bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flicker: A review of temporal light modulation stimulus, responses, and measures
Authors: Miller NJ , Leon FA , Tan J , Irvin L 
Published: August 2022

Flicker has been an important lighting system consideration for over a century. More precise terms are temporal light modulation (TLM) as the stimulus, and responses to TLM as the unwanted visual, cognitive, or physiological consequences. As lighting technology evolved, different forms of TLM emerged, and so did responses to them. Today, some LED systems – encompassing the LED, driver, and control – can result in TLM causing severe unwanted effects, while other LED systems produce no unwanted effects at all. LED systems can deliver a much wider range of luminous waveforms than conventional lighting systems, some exhibiting very high modulation depths. More than any light source before, they can elicit perceptions of the phantom array. Direct flicker effects at modulation frequencies less than about 80 Hz and the stroboscopic effect at frequencies greater than 80 Hz are fairly well understood, but the phantom array effect needs more exploration and characterisation. This review focuses on the technology and research history that led to current metrics for quantifying TLM and human responses to TLM. Visually impaired individuals may exhibit alterations in their response to TLM, but such a discussion is beyond the intent of this review. Thus, the focus is on individuals with normal visual function.
Financial incentives and moral distress in Australian audiologists and audiometrists
Authors: Simpson Andrea , Fawcett Meg , McLeod Lily , Lin Jennifer , Tuncer Selda , Sarkic Bojana 
Published: August 2022

Introduction Financial incentive schemes have been commonly used by the hearing aid industry as a way of encouraging device sales. These schemes can lead to a conflict of interest as the hearing device dispenser is torn between personal reward over the best interests of their client. This conflict of interest has the potential for the dispenser to develop “moral distress”, a negative state of mind when an individual’s ethical values contrast with those of the employing organization. The purpose of this study was to investigate if there was a relationship between financial incentives and moral distress in Australian audiologists and audiometrists. Methods An online survey was distributed to all members of Audiology Australia and the Australian College of Audiology via email. Participants rated their perceived moral distress from 0 to 10 on the Moral Distress Thermometer and answered four questions about financial incentives in their respective workplace. Results A total of 65 participants, 42 females and 23 males, completed the online survey. A quarter of participants rated their moral distress corresponding to levels of uncomfortable or above. A statistically significant association was found between financial incentives, sales target setting, and higher perceived moral distress in participants. Conclusions For our sample, the implementation of financial incentives created ethical challenges for practicing audiologists and audiometrists. Modifications to employee rewards programs as well as a regulation of device sales are recommended.
Relationships Among Environmental Variables, Physical Capacity, Balance Self-Efficacy, and Real-World Walking Activity Post-Stroke
Authors: Miller Allison , Pohlig Ryan T. , Reisman Darcy S. 
Published: August 2022

Background: Social and physical environmental factors affect real-world walking activity in individuals with stroke. However, environmental factors are often non-modifiable, presenting a challenge for clinicians working with individuals with stroke whose real-world walking is limited due to environmental barriers. Objective: The purpose of this work was to test a model hypothesizing the relationships among environmental factors (specifically, living situation and area deprivation), modifiable factors, and real-world walking activity to understand opportunities for intervention. We hypothesized that balance self-efficacy would mediate the relationship between the environment and real-world walking and that physical capacity would moderate this mediation. Methods: This was a cross-sectional study of 282 individuals with chronic (≥6 months) stroke. We tested the indirect effect to determine if mediation was present. Multiple group structural equation modeling was used to test if physical capacity moderated this mediation. A χ2 difference test was used to compare the moderation model against the null (no moderation) model. Results: Balance self-efficacy mediated the relationship between area deprivation and real-world walking (indirect effect: β = −0.04, P = .04). Both the moderation and null models fit the data equally well statistically (χ2(5) = 6.9, P = .23). We therefore accepted the simpler (null) model and concluded that the mediation was not moderated. Conclusions: Targeting balance self-efficacy may be an effective approach to improving real-world walking in persons with stroke who experience barriers within the physical environment. A stroke survivor’s physical capacity may not impact this approach. Future work should consider utilizing more specific measures of the social and physical environment to better understand their influences on real-world walking activity in individuals with stroke. However, the results of this work provide excellent targets for future longitudinal studies targeting real-world walking activity in stroke.
Epidemiology of shoulder instability procedures: A comprehensive analysis of complications and costs
Authors: Best Matthew J , Wang Kevin Y , Nayar Suresh K , Agarwal Amil R , Kreulen R Timothy , Sharma Sribava , McFarland Edward G , Srikumaran Uma 
Published: August 2022

