bluuebunny/crossref_metadata_2025_split huggingface dataset:
gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit
Authors: Guebila Marouen Ben , Morgan Daniel C , Glass Kimberly , Kuijjer Marieke L , DeMeo Dawn L , Quackenbush John 
Published: February 2022

Abstract
Gene regulatory network inference allows for the modeling of genome-scale regulatory processes that are altered during development, in disease, and in response to perturbations. Our group has developed a collection of tools to model various regulatory processes, including transcriptional (PANDA, SPIDER) and post-transcriptional (PUMA) gene regulation, as well as gene regulation in individual samples (LIONESS). These methods work by postulating a network structure and then optimizing that structure to be consistent with multiple lines of biological evidence through repeated operations on data matrices. Although our methods are widely used, the corresponding computational complexity, and the associated costs and run times, do limit some applications. To improve the cost/time performance of these algorithms, we developed gpuZoo which implements GPU-accelerated calculations, dramatically improving the performance of these algorithms. The runtime of the gpuZoo implementation in MATLAB and Python is up to 61 times faster and 28 times less expensive than multi-core CPU implementation of the same methods. gpuZoo is available in MATLAB through the netZooM package https://github.com/netZoo/netZooM and in Python through the netZooPy package https://github.com/netZoo/netZooPy.
Herpes Zoster Following Recombinant Zoster Vaccine With or Without Concomitant Vaccination
Authors: Bruxvoort Katia J , Qian Lei , Wu Jun , Florea Ana , Ackerson Bradley , Sy Lina S , Vega Daily Leticia , Takhar Harpreet , Tseng Hung Fu 
Published: February 2022

Abstract

Background
The 2-dose recombinant zoster vaccine (RZV) series is recommended for prevention of herpes zoster (HZ) in adults aged ≥50 years, but data are limited on the impact of concomitant administration with other vaccines on subsequent HZ risk.

Methods
This cohort study included Kaiser Permanente Southern California members aged ≥50 years who received 2 doses of RZV 4 weeks to ≤6 months apart during 1 April 2018–30 September 2019. RZV recipients with and without same-day concomitant vaccination for either RZV dose were followed up for incident HZ beginning 31 days after the second RZV dose until 30 September 2020. The hazard ratio (HR) for HZ comparing RZV recipients with and without concomitant vaccination was estimated using Cox proportional hazards regression, adjusting for confounders.

Results
RZV with and without concomitant vaccination was received by 12 898 and 28 353 individuals, respectively. HZ occurred among 41 individuals with concomitant vaccination (incidence rate, 2.2 [95% confidence interval {CI}, 1.6–3.0] per 1000 person-years) and 136 without concomitant vaccination (3.4 [95% CI, 2.9–4.0] per 1000 person-years). The adjusted HR for HZ comparing RZV recipients with and without concomitant vaccination was 0.75 (95% CI, .53–1.08).

Conclusions
HZ risk was not significantly different between RZV recipients with and without concomitant vaccination, supporting recommendations allowing for concomitant administration of RZV with other vaccines.
Youth mental health-related presentations at a quaternary centre: Who comes, What are their needs, and Can we meet their needs
Authors: Lee Alison , Davidson Jana , Black Tyler , Kim Grace G , Doan Quynh 
Published: February 2022

Abstract

Background
Mental health issues are increasingly prevalent across Canada, reflected in rising presentations to emergency departments. To effectively address the needs of children and youth seeking mental health-related care in the emergency department and to judiciously use scarce mental health-related resources, we need to better identify the specific areas of psychosocial needs and accessibility of associated services.

Objective
To describe the types and severity of paediatric mental health-related presentations evaluated at a quaternary paediatric emergency department, and to explore the accessibility of community mental health-related resources.

Methods
We conducted a retrospective cohort study of children and youth presenting to a quaternary paediatric emergency department who were assessed using HEARTSMAP, a validated mental health assessment and management tool. We reported the proportion who sought care for a psychiatric, social, or youth health-related mental health complaint. We contacted community mental health-related resources for their estimated wait times to determine accessibility.

