bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph-based models of the Oenothera mitochondrial genome capture the enormous complexity of higher plant mitochondrial DNA organization
Authors: Fischer Axel , Dotzek Jana , Walther Dirk , Greiner Stephan 
Published: March 2022

Abstract
Plant mitochondrial genomes display an enormous structural complexity, as recombining repeat-pairs lead to the generation of various sub-genomic molecules, rendering these genomes extremely challenging to assemble. We present a novel bioinformatic data-processing pipeline called SAGBAC (Semi-Automated Graph-Based Assembly Curator) that identifies recombinogenic repeat-pairs and reconstructs plant mitochondrial genomes. SAGBAC processes assembly outputs and applies our novel ISEIS (Iterative Sequence Ends Identity Search) algorithm to obtain a graph-based visualization. We applied this approach to three mitochondrial genomes of evening primrose (Oenothera), a plant genus used for cytoplasmic genetics studies. All identified repeat pairs were found to be flanked by two alternative and unique sequence-contigs defining so-called ‘double forks’, resulting in four possible contig-repeat-contig combinations for each repeat pair. Based on the inferred structural models, the stoichiometry of the different contig-repeat-contig combinations was analyzed using Illumina mate-pair and PacBio RSII data. This uncovered a remarkable structural diversity of the three closely related mitochondrial genomes, as well as substantial phylogenetic variation of the underlying repeats. Our model allows predicting all recombination events and, thus, all possible sub-genomes. In future work, the proposed methodology may prove useful for the investigation of the sub-genome organization and dynamics in different tissues and at various developmental stages.
Combining cardiac monitoring with actigraphy aids nocturnal arousal detection during ambulatory sleep assessment in insomnia
Authors: Rösler Lara , van der Lande Glenn , Leerssen Jeanne , Vandegriffe Austin G , Lakbila-Kamal Oti , Foster-Dingley Jessica C , Albers Anne C W , van Someren Eus J W 
Published: March 2022

Abstract

Study Objectives
The objective assessment of insomnia has remained difficult. Multisensory devices collecting heart rate (HR) and motion are regarded as the future of ambulatory sleep monitoring. Unfortunately, reports on altered average HR or heart rate variability (HRV) during sleep in insomnia are equivocal. Here, we evaluated whether the objective quantification of insomnia improves by assessing state-related changes in cardiac measures.

Methods
We recorded electrocardiography, posture, and actigraphy in 33 people without sleep complaints and 158 patients with mild to severe insomnia over 4 d in their home environment. At the microscale, we investigated whether HR changed with proximity to gross (body) and small (wrist) movements at nighttime. At the macroscale, we calculated day-night differences in HR and HRV measures. For both timescales, we tested whether outcome measures were related to insomnia diagnosis and severity.

Results
At the microscale, an increase in HR was often detectable already 60 s prior to as well as following a nocturnal chest, but not wrist, movement. This increase was slightly steeper in insomnia and was associated with insomnia severity, but future EEG recordings are necessary to elucidate whether these changes occur prior to or simultaneously with PSG-indicators of wakefulness. At the macroscale, we found an attenuated cardiac response to sleep in insomnia: patients consistently showed smaller day-night differences in HR and HRV.

Conclusions
Incorporating state-related changes in cardiac features in the ambulatory monitoring of sleep might provide a more sensitive biomarker of insomnia than the use of cardiac activity averages or actigraphy alone.
Nurses' role in addressing social determinants of health
Authors: Tiase Victoria , Crookston Cathryn Degraff , Schoenbaum Anna , Valu Madelynn 
Published: March 2022

Abstract:
Nurses have a vital role in addressing social and health inequities to promote quality healthcare for all. This article discusses the tools to screen for social determinants of health (SDOH) and key considerations for nurses and nurse leaders to advance the integration of SDOH information into their workflows.
Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection
Authors: Jung Carrie E. , Estaki Mehrbod , Chopyk Jessica , Taylor Bryn C. , Gonzalez Antonio , McDonald Daniel , Shin Jenny , Ferrante Kimberly , Wasenda Erika , Lippmann Quinn , Knight Rob , Pride David , Lukacz Emily S. 
Published: March 2022

