bluuebunny/crossref_metadata_2025 huggingface dataset:
Barriers and Facilitators to Administering Burn Pit Registry Exams in VHA Facilities
Authors: Chen Patricia V , Christie Israel C , Godwin Kyler M , Han Jaehwan , Jani Nisha , Sotolongo Anays , Ali Asma , Helmer Drew A
Published: May 2024

Introduction

The Veterans Health Administration (VHA) established the Airborne Hazards and Open Burn Pit Registry (AHOBPR) in 2014 to address exposure concerns for veterans who have served in military operations in Southwest Asia and Afghanistan. By 2021, over 236,086 veterans completed the online questionnaire and 60% requested an AHOBPR examination. Of those requesting an exam, only 12% had an exam recorded in their medical record. This article summarizes barriers and facilitators to delivering AHOBPR exams and shares lessons learned from facilities who have successfully implemented burn pit exams for veterans.

Materials and Methods

We (I.C.C and J.H.) constructed a key performance measure of AHOBPR examination (the ratio of examinations performed in facility over examinations assigned to a facility) to identify top performing facilities and then used stratified purposeful sampling among high-performing sites to recruit a diverse set of facilities for participation. We (P.V.C. and A.A.) recruited and interviewed key personnel at these facilities about their process of administering burn pit exams. Rapid qualitative methods were used to analyze interviews.

Results

The ratio of exams performed to exams assigned ranged from 0.00 to 14.50 for the 129 facilities with available information. Twelve interviews were conducted with a total of 19 participants from 10 different facilities. We identified 3 barriers: Unclear responsibility, limited incentives and competing duties for personnel involved, and constrained resources. Facilitators included the presence of an internal facilitator, additional staff support, and coordination across a facility’s departments to provide care.

Conclusions

Gaps across many VHA facilities to provide AHOBPR exams may be understood as stemming from organizational issues related to clear delegation of responsibility and staffing issues. VHA facilities that wish to increase AHOBPR exams for veterans may need additional administrative and medical staff.
p21/Zbtb18 repress the expression of cKit to regulate the self-renewal of hematopoietic stem cells
Authors: Wang Nini , Yang Shangda , Li Yu , Gou Fanglin , Lv Yanling , Zhao Xiangnan , Wang Yifei , Xu Chang , Zhou Bin , Dong Fang , Ju Zhenyu , Cheng Tao , Cheng Hui
Published: May 2024

The maintenance of hematopoietic stem cells (HSCs) is a complex process involving numerous cell-extrinsic and -intrinsic regulators. The first member of the cyclin-dependent kinase family of inhibitors to be identified, p21, has been reported to perform a wide range of critical biological functions, including cell cycle regulation, transcription, differentiation, and so on. Given the previous inconsistent results regarding the functions of p21 in HSCs in a p21-knockout mouse model, we employed p21-tdTomato (tdT) mice to further elucidate its role in HSCs during homeostasis. The results showed that p21-tdT+ HSCs exhibited increased self-renewal capacity compared to p21-tdT− HSCs. Zbtb18, a transcriptional repressor, was upregulated in p21-tdT+ HSCs, and its knockdown significantly impaired the reconstitution capability of HSCs. Furthermore, p21 interacted with ZBTB18 to co-repress the expression of cKit in HSCs and thus regulated the self-renewal of HSCs. Our data provide novel insights into the physiological role and mechanisms of p21 in HSCs during homeostasis independent of its conventional role as a cell cycle inhibitor.
Existence and Nonexistence of Solutions of Minkowski-Curvature Problems in Exterior Domains
Authors: Chen Tianlan , Wu Haiyi
Published: May 2024

In this paper, we show some nonexistence results of radial solutions for the following Minkowski curvature problems in an exterior domain: $$ \begin{cases} \ -\text{div} \big(\phi(\nabla v(x))\big)=k(x)f(v(x)), \quad\quad x\in\Omega,\\ \ v=0\ \text{on} \ \partial\Omega, \qquad\lim\limits_{x\rightarrow\infty}v(x)=0\\ \end{cases} $$ for R sufficiently large, where $\phi(s)=\frac{s}{\sqrt{1-s^{2}}}$ for $s\in{\mathbb R}$ with $s^2\lt1,$  $\Omega=\{x\in{{\mathbb R}^{N}}:\ |x| \gt R\}$, $N\geq3$ is an integer, $|\cdot|$ denotes the Euclidean norm on $\mathbb{R}^{N}$, R is a positive parameter, $f:\mathbb{R}\rightarrow\mathbb{R}$ is an odd and locally Lipschitz continuous function and $k \in C^{1}(\mathbb{R}^{+},\ \mathbb{R}^{+})$ with $\mathbb{R}^{+}=(0, +\infty)$. We also apply the fixed-point index theory to establish the existence of positive radial solutions of the above problems for R sufficiently small.
Multidimensional neural representations of social features during movie viewing
Authors: Lee Masson Haemy , Chang Lucy , Isik Leyla
Published: May 2024

