bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA
Authors: Guo Longhua , Boocock James , Hilt Evann E. , Chandrasekaran Sukantha , Zhang Yi , Munugala Chetan , Sathe Laila , Alexander Noah , Arboleda Valerie A. , Flint Jonathan , Eskin Eleazar , Luo Chongyuan , Yang Shangxin , Garner Omai B. , Yin Yi , Bloom Joshua S. , Kruglyak Leonid 
Published: April 2022

Abstract
Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks.

Methods
The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020.

Results
We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region.

Conclusion
Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic.
Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p
Authors: Li Yuanfang , Yuan Pengtao , Fan Shengxin , Zhai Bin , Jin Wenjiao , Li Donghua , Li Hong , Sun Guirong , Han Ruili , Liu Xiaojun , Tian Yadong , Li Guoxi , Kang Xiangtao 
Published: April 2022

Abstract
Background
The characteristics of muscle fibers determine the growth and meat quality of poultry. In this study, we performed a weighted gene co-expression network analysis (WGCNA) on the muscle fiber characteristics and transcriptome profile of the breast muscle tissue of Gushi chicken at 6, 14, 22, and 30 weeks.

Results
A total of 27 coexpressed biological functional modules were identified, of which the midnight blue module had the strongest correlation with muscle fiber and diameter. In addition, 7 hub genes were found from the midnight blue module, including LC8 dynein light chain 2 (DYNLL2). Combined with miRNA transcriptome data, miR-148a-3p was found to be a potential target miRNA of DYNLL2. Experiments on chicken primary myoblasts (CPMs) demonstrated that miR-148a-3p promotes the expression of myosin heavy chain (MYHC) protein by targeting DYNLL2, proving that it can promote differentiation of myoblasts.

Conclusions
This study proved that the hub gene DYNLL2 and its target miR-148-3p are important regulators in chicken myogenesis. These results provide novel insights for understanding the molecular regulation mechanisms related to the development of chicken breast muscle.
Physiological and multi-omics responses of Neoporphyra haitanensis to dehydration-rehydration cycles
Authors: Wang Zekai , Lu Caiping , Chen Juanjuan , Luo Qijun , Yang Rui , Gu Denghui , Wang Tiegan , Zhang Peng , Chen Haimin 
Published: April 2022

Abstract
Background
Seaweeds in the upper intertidal zone experience extreme desiccation during low tide, followed by rapid rehydration during high tide. Porphyra sensu lato are typical upper intertidal seaweeds. Therefore, it is valuable to investigate the adaptive mechanisms of seaweed in response to dehydration-rehydration stress.

Results
A reduction in photosynthetic capacity and cell shrinkage were observed when N. haitanensis was dehydrated, and such changes were ameliorated once rehydrated. And the rate and extent of rehydration were affected by the air flow speed, water content before rehydration, and storage temperature and time. Rapid dehydration at high air-flow speed and storage at − 20 °C with water content of 10% caused less damage to N. haitanensis and better-protected cell activity. Moreover, proteomic and metabolomic analyses revealed the abundance members of the differentially expressed proteins (DEPs) and differentially abundant metabolites (DAMs) mainly involved in antioxidant system and osmotic regulation. The ascorbic acid-glutathione coupled with polyamine antioxidant system was enhanced in the dehydration response of N. haitanensis. The increased soluble sugar content, the accumulated polyols, but hardly changed (iso)floridoside and insignificant amount of sucrose during dehydration indicated that polyols as energetically cheaper organic osmolytes might help resist desiccation. Interestingly, the recovery of DAMs and DEPs upon rehydration was fast.

Conclusions
Our research results revealed that rapid dehydration and storage at − 20 °C were beneficial for recovery of N. haitanensis. And the strategy to resist dehydration was strongly directed toward antioxidant activation and osmotic regulation. This work provided valuable insights into physiological changes and adaptative mechanism in desiccation, which can be applied for seaweed farming.
Regional opening strategies with commuter testing and containment of new SARS-CoV-2 variants in Germany
Authors: Kühn Martin J. , Abele Daniel , Binder Sebastian , Rack Kathrin , Klitz Margrit , Kleinert Jan , Gilg Jonas , Spataro Luca , Koslow Wadim , Siggel Martin , Meyer-Hermann Michael , Basermann Achim 
Published: April 2022