Results
Of 1,530 paediatric emergency presentations, 98.8% of patients had psychiatric issues (40.1% were severe), 78.0% of patients had social issues (17.1% were severe), and 71.5% had youth health issues (18.1% were severe). We contacted 123 community mental health-related resources. Community youth health and social services were somewhat accessible, with 50.0% and 38.7%, respectively, able to intake youth within a week of referral. Community psychiatric programs were least accessible, with 59.3% having wait times greater than 1 month.

Conclusions
Many psychiatric concerns presenting in paediatric emergency departments have complex psychosocial challenges requiring non-psychiatric support. A need exists for improved accessibility to community psychiatric programs.
Two major metabolic factors for an efficient NADP-malic enzyme type C4 photosynthesis
Authors: Zhao Honglong , Wang Yu , Lyu Ming-Ju Amy , Zhu Xin-Guang 
Published: February 2022

Abstract
Compared to the large number of studies focused on the factors controlling C3 photosynthesis efficiency, there are relatively fewer studies of the factors controlling photosynthetic efficiency in C4 leaves. Here, we used a dynamic systems model of C4 photosynthesis based on maize (Zea mays) to identify features associated with high photosynthetic efficiency in NADP-malic enzyme (NADP-ME) type C4 photosynthesis. We found that two additional factors related to coordination between C4 shuttle metabolism and C3 metabolism are required for efficient C4 photosynthesis: (1) accumulating a high concentration of phosphoenolpyruvate through maintaining a large PGA concentration in the mesophyll cell chloroplast and (2) maintaining a suitable oxidized status in bundle sheath cell chloroplasts. These identified mechanisms are in line with the current cellular location of enzymes/proteins involved in the starch synthesis, the Calvin–Benson cycle and photosystem II of NADP-ME type C4 photosynthesis. These findings suggested potential strategies for improving C4 photosynthesis and engineering C4 rice.
Physical Therapist and Physical Therapist Student Knowledge, Confidence, Attitudes, and Beliefs About Providing Care for People With Dementia: A Mixed-Methods Systematic Review
Authors: Quick Stephen M , Snowdon David A , Lawler Katherine , McGinley Jennifer L , Soh Sze-Ee , Callisaya Michele L 
Published: February 2022

Abstract

Objective
The purpose of this study was to determine physical therapists’ and physical therapist students’ attitudes and beliefs, knowledge, and confidence in working with people with dementia.

Methods
This was a mixed-methods systematic review. Participants included physical therapists working in any clinical specialty and physical therapist students who had completed at least 1 clinical placement. Eleven databases were searched. The evidence was evaluated using the Joanna Briggs Institute Critical Appraisal Checklists. Data synthesis followed a convergent integrated approach according to Joanna Briggs Institute methodology for mixed-methods systematic reviews. Quantitative data were “qualitized” using thematic analysis and synthesized with qualitative data using thematic synthesis.

Results
Fifteen studies were included (9 quantitative and 6 qualitative studies). Seven key themes evolved. Five related to the belief that (1) working with people with dementia is complex and challenging; (2) opportunities for education in dementia care are lacking; (3) working with people with dementia is a specialized area of practice; (4) there are unsupportive systems for working with people with dementia; and (5) people with dementia deserve rehabilitation, but their potential to improve is less certain. One theme related to knowledge (lack of knowledge in some areas of dementia care), and 1 theme related to confidence (lack of confidence in working with people with dementia).

Conclusions
Physical therapists and physical therapist students believe that working with people with dementia can be challenging. The low levels of knowledge and confidence in areas important to working with people who have dementia suggest that more education about dementia is needed.

Impact
This mixed-methods systematic review highlights that physical therapists and physical therapist students believe that working with people who have dementia is complex and challenging. Physical therapists want more training and support in this growing area of practice.
Seroprevalence of Toxoplasma gondii infection among HIV-positive patients in Southwest Iran and associated risk factors: a case-control study
Authors: Nikbakht Gordafarin , Behrouzi Maryam , Mousavizadeh Ali , Pourabbas Bahman , Rezaei Zahra , Nouripour-Sisakht Sadegh , Arefkhah Nasir 
Published: February 2022

Abstract

Background
The current study aimed to determine the seroprevalence of Toxoplasma gondii infection among HIV-positive patients and healthy subjects.

