bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatic inflammatory pseudotumor-like follicular dendritic cell tumor with hepatic lymphoma history
Authors: Li Jiang , Tao Hai-su , Chen Dong , Huang Zhi-yong , Zhang Er-lei 
Published: October 2021

Abstract

Rationale:
Hepatic inflammatory pseudotumor (IPT)-like follicular dendritic cell (FDC) sarcoma is a very rare disease. Till now, only 19 cases were reported in the English literature. However, the coexistence of IPT-like sarcoma and non-Hodgkin lymphoma (NHL) in the same patient has never been reported. In this report, we presented a case of hepatic IPT-like FDC with hepatic NHL history of which both were successfully resected.

Patient concerns:
We reported a case of a 47-year-old male patient who presented with right upper abdominal discomfort. Nineteen years ago, he underwent liver resection of segment VII for hepatic NHL (B-cell lymphoma). He had a history of chronic hepatitis B virus infection. Serum alpha fetoprotein level was normal. However, imaging studies revealed a well-circumscribed, solid mass in the right hepatic lobe, he came back to the clinic because he was worried about a recurrence of the B-cell lymphoma.

Diagnoses:
Based on the patient's past medical history and magnetic resonance imaging results, and he was diagnosed as hepatocellular carcinoma or hepatic NHL preoperatively.

Interventions:
Right hemi-hepatectomy was performed on this patient.

Outcomes:
Histological report showed features of a mixture of chronic inflammatory cells and variable amounts of spindle cells. Also, immuno-histo-chemical studies demonstrated that all the tumor cells showed strong nuclear in situ labeling for EBV-encoded small RNAs and strongly positive stainings with CD21 and CD35. The patient tolerated the surgery well, recovered smoothly and he was discharged on postoperative day 7 (day 7). The patient is still disease free after a follow-up of over 50 months.

Conclusions:
To our knowledge, this is the first report demonstrating hepatic IPT-like FDC sarcoma in a patient with primary hepatic NHL history. In regards to treatment, complete surgical resection should be performed and would acquire excellent long-term outcomes.
Workplace Predictors of Quality and Safe Patient Care Delivery Among Nurses Using Machine Learning Techniques
Authors: Havaei Farinaz , Ji Xuejun Ryan , Boamah Sheila A. 
Published: October 2021

Background:
Working in unhealthy environments is associated with negative nurse and patient outcomes. Previous body of evidence in this area is limited as it investigated only a few factors within nurses' workplaces.

Purpose:
The purpose of this study was to identify the most important workplace factors predicting nurses' provision of quality and safe patient care using a 13-factor measure of workplace conditions.

Methods:
A cross-sectional correlational survey study involving 4029 direct care nurses in British Columbia was conducted using random forest data analytics methods.

Results:
Nurses' reports of healthier workplaces, particularly workload management, psychological protection, physical safety and engagement, were associated with higher ratings of quality and safe patient care.

Conclusion:
These workplace conditions are perceived to impact patient care through influencing nurses' mental health. To ensure a high standard of patient care, data-driven policies and interventions promoting overall nurse mental health and well-being are urgently required.
Weight-bearing status may influence rates of radiographic healing following reamed, intramedullary fixation of diaphyseal femur fractures
Authors: Flanagan Christopher D. , Joseph Noah M. , Copp Jonathan , Romeo Nicholas , Alfonso Nicholas , Hirschfeld Adam 
Published: October 2021

Abstract

Objective:
To investigate the effect of weight-bearing status on radiographic healing of diaphyseal femur fractures.

Design:
Retrospective 1:1 matched cohort study.

Setting:
Single-level 1 trauma center.

Participants:
One-hundred forty-four (N = 154) patients matched 1:1 in non-weight bearing (NWB) and weight-bearing as tolerated (WBAT) groups.

Intervention:
Non-weight bearing following reamed, statically locked intramedullary fixation of diaphyseal femur fracture, generally due to concurrent lower extremity fracture.

