bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated cell segmentation for reproducibility in bioimage analysis
Authors: Robitaille Michael C , Byers Jeff M , Christodoulides Joseph A , Raphael Marc P 
Published: January 2023

AbstractLive-cell imaging is extremely common in synthetic biology research, but its ability to be applied reproducibly across laboratories can be hindered by a lack of standardized image analysis. Here, we introduce a novel cell segmentation method developed as part of a broader Independent Verification & Validation (IV&V) program aimed at characterizing engineered Dictyostelium cells. Standardizing image analysis was found to be highly challenging: the amount of human judgment required for parameter optimization, algorithm tweaking, training and data pre-processing steps forms serious challenges for reproducibility. To bring automation and help remove bias from live-cell image analysis, we developed a self-supervised learning (SSL) method that recursively trains itself directly from motion in live-cell microscopy images without any end-user input, thus providing objective cell segmentation. Here, we highlight this SSL method applied to characterizing the engineered Dictyostelium cells of the original IV&V program. This approach is highly generalizable, accepting images from any cell type or optical modality without the need for manual training or parameter optimization. This method represents an important step toward automated bioimage analysis software and reflects broader efforts to design accessible measurement technologies to enhance reproducibility in synthetic biology research.
Phylodynamics of deer tick virus in North America
Authors: McMinn Rebekah J , Langsjoen Rose M , Bombin Andrei , Robich Rebecca M , Ojeda Erick , Normandin Erica , Goethert Heidi K , Lubelczyk Charles B , Schneider Elizabeth , Cosenza Danielle , Meagher Molly , Prusinski Melissa A , Sabeti Pardis C , Smith Robert P , Telford Sam R , Piantadosi Anne , Ebel Gregory D 
Published: January 2023

AbstractThe burden of ticks and the pathogens they carry is increasing worldwide. Powassan virus (POWV; Flaviviridae: Flavivirus), the only known North American tick-borne flavivirus, is of particular concern due to rising cases and the severe morbidity of POWV encephalitis. Here, we use a multifaceted approach to evaluate the emergence of the II POWV lineage, known as deer tick virus (DTV), in parts of North America where human cases occur. We detected DTV-positive ticks from eight of twenty locations in the Northeast USA with an average infection rate of 1.4 per cent. High-depth, whole-genome sequencing of eighty-four POWV and DTV samples allowed us to assess geographic and temporal phylodynamics. We observed both stable infection in the Northeast USA and patterns of geographic dispersal within and between regions. A Bayesian skyline analysis demonstrated DTV population expansion over the last 50 years. This is concordant with the documented expansion of Ixodes scapularis tick populations and suggests an increasing risk of human exposure as the vector spreads. Finally, we isolated sixteen novel viruses in cell culture and demonstrated limited genetic change after passage, a valuable resource for future studies investigating this emerging virus.
Caring for People with Severe Brain Injuries: Improving Health Care Professional Communication and Practice Through Online Learning
Authors: Latchem-Hastings Julie , Latchem-Hastings Geraldine , Kitzinger Jenny 
Published: January 2023

Introduction:
Severe brain injuries can leave people in prolonged disorder of consciousness resulting in multifaceted medical, nursing, and rehabilitative needs that can be challenging for even the most experienced multidisciplinary team. The complexities of care, communication with families, and best interest decision-making about medical interventions means there is a need for ongoing training in clinical, social, ethical, and legal aspects.

Methods:
Using a combination of group discussions, interviews, and questionnaires with learners, this article reports an evaluation of designing and delivering an interprofessional, online work-based course to health care professionals caring for prolonged disorder of consciousness patients.

Results:
There were challenges for staff uptake because of COVID-19, but engaging with it increased knowledge in defining and diagnosing patients' conditions, understanding multidisciplinary team roles, communicating with families, and navigating legal and ethical issues. Course participation also enhanced critical and reflective thinking skills, provided a sense of connection to other professionals, and generated plans to improve service provision.