Methods
This study was carried out on HIV-positive patients and healthy individuals in Southwest Iran. Five millilitres of venous blood samples were collected aseptically from each individual. Sera and buffy coats were isolated from each sample and evaluated for anti-Toxoplasma antibodies and T. gondii DNA using ELISA kit and real-time PCR, respectively. Statistical analysis was performed using SPSS 18 software.

Results
Of 64 AIDS/HIV-positive patients, six (9.3%, 95% CI 7.2 to 11.3%) were seropositive for only IgG and five (7.8%, 95% CI 6.0 to 9.5%) were seropositive for both IgG and IgM. Moreover, among 64 healthy controls, 10 (15.6%, 95% CI 12.1 to 19.0%) were seropositive for only IgG and 2 (3.1%, 95% CI 2.4 to 3.7%) were seropositive for both IgG and IgM. Toxoplasma gondii DNA was detected in six samples (9.3%, 95% CI 7.2 to 11.3%) in the AIDS/HIV-positive patients group and eight samples (5.95%, 95% CI 4.6 to 7.2%) in the control group using real-time PCR. Consumption of undercooked meat was documented as an associated risk factor for T. gondii seropositivity in AIDS patients (OR 4.06, 95% CI 0.966 to 17.09; p=0.045).

Conclusions
Our findings showed a lower prevalence of Toxoplasma infection in AIDS/HIV-positive patients vs healthy controls; however, a considerable number of AIDS/HIV-positive patients were also seen to be at risk of toxoplasmosis. Based on the findings, screening and prophylaxis for toxoplasmosis should be implemented for all AIDS/HIV-positive patients in Southwest Iran.
Expanding Inpatient Addiction Consult Services Through Accountable Care Organizations for Medicaid Enrollees: A Modeling Study
Authors: King Caroline A. , Cook Ryan , Korthuis P. Todd , McCarty Dennis , Morris Cynthia D. , Englander Honora 
Published: February 2022

Introduction
Addiction consult services (ACS) care for hospitalized patients with substance use disorder, including opioid use disorder (OUD). Medicaid Accountable Care Organizations (ACOs) could enhance access to ACS. This study extends data from Oregon’s only ACS to Oregon’s 15 regional Medicaid Coordinated Care Organizations (CCOs) to illustrate the potential value of enhanced in- and out-patient care for hospitalized patients with OUD. The study objectives were to estimate the effects of (1) expanding ACS care through CCOs in Oregon, and (2) increasing community treatment access within CCOs, on post-discharge OUD treatment engagement.

Methods
We used a validated Markov model, populated with Oregon Medicaid data from April 2015 to December 2017, to estimate study objectives.

Results
Oregon Medicaid patients hospitalized with OUD with care billed to a CCO (n = 5878) included 1298 (22.1%) patients engaged in post-discharge OUD treatment. Simulation of referral to an ACS increased post-discharge OUD treatment engagement to 47.0% (95% confidence interval [CI] 45.7%, 48.3%), or 2684 patients (95% CI 2610, 2758). Ten of fifteen (66.7%) CCOs had fewer than 20% of patients engage in post-discharge OUD care. Without ACS, increasing outpatient treatment such that 20% of patients engage increased the patients engaging in post-discharge OUD care from 12.9% or 296 patients in care at baseline to 20% (95% CI 18.1%, 21.4%) or 453 (95% CI 416, 491).

Discussion
ACOs can improve care for patients hospitalized with OUD. Implementing ACS in ACO networks can potentially improve post-discharge OUD treatment engagement, but community treatment systems must be prepared to accept more patients as inpatient addiction care improves.
Tanning Beds, Rue, and Major Burns: An Alarming Association
Authors: Pérez-Camelo Juan Sebastián , Barrios Valeria , Gómez-Ortega Viviana 
Published: February 2022

