavior (DEB), isolated RBD (iRBD), and controls.

Methods
In this retrospective study, we comparatively analyzed 18 PTSD with DEB (PTSD+DEB), 18 PTSD without DEB, 15 iRBD, and 51 controls matched for age and sex. We reviewed medical records to determine PTSD clinical features and quantitatively analyzed RSWA. We used nonparametric analyses to compare clinical and polysomnographic features.

Results
PTSD patients, both with and without DEB, had significantly higher RSWA than controls (all p &lt; .025, excepting submentalis phasic duration in PTSD+DEB). Most RSWA measures were also higher in PTSD+DEB than in PTSD without DEB patients (all p &lt; .025).

Conclusions
PTSD patients have higher RSWA than controls, whether DEB is present or not, indicating that REM sleep atonia control is abnormal in chronic PTSD. Further prospective studies are needed to determine whether neurodegenerative risk and disease markers similar to RBD might occur in PTSD patients.
Telehealth Evaluation of Pediatric Neurodevelopmental Disabilities During the COVID-19 Pandemic: Clinician and Caregiver Perspectives
Authors: McNally Keehn Rebecca , Enneking Brett , James Cristina , Tang Qing , Rouse Maura , Hines Elesia , Raches Christine , Etling Allison 
Published: December 2021

Abstract:

Objective:
The objective of this study was to present clinician and caregiver perspectives regarding telehealth neurodevelopmental evaluation delivered at the onset of the coronavirus disease 2019 (COVID-19) pandemic. Specifically, we sought to describe telehealth neurodevelopmental evaluations, examine associations between child characteristics and diagnostic factors, determine the impact of technology and family barriers, and report on clinician and caregiver satisfaction with telehealth evaluation.

Methods:
In response to the COVID-19 pandemic, in-person clinical services at a large children's hospital neurodevelopmental clinic were transitioned to telehealth. Data are presented for 254 remote evaluations of children (18–212 months; referral concern: 51% autism spectrum disorder [ASD], 24% developmental delay/intellectual disability, 25% other neurodevelopmental concern) conducted from May to July 2020. Data were gathered from electronic health records as well as clinician and caregiver surveys.

Results:
A clinical diagnosis was provided in 72% of telehealth evaluations. Clinicians rated diagnostic certainty as “completely” or “somewhat” certain in 74% of evaluations. Certainty ratings were higher for evaluations in which a diagnosis of ASD was provided. Although technology and family challenges were reported, clinicians rarely identified these as disruptive to the evaluation process. Clinicians reported satisfaction with various aspects of delivering telehealth. Caregivers endorsed high satisfaction with receipt of telehealth and reduced travel burden.

Conclusion:
The COVID-19 pandemic has rapidly transformed service delivery for individuals with neurodevelopmental disabilities and provided an unprecedented opportunity to evaluate the deployment of telehealth evaluation to meet the need for ongoing diagnostic care. Our findings suggest that telehealth holds significant promise for neurodevelopmental assessment both within the context of a global pandemic and beyond.
Foot Wounds and the Reconstructive Ladder
Authors: Simman Richard , Abbas Fuad-Tahsin 
Published: December 2021

Background:
Foot soft tissue coverage represents a challenge to reconstructive surgeons due to a lack of donor sites for this specialized skin. This glabrous tethered thick skin is designed to withstand weight bearing stress and is hard to replace. The limited arch of rotation of foot local flaps contributes to further difficulties. In this study, we share our experience in foot soft tissue loss coverage using techniques tailored to each wound presentation.

Methods:
This case series presents eight patients with wounds of the plantar and dorsal surfaces of the foot, heel, and ankle. Closure techniques were selected and planned based on wound presentation and comorbidity status.

Results:
Patients’ mean age at surgery was 61 years. Etiologies of wounds include trauma, frostbite, diabetic ulceration, malignancy, pressure ulcer with osteomyelitis, and necrotizing infection. Coverage techniques included split and full-thickness skin graft, medial plantar arch pinch graft, cultured epithelial autograft, Hyalomatrix wound device, EpiFix tissue matrix, pedicle flap, and free rectus flap. Complete soft tissue coverage was achieved in each case within reasonable postoperative periods, and ambulation was preserved and/or restored.