(Abstracted from Female Pelvic Med Reconstr Surg 2022;28:20–26)
Up to 50% of women will have at least 1 urinary tract infection (UTI) in their lifetime, and 2% to 5% will experience recurrent UTIs (rUTIs). Postmenopausal women are disproportionately affected by both UTI and rUTI.
Randomized Trial of Cytoreductive Surgery for Relapsed Ovarian Cancer
Authors: Harter Philipp , Sehouli Jalid , Vergote Ignace , Ferron Gwenael , Reuss Alexander , Meier Werner , Greggi Stefano , Mosgard Berit J. , Selle Frederic , Guyon Frederic , Pomel Christophe , Lécuru Fabrice , Zang Rongyu , Avall-Lundqvist Elisabeth , Kim Jae‐Weon , Ponce Jordi , Raspagliesi Francesco , Kristensen Gunnar , Classe Jean-Marc , Hillemanns Peter , Jensen Pernille , Hasenburg Annette , Ghaem-Maghami Sadaf , Mirza Mansoor R. , Lund Bente , Reinthaller Alexander , Santaballa Ana , Olaitan Adeola , Hilpert Felix , du Bois Andreas 
Published: March 2022

(Abstracted from N Engl J Med 2021;385:2123–2131)
Standard of care treatment for advanced ovarian cancer involves primary macroscopic resection of all tumor followed by platinum-based combination chemotherapy with or without additional systemic therapy including bevacizumab or a poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitor. The Descriptive Evaluation of Preoperative Selection Criteria for Operability in Recurrent Ovarian Cancer (DESKTOP) series aims to assess the role of surgery in management of recurrent ovarian cancer.
Is maternal employment site a source of exposure misclassification in studies of environmental exposures and birth outcomes? A simulation-based bias analysis of haloacetic acids in tap water and hypospadias
Authors: Zaganjor Ibrahim , Keil Alexander P. , Luben Thomas J. , Desrosiers Tania A. , Engel Lawrence S. , Reefhuis Jennita , Michalski Adrian M. , Langlois Peter H. , Olshan Andrew F. ,   The National Birth Defects Prevention Study
Published: March 2022

Background:
In population research, exposure to environmental contaminants is often indirectly assessed by linking residence to geocoded databases of environmental exposures. We explored the potential for misclassification of residence-based environmental exposure as a result of not accounting for the workplace environments of employed pregnant women using data from a National Birth Defects Prevention Study (NBDPS) analysis of drinking water haloacetic acids and hypospadias.

Methods:
The original analysis used NBDPS data from women with haloacetic acid exposure information in eight states who delivered an infant with second- or third-degree hypospadias (cases) or a male infant without a birth defect (controls) between 2000 and 2005. In this bias analysis, we used a uniform distribution to randomly select 11%–14% of employed women that were assumed to change municipal water systems between home and work and imputed new contaminant exposures for tap water beverages consumed at work among the selected women using resampled values from the control population. Multivariable logistic regression was used to estimate the association between hypospadias and haloacetic acid ingestion with the same covariates and exposure cut-points as the original study. We repeated this process across 10,000 iterations and then completed a sensitivity analysis of an additional 10,000 iterations where we expanded the uniform distribution (i.e., 0%, 28%).

Results:
In both simulations, the average results of the 10,000 iterations were nearly identical to those of the initial study.

Conclusions:
Our results suggest that household estimates may be sufficient proxies for worksite exposures to haloacetic acids in tap water.
Dosing for Personalized Prophylaxis in Hemophilia A Highly Varies on the Underlying Population Pharmacokinetic Models
Authors: Uster David W. , Chowdary Pratima , Riddell Anne , Garcia Cecilia , Aradom Elsa , Musarara Molly , Wicha Sebastian G. 
Published: March 2022

Background:
Model-informed personalized prophylaxis with factor VIII (FVIII) replacement therapy aimed at higher trough levels is becoming indispensable for patients with severe hemophilia A. This study aimed to identify the most suitable population pharmacokinetic (PK) models for personalized prophylaxis using various FVIII products and 2 clinical assays and to implement the most suitable one in open-access software.

Methods:
Twelve published population PK models were systematically compared to predict the time above target (TaT) for a reference dosing occasion. External validation was performed using a 5-point PK data from 39 adult patients with hemophilia A with FVIII measured by chromogenic substrate (CSA) and 1-stage assays (OSAs) using NONMEM under 3 different conditions: a priori (with all FVIII samples blinded), a posteriori (with 1 trough sample), and general model fit (with all FVIII samples including the reference dosing occasion provided).