Summary:
Skin contact with phytotoxic chemicals present in Ruta graveolens L. and UV light exposure might cause a nonallergic contact dermatitis known as phytophotodermatitis. We present a major burns case report associated with the use of rue (an herb used in Colombia for cultural beliefs) before entering a tanning bed. The patient presented superficial wounds that evolved to deeper ones in a phytophotodermatitis reaction that acted as a chemical burn. The patient presented an estimated percentage of total burn surface area of 85% with second-degree burns. It took two and a half months to apply multiple debridements and bandage coverage before discharge. One month later, the patient presented a dark purplish pigmentation mainly in the lower limbs. Since ancient times, rue has been used as part of medical pharmacy, insecticidal activities, and for superstitious purposes. In many countries, rue is used as part of an elixir that helps with bad luck, envy, and anguish, and the risks associated with those uses are unknown. This is a critical and alarming public health problem. Awareness of possible complications that could develop after rue and tanning beds should encourage patients and physicians to prevent and treat this dangerous combination.
Sexual Assault Nurse Examiner Training: A Review of Literature and Implication for Nursing Education and Service to Rural Communities
Authors: Sheeran Beth , Kiser Lisa , Williams-Gilbert Wendy , Enslow Electra 
Published: February 2022

ABSTRACT
Sexual assault nurse examiners (SANEs) play a critical role in providing quality care to patients who have experienced sexual violence. Recent national legislative initiatives have been launched both to better explore state-specific needs in regard to training SANE nurses as well as pilot programs that will establish evidence-based methods of expanding SANE training to remote, rural, and underserved communities.
A scoping literature review was conducted to identify best practices in SANE training as well as implications for delivering this education to rural and underserved communities. This review analyzed the scientific strengths and weaknesses of existing research, provided an overview of findings within the literature, and identified areas where further research could be directed to inform local, state, and national strategy on SANE education.
Blended learning programs that pair online education with simulated clinical experiences are promising alternatives to the traditional classroom experience; however, more research is needed to know how to enhance retention and engagement of nurses utilizing these methods to obtain preliminary SANE training.
Building a Capacity of Sexual Assault Nurse Examiners in an Underserved U.S.–Mexico Border Region
Authors: Torregosa Marivic B. , Chaudhuri Nandita , del Rosario Benavides Maria , Jackson Anthony 
Published: February 2022

ABSTRACT
Sexual assault nurse examiners (SANEs) conduct medical forensic examinations for persons who have been sexually assaulted. Positive psychological effects, high prosecution rates, and increased victim self-efficacy to seek resources for recovery were reported among sexual assault victims who received forensic care from SANEs. However, such endeavors may be very challenging to achieve because of the severe shortage of certified SANEs. This article will describe how one institution located in a medically underserved U.S.–Mexico border town built a SANE program to increase the capacity of SANEs in the region through 3-year grant funding. The lessons learned, challenges faced during implementation, and sustainability plans including integrating SANEs into the local medicolegal system to seek justice for sexual assault victims are critically addressed in this article.
Sudden Death in Diabetic Ketoacidosis Complicated by Sickle Cell Trait
Authors: Dau Georgia E. , Shah Jamie J. , Walsh John C. , Berran Philip J. 
Published: February 2022

Abstract
In a sudden death investigation of a service member with sickle cell trait (SCT), evidence of sickle cell crisis further complicated by coexisting, undiagnosed diabetic ketoacidosis called into question the synergistic effects of diabetic ketoacidosis on red blood cell sickling. Sickle cell trait affects more than 4 million people in the United States (US) with the highest prevalence in non-Hispanic Blacks (7%–9%; Mil Med 2017;182(3):e1819–e1824). The heterozygous state of sickled hemoglobin was previously considered a benign condition causing sickling during hypoxic, high-stress conditions such as exercise and high altitude (Am Assoc Clin Chem 2017). However, research within the last decade shows evidence of sudden death among SCT patients (J Forensic Sci 2011;56(5):1352–1360). It has been shown that the presence of sickled hemoglobin artificially lowers levels of hemoglobin A1c making it a less effective biomarker for red blood cell glycosylation over time in sickle cell patients (JAMA 2017;317(5):507–515). The limited scope of medical understanding of the effects of SCT in combination with other comorbidities requires further investigation and better diagnostic criteria. The uniqueness of the US Military and its screening program for sickle cell disease (SCD) and SCT allows for more detection. Since May 2006, newborn screening for SCD/SCT has been a national requirement; however, anyone older than 14 years may not know their SCD/SCT status (Semin Perinatol 2010;34(2):134–44). The previous absence of such national screening makes it more challenging to identify SCT and SCD patients even within high-risk populations. Furthermore, patients may not know or understand the results of their SCD/SCT status testing. International standards for the autopsy of decedents with SCD and SCT exist (R Coll Pathol 2017). Within the US, testing of vitreous electrolytes is a common practice in suspected natural death cases, but a review of the US literature did not demonstrate any autopsy standards or recommendations for persons with SCT or high-risk persons for sickling pathologies. The identification of a new diagnosis of type 2 diabetes mellitus, as the cause of death, is not uncommon; however, this case indicates that type 2 diabetes mellitus was not the sole contributing factor. It further illustrates that the US may be underestimating the impact of SCD and SCT as a cause of death, a contributing factor to death, and its synergistic effects with other pathologic processes. We propose a stringent literature review in conjunction with a review of international autopsy standards to develop national autopsy standards and possible SCT/SCD screening recommendations for high-risk persons at the time of autopsy.
Do Websites Serve Our Patients Well? A Comparative Analysis of Online Information on Cosmetic Injectables
Authors: Patel Anooj A. , Joshi Chitang , Varghese Jeffrey , Hassan Abbas M. , Janis Jeffrey E. , Galiano Robert D. 
Published: February 2022