AbstractBackgroundDespite the vaccination process in Germany, a large share of the population is still susceptible to SARS-CoV-2. In addition, we face the spread of novel variants. Until we overcome the pandemic, reasonable mitigation and opening strategies are crucial to balance public health and economic interests.MethodsWe model the spread of SARS-CoV-2 over the German counties by a graph-SIR-type, metapopulation model with particular focus on commuter testing. We account for political interventions by varying contact reduction values in private and public locations such as homes, schools, workplaces, and other. We consider different levels of lockdown strictness, commuter testing strategies, or the delay of intervention implementation. We conduct numerical simulations to assess the effectiveness of the different intervention strategies after one month. The virus dynamics in the regions (German counties) are initialized randomly with incidences between 75 and 150 weekly new cases per 100,000 inhabitants (red zones) or below (green zones) and consider 25 different initial scenarios of randomly distributed red zones (between 2 and 20% of all counties). To account for uncertainty, we consider an ensemble set of 500 Monte Carlo runs for each scenario.ResultsWe find that the strength of the lockdown in regions with out of control virus dynamics is most important to avoid the spread into neighboring regions. With very strict lockdowns in red zones, commuter testing rates of twice a week can substantially contribute to the safety of adjacent regions. In contrast, the negative effect of less strict interventions can be overcome by high commuter testing rates. A further key contributor is the potential delay of the intervention implementation. In order to keep the spread of the virus under control, strict regional lockdowns with minimum delay and commuter testing of at least twice a week are advisable. If less strict interventions are in favor, substantially increased testing rates are needed to avoid overall higher infection dynamics.ConclusionsOur results indicate that local containment of outbreaks and maintenance of low overall incidence is possible even in densely populated and highly connected regions such as Germany or Western Europe. While we demonstrate this on data from Germany, similar patterns of mobility likely exist in many countries and our results are, hence, generalizable to a certain extent.
X-linked hyper IgM syndrome with severe eosinophilia: a case report and review of the literature
Authors: Li He , Cao Yang , Ma Jijun , Li Chongwei 
Published: April 2022

Abstract
Background
Hyper IgM syndromes (HIGMS) are a group of rare primary immunodeficiency disorders. There are limited reports about HIGMS combined with severe eosinophilia.

Case presentation
In this report, we described a 2-year-old boy with chronic cough and symptoms of hypoxia. Lung computed tomography (CT) scan showed that diffuse ground-glass changes and eosinophils in peripheral blood increased significantly. Subsequent tests revealed a notable decrease in serum IgG and IgA. The lymphocyte subgroup classification was basically normal. Pneumocystis jirovecii were detected from the bronchoalveolar lavage fluid (BALF) of the patient by metagenomic next-generation sequencing (mNGS). After treatments of caspofungin combined with sulfamethoxazole, intravenous immunoglobulin (IVIG) replacement and anti-inflammatory steroid, the clinical symptoms and pulmonary imaging noticeably improved. The absolute eosinophil count (AEC) also returned to normal range. X-linked hyper IgM syndrome was confirmed by gene test. Two months after the diagnosis, the patient underwent allogeneic stem cell transplantation (HSCT) and has recovered well.

Conclusions
Children with HIGMS are prone to opportunistic infections such as Pneumocystis jirovecii pneumonia (PJP). Diffuse interstitial lung disease and hypoglobulinemia in a young child predict the diagnosis of a primary immunodeficiency (PID). mNGS has obvious advantages for obtaining etiological diagnosis of children with PIDs. Severe eosinophilia is rarely reported in this kind of PIDs. Considering literature review and the corresponding reaction to steroid, we proposed that eosinophilia in HIGMS might be related to infections. Steroid therapy can quickly relieve eosinophilia but is easy to rebound if the reduction is too fast. Once the diagnosis of HIGMS is confirmed, the earlier the HSCT, the better the prognosis.
Retention on antiretroviral therapy in person with HIV and viral hepatitis coinfection in Ethiopia: a retrospective cohort study
Authors: Seyoum Eleni , Demissie Meaza , Worku Alemayehu , Mihret Adane , Abdissa Alemseged , Berhane Yemane 
Published: April 2022

Abstract
Background
HIV coinfection with viral hepatitis B (HBV) or viral hepatitis C (HCV) is not uncommon in Ethiopia. Although the coinfections are presumed to interfere with antiretroviral treatment (ART), this is not widely studied in Sub-Saharan African settings. This study was conducted to determine ART retention in persons coinfected with HIV + HBV or HIV + HCV.

Methods
We reviewed the medical records of HIV-positive adults who initiated ART between 2011 to 2018 in four high-burden hospitals of Addis Ababa. Retention in care was the primary outcome of the study, which was compared between HIV and either HBV or HCV coinfected persons, and HIV-monoinfected persons. A parametric Gompertz regression model was used to compare retention between the coinfected and monoinfected groups.