Discussion:
Online learning that enables health care professionals to engage at their own pace and also come together as an interprofessional community can provide invaluable continuing professional development and help to enhance joined up, holistic patient care. However, achieving this requires significant investment in creating research-led, multimedia, learning materials, and courses that include synchronous and asynchronous delivery to combine flexible study with the opportunity for peer networks to form. It also depends on a commitment from organizations to support staff online continuing professional development.
The Effect of Abdominal Massage on Discharge and Ventilator-Associated Pneumonia in Enterally Fed Patients Connected to Mechanical Ventilation
Authors: Eskici İlgin Vesile , Özer Nadiye 
Published: January 2023

Abstract

Purpose
The present research was conducted to reveal the impact of abdominal massage on enteral nutrition–induced ventilator-associated pneumonia and the gastrointestinal system in mechanically ventilated patients.

Materials and Methods
The present research is a prospective, randomized, controlled clinical trial. This study was completed with 63 patients (31 in the experimental group and 32 in the control group). Data collection was performed using a patient information form, a patient follow-up form, and the Bristol Stool Scale. After patients were under mechanical ventilation for 48 hours, the data collection tools were filled out twice a day for 3 days by visiting the mechanical ventilation patients. The experimental group received 15 minutes of abdominal massage twice a day before nursing care was delivered in the morning and the evening.

Results
According to the intergroup evaluations, the experimental group had lower gastric residual volume and abdominal distension, types of stool closer to normal, and higher defecation frequency. Differences between the groups were statistically significant (P < .05). In accordance with the intragroup evaluations, the experimental group had lower gastric residual volume, abdominal distension, and ventilator-associated pneumonia. The difference between the groups was revealed to be statistically significant (P < .05).

Conclusion
Abdominal massage reduces ventilator-associated pneumonia development to a statistically significant degree. Furthermore, it decreases gastric residual volume and abdominal distension, causes stools to be closer to the normal/ideal stool, increases defecation frequency, and regulates bowel movements and excretion (P < .05).
Mobile Source Benzene Regulations and Risk of Childhood and Young Adult Hematologic Cancers in Alaska: A Quasi-experimental Study
Authors: Nethery Rachel C. , Vega Sofia , Frazier A. Lindsay , Laden Francine 
Published: January 2023

Background:
We aimed to evaluate the impact of the EPA’s Mobile Source Air Toxics rules (MSAT), which targeted benzene emissions, on childhood and young adult leukemia and lymphoma incidence in Alaska.

Methods:
MSAT was implemented in 2011 and produced a dramatic decline in ambient benzene in Alaska. Due to previous benzene-related regulations enacted in the continental United States, MSAT had relatively modest impacts in other states. This created quasi-experimental conditions leveraged in this study. Using 2-year state-level incidence rates of childhood and young adult leukemia and lymphoma for each US state 2001–2018, we examined MSAT-attributable changes in incidence by applying a difference-in-differences approach.

Results:
We found evidence of a substantial reduction associated with MSAT in incidence of childhood and young adult lymphoma (–1.23 [–1.84, –0.62] cases per 100,000), but not in leukemia (–0.13 [–0.77, 0.51] cases per 100,000).

Conclusions:
Our findings are consistent with the hypothesis that MSAT, which reduced benzene levels in Alaska, led to a decline in lymphoma incidence in children and young adults.
Microbial Keratitis Isolates at a Midwestern Tertiary Eye Care Center
Authors: Kang Linda , Lu Ming-Chen , Niziol Leslie M. , Greenwald Miles F. , Mian Shahzad I. , Thibodeau Alexa , Pawar Mercy , Lephart Paul R. , Woodward Maria A. 
Published: January 2023

Purpose:
The aim of the study was to describe the pathogen, antimicrobial susceptibility, and trends over time of microbial keratitis (MK) at a Midwestern tertiary eye center.

Methods:
Patients with MK were identified in the electronic health record from August 2012 to December 2021. Diagnostic laboratory tests with an MK diagnosis were identified and classified as laboratory positive or laboratory negative. Laboratory-positive infections were categorized as bacterial (gram-positive, gram-negative, or acid-fast bacilli), fungal, viral, Acanthamoeba, or polymicrobial. Antimicrobial susceptibilities were obtained. Trends over time were assessed using linear regression.