Background:
Patients access online cosmetic health information to help with decision making. This information is unregulated, variable in quality, and may be biased. This study compared the most popular cosmetic injectables websites to assess their readability, quality, and technical performance.

Methods:
A Google search for “Botox” (botulinum toxin type A) and “fillers” was performed in July of 2020, identifying the most popular health information websites. Sites were analyzed for their readability and quality of health information using the validated DISCERN criteria and the Health on the Net Foundation Code of Conduct principles. Technical qualities were evaluated using two website performance algorithms, WooRank and WebsiteGrader.

Results:
Eighty-five websites were analyzed (13 academic/hospital websites, seven commercial websites, 25 private practice board-certified websites, seven private practice not-board-certified websites, 16 online health reference websites, and 17 other websites). The mean readability consensus score was 11 (eleventh grade reading level). The mean DISCERN quality scores were higher for online health reference websites compared to academic/hospital websites (p = 0.045), commercial websites (p = 0.045), private practice board-certified websites (p < 0.001), and private practice not-board-certified websites (p = .002). No correlation between a website’s rank and its DISCERN score was found (ρ = −0.07; p = 0.49).

Conclusions:
Cosmetic injectable websites are too difficult to read by the sixth grade standard recommended by the National Institutes of Health and the American Medical Association. Online health reference sites are higher in quality than physician sites. This has implications for the ability of many patients to be fully informed consumers. The readability, quality, and technical aspects of websites may affect the overall accessibility of patient health information.
Exploring Changes in Patient Safety Incidents During the COVID-19 Pandemic in a Canadian Regional Hospital System: A Retrospective Time Series Analysis
Authors: Lombardi Julia , Strobel Stephenson , Pullar Virginia , Senthil Pooja , Upadhye Suneel , Khemani Ekta 
Published: February 2022

Objectives
The COVID-19 pandemic has placed unprecedented strain on healthcare systems and may have consequential impacts on patient safety incidents (PSIs). The primary objective of this study was to examine the impact of the COVID-19 pandemic on PSIs reported in Niagara Health.

Methods
Flexible Farrington models were used to retrospectively detect weeks from January to September 2020 where PSI counts were significantly above expected counts. Incident counts were adjusted to weekly inpatient-days. Outcomes included overall incident numbers, incidents by category, and incidents by ward type.

Results
The overall number of PSIs across Niagara Health did not increase during the first wave of the COVID-19 pandemic. However, significant increases in falls were observed, suggesting that other types of incidents decreased. Falls increased by 75% from February to March 2020, coinciding with the onset of the first wave of the pandemic. Further investigation by unit type revealed that the number of falls increased specifically on internal medicine and complex continuing care wards.

Conclusions
Despite no observed changes in overall number, significant composition shifts in PSIs occurred during the first wave of the COVID-19 pandemic, with increased falls on internal medicine and complex continuing care wards. Possible explanations include restrictions on patient visitation, reduced patient contact/supervision, and/or personal protective equipment requirements. Providers should maintain a particularly high vigilance for patient falls during pandemic outbreaks, and hospitals should consider targeting resources to higher-risk locations. The results of this study reinforce the need for ongoing pandemic PSI monitoring and rapidly adaptive responses to new patient safety concerns.