The social world is dynamic and contextually embedded. Yet, most studies utilize simple stimuli that do not capture the complexity of everyday social episodes. To address this, we implemented a movie viewing paradigm and investigated how everyday social episodes are processed in the brain. Participants watched one of two movies during an MRI scan. Neural patterns from brain regions involved in social perception, mentalization, action observation and sensory processing were extracted. Representational similarity analysis results revealed that several labeled social features (including social interaction, mentalization, the actions of others, characters talking about themselves, talking about others and talking about objects) were represented in the superior temporal gyrus (STG) and middle temporal gyrus (MTG). The mentalization feature was also represented throughout the theory of mind network, and characters talking about others engaged the temporoparietal junction (TPJ), suggesting that listeners may spontaneously infer the mental state of those being talked about. In contrast, we did not observe the action representations in the frontoparietal regions of the action observation network. The current findings indicate that STG and MTG serve as key regions for social processing, and that listening to characters talk about others elicits spontaneous mental state inference in TPJ during natural movie viewing.
Australasian Sleep Association 2024 guidelines for sleep studies in adults
Authors: Ellender Claire M , Ruehland Warren R , Duce Brett , Joyce Rosemarie , Worsnop Christopher , Mercer Jeremy , Naughton Matthew , Hukins Craig A , Wheatley John , Cunnington David
Published: May 2024

Executive summary: This document is a consensus statement of a subcommittee of experienced sleep physicians and scientists, tasked to review the literature and formulate recommendations on the indications, performance, and reporting of sleep studies, to update clinical practice from the 2017 Australasian Sleep Association (ASA) guidelines for sleep studies in adults (Douglas JA, Chai-Coetzer CL, McEvoy D, et al. Guidelines for sleep studies in adults - a position statement of the Australasian Sleep Association. Sleep Med. 2017;36(Suppl 1):S2–S22. doi:10.1016/j.sleep.2017.03.019). This document moves the focus beyond important discussions outlined in the 2017 guidelines, particularly surrounding the sensitivity and specificity of validated questionnaires and home sleep studies. The 2024 guide outlines the performance of the broad range of sleep testing available for the investigations of sleep disorders in adults including indications, strengths, limitations, and reporting standards.
Prevalence and mortality of haemophagocytic lymphohistiocytosis in dengue fever: a systematic review and meta-analysis
Authors: Ong Leong Tung , Balasubramaniam Roovam
Published: May 2024

Background

Haemophagocytic lymphohistiocytosis (HLH) is a rare complication of dengue fever with potentially life-threatening consequences and high mortality. Therefore, this study aims to investigate the prevalence, management and outcome of HLH in dengue fever.

Methods

The major electronic databases, including PubMed, ScienceDirect and Ovid SP, were searched from inception until 31 January 2024 to identify relevant studies. Pooled prevalence and mortality were calculated using the random-effects generic inverse variance model with a 95% CI. All the statistical analysis was conducted using R programming.

Results

A total of nine studies with 157 patients with HLH, 576 patients with severe dengue and 5081 patients with dengue fever were included in this meta-analysis. The prevalence of HLH in severe dengue (22.1%, 95% CI 8.07 to 48.0%) was significantly higher than the prevalence in dengue fever (3.12%, 95% CI 0.37 to 21.9%). The prevalence of HLH in severe dengue was higher in the paediatric population (22.8%, 95% CI 3.9 to 68.4%) compared with the adult population (19.0%, 95% CI 3.0 to 63.9%). The overall mortality rate was 20.2% (95% CI 9.7 to 37.2%).

Conclusion

The prevalence of dengue-associated HLH was low in patients with dengue fever but is significantly higher in patients with severe dengue and a high mortality rate.
First-Trimester Ultrasound Screening in Routine Obstetric Practice
Authors: Bromley Bryann , Platt Lawrence D.
Published: May 2024

Technologic advances and ultrasonographer–physician experience in fetal imaging have led to significant improvements in our ability to distinguish between normal and abnormal fetal structural development in the latter part of the first trimester. As a critical component of pregnancy care, assessment of fetal anatomy at the end of the first trimester with a standardized imaging protocol should be offered to all pregnant patients regardless of aneuploidy screening results because it has been demonstrated to identify approximately half of fetal structural malformations. Early identification of abnormalities allows focused genetic counseling, timely diagnostic testing, and subspecialist consultation. In addition, a normal ultrasound examination result offers some degree of reassurance to most patients. Use of cell-free DNA alone for aneuploidy screening while foregoing an accompanying early anatomic evaluation of the fetus will result in many anomalies that are typically detected in the first trimester not being identified until later in pregnancy, thus potentially diminishing the quality of obstetric care for pregnant individuals and possibly limiting their reproductive options, including pregnancy termination.
Biomechanical Effect of Different Posterior Fixation Techniques on Stability and Adjacent Segment Degeneration in Treating Thoracolumbar Burst Fracture With Osteoporosis
Authors: Zhang Guodong , Li Jianyi , Zhang Li , Song Jie , Shao Jiale , Lv Changlin , Bai Tianyu , Du Yukun , Xi Yongming
Published: May 2024

Study Design.

Finite element analysis.

Objective.

To investigate the biomechanical effect of four posterior fixation techniques on stability and adjacent segment degeneration in treating thoracolumbar burst fractures with osteoporosis.

Summary of Background Data.

In terms of stability and adjacent segment degeneration, there remains no consensus or guidelines on the optimal technique for the treatment of thoracolumbar burst fractures in patients with osteoporosis.