Background Recurrent shoulder instability is a debilitating condition that can lead to chronic pain, decreased function, and inability to return to activities or sport. This retrospective epidemiology study was performed to report 90-day postoperative complications and costs of Latarjet, anterior bone block reconstruction, arthroscopic, and open Bankart repair for shoulder instability. Methods Patients 18 years and older who underwent four primary shoulder surgeries from 2010 to 2019 were identified using national claims data. Patient demographics, comorbidities, and 90-day postoperative complications were analyzed using univariate analysis and multivariable logistic regression. Total and itemized 90-day reimbursements were determined for each procedure. Results The 90-day medical and surgery-specific complication rates were highest for anterior bone block reconstruction, followed by Latarjet. Arthroscopic Bankart repair had the highest 90-day costs and primary procedure costs compared to other procedures. Conclusion Anterior bone block reconstruction and Latarjet procedures were associated with the highest rates of 90-day medical and surgery-specific complications, while arthroscopic Bankart repair was associated with the highest costs.
Patient and clinician experiences of remote consultation during the SARS-CoV-2 pandemic: A service evaluation
Authors: Schutz Sue , Walthall Helen , Snowball Joanna , Vagner Raluca , Fernandez Nicola , Bartram Emilia , Merriman Clair 
Published: August 2022

Objectives During the SARS-CoV-2 pandemic, clinicians were instructed to move all but emergency consultations to remote means to reduce the spread of the virus. The aim of this study was to evaluate patients’ and clinicians’ experiences of moving to remote means of consultation with their health care professionals during the SARS-CoV-2 pandemic. Methods The study design was a qualitative service evaluation. Twenty-six clinicians and forty-eight patients who met the inclusion criteria consented to be interviewed. Clinician participants were from either medical, nursing, or allied health professional backgrounds. Patients were recruited from diabetes, acute care, and haematology and cancer areas. Data analysis was conducted using a thematic analysis framework. Results Following coding and thematic analysis of the data collected from clinicians, five themes were identified: personal and professional well-being; providing a safe and high-quality experience; adapting to a new way of working; making remote consultations fit for purpose and an awareness of altered dynamics during consultation. Patient data was coded into 3 themes: remote consultation adds value; remote consultation brings challenges and concerns about remote consultation. Conclusions Clinician and patient experiences reported here are reflected in the literature. The study indicates that remote consultation is not suitable for all patients and in all contexts. Whilst maintaining the benefits to patients, remote means of consultation needs organisational support and preparation. A way forward that maintains the benefits whilst addressing concerns seems urgent.
Overall and patient-level comparative effectiveness of dimethyl fumarate and fingolimod: A precision medicine application to the Observatoire Français de la Sclérose en Plaques registry
Authors: Simoneau Gabrielle , Jiang Xiaotong , Rollot Fabien , Tian Lu , Copetti Massimiliano , Guéry Matthieu , Ruiz Marta , Vukusic Sandra , de Moor Carl , Pellegrini Fabio ,   on behalf of OFSEP investigators
Published: August 2022

Background Comparing real-world effectiveness and tolerability of therapies for relapsing-remitting multiple sclerosis is increasingly important, though average treatment effects fail to capture possible treatment effect heterogeneity. With the clinical course of the disease being highly heterogeneous across patients, precision medicine methods enable treatment response heterogeneity investigations. Objective To compare real-world effectiveness and discontinuation profiles between dimethyl fumarate and fingolimod while investigating treatment effect heterogeneity with precision medicine methods. Methods Adults initiating dimethyl fumarate or fingolimod as a second-line therapy were selected from a French registry. The primary outcome was annualized relapse rate at 12 months. Seven secondary outcomes relative to discontinuation and disease progression were considered. A precision medicine framework was used to characterize treatment effect heterogeneity. Results Annualized relapse rates at 12 months were similar for dimethyl fumarate and fingolimod. The odd of treatment persistence was 47% lower for patients treated with dimethyl fumarate relative to those treated with fingolimod (odds ratio: 0.53, 95% confidence interval: 0.39, 0.70). None of the five precision medicine scoring approaches identified treatment heterogeneity. Conclusion These findings substantiated the similar effectiveness and different discontinuation profiles for dimethyl fumarate and fingolimod as a second-line therapy for relapsing-remitting multiple sclerosis, with no significant effect heterogeneity observed.
Single-cell analysis of acute lymphoblastic and lineage-ambiguous leukemia: approaches and molecular insights
Authors: Iacobucci Ilaria , Witkowski Matthew T. , Mullighan Charles G. 
Published: August 2022