Conclusions:
Foot soft tissue reconstruction is challenging and should be planned carefully due to the required specialized skin replacement. Primary closure should be considered first and attempted if possible. Technique escalation in accordance with the reconstructive ladder should be undertaken based on wound etiology, presentation, amount and nature of tissue loss, available resources, and surgeon experience.
Frequency, Characteristics and Complications of COVID-19 in Hospitalized Infants
Authors: Hobbs Charlotte V. , Woodworth Kate , Young Cameron C. , Jackson Ashley M. , Newhams Margaret M. , Dapul Heda , Maamari Mia , Hall Mark W. , Maddux Aline B. , Singh Aalok R. , Schuster Jennifer E. , Rowan Courtney M. , Fitzgerald Julie C. , Irby Katherine , Kong Michele , Mack Elizabeth H. , Staat Mary A. , Cvijanovich Natalie Z. , Bembea Melania M. , Coates Bria M. , Halasa Natasha B. , Walker Tracie C. , McLaughlin Gwenn E. , Babbitt Christopher J. , Nofziger Ryan A. , Loftis Laura L. , Bradford Tamara T. , Campbell Angela P. , Patel Manish M. , Randolph Adrienne G. ,   for the Overcoming COVID-19 Investigators
Published: December 2021

Background:
Previous studies of severe acute respiratory syndrome coronavirus 2 infection in infants have incompletely characterized factors associated with severe illness or focused on infants born to mothers with coronavirus disease 2019 (COVID-19). Here we highlight demographics, clinical characteristics and laboratory values that differ between infants with and without severe acute COVID-19.

Methods:
Active surveillance was performed by the Overcoming COVID-19 network to identify children and adolescents with severe acute respiratory syndrome coronavirus 2–related illness hospitalized at 62 sites in 31 states from March 15 to December 27, 2020. We analyzed patients >7 days to <1 year old hospitalized with symptomatic acute COVID-19.

Results:
We report 232 infants >7 days to <1 year of age hospitalized with acute symptomatic COVID-19 from 37 US hospitals in our cohort from March 15 to December 27, 2020. Among 630 cases of severe COVID-19 in patients >7 days to <18 years old, 128 (20.3%) were infants. In infants with severe illness from the entire study period, the median age was 2 months, 66% were from racial and ethnic minority groups, 66% were previously healthy, 73% had respiratory complications, 13% received mechanical ventilation and <1% died.

Conclusions:
Infants accounted for over a fifth of children <18 years of age hospitalized for severe acute COVID-19, commonly manifesting with respiratory symptoms and complications. Although most infants hospitalized with COVID-19 did not suffer significant complications, longer term outcomes remain unclear. Notably, 75% of infants with severe disease were <6 months of age in this cohort study period, which predated maternal COVID-19 vaccination, underscoring the importance of maternal vaccination for COVID-19 in protecting the mother and infant.
Management of post-cervical laminectomy fusion pain syndrome with a successful trial of spinal cord stimulation
Authors: Dahbour Layth , Wright Thelma B. , Rusha Laert , Uppal Pushpinder , Gattu Kanchana , Lee Seung J. , Watterworth Blake , Stansbury Lynn 
Published: December 2021

Abstract

Introduction:
Spinal cord stimulation has been shown to be beneficial in various postsurgical neuropathic pain syndromes, but the already small cervical epidural space due to epidural fibrosis makes cervical spinal cord stimulator placement very difficult. We present a case of successful cervical cord stimulator implantation in a patient with a history of anterior cervical discectomy and fusion, posterior cervical fusion, and significant epidural fibrosis.

Methods:
A 48-year-old woman with a history of type 2 diabetes, nonalcoholic steatohepatitis, and fibromyalgia presented with trauma-induced cervicalgia and bilateral upper extremity radiculopathy.

Results:
In a 4-day trial of stimulation, she reported an 80% reduction of her pain and significant improvement in her quality of life.

Discussion:
Although anecdotal evidence and case series have shown spinal cord stimulation to be successful in cervical failed back surgery syndrome, we are the first to discuss the technical challenges and complications associated with epidural fibrosis.
Effect of HIV Self-Testing on PrEP Adherence Among Gender-Diverse Sex Workers in Uganda: A Randomized Trial
Authors: Mujugira Andrew , Nakyanzi Agnes , Nabaggala Maria S. , Muwonge Timothy R. , Ssebuliba Timothy , Bagaya Monica , Nampewo Olivia , Sapiri Oliver , Nyanzi Kikulwe R. , Bambia Felix , Nsubuga Rogers , Serwadda David M. , Ware Norma C , Baeten Jared M. , Haberer Jessica E. 
Published: December 2021

Background:
HIV self-testing (HIVST) and pre-exposure prophylaxis (PrEP) are complementary tools that could empower sex workers to control their HIV protection, but few studies have jointly evaluated PrEP and HIVST in any setting.