Materials and Methods.

Images of CT scans were imported into MIMICS and further processed by Geomagic to build three-dimensional models of the T10-L5 region. A v-shaped osteotomy was performed on the L1 vertebral body to simulate a burst fracture in the setting of osteoporosis. Subsequently, four fixation techniques were designed using SolidWorks software. Range of motion (ROM) of the global spine, ROM distribution, ROM of adjacent segment, Von Mises stress on adjacent intervertebral disks, and facet joints were analyzed.

Results.

Among the four groups, the cortical bone screw fixation (CBT) showed the highest global ROM at 1.86°, while long-segmented pedicle screw fixation (LSPS) had the lowest global ROM at 1.25°. The LSPS had the smallest percentage of ROM of fractured vertebral body to fixed segment at 75.04%, suggesting the highest stability after fixation. The maximum ROM of the adjacent segment was observed in the CBT at 1.32°, while the LSPS exhibited the smallest at 0.89°. However, the LSPS group experienced larger maximum stress on the adjacent intervertebral disks (9.60 MPa) and facet joints (3.36 MPa), indicating an increasing risk of adjacent segment disease.

Conclusion.

LSPS provided the greatest stability, while CBT provided the smallest amount of stability. However, the elevated stress on adjacent intervertebral disks and facet joints after LSPS fixation increased the possibility of adjacent segment degeneration. Cement-augmented pedicle screw fixation (CAPS) and combined cortical bone screw and pedicle screw fixation (CBT-PS) demonstrated significant biomechanical advantages in providing moderate fixation strength while reducing stress on the intervertebral disks and facet joints.
Photochemical Crosslinking of Tarsal Collagen as a Treatment for Eyelid Laxity: Evaluation in Ex Vivo Human Tissue
Authors: Manta Alexandra I. , Pop Nadja E. , Tripon Robert G. , Vultur Florina , Suzuki Shuko , Cordos Bogdan A. , Radu Carmen C. , Hogea Timur , Carasca Cosmin , Horvath Karin U. , Muntean George A. , Siserman Vasile C. , Cotoi Ovidiu S. , Radford Mark H. B. , Chirila Traian V.
Published: May 2024

Purpose:

Experimental investigation in human eyelids to confirm that exposing excised tarsal plates to ultraviolet-A radiation can induce a stiffening effect through the riboflavin-photosensitized crosslinking of tarsal collagen.

Methods:

Thirteen tarsal plates excised from nonfrozen human cadavers were irradiated with ultraviolet-A rays (365 nm wavelength) at an irradiance of 75 mW/cm2 for 3 minutes, equivalent to a radiation fluence of 13.5 J/cm2, in the presence of a riboflavin derivative as a photosensitizer. The tensile stress (strength) and Young’s modulus (stiffness) of both nonirradiated and irradiated specimens were measured with the BioTester 5000 in the uniaxial mode at a strain of 10% and analyzed statistically. Individual specimens excised from 2 cadavers were also examined by routine histopathologic protocols to assess the effect of radiation on the Meibomian glands and collagen organization.

Results:

The irradiation enhanced both stiffness and strength of the human tarsal specimens, the difference between the test samples and controls being statistically significant (p < 0.0002 for n = 13). Histology indicated no damage to tarsal connective tissue or to Meibomian glands, and revealed a more compact packing of the collagen network located around the glands, which may be beneficial. The existence of collagen compaction was also supported by the reduction of samples’ thickness after irradiation (p = 0.0645).

Conclusions:

The irradiation of tarsal tissue with ultraviolet-A light of tarsus appears to be a safe and effective method for reducing eyelid laxity in human patients.
Research progress on ultrastructure of Treponema pallidum subspecies pallidum
Authors: Wang Si-Ning , Zhang Rui-Li
Published: May 2024

The ultrastructure of Treponema pallidum, the causative pathogen of syphilis, remains unclarified because of the difficulty of long-term culture in vitro. However, research on the ultrastructure of T. pallidum has made great progress in recent years with the success of long-term culture of T. pallidum in vitro and the development of gene sequencing technology and electron microscopy. This review summarizes the research progress on the ultrastructure of T. pallidum.
Cultivating a “Feminine” Surgical Culture: Lessons from Indonesia
Authors: Sanders Hayley M. , Cullen Clara M. , Benítez Trista M. , Prasetyono Theddeus , Chung Kevin C.
Published: May 2024

Background:

Although the number of female physicians in the United States has been increasing, most practicing surgeons in the United States are men. By contrast, Indonesia has achieved notable gender parity among surgeons, with the number of women practicing as plastic surgeons projected to soon surpass that of men. Achieving greater female representation in plastic surgery is important for delivering high-quality care, especially in the face of physician shortages and high burnout rates.

Methods:

This survey study was conducted at the 26th annual scientific meeting of the Indonesian Association of Plastic Reconstructive and Aesthetic Surgeons, in Manado, Indonesia, in August 2023. Respondents were asked about their perceptions of plastic surgery, mentorship, career motivations, and caregiving responsibilities. Responses were scored using a 3-point Likert scale of agreement with statements (disagree, neutral, or agree); χ2 and Fisher exact tests were performed to assess differences in responses by sex.