Main Outcome Measurement:
Postoperative radiographic healing using modified Radiographic Union Scale for Tibia fractures (mRUST) scores.

Results:
Groups were well matched on age, sex, race, prevalence of tobacco and alcohol use, diabetes mellitus status, Injury Severity Score, fracture pattern and shaft location, vascular injury, open fracture prevalence, and operative characteristics. Radiographic follow-up was similar between groups (231 vs 228 days, P = .914). At 6 to 8 weeks status post intramedullary fixation, the median mRUST score in the NWB group (9) was lower than that of the WBAT group (10) (mean: 8.4 vs 9.7, P = .004). At 12 to 16 weeks, the median mRUST in the NWB group (10) was again lower than the WBAT group (12) (mean: 9.9 vs 11.7, P = .003). The median number of days to 3 cortices of bridging callous was 85 in the WBAT group, compared with 122 in the NWB group (P = .029). Median time to mRUST scores of 12 (111 vs 162 days, P = .008), 13 (218 vs 278 days, P = .023), and 14 (255 vs 320 days, P = .028) were all longer in the NWB group compared with the WBAT group.

Conclusions:
Non-weight bearing after intramedullary fixation of diaphyseal femur fractures delays radiographic healing, with median time to 3 cortices of bridging callous increased from 85 days in WBAT groups to 122 days in NWB groups. These results provide clinicians with an understanding of the expected postoperative course, as well as further support the need to expeditiously advance weight-bearing status.

Level of Evidence: IV
Description and Functional Outcomes of a Novel Interdisciplinary Rehabilitation Program for Hospitalized Patients With COVID-19
Authors: Patel Nija , Steinberg Chelsea , Patel Ruchi , Chomali Cheryl , Doulatani Gargi , Lindsay Leroy , Jaywant Abhishek 
Published: October 2021

Objectives
The aims of the study were to describe an interdisciplinary inpatient rehabilitation program for patients recovering from COVID-19 and to evaluate functional outcomes.

Design
This is an analysis of retrospective data captured from the electronic health record of COVID-19 patients admitted to the rehabilitation unit (N = 106). Rehabilitation approaches are described narratively. Functional gain was evaluated using the Activity Measure for Postacute Care 6 Clicks, basic mobility and daily activities.

Results
Interdisciplinary approaches were implemented to address the medical, physical, communication, cognitive, and psychosocial needs of COVID-19 patients. COVID-19 patients exhibited significant improvements in basic mobility (Activity Measure for Postacute Care for basic mobility, P < 0.001, Cohen d = 1.35) and daily activities (Activity Measure for Postacute Care for daily activities, P < 0.001, Cohen d = 1.06) from admission to discharge. There was an increase in ambulatory distance as well as the percentage of the patients who were able to breathe on room air. At discharge, fewer patients required supplemental oxygen on exertion. Eighty percent of the patients were discharged home after an average length of stay of 17 days. Greater functional improvement was associated with younger age, longer intubation duration, and participation in psychotherapy, but not a history of delirium during hospitalization.

Conclusions
Early rehabilitation is associated with improved mobility and independence in activities of daily living after COVID-19.
The Hirsch Index and Self-Citation in Academic Physiatry Among Graduate Medical Education Program Directors
Authors: Pfirrman Scott J. , Yheulon Christopher G. , Parziale John R. 
Published: October 2021