Methods:
The Empower Study was an open-label randomized trial in Uganda. Sex workers were offered F/tenofovir disoproxil fumarate and randomized 1:1 to monthly HIVST and quarterly in-clinic testing (intervention) or quarterly in-clinic HIV testing alone (standard of care) and followed up for 12 months. PrEP adherence was measured using electronic adherence monitoring and tenofovir diphosphate (TFV-DP) levels in dried blood spots. Adherence outcomes and sexual behaviors were compared by arm using generalized estimating equation models.

Results:
We enrolled 110 sex workers: 84 cisgender women, 14 transgender women, 10 men who have sex with men, and 2 transgender men. The median age was 23 years. The 12-month retention was 75%. Nearly all (99.4%) used ≥1 HIVST kit. The proportion with TFV-DP levels ≥700 fmol/punch in the HIVST and standard of care arms at the 3-, 6-, 9-, and 12-month visits was 2.4%, 2.3%, 0%, and 0% and 7.9%, 0%, 0%, and 0%, respectively, with no differences by randomization arm (P > 0.2). Self-reported condomless sex acts with paying partners was similar by arm [adjusted incidence rate ratio 0.70; 95% confidence interval (CI): 0.42 to 1.17; P = 0.18]. One seroconversion occurred (HIV incidence, 0.9/100 person-years); TFV-DP was not detected at any visit.

Conclusions:
A gender-diverse sample of sex workers in Uganda used HIVST but not daily oral PrEP for HIV protection. Alternate approaches to promote PrEP use, including long-acting formulations, should be considered in this population.
The Impact of Income and Social Mobility on Colorectal Cancer Outcomes and Treatment
Authors: Poulson Michael R. , Geary Alaina , Annesi Chandler , Dechert Tracey , Kenzik Kelly , Hall Jason 
Published: December 2021

Objective:
To determine the impact of income mobility on racial disparities in colorectal cancer.

Background:
There are well-documented disparities in colorectal cancer treatment and outcomes between Black and White patients. Socioeconomic status, insurance, and other patient-level factors have been shown important, but little has been done to show the discriminatory factors that lead to these outcomes.

Methods:
Data were obtained from the Surveillance Epidemiology and End-Results database for Black and White patients with colorectal cancer between 2005 and 2015. County level measures of Black (BIM) and White income mobility (WIM) were obtained from the Opportunity Atlas as a measure of intergenerational poverty and social mobility. Regression models were created to assess the relative risk of advanced stage at diagnosis (Stage IV), surgery for localized disease (Stage I/II), and cancer-specific mortality.

Results:
There was no significant association of BIM or WIM on advanced stage at diagnosis in Black or White patients. An increase of $10,000 of BIM was associated with a 9% decrease in hazards of death for both Black (hazard ratio 0.91, 95% confidence interval 0.86,0.95) and White (0.91, 95%CI 0.90,0.93) patients, while the same increase in WIM was associated with no significant difference in hazards among Black patients (hazard ratio 0.99, 95% confidence interval 0.97,1.02). There were no predicted racial differences in hazards of death at high levels of BIM.

Conclusions:
Increased Black income mobility significantly improves survival for both Black and White patients. Interventions aimed at increasing economic and social mobility could significantly decrease mortality in both Black and White patients while alleviating disparities in outcomes.
Outcomes After Independent Trainee Versus Consultant-led Emergency Laparotomy
Authors: Rahman Saqib A. , Pickering Oliver , Tucker Vanessa , Mercer Stuart J. , Pucher Philip H. 
Published: December 2021

Objective:
We utilized a population dataset to compare outcomes for patients where surgery was independently performed by trainees to cases led by a consultant.

Summary of Background Data:
Emergency laparotomy is a common, high-risk, procedure. Although trainee involvement to improve future surgeons’ experience and ability in the management of such cases is crucial, some studies have suggested this is to the detriment of patient outcomes. In the UK, appropriately skilled trainees may be entrusted to perform emergency laparotomy without supervision of a consultant (attending).

Methods:
Patients who underwent emergency laparotomy between 2013 and 2018 were identified from the National Emergency Laparotomy Audit of England and Wales. To reduce selection and confounding bias, the inverse probability of treatment weighting approach was used, allowing robust comparison of trainee-led and consultant-led laparotomy cases accounting for eighteen variables, including details of patient, treatment, pathology, and preoperative mortality risk. Groups were compared for mortality and length of stay.

Results:
A total of 111,583 patients were included in the study. The operating surgeon was a consultant in 103,462 cases (92.7%) and atrainee in 8121 cases (7.3%). Mortality at discharge was 11.6%. Trainees were less likely to operate on high-risk and colorectal cases. After weighting, mortality (12.2% vs 11.6%, P = 0.338) was equivalent between trainee- and consultant-led cases. Median length of stay was 11 (interquartile range 7, 19) versus 11 (7, 20) days (P = 0.004), respectively. Trainee-led operations reported fewer cases of blood loss >500mL (9.1% vs 11.1%, P < 0.001).