Results:
On average, the baseline covariate models overpredicted TaT (a priori; bias −3.8 hours to 49.6 hours). When additionally including 1 previous trough FVIII sample before the reference dosing occasion (a posteriori), only 50% of the models improved in bias (−1.0 hours to 36.5 hours) and imprecision (22.4 hours and 60.7 hours). Using all the time points (general model fit), the models accurately predicted (individual TaT less than ±12 hours compared with the reference) 62%–90% and 33%–74% of the patients using CSA and OSA data, respectively. Across all scenarios, predictions using CSA data were more accurate than those using the OSA data.

Conclusions:
One model performed best across the population (bias: −3.8 hours a priori, −1.0 hours a posteriori, and 0.6 hours general model fit) and acceptably predicted 44% (a priori) to 90% (general model fit) of the patients. To allow the community-based evaluation of patient–individual FVIII dosing, this model was implemented in the open-access model-informed precision dosing software “TDMx.”
Relationship of sleep disorders with long-term complications and health-related quality of life in people with well-controlled human immunodeficiency virus
Authors: Yoshino Yusuke , Wakabayashi Yoshitaka , Kitazawa Takatoshi 
Published: March 2022

Abstract
Although sleep disorders are common in patients with human immunodeficiency virus (HIV) infection, they have not been adequately evaluated under currently advanced treatments, mainly with integrase strand transfer inhibitors. However, the relationship of sleep disorders with long-term complications and quality of life (QOL) status in patients infected with HIV is still poorly understood. Such associations are important in the management of outpatients with HIV. Hence, this study aimed to evaluate these associations.
This cross-sectional observational study assessed the QOL changes of patients with HIV before and after the treatment regimen change. Male patients with well-controlled HIV who attended our hospital and changed HIV medications for reasons other than treatment failure between October 2019 and September 2021 were included. At the time of regimen change, sleep disorder status was assessed according to the Pittsburgh sleep quality index (PSQI), and health-related QOL (HRQOL) was assessed using the medical outcomes study 8-item short form health survey. In addition, we collected information on age, blood tests, and long-term comorbid conditions present during the evaluation. The HIV treatment regimen was also reviewed.
Out of 45 male Japanese patients with HIV that were included in this study, 24 (53.3%) and 21 (46.7%) were classified into the sleep disorder group and nonsleep disorder group, respectively, according to their PSQI scores. The sleep disorder group had a significantly lower HRQOL mental component summary (P = .0222) than the nonsleep disorder group. The prevalence rates of hypertension, dyslipidemia, and diabetes mellitus were not significantly different between the 2 groups. In addition, a significant correlation was observed between PSQI scores and the HRQOL status (mental component summary, P = .0450; physical component summary, P = .0350).
Sleep disorders remain common in patients with well-controlled HIV infection receiving current treatment. Sleep disorder is significantly associated with a low HRQOL in these patients. Hence, sleep status evaluation is necessary to improve HIV management.
Assessment of quality of life and activities of daily living among elderly patients with hypertension and impaired physical mobility in home health care by antihypertensive drugs plus acupuncture
Authors: Huang Kuei-Yu , Chang Ching-Hao , Yu Kai-Chiang , Hsu Chung-Hua 
Published: March 2022