Results:
Of 3288 patients with MK identified, 1012 (30.8%) had laboratory tests performed. Laboratory-positive infections (n = 499, 49.3%) were bacterial in 73.5% (n = 367) of cases, fungal in 7.8% (n = 39), viral in 1.6% (n = 8), Acanthamoeba in 1.4% (n = 7), and polymicrobial in 15.6% (n = 78). Of bacterial infections, 70% (n = 257) were gram-positive, with coagulase-negative Staphylococcus (CoNS; 31%) and Staphylococcus aureus (S. aureus; 23%) as the most common pathogens. Bacteria were acid-fast bacilli in 1.9% (n = 7) of cases and gram-negative in 28.1% (n = 103), with Pseudomonas aeruginosa as the predominant pathogen (47.7%). S. aureus showed antibiotic resistance from 0% (vancomycin and gentamicin) to 50% (erythromycin); CoNS from 0% (vancomycin, gentamicin, and moxifloxacin) to 64% (erythromycin). The rate of laboratory-negative MK significantly increased over time (slope estimate = 2.1% per year, P = 0.034). Rates of bacterial, fungal, viral, Acanthamoeba, and polymicrobial infections were stable over time (all slope P > 0.05).

Conclusions:
Bacterial keratitis accounted for most MK cases. Gram-positive bacteria were the most common isolates. CoNS and S. aureus were universally susceptible to vancomycin. Rates of MK infection types were stable over time.
Descriptive Epidemiology of High School Swimming and Diving Injuries
Authors: Belilos Eleanor , Jow Steven , Maxwell Matthew 
Published: January 2023

Objective:
Using data from a longitudinal national sports injury surveillance program, this study aimed to calculate injury rates and describe injury patterns across high school swimmers and divers.

Design:
Descriptive Epidemiological Study. Athletic trainers (ATs) from participating high schools reported injuries from swimming and diving programs for the High School Reporting Information Online system.

Setting:
Convenience sample of high school boys and girls' swimming and diving injuries during the 2008 to 2019 school years.

Patients or other Participants:
High school boy and girl swimmers and divers (aged ∼14-18 years).

Independent Variables:
Exposure data on gender, location of injury (practice vs competition), mechanism of injury, and sport (swimming vs diving).

Main Outcome Measures:
Injury rates, rate ratios (RRs) with 95% confidence intervals, and other descriptive statistics were performed.

Results:
563 swimming and diving injuries occurred during 2 171 260 athlete exposures (0.26 per 1000 athlete exposures). Girls had higher injury rates than boys overall (RR 1.57, P < 0.05), in practice (RR 1.53, P < 0.05), and competition (RR 1.81, P < 0.05). In swimmers, most injuries were to the shoulder (48.6%), associated with the freestyle (67.3%), and classified as overuse/chronic (58.0%). Among divers, most injuries were to the head/face (36.6%) and from contact with the playing surface (68.3%).

Conclusions:
Girls had statistically significantly higher injury rates than boys. The shoulder and head/face were the most injured body parts in swimmers and divers, respectively. Swimming injuries were most frequently of an overuse etiology, whereas diving injuries were more likely traumatic. Coaches and ATs should be aware of these findings to develop targeted strategies for injury prevention.
Expanding access to difficult urinary catheter insertion services through a novel nurse practitioner-led team
Authors: Hackett Anna , Wells Celia , Drew Lora , Curto Joseph , Ennis-Welch Petrona , Zafra Kimberly , Bass Kathryn , Rosen Daniel , Gupta Rohit , Kohli-Seth Roopa 
Published: January 2023

ABSTRACT

Background:
Within the United States health care system, one of the most common procedures performed daily is urinary catheterization. Oftentimes, the urinary catheter is placed by nursing personnel without any difficulty. Although the procedure is usually simple and routine, there are instances in which placement can be problematic.

Local Problem:
Urology is one of the smallest surgical subspecialties, with intermittent availability given active commitments in the operating room and clinic. This opened an opportunity for nurse practitioners (NPs) at an urban quaternary care hospital to further enhance their skill set in the care of these patients.

Methods:
Fifteen Rapid Response Team NPs were selected based on specific criteria. Their roles expanded to include consults for difficult urinary catheter insertions.

Intervention:
A 2-step training program was implemented for NPs to develop proficiency in inserting urinary catheters in patients with new or known urologic conditions.

Results:
Of the 391 catheter consults made to the NP group, 73 (18.7%) of them required urology follow-up.

