bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program
Authors: Goswami Chirayu , Sheldon Michael , Bixby Christian , Keddache Mehdi , Bogdanowicz Alexander , Wang Yihe , Schultz Jonathan , McDevitt Jessica , LaPorta James , Kwon Elaine , Buyske Steven , Garbolino Dana , Biloholowski Glenys , Pastuszak Alex , Storella Mary , Bhalla Amit , Charlier-Rodriguez Florence , Hager Russ , Grimwood Robin , Nahas Shareef A. 
Published: April 2022

Abstract
Background
The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021.

Methods
RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina’s Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID.

Results
An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron.

Conclusion
These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.
Damaging novel mutations in PIGN cause developmental epileptic-dyskinetic encephalopathy: a case report
Authors: Tian Maoqiang , Chen Jing , Li Juan , Pan Hong , Lei Wenting , Shu Xiaomei 
Published: April 2022

Abstract
Background
Mutations in PIGN, resulting in a glycosylphosphatidylinositol (GPI) anchor deficiency, typically leads to multiple congenital anomalies-hypotonia-seizures syndrome. However, the link between PIGN and epilepsy or paroxysmal non-kinesigenic dyskinesia (PNKD) is not well-described. This study reported a patient with PIGN mutation leading to developmental and epileptic encephalopathy and PNKD, to expand upon the genotype–phenotype correlation of PIGN.

Case presentation
During the first 10 days of life, a girl exhibited paroxysmal staring episodes with durations that ranged from several minutes to hours. These episodes occurred 2–5 times daily and always occurred during wakefulness. Ictal electroencephalography revealed no abnormalities, and PNKD was diagnosed. The patient also exhibited severely delayed psychomotor development and generalized seizures at the age of 4 months. Results of brain magnetic resonance imaging and metabolic screenings were normal, but trio-based whole-exome sequencing identified two novel compound heterozygous PIGN mutations (NM_176787; c.163C > T [p.R55 > X] and c.283C > T [p.R95W]). Flow cytometry analysis of the patient’s granulocytes revealed dramatically reduced expression of GPI-anchored proteins. This indicated that the mutations compromised GPI functions. The patient got seizure-free for 1 year, and her dyskinesia episodes reduced significantly (1–2 times/month) after treatment with levetiracetam (600 mg/day) and clonazepam (1.5 mg/day). No progress was observed with respect to psychomotor development; however, no craniofacial dysmorphic features, cleft lip/palate, brachytelephalangy with nail hypoplasia, and internal malformations have been observed until now (6 years of age).

Conclusion
This is the first study to document developmental and epileptic encephalopathy with PNKD in a human with PIGN mutations. This report expanded our understanding of the genotype–phenotype correlation of PIGN, and PIGN may be considered a potentially relevant gene when investigating cases of epilepsy or PNKD.
Advances in our understanding of the molecular pathogenesis of necrotizing enterocolitis
Authors: Cai Xue , Golubkova Alena , Hunter Catherine J. 
Published: April 2022

AbstractNecrotizing enterocolitis (NEC) is a multifactorial and complex disease. Our knowledge of the cellular and genetic basis of NEC have expanded considerably as new molecular mechanisms have been identified. This article will focus on the current understanding of the molecular pathogenesis of NEC with a focus on the inflammatory, immune, infectious, and genetic mechanisms that drive disease development.
The experience of participating in an internet-based cognitive behavioral therapy program among patients with cardiovascular disease and depression: a qualitative interview study
Authors: Westas Mats , Mourad Ghassan , Andersson Gerhard , Neher Margit , Lundgren Johan , Johansson Peter 
Published: April 2022

Abstract
Background
Depression in conjunction with cardiovascular disease (CVD) is associated with worsening in CVD, higher mortality, and poorer quality of life. Despite the poor outcomes there is a treatment gap of depression in CVD patients. Recently we found that an Internet-based cognitive behavioral therapy (iCBT) tailored for CVD patients led to reduced symptoms of depression. However, we still have little knowledge about CVD patients’ experiences of working with iCBT. The aim of this study was therefore to explore CVD patients’ experiences of engaging in a tailored iCBT program.

Methods
A qualitative interview study using inductive thematic analysis. Data was obtained from 20 patients with CVD and depressive symptoms who had participated in a randomized controlled trial (RCT) evaluating the impact of a nine-week iCBT program on depression.