Abstract
The Hirsch Index is a measure of academic productivity which captures both the quantity and quality of an author’s output. A well-accepted bibliometric, the Hirsch Index still may be influenced by self-citation, which has been assessed in other medical and surgical specialties. This study aims to evaluate research output and self-citation in physiatry, establishing a benchmark for the field, in addition to identifying differences between physical medicine and rehabilitation subspecialties. This study identified physical medicine and rehabilitation residency and fellowship program directors and analyzed the number of publications, citations, self-citations, and h-indices. A total of 169 program directors were identified, and the mean number ± SD of publications, citations, and Hirsch Index for the cohort were 16.7 ± 29.5, 348 ± 753, and 5.7 ± 6.7, respectively. When self-citation was excluded, less than 2% of program directors (3 of 169) had changes in Hirsch Index greater than one integer, and none greater than two integers. The Hirsch Index remained unchanged for 90% (152 of 169). Spinal cord injury fellowship directors had significantly higher mean number of publications (28, P = 0.04), mean number of citations (672, P = 0.03), and Hirsch Index (9.2, P < 0.01; 95% confidence interval). Overall, self-citation is infrequent in physical medicine and rehabilitation, and spinal cord injury directors had more robust academic profiles.
Role of Adjuvant Therapy in Esophageal Cancer Patients After Neoadjuvant Therapy and Esophagectomy
Authors: Lee Yung , Samarasinghe Yasith , Lee Michael H. , Thiru Luxmy , Shargall Yaron , Finley Christian , Hanna Wael , Levine Oren , Juergens Rosalyn , Agzarian John 
Published: October 2021

Objective:The aim of this study was to analyze esophageal cancer patients who previously underwent neoadjuvant therapy followed by a curative resection to determine whether additional adjuvant therapy is associated with improved survival outcomes.Summary Background Data:Neoadjuvant therapy followed by surgery is the standard of care for locally advanced esophageal cancer, whereas adjuvant therapy is typically employed for patients with residual disease. However, the role of adjuvant therapy after a curative resection is still uncertain.Methods:MEDLINE, EMBASE, and CENTRAL databases were searched for studies comparing patients with esophageal cancer who underwent neoadjuvant therapy and curative resection with and without adjuvant therapy. Primary outcome was overall survival (OS), and random effects meta-analysis was conducted where appropriate. Grading of recommendations, assessment, development, and evaluation was used to assess the certainty of evidence.Results:Ten studies involving 6462 patients were included. When compared to patients who received neoadjuvant therapy and esophagectomy alone, adjuvant therapy groups experienced a significant decrease in mortality by 48% at 1 year (Risk Ratio (RR) 0.52, 95% confidence interval [CI] 0.41–0.65,P< 0.001,moderate certainty). This reduction in mortality was carried through to 5-year follow-up (RR 0.91, 95% CI 0.86–0.96,P< 0.001,moderate certainty). The difference between the adjuvant therapy and the control group was uncertain regarding the secondary outcomes.Conclusion:Adjuvant therapy after neoadjuvant treatment and esophagectomy with negative resection margins provide an improved OS at 1 and 5 years with moderate to high certainty of evidence, but the benefit for disease-free survival and locoregional/distal recurrence remain uncertain due to limited reporting of these outcomes.
Rotational Activity Around an Obstacle in 2D Cardiac Tissue in Presence of Cellular Heterogeneity
Authors: Konovalov Pavel , Mangileva Daria , Dokuchaev Arsenii , Solovyova Olga , Panfilov Alexander V. 
Published: October 2021

AbstractWaves of electrical excitation rotating around an obstacle is one of the important mechanisms of dangerous cardiac arrhythmias occurring in the heart damaged by post-infarction scar. Such a scar also has a border zone around it, which has electrophysiological properties different from the rest of normal myocardial tissue. Spatial patterns of wave rotation in the presence of such tissue heterogeneity are poorly studied. In this paper we perform a comprehensive numerical study of various regimes of rotation of a wave in a plane layer of the ventricular tissue around an obstacle surrounded by a gray zone. We use a TP06 cellular ionic model which reproduces the electrophysiological properties of cardiomyocytes in the left ventricle of human heart. We vary the extent of obstacle and gray zone and study the pattern of wave rotation and its period. We observed different regimes of wave rotation that can be subdivided into several classes: (1) functional rotation and (2) scar rotation regimes, which were identified in the previous studies, and new (3) gray zone rotation regime: where the wave instead of rotation around the obstacle, rotates around the gray zone (an area of tissue heterogeneity) itself. For each class, the period of rotation is determined by different factors, which we discuss and quantify. We also found that due to regional pathological remodeling of myocardial tissue, we can obtain additional regimes associated with dynamical instabilities of two types which may affect or not affect the period of rotation.
A cell-based screen identifies HDAC inhibitors as activators of RIG-I signaling
Authors: Fraile-Bethencourt Eugenia , Foss Marie H , Nelson Dylan , Malhotra Sanjay V , Anand Sudarshan 
Published: October 2021