Results
A total of 132 coinfected persons and 514 HIV-monoinfected individuals who initiated ART in 2011–2018 were compared. At 12-months of follow-up, 81.06% [95% CI: 73.3–86.9%] of the coinfected and 86.96% [95% CI: 83.7–89.6%] of the monoinfected were still on ART care. Cumulative retention in the coinfected group was 68.93% [60.4–76.3%] versus 80.35% [76.6–83.5%, p = 0.0048] in the monoinfected group. The cumulative retention was lower (61.25, 95% CI: 49.9–71.4%) in male coinfected patients than male monoinfected patients (77.77, 95% CI: 71.8–82.7%, p = 0.0041). In contrast, cumulative retention was similar in females in the coinfected group (80.76, 95% CI:67.3–89.5%) versus the monoinfected group (82.29, 95% CI:77.4–86.3%, p = 0.792). Overall, HIV-positive with viral hepatitis coinfection were 24 and 31% less likely to still be on ART care than the monoinfected group at 12 months and overall, with sub-distribution adjusted hazard ratio (AHR) of 0.76(95% CI:0.61–0.96, p = 0.021) and 0.69(95% CI:0.54–0.87, p = 0.002) respectively.

Conclusions
We observed that coinfected individuals are less likely to stay on ART than HIV monoinfected individuals. The low retention in the coinfected group from this study may affect the success of survival gained in people living with HIV (PLHIV) in the long term. More concerted efforts need to be made to retain coinfected individuals at least at the level of monoinfected persons on long-term ART care. Future studies are needed to better understand the difference in retention, preferable in a prospective manner.
Lifetime impact of being underweight or overweight/obese during childhood in Vietnam
Authors: Baek Yeji , Owen Alice J. , Fisher Jane , Tran Thach , Ademi Zanfina 
Published: April 2022

Abstract
Background
There is limited evidence about lifetime burden of child malnutrition. This study aimed to estimate the lifetime impact of being underweight or overweight/obese during childhood in Vietnam.

Methods
We developed a life table model in combination with a Markov model for Vietnamese children aged 5–19 years and simulated until they reached 75 years of age or died using published data. The starting year was 2019 and the model estimated number of deaths, years of life lived and quality-adjusted life years (QALY) with an annual discount rate of 3%. We performed scenario, one-way, and probabilistic sensitivity analyses to assess the impact of uncertainties in input parameters.

Results
The model estimated 9.68 million deaths (6.44 million men and 3.24 million women), 622 million years of life lived (317 million men and 305 million women), and 601 million QALYs (308 million men and 293 million women). Scenario analyses showed that the reduction in either underweight or overweight/obesity alone, and reduction in both underweight and overweight/obesity resulted in fewer deaths, more years of life lived and more QALYs gained. In the scenario where everyone was a healthy weight, the model estimated 577,267 fewer deaths (6.0% less), 2 million more years of life lived (0.3% more), and 3 million QALYs gained (0.6% more) over base-case results which represents current situation in Vietnam.

Conclusions
Our results suggest that addressing underweight and overweight/obesity will contribute to reducing deaths and increasing years of life lived and QALYs. Policies and interventions in alignment with Sustainable Development Goals to address underweight and overweight/obesity are necessary to achieve health for all.
Identifying and articulating the student experience in the Intercalated Enrichment Year
Authors: Wan Eric Yuk Fai , Li Zhihao , Sun Kai Sing , Chan Karina Hiu Yen , Cheng Will Ho Gi , Chen Julie Yun , Chin Weng Yee , Lam Tai Pong , Tipoe George Lim , Wong Gordon Tin Chun , Chan Sarah So Ching , Lam Cindy Lo Kuen 
Published: April 2022

Abstract
Background
Benefits of intercalation during an undergraduate medical degree are well-recognized. The University of Hong Kong implemented a compulsory Enrichment Year (EY) in its Bachelor of Medicine and Bachelor of Surgery degree programme (MBBS) in 2016. In their third year of study, students could work on an area of interest in any of three programme categories (i) intercalation/ university exchange (IC); (ii) research (RA); (iii) service/ humanitarian work (SH). This study aimed to explore the barriers, enablers, and overall student learning experiences from the first cohort of EY students in order to inform future development of the EY.

Methods
An exploratory sequential mixed-method study in 2019-20. Twenty students were purposively selected to attend three semi-structured focus group interviews. Conventional thematic analysis was employed and results assisted the design of a cross-sectional questionnaire. Sixty-three students completed the questionnaire. ANOVA or chi-square test was used to compare the difference in student’s characteristics, barriers, enablers and perspectives on EY between programme categories. Adjusting student’s characteristics, logistic regressions were conducted to identify the effect of programme categories on the EY experience.