Results
Three main themes emerged: (1) Taking control of the disease, (2) Not just a walk in the park, and (3) Feeling a personal engagement with the iCBT program. The first theme included comments that the tailored program gave the patients a feeling of being active in the treatment process and helped them achieve changes in thoughts and behaviors necessary to take control of their CVD. The second theme showed that patients also experienced the program as demanding and emotionally challenging. However, it was viewed as helpful to challenge negative thinking about living with CVD and to change depressive thoughts. In the third theme patients reported that the structure inherent in the program, in the form of organizing their own health and the scheduled feedback from the therapist created a feeling of being seen as an individual. The feeling of being acknowledged as a person also made it easier to continuously work with the changes necessary to improve their health.

Conclusions
Engaging in an iCBT program tailored for patients with CVD and depression was by the patients perceived as helpful in the treatment of depression. They experienced positive changes in emotions, thoughts, and behaviors which a result of learning to take control of their CVD, being confirmed and getting support. The patients considered working with the iCBT program as demanding and emotionally challenging, but necessary to achieve changes in emotions, thoughts, and behaviors.
The effect of exercise on resilience, its mediators and moderators, in a general population during the UK COVID-19 pandemic in 2020: a cross-sectional online study
Authors: Lancaster Molly Rose , Callaghan Patrick 
Published: April 2022

Abstract
Background
Resilience is central to positive mental health and well-being especially when faced with adverse events. Factors such as exercise, location, sleep, mental health, and personality are moderators and mediators of resilience. However, the impact of these factors on resilience during severe adverse events are unknown. The present study examined how the COVID-19 pandemic affected resilience and its moderators and mediators by investigating whether there was a difference in resilience and quality of life between people with varying levels of exercise, including those who changed their exercise levels pre and during a COVID-19-related lockdown, and whether location affected the relationship between levels of exercise and resilience and quality of life.

Methods
Following ethical approval, a cross-sectional online survey capturing data on self-reported key moderators and mediators of resilience before and during the COVID-19 lockdown imposed on the 23rd March 2020 in the UK was distributed via social media and completed over a three week time period during July 2020 via a self-selecting sample of the general population (N = 85). The key moderators and mediators of resilience the survey assessed were exercise, location, life-orientation, mental health, and sleep quality. All data were self-reported.

Results
Participants’ exercise intensity level increased as resilience increased (F(2,82) = 4.22, p = .003: Wilks’ lambda = .82, partial n2 = 0.09). The relationship between exercise, and resilience and quality of life was independent of sleep and mental health status pre-lockdown (p = .013, p = .027 respectively). In the face of the COVID-19 pandemic, this relationship was dependent on mental health but not sleep quality (p = <.001 for resilience p = .010 for quality of life). There were no statistically significant differences between participants living in urban or rural locations.

Conclusion
Exercise is strongly correlated to resilience and during a pandemic such as COVID-19 it becomes a mechanism in which to moderate resilience. The relationship between exercise and resilience is supported by this study. The influence that a pandemic had on mental health is mediated by its effect on quality of life.
Factors related to parents’ adherence to childhood immunization
Authors: Hobani Fatimah , Alhalal Eman 
Published: April 2022

AbstractBackgroundImmunizations protect children from deadly infectious diseases. Yet, there is still insufficient understanding of the factors associated with parents’ non-adherence to immunizations in contexts outside of Western countries. The aim of this study is twofold: (a) to investigate non-adherence to immunizations for children aged 6 months to 6 years in Saudi Arabia based on the number of immunizations missing or delayed by more than one month; and (b) to examine the underlying factors that predict the extent of non-adherence based on the Health Belief Model framework.MethodsA cross-sectional study was carried out in 22 randomly selected primary health care centers. Structured interviews were also conducted to collect data using the modified Health Belief Model questionnaire. Multiple regression analysis was used to assess the predictors of the extent of non-adherence.ResultsBased on data from 220 participants, 51.8% of parents did not adhere with childhood immunizations. There was no significant relationship between parents’ sociodemographic characteristics and the extent of their hesitancy about children’s immunizations. The linear combination of perception of infectious disease severity, perception of their children’s susceptibility, perception of immunization benefits, perception of fewer barriers to obtaining immunizations, cues to action related to immunizations, and self-efficacy predicted the extent of non-adherence to immunizations (F (11.220) = 2.595,p < 0.001) and explained 12% of its variance. Yet, only perceived children’s susceptibility, perceived barriers, and self-efficacy independently predicted parents’ non-adherence.ConclusionSaudi Arabia’s high proportion of non-adherence to childhood immunizations should be addressed. For instance, a health education program could be developed to increase parents’ awareness that their children are susceptible to health risks. Paying a special attention to existing barriers in accessing and receiving the immunizations is crucial. In addition, building parents’ self-efficacy, which is confident in making healthy decisions, such as keeping their children’s immunizations up to date, is important.
Characterizing tobacco and marijuana use among youth combustible tobacco users experiencing homelessness – considering product type, brand, flavor, frequency, and higher-risk use patterns and predictors
Authors: Glasser Allison M. , Hinton Alice , Wermert Amy , Macisco Joseph , Nemeth Julianna M. 
Published: April 2022