Conclusion:
This program can benefit patients by potentially reducing catheter-related complications and associated length of stay.
Prevalence and Correlates of Hair Pulling Disorder and Skin Picking Disorder in an Acute Psychiatric Sample
Authors: Snorrason Ivar , Keuthen Nancy J. , Beard Courtney , Björgvinsson Thröstur 
Published: January 2023

Abstract
Hair pulling disorder (HPD; trichotillomania) and skin picking disorder (SPD; excoriation disorder) are understudied psychiatric disorders. The aim of this study was to examine the prevalence and correlates of HPD and SPD in an acute psychiatric sample. Semistructured interviews and self-report measures were administered to patients in a psychiatric partial hospital (N = 599). The past-month prevalence of HPD and SPD was 2.3% and 9%, respectively. HPD and SPD had highly similar clinical characteristics and a strong co-occurrence. Patients with HPD/SPD were significantly younger than other patients and more likely to be female. Logistic regression controlling for age and sex showed that diagnosis of HPD/SPD was not significantly associated with suicidal ideation, suicidal behaviors, nonsuicidal self-injury, or emotional disorder diagnoses (e.g., borderline personality disorder, major depressive disorder). HPD/SPD status was significantly associated with an increased risk of generalized anxiety disorder. However, patients with HPD/SPD did not differ from other patients on self-report measures of generalized anxiety, depression, and distress intolerance. HPD and SPD are common and frequently co-occurring disorders in psychiatric settings.
Association Between Cannabis and Violence in Community-Dwelling Patients With Severe Mental Disorders
Authors: Hudon Alexandre , Dellazizzo Laura , Phraxayavong Kingsada , Potvin Stéphane , Dumais Alexandre 
Published: January 2023

Abstract
The objective of this cross-sectional study was to identify cannabis-related features and other characteristics predictive of violence using a data-driven approach in patients with severe mental disorders (SMDs). A Least Absolute Shrinkage and Selection Operator regularization regression model was used on the database consisting of 97 patients with SMD who completed questionnaires measuring substance use and violence. Cannabis use, particularly related to patients' decision to consume or time spent using, was a key predictor associated with violence. Other patterns of substance use and personality traits were identified as strong predictors. Regular patterns of cannabis use and interpersonal issues related to cannabis/stimulant abuse were inversely correlated to violence. This study identified the effect of several predictors correlated to violence in patients with SMD using a regularization regression model. Findings open the door to better identify the profiles of patients that may be more susceptible to perpetrate violent behaviors.
Spontaneous Recanalization of Internal Carotid Artery Occlusion
Authors: Zhang Sarah Y. , Blacquiere Dylan , Dewar Brian , Stotts Grant , Dowlatshahi Dar 
Published: January 2023

Introduction:
Spontaneous recanalization of an occluded internal carotid artery (ICA) is thought to be unlikely. However, there has been a growing number of reports describing this phenomenon. Despite this, the frequency, time course, and mechanism of spontaneous recanalization remain unknown. In this paper, we describe a patient with a symptomatic recanalization of an occluded left ICA.

Case Report:
A 70-year-old woman presented with transient speech arrest and right upper extremity weakness related to an occluded ICA. After 3 days, her weakness and aphasia reappeared and worsened transiently. A repeat computed tomography angiography revealed recanalization of the occluded ICA, as well as new ischemic changes in the previously hypoperfused left insular region. This finding changed the management from medical management to revascularization with a stent, after which the patient was discharged home with acetylsalicylic acid and clopidogrel.

Conclusions:
Although previously thought to be a rare occurrence, spontaneous recanalization is not uncommon. Further research into this phenomenon as proper identification and characterization of this phenomenon can influence follow-up and management.
The Influence of Pterygium on Meibomian Glands and Dry Eye Parameters
Authors: Devebacak Ali , Teker M. Esat , Palamar Melis 
Published: January 2023

ABSTRACT

Significance
Mechanical factors are also associated with Meibomian gland dysregulation in patients with pterygium. Dry eye parameters were assessed, and the results support the association between pterygium and dry eye disease.

Purpose
To investigate how Meibomian gland dysfunction and dry eye parameters relate to the existence of pterygium.

Methods
Patients with pterygium and healthy volunteers of similar age and demographic characteristics were included. Schirmer 1 test, Ocular Surface Disease Index (OSDI) score, fluorescein tear film break-up time and ocular surface staining scores (Oxford score) were recorded. Meiboscores were estimated based on Meibomian gland loss rate on infrared meibography (SL-D701; Topcon, Netherlands). The symmetry of Meibomian gland loss with respect to eyelid midline was assessed.