Results:

In this validated survey of 175 plastic surgeon trainees and attendings, there were no significant differences between sexes in the perception and roles of mentorship in preparing for a career in plastic surgery. Respondents from both sexes espoused optimistic views on work–life balance items, including time for family and friends and flexibility of work schedules.

Conclusions:

Indonesia can serve as a model for encouraging greater gender parity in plastic surgery. Community-level interventions, such as family leave policies, childcare provisions, and initiatives to promote an inclusive culture, will create a more supportive workplace to increase women’s representation in plastic surgery in the United States and around the world.
FDG PET/CT Findings of Primary Pulmonary Choriocarcinoma in a Postmenopausal Woman
Authors: Zhang Jun , Dong Aisheng , Wang Yang
Published: May 2024

Choriocarcinomas usually occur in the genital tracts of reproductive-age women after a gestational event. Primary pulmonary choriocarcinoma is very rare. We describe FDG PET/CT findings of primary pulmonary choriocarcinoma with multiple intrapulmonary metastases in a postmenopausal woman with elevated serum beta human chorionic gonadotropin level. On FDG PET/CT, the large primary lung tumor showed intense FDG uptake (SUVmax, 46), and the small intrapulmonary metastases showed variable FDG uptake (SUVmax, 27). Primary pulmonary choriocarcinoma should be included in the differential diagnosis of FDG-avid pulmonary lesions with elevated serum beta human chorionic gonadotropin levels, including metastatic choriocarcinoma and lung cancer.
Upper Extremity Nerve Transfers for Treatment of Nerve Injury After Cervical Spine Surgery
Authors: Doucet Véronique M. , Clark Tod A. , Giuffre Jennifer L.
Published: May 2024

Purpose

Nerve transfers to restore or augment function after spinal cord injury is an expanding field. There is a paucity of information, however, on the use of nerve transfers for patients having undergone spine surgery. The incidence of neurologic deficit after spine surgery is rare but extremely debilitating. The purpose of this study was to describe the functional benefit after upper extremity nerve transfers in the setting of nerve injury after cervical spine surgery.

Methods

A single-center retrospective review of all patients who underwent nerve transfers after cervical spine surgery was completed. Patient demographics, injury features, spine surgery procedure, nerve conduction and electromyography study results, time to referral to nerve surgeon, time to surgery, surgical technique and number of nerve transfers performed, complications, postoperative muscle testing, and subjective outcomes were reviewed.

Results

Fourteen nerve transfers were performed in 6 patients after cervical spine surgery. Nerve transfer procedures consisted of a transfer between a median nerve branch of flexor digitorum superficialis into a biceps nerve branch, an ulnar nerve branch of flexor carpi ulnaris into a brachialis nerve branch, a radial nerve branch of triceps muscle into the axillary nerve, and the anterior interosseous nerve into the ulnar motor nerve. Average patient age was 55 years; all patients were male and underwent surgery on their left upper extremity. Average referral time was 7 months, average time to nerve transfer was 9 months, and average follow-up was 21 months. Average preoperative muscle grading was 0.9 of 5, and average postoperative muscle grading was 4.1 of 5 (P < 0.00001).

Conclusions

Upper extremity peripheral nerve transfers can significantly help patients regain muscle function from deficits secondary to cervical spine procedures. The morbidity of the nerve transfers is minimal with measurable improvements in muscle function.
Application of Carbon Nanoparticles in Transoral Endoscopic Thyroidectomy Vestibular Approach for Unilateral Papillary Thyroid Cancer
Authors: Zhang Wei-dong , Le Qi , Yu Ke-jie , Wang Ying-chun , Wu Xian-jiang
Published: May 2024

Background:

Transoral endoscopic thyroidectomy vestibular approach (TOETVA) is newly applied technology. Carbon nanoparticles (CNs) are novel lymph node tracers that have been widely used in China to help remove central lymph nodes (CLNs) and protect the parathyroid glands (PGs) in open thyroid cancer surgery. This study is to evaluate the effectiveness and safety of CNs in TOETVA.

Materials and Methods:

A total of 158 patients who underwent TOETVA with unilateral papillary thyroid carcinoma were enrolled in this study from March 2019 to February 2022. The participants were divided into a CNs group (n=88) and a control group (n=70), based on whether they received a intraoperative injection of CNs or not. Meanwhile, the CNs group were additionally divided into 2 subgroups, leakage subgroup (n=26) and standard subgroup (n=62). The 2 groups and subgroups were compared in terms of patient characteristics, perioperative clinical results, and postoperative outcomes.

Results:

All common metrics had no significant differences were found between the CNs group and the control group (P>0.05). The standard subgroup of CNs group had advantage over the control group on PGs identification (59/62 vs. 59/70 for superior PG, 56/62 vs. 52/70 for inferior PG, P<0.05). Moreover, the standard subgroup harvested more CLNs than the control group (8.97±2.96 vs. 7.47±2.93, P<0.05). More operation time was spent on the leakage subgroup of CNs group than the control group (160.00±17.61 vs. 140.00±13.32, P<0.05). Meanwhile, the leakage subgroup had disadvantage on intraoperative hemorrhage (26.15±10.80 vs. 21.21±7.09, P<0.05) and hospital durations (4.96±0.72 vs. 4.57±0.69, P<0.05). Furthermore, the leakage group identified fewer inferior PG than the control group (7/26 vs. 52/70, P<0.05). Contrary to the standard subgroup, the CLNs of the leakage subgroup was also unsatisfactory compared with the control group (4.96±1.84 vs. 7.47±2.93, P<0.05).