Abstract
Background
Cigarette smoking is three times more prevalent among youth experiencing homelessness compared with the general population. Co-use of tobacco and marijuana is also common. The aim of this study is to characterize tobacco and marijuana use among youth experiencing homelessness who use combustible tobacco in a Midwestern city to inform smoking cessation intervention.

Methods
This study included 96 youth (ages 14–24 years; 52% male, 39% female, 5% transgender/non-binary) attending a homeless drop-in center who had used at least one combustible tobacco product in the past week. We assessed past-month use of tobacco products and marijuana, other product use characteristics (e.g., frequency, brand and flavor), and psychosocial predictors of more frequent (i.e., daily) use of combustible tobacco and marijuana.

Results
Most youth experiencing homelessness with past-week combustible tobacco use had used cigarettes (n = 85, 88.5%), cigars (n = 89, 92.7%), and marijuana (n = 82, 85.4%) in the past month. One-third (n = 34) used electronic vapor products (EVPs), 19.8% (n = 19) smoked hookah, and 11.5% (n = 11) used smokeless tobacco (ST). Most marijuana users co-administered with tobacco (n = 67, 69.8%). Daily combustible tobacco smoking was associated with having a child and smoking out of boredom/habit. Daily marijuana use was associated with using substances to cope with one’s housing situation. Newport (n = 66, 72.5%) and Black & Mild (n = 48, 51.1%) were the most popular brands of cigarettes and cigars among ever users. Most non-combustible tobacco ever users reported not having a usual brand (EVPs: n = 51, 73.9%; ST: n = 16, 57.1%). Cigar smokers reported the most varied selection of flavors.

Conclusions
Young combustible tobacco users experiencing homelessness engage in high-risk use patterns, including poly-tobacco use, co-use of tobacco with marijuana, and frequent combustible product use. Interventions that consider the full context of tobacco and marijuana use are needed to support smoking cessation in this population.
Trends in growth and nutritional status of high school graduates in Hangzhou, China, 2011–2020
Authors: Duan Xu , Zhou Yi-nan , Chen Yun 
Published: April 2022

Abstract
Background
During past decades, there was a positive trend in growth and nutrition status of adolescents in China, but there was significant regional disparity. The purpose of this study is to investigate the trends in growth and nutritional status of high school graduates in Hangzhou between 2011 and 2020.

Methods
High school graduates (Grade 12) who finished the physical examination of the national college entrance examination between 2011 and 2020 (n=481,353)were included in this study. Data were obtained from the database of physical examination of the national college entrance exam. Height and weight were measured; body mass index (BMI) was calculated from height and weight. Thinness, overweight and obesity were defined according to the International Obesity Task Force criteria. For the vast majority of the high school graduates were 18 years old or nearly 18 years old, the cutoffs of 18 years were adopted. Those are 18.5, 25 and 30 kg/m2, for thinness, overweight and obesity respectively.

Results
There was a significant growth trend in height, weight and BMI in both sexes (P < 0.001). Height increased by 1.80 cm in boys and 1.45 cm in girls. Weight increased by 4.62 kg in boys and 2.51 kg in girls. BMI increased by 1.09 kg/m2 in boys and 0.60 kg/m2 in girls. An increase trend was found in the prevalence of overweight and obesity in both sexes (P < 0.001). Overweight increased by 7.43% (from 9.05 to 16.48%) among boys and 4.05% (from 4.57 to 8.62%) among girls. Obesity increased by 3.85% (from 2.29 to 6.14%) among boys and 1.76% (from 0.64 to 2.40%) among girls. The prevalence of thinness fluctuated in both boys and girls, 12.42–15.59% among boys and 18.97–23.68% among girls. Boys had higher odds of overweight and obesity and lower odds of thinness than girls (P < 0.001).