Results
54 eyes with pterygium (Group 1) and 50 eyes of healthy volunteers (Group 2) were included. The mean ages were 54.0 ± 12.3 and 52.3 ± 8.0 years, respectively. Schirmer 1 test results and tear film break-up time were lower in Group 1 (P = .007, p < .001). Oxford and OSDI scores were significantly higher in Group 1 (P = .009, p < .001). The mean meiboscores were significantly higher in Group 1 (P < .001). There was Meibomian gland depletion in 90.7% (49:54) of Group 1 and 32% (16:50) of Group 2 (P < .001). Meibomian gland loss region was distributed asymmetrically in 75.5% (37:49) of the eyes in Group 1, but not in any of the eyes in Group 2. The asymmetry was located on the side where the pterygium was detected in 94.5% (35:37) of these eyes.

Conclusions
Meibomian glands are influenced morphologically and functionally in eyes with pterygium. The overlap of the pterygium location and Meibomian gland abnormality suggests a direct mechanical relationship. In managing pterygium patients, the possibility of Meibomian gland dysfunction and associated evaporative dry eye should be considered.
Intraobserver and Interobserver Consistency Evaluation of Carotid Plaque Volume Measured by Different 3-Dimensional Ultrasound Methods
Authors: Ren Ling , Yan Lin , Fei Xiang , Luo Yukun 
Published: January 2023

Abstract
This study aims to evaluate the accuracy of the semiautomatic planimetric measurement (SAPM) method and the necessity of manually adjusted boundary measurement in 3-dimensional ultrasound measurement of plaque volume. A total of 50 patients with 82 plaques in the common carotid arteries between December 2020 and March 2021 were included in this study. Two observers measured the 3-dimensional volume of plaque for each patient in 3 different methods (contour tracing method [CTM], SAPM method without manually adjusted boundary [SAPM1], and SAPM method with manually adjusted boundary [SAPM2]). The difference in measurement time between the 3 methods was evaluated by Kruskal-Wallis H test. Intraclass correlation coefficient and 95% confidence interval were used to evaluate the intraobserver and interobserver reliability of the 3 measurement modes. The Bland-Altman analysis was used to assess the agreement, which was expressed as the mean difference with the 95% limits of agreement (LOA). The difference in measurement time between the 3 methods was statistically significant (P < 0.001). Both observers' intraobserver and interobserver reliability showed well in the 3 methods (all of the intraclass correlation coefficients were >0.75). The mean differences of the plaque volume measurement were 38.17, 26.42, and 11.75 mm3, respectively. The agreement between CTM and SAPM2 was the best, and LOA was −57.00 to 80.51. The agreement between SAPM1 and SAPM2 and the agreement between SAPM1 and CTM were similar, and the LOAs were −126.10 to 202.40 and −158.00 to 210.80, respectively. The SAPM method may be recommended to measure plaque volume in clinical practice.
Solitary-like and modulated wavepackets in the Couette–Taylor flow with a radial temperature gradient
Authors: Kang Changwoo , Yoshikawa Harunori N. , Ntarmouchant Ziad , Prigent Arnaud , Mutabazi Innocent 
Published: January 2023

We have performed numerical and experimental studies of the flow in a large aspect ratio Couette–Taylor system with a rotating inner cylinder and a fixed radial temperature gradient. The base flow state is a superposition of an azimuthal flow induced by rotation and an axial large convective cell induced by the temperature gradient. For a relatively large temperature gradient, the rotation rate of the inner cylinder destabilizes the convective cell to give rise to travelling wave pattern through a subcritical bifurcation. This wave pattern is associated with a temperature mode and it consists of helical vortices travelling in the annulus. In a small range of the rotation rate, helical vortices have longitudinal meandering leading to the formation of kinks randomly distributed, leading to spatio-temporal disordered patterns. The flow becomes regular for a large interval of rotation rate. The friction, the momentum and the heat transfer coefficients are computed and found to be independent of the heating direction.This article is part of the theme issue ‘Taylor–Couette and related flows on the centennial of Taylor's seminalPhilosophical Transactionspaper (part 1)’.