Conclusions:

The application of CNs suspension tracing technology has a definite effect in TOETVA. It can improve the thoroughness of lymph node dissection in the central region and enhance recognition of the PG. However, refined extracapsular anatomy is indispensable to prevent CN leakage. Leaked CNs will also be counterproductive to the operation.
Sex differences emerge after the menopause transition: Females show accelerated decline in episodic memory for spatial context at midlife
Authors: LaPlume Annalise Aleta , Lissaman Rikki , Kearley Julia , Rajah Maria Natasha
Published: May 2024

Background and Objectives

The ability to remember past events in rich contextual detail (episodic memory) declines with advancing age, with accelerated decline around midlife. Past research indicates there may be sex differences in cognitive aging trajectories and risk for age-related neurodegenerative diseases, i.e. Alzheimer’s Disease. Yet, little is known about how biological sex affects episodic memory in the adult lifespan. We examined age differences in episodic memory for spatial context in males and females.

Research Design and Methods

192 adults aged 21 to 65 (M=44,SD=13, 134 females) completed a face-location task measuring spatial context memory (correct spatial context retrieval rates) and facial item memory (correct recognition rates), and the California Verbal Learning Test version II (CVLT-II) measuring verbal item memory (long free recall, cued recall, and recognition rates). Changepoint regression analysis was used to estimate the slope of memory across age and any significant shifts in the slope (indicating critical transition periods).

Results

Regression analyses revealed that the best-fitting model for females on spatial context memory accuracy was a one-changepoint model, with gradual decline of 2% (SE=1) fewer correct responses per year of age from age 21 until age 50 (95% CI 41, 58), shifting to more rapid decline of 4% (SE=1) fewer correct responses per year of age until age 65. The best fitting model for males on spatial context memory accuracy was linear, with no significant changes across ages. The best fitting models for both sexes were linear for facial item memory accuracy, spatial context memory and facial item memory reaction times, and verbal item memory accuracy.

Discussion and Implication

Males and females show similar decline on spatial context memory from young adulthood until midlife, after which females show greater decline than males. Importantly, disaggregating by sex indicated that past midlife effects on episodic memory for context may be driven by a specific group of females (post-menopausal), as accelerated decline occurred at the same time as menopause in midlife females and did not occur in midlife males.

Translational Significance

Problem Addressed

We use changepoint regression to examine how biological sex influences age differences in remembering the context of past events (episodic memory).

Main outcome

Females, but not males, showed significantly greater decline on spatial context memory (i.e., correctly recalling the location of previously learned information) after age 50, which aligns with the time of menopause in midlife females.

Implications for Translation

Episodic memory for spatial context shows accelerated decline in females after midlife compared to before midlife, but not in midlife males, indicating the potential influence of menopause on aging of memory.
Fluctuation-Driven Morphological Patterning: A Novel Approach to Morphogenesis
Authors: Agam Oded , Braun Erez
Published: May 2024

Recent experimental investigations intoHydraregeneration revealed a remarkable phenomenon: the morphological transformation of a tissue fragment from the incipient spherical configuration to a tube-like structure - the hallmark of a matureHydra- has the dynamical characteristics of a first-order phase-transition, with calcium field fluctuations within the tissue playing an essential role. This morphological transition was shown to be generated by activation over an energy barrier within an effective potential that underlies morphogenesis. Inspired by this intriguing insight, we propose a novel mechanism where stochastic fluctuations drive the emergence of morphological patterns. Thus, the inherent fluctuations determine the nature of the dynamics and are not incidental noise in the background of the otherwise deterministic dynamics. Instead, they play an important role as a driving force that defines the attributes of the pattern formation dynamics and the nature of the transition itself. Here, we present a simple model that captures the essence of this novel mechanism for morphological pattern formation. Specifically, we consider a one-dimensional tissue arranged as a closed contour embedded in a two-dimensional space, where the local curvature of the contour is coupled to a non-negative scalar field. An effective temperature parameter regulates the strength of the fluctuations in the system. The tissue exhibits fluctuations near a circular shape at sufficiently low coupling strengths, but as the coupling strength exceeds some critical value, the circular state becomes unstable. The nature of the transition to the new state, namely whether it is a first-order-like or a second-order-like transition, depends on the temperature and the effective cutoff on the wavelength of the spatial variations in the system. It is also found that entropic barriers separate the various metastable states of the system.
scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison
Authors: Ferrena Alexander , Zheng Xiang Yu , Jackson Kevyn , Hoang Bang , Morrow Bernice , Zheng Deyou
Published: May 2024

Single-cell transcriptomics profiling has increasingly been used to evaluate cross-group differences in cell population and cell-type gene expression. This often leads to large datasets with complex experimental designs that need advanced comparative analysis. Concurrently, bioinformatics software and analytic approaches also become more diverse and constantly undergo improvement. Thus, there is an increased need for automated and standardized data processing and analysis pipelines, which should be efficient and flexible too. To address these, we develop thesingle-cellDifferentialAnalysis andProcessingPipeline (scDAPP), a R-based workflow for comparative analysis of single cell (or nucleus) transcriptomic data between two or more groups and at the levels of single cells or “pseudobulking” samples. The pipeline automates many steps of pre-processing using data-learnt parameters, uses previously benchmarked software, and generates comprehensive intermediate data and final results that are valuable for both beginners and experts of scRNA-seq analysis. Moreover, the analytic reports, augmented by extensive data visualization, increase the transparency of computational analysis and parameter choices, while facilitate users to go seamlessly from raw data to biological interpretation.