AbstractEnhancing the immune microenvironment in cancer by targeting the nucleic acid sensors is becoming a potent therapeutic strategy. Among the nucleic acid sensors, activation of the RNA sensor Retinoic Acid-inducible Gene (RIG-I) using small hairpin RNAs has been shown to elicit powerful innate and adaptive immune responses. Given the challenges inherent in pharmacokinetics and delivery of RNA based agonists, we set out to discover small molecule agonists of RIG-I using a cell-based assay. To this end, we established and validated a robust high throughput screening assay based on a commercially available HEK293 reporter cell line with a luciferase reporter downstream of tandem interferon stimulated gene 54 (ISG54) promoter elements. We first confirmed that the luminescence in this cell line is dependent on RIG-I and the interferon receptor using a hairpin RNA RIG-I agonist. We established a 96-well and a 384-well format HTS based on this cell line and performed a proof-of-concept screen using an FDA approved drug library of 1200 compounds. Surprisingly, we found two HDAC inhibitors Entinostat, Mocetinostat and the PLK1 inhibitor Volasertib significantly enhanced ISG-luciferase activity. This luminescence was substantially diminished in the null reporter cell line indicating the increase in signaling was dependent on RIG-I expression. Combination treatment of tumor cell lines with Entinostat increased RIG-I induced cell death in a mammary carcinoma cell line that is resistant to either Entinostat or RIG-I agonist alone. Taken together, our data indicates an unexpected role for HDAC1,-3 inhibitors in enhancing RIG-I signaling and highlight potential opportunities for therapeutic combinations.
SVAT: Secure Outsourcing of Variant Annotation and Genotype Aggregation
Authors: Kim Miran , Wang Su , Jiang Xiaoqian , Harmanci Arif 
Published: October 2021

AbstractBackgroundSequencing of thousands of samples provides genetic variants with allele frequencies spanning a very large spectrum and gives invaluable insight for genetic determinants of diseases. Protecting the genetic privacy of participants is challenging as only a few rare variants can easily re-identify an individual among millions. In certain cases, there are policy barriers against sharing genetic data from indigenous populations and stigmatizing conditions.ResultsWe present SVAT, a method for secure outsourcing of variant annotation and aggregation, which are two basic steps in variant interpretation and detection of causal variants. SVAT uses homomorphic encryption to encrypt the data at the client-side. The data always stays encrypted while it is stored, in-transit, and most importantly while it is analyzed. SVAT makes use of a vectorized data representation to convert annotation and aggregation into efficient vectorized operations in a single framework. Also, SVAT utilizes a secure re-encryption approach so that multiple disparate genotype datasets can be combined for federated aggregation and secure computation of allele frequencies on the aggregated dataset.ConclusionsOverall, SVAT provides a secure, flexible, and practical framework for privacy-aware outsourcing of annotation, filtering, and aggregation of genetic variants. SVAT is publicly available for download from https://github.com/harmancilab/SVAT
Nanoparticle Shape Governs Immunomodulation of MUC1 Antigen to Develop Anti-cancer Vaccine
Authors: Toraskar Suraj , Chaudhary Preeti Madhukar , Kikkeri Raghavendra 
Published: October 2021