Abstract
Despite recent progress in identifying the genetic drivers of acute lymphoblastic leukemia (ALL), prognosis remains poor for those individuals who experience disease recurrence. Moreover, acute leukemias of ambiguous lineage lack a biologically informed framework to guide classification and therapy. These needs have driven the adoption of multiple complementary single-cell sequencing approaches to explore key issues in the biology of these leukemias, including cell of origin, developmental hierarchy and ontogeny, and the molecular heterogeneity driving pathogenesis, progression, and therapeutic responsiveness. There are multiple single-cell techniques for profiling a specific modality, including RNA, DNA, chromatin accessibility and methylation; and an expanding range of approaches for simultaneous analysis of multiple modalities. Single-cell sequencing approaches have also enabled characterization of cell-intrinsic and -extrinsic features of ALL biology. In this review we describe these approaches and highlight the extensive heterogeneity that underpins ALL gene expression, cellular differentiation, and clonal architecture throughout disease pathogenesis and treatment resistance. In addition, we discuss the importance of the dynamic interactions that occur between leukemia cells and the nonleukemia microenvironment. We discuss potential opportunities and limitations of single-cell sequencing for the study of ALL biology and treatment responsiveness.
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis
Authors: Wan Ling , Song Justin , He Virginia , Roman Jennifer , Whah Grace , Peng Suyuan , Zhang Luxia , He Yongqun 
Published: August 2022

AbstractBackgroundThe 10th and 9th revisions of the International Statistical Classification of Diseases and Related Health Problems (ICD10 and ICD9) have been adopted worldwide as a well-recognized norm to share codes for diseases, signs and symptoms, abnormal findings, etc. The international Consortium for Clinical Characterization of COVID-19 by EHR (4CE) website stores diagnosis COVID-19 disease data using ICD10 and ICD9 codes. However, the ICD systems are difficult to decode due to their many shortcomings, which can be addressed using ontology.MethodsAn ICD ontology (ICDO) was developed to logically and scientifically represent ICD terms and their relations among different ICD terms. ICDO is also aligned with the Basic Formal Ontology (BFO) and reuses terms from existing ontologies. As a use case, the ICD10 and ICD9 diagnosis data from the 4CE website were extracted, mapped to ICDO, and analyzed using ICDO.ResultsWe have developed the ICDO to ontologize the ICD terms and relations. Different from existing disease ontologies, all ICD diseases in ICDO are defined as disease processes to describe their occurrence with other properties. The ICDO decomposes each disease term into different components, including anatomic entities, process profiles, etiological causes, output phenotype, etc. Over 900 ICD terms have been represented in ICDO. Many ICDO terms are presented in both English and Chinese. The ICD10/ICD9-based diagnosis data of over 27,000 COVID-19 patients from 5 countries were extracted from the 4CE. A total of 917 COVID-19-related disease codes, each of which were associated with 1 or more cases in the 4CE dataset, were mapped to ICDO and further analyzed using the ICDO logical annotations. Our study showed that COVID-19 targeted multiple systems and organs such as the lung, heart, and kidney. Different acute and chronic kidney phenotypes were identified. Some kidney diseases appeared to result from other diseases, such as diabetes. Some of the findings could only be easily found using ICDO instead of ICD9/10.ConclusionsICDO was developed to ontologize ICD10/10 codes and applied to study COVID-19 patient diagnosis data. Our findings showed that ICDO provides a semantic platform for more accurate detection of disease profiles.
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions
Authors: Nishizaki Sierra S. , Boyle Alan P. 
Published: August 2022

Abstract
Motivation
Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor’s motif.

Results
SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease.

Availability and Implementation
SEMplMe is available from https://github.com/Boyle-Lab/SEMplMe.
Effects of silicon application on leaf structure and physiological characteristics of Glycyrrhiza uralensis Fisch. and Glycyrrhiza inflata Bat. under salt treatment
Authors: Shen Zihui , Cheng Xiaojiao , Li Xiao , Deng Xianya , Dong Xiuxiu , Wang Shaoming , Pu Xiaozhen 
Published: August 2022

Abstract
Background
Soil salinization leads to a significant decline in crop yield and quality, including licorice, an important medicinal cash crop. Studies have proofed that the application of exogenous silicon can significantly improve the ability of licorice to resist salt stress, however, few studies concentrated on the effects of foliar silicon application on the morphology, physiological characteristics, and anatomical structure of licorice leaves under salt stress. In this study, the effects of Si (K2SiO3) on the structural and physiological characteristics of Glycyrrhiza uralensis Fisch. and G. inflata Bat. leaves under different salt concentrations (medium- and high-salt) were studied.