Conclusions
There is a positive trend in growth and nutritional status of high school graduates in Hangzhou. However, there is still a considerable prevalence of thinness, it indicates a double burden of undernutrition and overnutrition.
Influence of frailty and its interaction with comorbidity on outcomes among total joint replacement
Authors: Lian Qiang , Li Kangxian , Yang Qinfeng , Lian Yun , Zhao Mingchen , Shi Zhanjun , Wang Jian , Zhang Yang 
Published: April 2022

Abstract
Background
Patients with frailty get more and more attention in clinical practice. Yet, no large-scale studies have explored the impact of frailty on the perioperative acute medical and surgical complications following TJA. what is more, comorbid diseases may lead, at least additively, to the development of frailty. There also no studies to find the possible interaction between comorbidity and frailty on the postoperative complications after TJA.

Methods
Discharge data of 2,029,843 patients who underwent TJA from 2005 to 2014 from the National Inpatient Sample (NIS) database, which was analyzed using cross-tabulations and multivariate regression modeling. Frailty was defined based on frailty-defining diagnosis clusters from frailty-defining diagnosis indicator of Johns Hopkins Adjusted Clinical Groups.

Results
Among patients who underwent total joint replacement surgeries, 50,385 (2.5%) were identified as frail. Frailty is highly associated with old age, especially for those over the age of 80, meanwhile females and black races have a high Charlson comorbidity index (CCI) of ≥ 3, together with emergency/urgent admission and teaching hospital. While comorbidity is associated with greater odds of acute medical complications, and frailty has a better predictive effect on in-hospital deaths, acute surgical complications. Furthermore, frailty did not show an enhancement in the predictive power of the Charlson comorbidity score for postoperative complications or in-hospital deaths but postoperative LOS and hospitalization costs.

Conclusion
Frailty can be used to independently predicted postoperative surgical and medical complications, which also has a synergistic interaction with comorbidity for patients who are preparing to undergo TJA.
Acceptability, simplicity, and relevance of the new human papillomavirus/DNA test among 35-year-old ever-married women in a district of Sri Lanka: focus group discussions
Authors: Perera K. C. , Mapitigama K. N. , Abeysena T. C. 
Published: April 2022

Abstract
Background
Two major drawbacks of the present cervical cancer screening programme in Sri Lanka are, the suboptimal sensitivity of the pap smear and the low coverage. The sensitivity of the HPV/DNA screening test is high. The objective of the study was to explore the acceptability relevance and simplicity of the new HPV/DNA screening implementation among ever-married women in a district of Sri Lanka.

Methods
Focus group discussions (FGD) (n = 3) in the public health divisions of the Kalutara district were used to collect data during December 2018. The study population comprised of ever-married women 35 years old, who, carried out an HPV/DNA test at a community Well Woman Clinics (WWCs) (n = 89). A list of WWCs was prepared according to an alphabetical order under urban, rural, and estate sector categories and allocated a number. One WWC was selected from each sector randomly for the three FGDs representing the estate, rural, and urban clinics. A convenient sampling technique was used to select participants for each FGD (n = 8). The information collected at each interview was summarized at the end of each interview. The analysis was done with manual content.

Results
Most of the participants were Sinhalese (n = 17, 70.9%), Buddhist (n = 18, n = 75%), and non-working (n = 18, n = 75%). The community awareness of HPV/DNA screening and field staff performance were highly appreciated by most of the participants. Most were aware of the high sensitivity of the HPV/DNA test, therefore the early detection rate of cervical cancer precursors is high. Most of the participants expressed the HPV/DNA test as a convenient and neutral test. Most were mentioned the necessity of repeated clinic visits for the pap test and colposcopy in HPV/DNA screened positive follow-up but there was marked acceptability (n = 23, 95.8%) for HPV/DNA test.

Conclusions
Acceptability of the new HPV/DNA screening test was high. Most of the participants perceived the HPV/DNA test to be simple and also relevant. Therefore, the HPV/DNA screening test can be recommended to be incorporated into the National Cervical Cancer Screening Programme as its suitability was well explored in the Sri Lankan setting.