AbstractBackground:To evaluate the efficacy of acupuncture in improving quality of life (QOL) and activities of daily living among elderly patients with hypertension and impaired physical mobility in home health care.Methods:Seventy participants were allocated randomly to receive either acupuncture together with antihypertensive drugs (n = 35) or antihypertensive drugs only (n = 35). Acupuncture was conducted twice a week for 12 consecutive weeks, each lasting 30 minutes. Acupuncture points San Yin Jiao, Xue Hai, Taichong, Zusanli, and Hegu acupuncture points were used bilaterally. The primary outcome was change in QOL score, evaluating by Short-Form 36 Item Health Survey (SF-36). Secondary outcomes were changes in Barthel index score and blood pressure. Besides, pain evaluation by Visual analog scale, among acupuncture and control subgroups in participants with diagnosis with disease of the musculoskeletal system and connective tissue (ICD-9: 710-739).Results:Thirty-one participants in each of the acupuncture group and the control group completed the study. After 12 weeks of treatment, compared with the control group, the combination of antihypertensive treatments and acupuncture helped to improve bodily pain (P= .03), physical component summary (P= .04), mental health (P< .001), mental component summary (P= .008), Barthel index (P= .02), and systolic blood pressure (P= .01). In contrast, the control group showed no significant changes. Change in pain score revealed that there were a significant between-group differences after 6weeks (P= .01) and 12weeks of treatment (P= .001).Conclusion:The results of the study suggested that in home health care elderly patients with hypertension and impaired physical mobility, antihypertensive drugs combined with acupuncture therapy will be more beneficial to improve QOL, activities of daily living, and blood pressure.
Construction of miRNA-regulated drug-pathway network to screen drug repurposing candidates for multiple sclerosis
Authors: Kong Xiaotong , Wang Jianjian , Cao Yuze , Lu Xiaoyu , Zhang Huixue , Zhang XiaoMing , Bo Chunrui , Bai Ming , Li Shuang , Jiao Yang , Wang Lihua 
Published: March 2022

AbstractGiven the high disability rate of multiple sclerosis (MS), there is a need for safer and more effective therapeutic agents. Existing literature highlights the prominent roles of miRNA in MS pathophysiology. Nevertheless, there are few studies that have explored the usefulness of existing drugs in treating MS through potential miRNA-modulating abilities.The current investigation identifies genes that may exacerbate the risk of MS due to their respective miRNA associations. These findings were then used to determine potential drug candidates through the construction of miRNA-regulated drug-pathway network through genes. We uncovered a total of 48 MS risk pathways, 133 MS risk miRNAs, and 186 drugs that can affect these pathways. Potential MS risk miRNAs that are also regulated by therapeutic candidates were hsa05215 and hsa05152. We analyzed the properties of the miRNA-regulated drug-pathway network through genes and uncovered a number of novel MS agents by assessing their respective Z-values.A total of 20 likely drug candidates were identified, including human immunoglobulin, aspirin, alemtuzumab, minocycline, abciximab, alefacept, palivizumab, bevacizumab, efalizumab, tositumomab, minocycline, etanercept, catumaxomab, and sarilumab. Each of these agents were then explored with regards to their likely mechanism of action in treating MS.The current investigation provides a fresh perspective on MS biological mechanisms as well as likely treatment strategies.
A holistic investigation of the global outcomes of spontaneous pneumothorax during 1980-2021, including the COVID-19 pandemic A bibliometric approach
Authors: Baldemir Ramazan , Ülger Gulay 
Published: March 2022

Abstract

Background:
During coronavirus pandemic, despite the increase in the number of studies on spontaneous pneumothorax (SP), there is not enough bibliometric study in the literature. In this study, it was aimed to analyze scientific articles published on SP.

Methods:
Studies published on SP between 1980 and 2021 were obtained from the Web of Science database and analyzed using statistical and bibliometric methods. Spearman correlation coefficient was used for correlation studies. The exponential smoothing estimator was used to forecast publication trend for coming years. Network visualization maps were used to analyze citations and identify trending topics.

Results:
A total of 2422 publications were found. 1403 (57.9%) of these publications were articles. The articles on SP have increased with a non-linear trend in recent years. The top 5 contributors to the literature were USA (231, 16.4%), Japan (161, 11.4%), United Kingdom (98, 6.9%), France (81, 5.7%), and Taiwan (78, 5.5%). The top 3 most active institutions were National Taiwan University Hospital (22, 1.5%), Catholic University Korea (19, 1.3%), and National Taiwan University (19, 1.3%). The top 3 journals that published the most articles were Chest (51), Annals of Thoracic Surgery (46), and Journal of Thoracic Disease (45). The most studied subjects were primary SP, recurrence, thoracoscopy, pleurodesis, video-assisted thoracoscopic surgery, COVID-19, video-assisted thoracic surgery, chest tube(s), and secondary spontaneous pneumothorax. According to trend topics analysis, the keywords studied in recent years are COVID-19, chest tubes, pneumonia, subcutaneous emphysema, risk factors, dyspnea, primary SP, FLCN gene, tension pneumothorax, uniportal, postoperative recurrence, secondary spontaneous pneumothorax, chronic obstructive pulmonary disease, and uniportal.