Availability and Implementation

scDAPP is freely available for non-commercial usage as an R package under the MIT license. Source code, documentation and sample data are available at the GitHub (https://github.com/bioinfoDZ/scDAPP).
Geometrically-engineered organoid units and their assembly for pre-construction of organ structures
Authors: Kadotani Ayaka , Hayase Gen , Yoshino Daisuke
Published: May 2024

Regenerative medicine is moving from the nascent to the transitional stage as researchers are actively engaged in creating mini-organs from pluripotent stem cells to construct artificial models of physiological and pathological conditions. Currently, mini-organs can express higher-order functions, but their size is limited to the order of a few millimeters. Therefore, one of the ultimate goals of regenerative medicine, “organ replication and transplantation with organoid,” remains a major obstacle. 3D bioprinting technology is expected to be an innovative breakthrough in this field, but various issues have been raised, such as cell damage, versatility of bioink, and printing time. In this study, we established a method for fabricating, connecting, and assembling organoid units of various shapes independent of cell type, extracellular matrix, and adhesive composition (unit construction method). We also fabricated kidney tissue-like structures using three types of parenchymal and interstitial cells that compose the human kidney and obtained findings suggesting the possibility of crosstalk between the units. We anticipate that this technique will bring us closer to the realization of highly efficient and rapid fabrication of full-scale organoids that can withstand organ transplantation.
Impact Of Learned Helplessness On Cognitive Performance And Resting-State Connectivity: An fMRI Study
Authors: Lechat Pierre , Alonso-Ortiz Eva , Bassetto Jean-Samuel
Published: May 2024

1.1

Learned helplessness (LH) is the phenomenon of resignation in the face of a problematic situation and is caused by the feeling of lacking control in a situation due to internal or external factors. This means that an individual does not seek to resolve the situation they are confronted with and consciously or unconsciously chooses to be passive. The Dorsal Raphe Nucleus (DRN) core could be at the root of the persistent action of the LH phenomenon and influences regions such as the striatum and amygdala. It is thought that the LH phenomenon could affect self-perception and it has been shown that the default mode network (DMN) is often associated with self-reflection during the resting state (RS) phase. It is therefore possible that LH influences both self-perception and the DMN. Based on previous studies, we investigated how LH affects participants. We used functional MRI (fMRI) to test this hypothesis. Participants were divided into two groups, subjected to solvable (control group), and solvable plus unsolvable (LH group) cognitive tasks. We also measured electrodermal signals, OCEAN (Openness, Conscientiousness, Extraversion, Agreeableness, Neuroticism) personality scores, variables related to the anagram resolution, and related these to LH. The study revealed significant differences in the RS contrast between the two groups, with the Posterior Cingulate Cortex (PCC) (an area of the DMN) being more connected to the DRN in the LH group than in the control group, and a portion of the Superior Temporal Gyrus being more connected to the PCC in the control group than in the LH group. These results suggest that LH may have a direct impact on the DMN and could lead to the start of long-term changes.
Automatic Lymph Nodes Segmentation and Histological Status Classification on Computed Tomography Scans Using Convolutional Neural Network
Authors: Shevtsov Alexey , Tominin Iaroslav , Tominin Vladislav , Malevanniy Vsevolod , Esakov Yury , Tukvadze Zurab , Nefedov Andrey , Yablonskii Piotr , Gavrilov Pavel , Kozlov Vadim , Blokhina Mariya , Nalivkina Elena , Gombolevskiy Victor , Vasilev Yuriy , Dugova Mariya , Chernina Valeria , Omelyanskaya Olga , Reshetnikov Roman , Blokhin Ivan , Belyaev Mikhail
Published: May 2024

Abstract

Lung cancer is the second most common type of cancer worldwide, making up about 20% of all cancer deaths with less than 10% 5-year survival rate for the very late stage. The recent guidelines for the most common non-small-cell lung cancer (NSCLC) type recommend performing staging based on the 8th edition of TNM classification, where the mediastinal lymph node involvement plays a key role. However, most of the non-invasive methods have a very limited level of sensitivity and are relatively accurate, but invasive methods can be contradicted for some patients. Current advances in Deep Learning show great potential in solving such problems. Still, most of these works focus on the algorithmic side of the problem, not the clinical relevance. Moreover, none of them addressed individual lymph node malignancy classification problem, restricting the indirect analysis of the whole study, and limiting the interpretability of the result without giving an option for cliniciansto validate the result. This work mitigates these gaps, proposing a multi-step algorithm for each visible mediastinal lymph node segmentation and assessing the probability of its involvement in themetastatic process, using the results of histological verification on training. The developed pipelineshows 0.74 ± 0.01 average Recall with 0.53 ± 0.26 object Dice Score for the clinically relevant lymph nodes segmentation task and 0.73 ROC AUC for patient’s N-stage prediction, outperformingtraditional size-based criteria.
Nowhere to Go: A parallel convergent mixed methods study examining the health of people who experience emergency shelter service restrictions
Authors: Bansal Suraj , Pelino Stephanie Di , Pierre Jammy , Chan Kathryn , Lee Amanda , Liu Rachel , Mancini Olivia , Pitkas Avital , Kouyoumdjian Fiona , Lamarche Larkin , Lennox Robin , McIlveen Marcie , O’Shea Timothy , Bodkin Claire
Published: May 2024