Results
Compared with the control (without salt), the plant height, total dry weight, leaf area, leaf number, relative water content, xylem area, phloem area, ratio of palisade to spongy tissue, gas exchange parameters, and photosynthetic pigment content of both licorice varieties were significantly reduced under high-salt (12S) conditions. However, the thickness of the leaf, palisade tissue, and spongy tissue increased significantly. Applying Si to the leaf surface increased the area of the vascular bundle, xylem, and parenchyma of the leaf’s main vein, promoted water transportation, enhanced the relative leaf water content, and reduced the decomposition of photosynthetic pigments. These changes extended the area of photosynthesis and promoted the production and transportation of organic matter. G. uralensis had a better response to Si application than did G. inflata.

Conclusions
In conclusion, foliar application of Si can improve water absorption, enhance photosynthesis, improve photosynthetic capacity and transpiration efficiency, promote growth and yield, and alleviate the adverse effects of salt stress on the leaf structure of the two kinds of licorice investigated.
A comparison of statistical methods for modeling count data with an application to hospital length of stay
Authors: Fernandez Gustavo A. , Vatcheva Kristina P. 
Published: August 2022

Abstract
Background
Hospital length of stay (LOS) is a key indicator of hospital care management efficiency, cost of care, and hospital planning. Hospital LOS is often used as a measure of a post-medical procedure outcome, as a guide to the benefit of a treatment of interest, or as an important risk factor for adverse events. Therefore, understanding hospital LOS variability is always an important healthcare focus. Hospital LOS data can be treated as count data, with discrete and non-negative values, typically right skewed, and often exhibiting excessive zeros. In this study, we compared the performance of the Poisson, negative binomial (NB), zero-inflated Poisson (ZIP), and zero-inflated negative binomial (ZINB) regression models using simulated and empirical data.

Methods
Data were generated under different simulation scenarios with varying sample sizes, proportions of zeros, and levels of overdispersion. Analysis of hospital LOS was conducted using empirical data from the Medical Information Mart for Intensive Care database.

Results
Results showed that Poisson and ZIP models performed poorly in overdispersed data. ZIP outperformed the rest of the regression models when the overdispersion is due to zero-inflation only. NB and ZINB regression models faced substantial convergence issues when incorrectly used to model equidispersed data. NB model provided the best fit in overdispersed data and outperformed the ZINB model in many simulation scenarios with combinations of zero-inflation and overdispersion, regardless of the sample size. In the empirical data analysis, we demonstrated that fitting incorrect models to overdispersed data leaded to incorrect regression coefficients estimates and overstated significance of some of the predictors.

Conclusions
Based on this study, we recommend to the researchers that they consider the ZIP models for count data with zero-inflation only and NB models for overdispersed data or data with combinations of zero-inflation and overdispersion. If the researcher believes there are two different data generating mechanisms producing zeros, then the ZINB regression model may provide greater flexibility when modeling the zero-inflation and overdispersion.
What next for the polyclinic? New models of primary health care are required in many former Soviet Union countries
Authors: Edwards Nigel , Sheiman Igor 
Published: August 2022

Abstract
Background
There is unfinished reform in primary care in Russia and other former Soviet Union (FSU) countries. The traditional ‘Semashko’ multi-specialty polyclinic model has been retained, while its major characteristics are increasingly questioned. The search for a new model is on a health policy agenda. It is relevant for many other countries.

Objectives
In this paper, we explore the strengths and weaknesses of the multi-specialty polyclinic model currently found in Russia and other FSU countries, as well as the features of the emerging multi-disciplinary and large-scale primary care models internationally. The comparison of the two is a major research question. Health policy implications are discussed.

Methods
We use data from two physicians’ surveys and recent literature to identify the characteristics of multi-specialty polyclinics, indicators of their performance and the evaluation in the specific country context. The review of the literature is used to describe new primary care models internationally.

Results
The Semashko polyclinic model has lost some of its original strengths due to the excessive specialization of service delivery. We demonstrate the strengths of extended practices in Western countries and conclude that FSU countries should “leapfrog” the phase of developing solo practices and build a multi-disciplinary model similar to the extended practices model in Europe. The latter may act as a ‘golden mean’ between the administrative dominance of the polyclinic model and the limited capacity of solo practices. The new model requires a separation of primary care and outpatient specialty care, with the transformation of polyclinics into centers of outpatient diagnostic and specialty services that become part of hospital services while working closely with primary care.

Conclusion
The comprehensiveness of care in a big setting and potential economies of scale, which are major strengths of the polyclinic model, should be retained in the provision of specialty care rather than primary care. Internationally, there are lessons about the risks associated with models based on narrow specialization in caring for patients who increasingly have multiple conditions.