AbstractT-cell-dependent immunomodulation of carbohydrate antigens under benign conditions is the most promising approach for carbohydrate-based vaccine development. However, to achieve such adaptive immune responses, well-defined multifunctional nanocarriers loaded with immunogenic materials must be explored. Current efforts to use gold nanoparticles (AuNPs) as antigen carriers in vaccine development have conveniently introduced considerable diversity. Here, we show that the shape of AuNPs markedly influences carbohydrate-based antigen processing in murine dendritic cells (mDCs) and subsequent T-cell activation. In the study, CpG-adjuvant coated sphere-, rod-, and star-shaped AuNPs were conjugated to the tripodal Tn-glycopeptide antigen to study their DC uptake and the activation of T-cells in the DCs/T-cell co-culture assay. Our results showed that sphere- and star-shaped AuNPs displayed relatively weak receptor-mediated uptake but induced a high level of T helper-1 (Th1) biasing immune responses compared with rod-shaped AuNPs, showing that receptor-mediated uptake and cytokine secretion of nanostructures are two independent mechanisms. Significantly, the shapes of AuNPs and antigen/adjuvant conjugation synergistically work together to modulate the effective anti-Tn-glycopeptide immunoglobulin (IgG) antibody response after in vivo administration of the AuNPs. These results show that by varying the shape parameter, one can alter the immunomodulation, leading to the development of carbohydrate vaccines.
Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica
Authors: Baisya Dipankar , Ramesh Adithya , Schwartz Cory , Lonardi Stefano , Wheeldon Ian 
Published: October 2021

AbstractGenome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that could be broadly applied to fungal species, prokaryotes, and other non-conventional organisms.
Towards real-world neuroscience using mobile EEG and augmented reality
Authors: Krugliak Alexandra , Clarke Alex 
Published: October 2021

AbstractOur visual environment impacts multiple aspects of cognition including perception, attention and memory, yet most studies traditionally remove or control the external environment. As a result, we have a limited understanding of neurocognitive processes beyond the controlled lab environment. Here, we aim to study neural processes in real-world environments, while also maintaining a degree of control over perception. To achieve this, we combined mobile EEG (mEEG) and augmented reality (AR), which allows us to place virtual objects into the real world. We validated this AR and mEEG approach using a well-characterised cognitive response - the face inversion effect. Participants viewed upright and inverted faces in three EEG tasks (1) a lab-based computer task, (2) walking through an indoor environment while seeing face photographs, and (3) walking through an indoor environment while seeing virtual faces. We find greater low frequency EEG activity for inverted compared to upright faces in all experimental tasks, demonstrating that cognitively relevant signals can be extracted from mEEG and AR paradigms. This was established in both an epoch-based analysis aligned to face events, and a GLM-based approach that incorporates continuous EEG signals and face perception states. Together, this research helps pave the way to exploring neurocognitive processes in real-world environments while maintaining experimental control using AR.
Computational model of 3D cell migration based on the molecular clutch mechanism
Authors: Campbell Samuel , Zitnay Rebecca , Mendoza Michelle , Bidone Tamara C 
Published: October 2021

AbstractThe external environment is a regulator of cell activity. Its stiffness and microstructure can either facilitate or prevent 3D cell migration in both physiology and disease. 3D cell migration results from force feedbacks between the cell and the extracellular matrix (ECM). Adhesions regulate these force feedbacks by working as molecular clutches that dynamically bind and unbind the ECM. Because of the interdependency between ECM properties, adhesion dynamics, and cell contractility, how exactly 3D cell migration occurs in different environments is not fully understood. In order to elucidate the effect of ECM on 3D cell migration through force-sensitive molecular clutches, we developed a computational model based on a lattice point approach. Results from the model show that increases in ECM pore size reduce cell migration speed. In contrast, matrix porosity increases it, given a sufficient number of ligands for cell adhesions and limited crowding of the matrix from cell replication. Importantly, these effects are maintained across a range of ECM stiffnesses’, demonstrating that mechanical factors are not responsible for how matrix microstructure regulates cell motility.