Background

Emergency shelters offer temporary sleeping accommodation to people deprived of housing and connect them to services. Service restriction is the practice of limiting or denying someone access to emergency shelters. This parallel convergent mixed methods study describes the characteristics, healthcare utilization, and morbidity of people experiencing service restrictions in Hamilton, Ontario, and explores the relationship between health and service restriction.

Methods

We recruited 20 people who had experienced service restriction and accessed healthcare from the Shelter Health Network clinic. We conducted semi-structured interviews and performed reflexive thematic analysis. We reviewed participants’ medical records from January 1, 2018 to December 31, 2021 to calculate simple descriptive statistics. Mixing our qualitative and quantitative results, we generated narrative metainferences. We employed community-based research principles, including a research team with lived and living experiences of being service restricted, implementing service restrictions, or providing care to people experiencing service restrictions.

Results

We generated six themes: 1) Losing your home shouldn’t mean losing your humanity, 2) Where am I supposed to go?, 3) The snakes and ladders of service restrictions, 4) Abandoned to survive, 5) Constantly criminalized, 6) Harnessing the wisdom of community. Participants averaged 17.4 primary care visits, 11 emergency department visits, and 4 hospital admissions over 4 years. The most common reasons for visit were infections, traumatic injuries, and substance use-related concerns. Narrative metainferences highlighted how people experience dehumanization when accessing shelters or healthcare; how service restrictions and encampment living contribute to infections; the lack of practical supports for people using substances in shelters; the ubiquitous criminalization of people experiencing homelessness; and the care people practice for one another to reduce substance-related harms.

Conclusions

Participants’ high healthcare need and utilization was shaped by criminalization, stigma, societal abandonment, and abstinence-based substance use policies. Participants practiced care for themselves and others to navigate these barriers. Shelters should have a transparent service restriction process and employ harm reduction practices. Healthcare should provide affirming and accessible treatment for common conditions. Social and health services must contend with broader social forces while building on the strengths of people with lived experience to improve the health of people who are service restricted.
Risk prediction tools for pressure injury occurrence: An umbrella review of systematic reviews reporting model development and validation methods
Authors: Hillier Bethany , Scandrett Katie , Coombe April , Hernandez-Boussard Tina , Steyerberg Ewout , Takwoingi Yemisi , Velickovic Vladica , Dinnes Jacqueline
Published: May 2024

Background

Pressure injuries (PIs) place a substantial burden on healthcare systems worldwide. Risk stratification of those who are at risk of developing PIs allows preventive interventions to be focused on patients who are at the highest risk. The considerable number of risk assessment scales and prediction models available underscore the need for a thorough evaluation of their development, validation and clinical utility.

Our objectives were to identify and describe available risk prediction tools for PI occurrence, their content and development and validation methods used.

Methods

The umbrella review was conducted according to Cochrane guidance. MEDLINE, Embase, CINAHL, EPISTEMONIKOS, Google Scholar and reference lists were searched to identify relevant systematic reviews. Risk of bias was assessed using adapted AMSTAR-2 criteria. Results were described narratively. All included reviews contributed to build a comprehensive list of risk prediction tools.

Results

We identified 32 eligible systematic reviews only seven of which described the development and validation of risk prediction tools for PI. Nineteen reviews assessed the prognostic accuracy of the tools and 11 assessed clinical effectiveness. Of the seven reviews reporting model development and validation, six included only machine learning models. Two reviews included external validations of models, although only one review reported any details on external validation methods or results. This was also the only review to report measures of both discrimination and calibration. Five reviews presented measures of discrimination, such as area under the curve (AUC), sensitivities, specificities, F1 scores and G-means. For the four reviews that assessed risk of bias assessment using the PROBAST tool, all models but one were found to be at high or unclear risk of bias.

Conclusions

Available tools do not meet current standards for the development or reporting of risk prediction models. The majority of tools have not been externally validated. Standardised and rigorous approaches to risk prediction model development and validation are needed.

Registration

The protocol was registered on the Open Science Framework (https://osf.io/tepyk).
Vertebral and Carotid Artery Stenosis after Irradiation Both Raise Ischemic Stroke Risk in Head and Neck Cancer Patients
Authors: Jiang Jian-Lin , Chang Joseph Tung-Chieh , Huang Bing-Shen , Chang Ting-Yu , Sung Pi-Shan , Wei Yi-Chia , Lin Chien-Yu , Yeh Chih-Hua , Fan Kang-Hsing , Liu Chi-Hung
Published: May 2024

Purpose

To study the risk of ischemic stroke (IS) following carotid (CAS) or vertebral artery stenosis (VAS) in head and neck cancer (HNC) patients after radiation therapy (RT).