Conclusions:
Major laparotomy maybe safely entrusted to appropriately skilled trainees without impacting patient outcomes.
The American College of Surgeons Entering Resident Readiness Assessment (ACS ERRA)
Authors: Park Yoon Soo , Sachdeva Ajit K. , Liscum Kathy , Alseidi Adnan , Gesbeck Melissa , Blair Patrice Gabler , Salcedo Edgardo , Sullivan Maura , Bordage Georges 
Published: December 2021

Objective:
To gather validity evidence supporting the use and interpretation of scores from the American College of Surgeons Entering Resident Readiness Assessment (ACS ERRA) Program.

Summary and Background Data:
ACS ERRA is an online formative assessment program developed to assess entering surgery residents’ ability to make critical clinical decisions, and includes 12 clinical areas and 20 topics identified by a national panel of surgeon educators and residency program directors.

Methods:
Data from 3 national testing administrations of ACS ERRA (2018–2020) were used to gather validity evidence regarding content, response process, internal structure (reliability), relations to other variables, and consequences.

Results:
Over the 3 administrations, 1975 surgery residents participated from 125 distinct residency programs. Overall scores [Mean = 64% (SD = 7%)] remained consistent across the 3 years (P = 0.670). There were no significant differences among resident characteristics (gender, age, international medical graduate status). The mean case discrimination index was 0.54 [SD = 0.15]. Kappa inter-rater reliability for scoring was 0.87; the overall test score reliability (G-coefficient) was 0.86 (Ф-coefficient = 0.83). Residents who completed residency readiness programs had higher ACS ERRA scores (66% versus 63%, Cohen’s d = 0.23, P < 0.001). On average, 15% of decisions made (21/140 per test) involved potentially harmful actions. Variability in scores from graduating medical schools (7%) carried over twice as much weight than from matched residency programs (3%).

Conclusions:
ACS ERRA scores provide valuable information to entering surgery residents and surgery program directors to aid in development of individual and group learning plans.
Scaffolding layered control architectures through constraint closure: insights into brain evolution and development
Authors: Wilson Stuart P. , Prescott Tony J. 
Published: December 2021

The functional organization of the mammalian brain can be considered to form a layered control architecture, but how this complex system has emerged through evolution and is constructed during development remains a puzzle. Here we consider brain organization through the framework of constraint closure, viewed as a general characteristic of living systems, that they are composed of multiple sub-systems that constrain each other at different timescales. We do so by developing a new formalism for constraint closure, inspired by a previous model showing how within-lifetime dynamics can constrain between-lifetime dynamics, and we demonstrate how this interaction can be generalized to multi-layered systems. Through this model, we consider brain organization in the context of two major examples of constraint closure—physiological regulation and visual orienting. Our analysis draws attention to the capacity of layered brain architectures to scaffold themselves across multiple timescales, including the ability of cortical processes to constrain the evolution of sub-cortical processes, and of the latter to constrain the space in which cortical systems self-organize and refine themselves.This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.
Computational validity: using computation to translate behaviours across species
Authors: Redish A. David , Kepecs Adam , Anderson Lisa M. , Calvin Olivia L. , Grissom Nicola M. , Haynos Ann F. , Heilbronner Sarah R. , Herman Alexander B. , Jacob Suma , Ma Sisi , Vilares Iris , Vinogradov Sophia , Walters Cody J. , Widge Alik S. , Zick Jennifer L. , Zilverstand Anna 
Published: December 2021

We propose a new conceptual framework (computational validity) for translation across species and populations based on the computational similarity between the information processing underlying parallel tasks. Translating between species depends not on the superficial similarity of the tasks presented, but rather on the computational similarity of the strategies and mechanisms that underlie those behaviours. Computational validity goes beyond construct validity by directly addressing questions of information processing. Computational validity interacts with circuit validity as computation depends on circuits, but similar computations could be accomplished by different circuits. Because different individuals may use different computations to accomplish a given task, computational validity suggests that behaviour should be understood through the subject's point of view; thus, behaviour should be characterized on an individual level rather than a task level. Tasks can constrain the computational algorithms available to a subject and the observed subtleties of that behaviour can provide information about the computations used by each individual. Computational validity has especially high relevance for the study of psychiatric disorders, given the new views of psychiatry as identifying and mediating information processing dysfunctions that may show high inter-individual variability, as well as for animal models investigating aspects of human psychiatric disorders.
This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.