Conclusion:
In this comprehensive bibliometric study, we summarized 1403 articles about SP, which has an increasing trend in the number of articles during the COVID-19 pandemic process. This article can be a useful resource for clinicians and scientists through presenting a summary of worldwide studies related to SP, including the ones during COVID-19 pandemic.
Time to Reflect and Take Action on Health Disparities and Health Inequities
Authors: Salmond Susan , Dorsen Caroline 
Published: March 2022

The United States healthcare system underperforms in healthcare access, quality, and cost resulting in some of the poorest health outcomes among comparable countries, despite spending more of its gross national product on healthcare than any other country in the world. Within the United States, there are significant healthcare disparities based on race, ethnicity, socioeconomic status, education level, sexual orientation, gender identity, and geographic location. COVID-19 has illuminated the racial disparities in health outcomes.
This article provides an overview of some of the main concepts related to health disparities generally, and in orthopaedics specifically. It provides an introduction to health equity terminology, issues of bias and equity, and potential interventions to achieve equity and social justice by addressing commonly asked questions and then introduces the reader to persistent orthopaedic health disparities specific to total hip and total knee arthroplasty.
Vasoplegic Shock Represents a Dominant Hemodynamic Profile of Multisystem Inflammatory Syndrome Following COVID-19 in Children and Adolescents
Authors: Alali Alexander , O’Neil Erika , Anders Marc , Abella Jayvee , Shekerdemian Lara S. , Vogel Tiphanie P. , Sexson Tejtel Kristen , Tume Sebastian C. 
Published: March 2022

OBJECTIVES:
The hemodynamic profile of multisystem inflammatory syndrome in children (MIS-C)–related shock remains poorly defined and, therefore, challenging to support with pharmacotherapy in the ICU. We aimed to evaluate the hemodynamic profile and vasoactive medication management used in MIS-C patients presenting to the ICU in shock and provide data from high-fidelity continuous cardiac output monitoring.

DESIGN
Single-center retrospective case-cohort study.

SETTING:
Pediatric and cardiac ICU in a quaternary-care hospital.

PATIENTS:
All patients who met U.S. Centers for Disease Control and Prevention criteria for MIS-C and who were admitted to the ICU between March 2020 and May 2021 required vasoactive support and were placed on continuous cardiac index (CCI) monitoring. Patients requiring extracorporeal life support were excluded.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Among 52 children with MIS-C presenting in shock and requiring vasoactive support, 14 patients (27%) were placed on CCI monitoring. These 14 patients had hyperdynamic cardiac index (CI) and low indexed systemic vascular resistance (SVRi) in the first 24 hours with normalization of CI and improved SVRi within the subsequent 24 hours.

CONCLUSIONS:
Further studies are needed to evaluate the difference between the use of vasoconstrictor versus vasodilators in pediatric patients with MIS-C because a phenotype with high CI and low SVRi may be important.
Education for Pediatric Gastroenterology Pathology Reports Increases Understanding Ahead of 21st Century Cures Act Rollout
Authors: Dunwoodie Leland , Vannilam Annette 
Published: March 2022

Background:
As a result of the 21st Century Cures Act, Pediatric Gastroenterology (Peds GI) patients and caregivers are receiving pathology reports directly on their online patient portal. This quality improvement project attempted to validate an educational handout about Peds GI pathology reports and identify areas for caregiver education.

Methods:
Caregivers (n = 59) of patients undergoing Peds GI procedures were surveyed about their knowledge of pathology reports. Caregivers’ responses to each of 4 questions were assessed before and after reading an educational handout. These 4 questions questioned the contents and creators of pathology reports, the role of pathologists, and caregiver confidence in interpreting pathology reports.

Results:
Nearly one-third of caregivers did not know the role of pathologists before education, and one-fifth of caregivers did not know the contents of a pathology report. Caregivers with less than a college degree (n = 21, P = 0.0089), and caregivers of patients undergoing their first procedure (n = 27, P = 0.0022) showed a significant improvement in responses after the educational handout.

Conclusions:
Educational handouts can increase caregiver understanding of pathology reports, especially for those with lower education levels or those with children undergoing their first procedure.