Methods

We included HNC patients who received RT between 2010 and 2023. They underwent regular head and neck imaging monitoring to evaluate cancer recurrence at the department of radiation-oncology and vascular examinations at the department of neurology. Patients were initially divided into nasopharyngeal carcinoma (NPC) and non-NPC groups. The primary outcome was the occurrence of IS after RT, and the secondary outcomes included the development of >50% CAS or >50% VAS after RT. Cox regression and Kaplan–Meier analyses were conducted to compare the outcomes of the study groups. Further analysis was conducted based on the presence or absence of >50% CAS or >50% VAS during the follow-up period.

Results

Of the 1,423 HNC patients, 19%, 6.8%, and 2.3% developed >50% CAS, >50% VAS, and IS during a 58-month follow-up. Compared with the NPC group, the non-NPC group exhibited a higher incidence of >50% CAS (25.4% vs. 10.7%, p<0.001) and >50% VAS (8.8% vs. 4.3%, p<0.001), but similar risks of IS. In patients with HNC, >50% CAS (adjusted hazard ratio [HR]=3.21, 95% confidence interval [CI]=1.53-6.71), and >50% VAS (adjusted HR=2.89, 95% CI=1.28-6.53) were both the independent predictors of IS. In the patients with NPC, >50% CAS was an independent predictor of anterior circulation IS (adjusted HR=4.39, 95% CI=1.17-16.47). By contrast, >50% VAS emerged as a predictor of posterior circulation IS in both the NPC (adjusted HR=15.02, 95% CI=3.76-60.06) and non-NPC groups (adjusted HR=13.59, 95% CI=2.21-83.46).

Conclusion

HNC patients with >50% CAS or >50% VAS after RT had an increased risk of IS within their corresponding vascular territory. CAS is a major predictor of IS in NPC patients, whereas VAS is a major predictor of IS in both NPC and non-NPC patients.
Statin Initiation and early stroke recurrence in the POINT Trial Population
Authors: Azizi Elham , Prabhakaran Shyam , Brorson James R.
Published: May 2024

Background and Purpose

Benefits of statin therapy in reducing the long-term risk of ischemic stroke are well-established, but the immediate effects of statin therapy on early stroke recurrence after an initial ischemic event are less clear.

Methods

In this secondary analysis of POINT data, we evaluated the effects of statins on early stroke recurrence (within 7 days) and recurrence over 90 days. We also examined the effect of early statin initiation in the subgroup of subjects not on statins prior to the index event using logistic and proportional hazards models.

Results

In the POINT trial, 175 of 267 (65.5%) of ischemic stroke recurrences were early (within 7 days). Baseline statin treatment at the time of study entry was marginally associated with a decrease in the odds of early ischemic stroke recurrence in adjusted logistical regression analysis (OR 0.70, 95% CI 0.50-0.99, p=0.04), but with a non-significant effect in adjusted Cox proportional hazard analysis (HR=0.72, 95% CI 0.52–1.01, p=0.05). In the subset of subjects not taking statin medications at baseline, initiation of statin treatment had no significant effect on the rate of early stroke recurrence (adjusted HR 0.80, 95% CI 0.54–1.20, p=0.22).

Conclusion

In the POINT trial population, prior treatment with statin was weakly associated with decreased risk of early recurrence of stroke. However initiating statin treatment had no detectable effect in reducing risk of early stroke recurrence. The POINT trial provides no evidence for an immediate protective effect of statins against stroke recurrence.
A description of Lineage 1Mycobacterium tuberculosisfrom Papua, Indonesia
Authors: Djunaedy Hanif A. K. , Febinia Clarissa A. , Hamers Raph L. , Baird Kevin , Elyazar Iqbal , Thuong Nguyen Thuy Thuong , Trimarsanto Hidayat , Malik Safarina G. , Thwaites Guy , van Crevel Reinout , Alisjahbana Bachti , Chaidir Lidya , Ashton Philip M.
Published: May 2024

Indonesia has the third highest number of tuberculosis (TB) patients infected with Mycobacterium tuberculosis (MTB) Lineage 1 (L1). Most of these MTB L1 cases can be found in Indonesia’s remote easternmost province of Papua, one of Indonesia’s most underdeveloped provinces with a particularly high burden for TB. In this study, we sequenced and described 42MTBL1 isolates from a well-characterized cohort of patients. We found a genetically diverseMTBL1 population with no association between pathogen genetic relatedness and place of residence or pathogen genetic relatedness and patient ethnicity, which could reflect mixing between different locales and ethnicities or our low sampling fraction. Only a small number showed genetic variants associated with drug resistance (5/42, 11.9%), probably due to a lack of effective treatment programs. The Papuan isolates showed similarities to other Island Southeast Asian Countries due to the high proportion of L1.2.1.2.1 (30/42, 71.4%), especially East Timor and the Philippines. This study fills a research gap of MTB L1 in Indonesian Papua and should serve as a stepping stone for further research in the region.