Results
Most students (95% in the questionnaire) agreed that EY was worthwhile and more rewarding than expected. EY was positively regarded for enhancing personal growth and interpersonal relationships. The main barriers were financial difficulties, scholarship issues and insufficient information beforehand. A few students had practical (i.e. accommodation, cultural adaptation) problems. Potential enablers included better financial support, more efficient information exchange and fewer assignments and preparation tasks. Similar barriers were encountered by students across all three categories of EY activities.

Conclusions
Personal growth was the most important benefit of the EY. Barriers were consistent with those identified in the literature except for cultural adaptation, which could be related to Hong Kong’s unique historical context. Financial limitation was the most concerning barrier, as it could result in unequal access to educational opportunities. Better and timely access to scholarships and other funding sources need to be considered.

Trial registration
Ethics approval was obtained from the local Institutional Review Board of The University of Hong Kong/Hospital Authority Hong Kong West Cluster (UW 19-585).
COVID-19 outbreak improves attractiveness of medical careers in Chinese senior high school students
Authors: Zhang Ruoxin , Pei Jianfeng , Wang Yanli , Wang Lei , Yeerjiang Yeerzhati , Gao Haifeng , Xu Wanghong 
Published: April 2022

Abstract
Background
The shortage of healthcare workers is becoming a serious global problem. The underlying reasons may be specific to the healthcare system in each country. Over the past decade, medicine has become an increasingly unpopular profession in China due to the heavy workload, long-term training, and inherent risks. The ongoing COVID-19 pandemic has placed the life-saving roles of healthcare professionals under the spotlight. This public health crisis may have a profound impact on career choices in Chinese population.

Methods
We conducted a questionnaire-based online survey among 21,085 senior high school students and 21,009 parents from 24 provinces (or municipalities) of China. We investigated the change of interest in medical study due to the outbreak of COVID-19 and the potential motivational factors based on the expectancy-value theory framework. Pearson correlation analysis was used to assess the correlation of static or dynamic interest in medical career pursuit with the reported number of COVID-19 cases. Logistic regression model was adopted to analyze the main factors associated with students’ choices.

Results
We observed an increased preference for medical study post the outbreak of COVID-19 in both students (17.5 to 29.6%) and parents (37.1 to 47.3%). Attainment value was found to be the main reason for the choice among students, with the contribution to society rated as the top motivation. On the other hand, the predominant demotivation in high school students was lack of interest, followed by concerns regarding violence against doctors, heavy workload, long-term training and heavy responsibility as a doctor. Additionally, students who were female, in the resit of final year, had highly educated parents and outside of Hubei province were significantly associated with a keen interest in pursuing medical study.

Conclusions
This is the first multi-center cross-sectional study exploring the positive change and motivations of students’ preferences in medical study due to the outbreak of COVID-19. Our results may help medical educators, researchers and policymakers to restructure medical education to make it more appealing to high school students, particularly, to develop a more supportive social and working environment for medical professionals to maintain the observed enhanced enthusiasm.
Using virtual reality in lumbar puncture training improves students learning experience
Authors: Vrillon Agathe , Gonzales-Marabal Laurent , Ceccaldi Pierre-François , Plaisance Patrick , Desrentes Eric , Paquet Claire , Dumurgier Julien 
Published: April 2022

AbstractBackgroundLumbar puncture (LP) is a commonly performed medical procedure in a wide range of indications. Virtual reality (VR) provides a stimulating, safe and efficient learning environment. We report the design and the evaluation of a three dimensions (3D) video for LP training.MethodsWe recorded a stereoscopic 180-degrees 3D video from two LPs performed in clinical settings in Fernand Widal Lariboisière University Hospital, Paris, France. The video was administered to third-year medical students as well as to a residents and attendings group during LP simulation-based training sessions.ResultsOn 168 participants (108 novice third-year medical students, and 60 residents and attendings with prior LP experience), satisfaction after video exposure was high (rated 4.7 ± 0.6 on a 5-point scale). No significant discomfort was reported (comfort score graded 4.5 ± 0.8 on 5). LP-naive students displayed higher satisfaction and perceived benefit than users with prior LP experience (overall,P < 0.05). Trainees evaluated favorably the 3D feature and supported the development of similar tutorials for other medical procedures (respectively, 3.9 ± 1.1 and 4.4 ± 0.9 on 5).ConclusionWe report our experience with a 3D video for LP training. VR support could increase knowledge retention and skill acquisition in association to LP simulation training.