bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)
Authors: Cho Chung Hyun , Park Seung In , Ciniglia Claudia , Yang Eun Chan , Graf Louis , Bhattacharya Debashish , Yoon Hwan Su
Published: August 2020

BackgroundThe Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). ResultsTo fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. ConclusionsThis high divergence was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.
Impact of the COVID-19 pandemic on mental health in pregnancy women: results from two cohort studies in China
Authors: Mei Hong , Li Na , Li Junwei , Zhang Dan , Cao Zhongqiang , Zhou Yongjie , Cao Jiangxia , Zhou Ai’fen
Published: August 2020

Background

The COVID-19 pandemic led to a global atmosphere of anxiety and depression. However, the impact of this disaster on mental health in pregnancy women was not clear.
Methods

Based on two cohort study, the Novel Coronavirus Disease Influenced Pregnant Cohort Study (NCP) set up during the COVID-19 epidemic and the Healthy Baby Cohort Study (HBC) set up in 2012, we compared the anxiety, depression and stress levels of pregnant women who did not or did go through the COVID-19 pandemic and analyzed the risk factors for mental health in pregnancy women.
Results

There were 784 and 2448 participants in the CNP and HBC studies involved in the analysis, respectively. We found that there were 23.09% and 4.72% pregnant women suffering for mild and moderate-to-several anxieties for those in the NCP study, and 21.53% and 3.06% in the HBC study. The mild and moderate-to-several depression rate was 25.89% and 11.35% for those in the NCP study, and 19.81% and 0.51% for those in the HBC study, respectively. No significant difference was found for anxiety, depression and stress levels was found at each gestational trimester (p > 0.05). The pandemic of COVID-19 was significantly associated with maternal depression and stress (p < 0.05), with the co-efficient and 95%CI as 0.37 (0.18, 0.55) and − 0.12 (-0.09, -0.32), respectively. Pregnant women with pre-pregnancy obesity, higher educational level or good sleep quality might have lower risks for anxiety, depression and stress compared with the referenced groups.
conclusions

The pandemic had a huge impact on depression, especially moderate-to-sever level, in pregnant women at whatever gestational week; and that pre-pregnancy obesity, highly educated and sleep well ones had less anxiety and depression risks. The society, especially the family members, should pay more attention to pregnant ones and give more social support to them.
Single-stage transverse process resection, debridement, interbody fusion, and internal fixation for the treatment of lumbar spinal tuberculosis via posterior-only approach
Authors: Li Zhongwei , Shuwen Zhang , He Miao , Cheng Hao , Zhao Dongming , Yang Xinming , Hali Habulihan
Published: August 2020

Background: Spinal tuberculosis (TB) is a less frequently reported infectious spinal pathology. There are controversies on the surgical intervention of lumbar spinal TB with neurological damage and paraspinal abscess. This retrospective study was conducted to determine the effectiveness of single-stage transverse process resection, debridement, interbody fusion, and internal fixation for the treatment of lumbar spinal TB via posterior-only approach.Methods: From January 2015 to June 2018, 32 consecutive patients (19 males and 13 females) with lumber spinal TB complicated with neurological damage and paraspinal abscess treated by single-stage transverse process resection, debridement, interbody fusion, and internal fixation were enrolled. Medical records, imaging studies, laboratory data were collected and summarized. Anti-TB drugs with HREZ chemotherapy regimen was administered to all patients. Surgical outcomes were evaluated based on visual analogue scale (VAS), American Spinal injury Association (ASIA) classification. The changes in C-reactive protein (CRP) levels, erythrocyte sedimentation rate (ESR), clinical symptoms and complications were investigated. Graft fusion was evaluated using Bridwell grading criteria.Results: The mean follow-up period was 20.41 ± 5.19 months. No implant failures were observed in any patients. Wound infection was observed in one patient. Solid bony fusion was achieved in 9 cases at 6 months and 23 cases at 12 months after operation. Kyphosis angle was 11.28 ± 4.01° at final follow-up. The levels of ESR and CRP were returned to normal at the final follow-up. VAS scores were significantly improved (P < 0.05). According to ASIA classification, 6 cases were classified as with grade D and 26 cases were classified as grade E at the last follow-up.Conclusion: Single-stage transverse process resection, debridement, interbody fusion, and internal fixation via posterior-only approach is a feasible and effective surgical therapy for lumbar spinal TB with neurological damage and paraspinal abscess.
Perceived Social support and compliance with stay-at-home orders during the COVID-19 outbreak: Evidence from Iran
Authors: Paykani Toktam , Zimet Geregory D. , Esmaeili Reza , khajedaluee Amir Reza , Khajedaluee Mohammad
Published: August 2020

Background
Strong evidence demonstrates that social support plays a key role in facilitating preventive health behaviors. The major aim of the current study was to assess the effects of perceived social support on compliance with stay-at-home advice in response to a COVID-19 outbreak during the Persian New Year (Nowruz) holydays, since Nowruz holidays of 2020 coincided with the peak of the coronavirus epidemic in Iran.
Methods
This cross-sectional survey was carried out based on phone interviews of 1073 adults aged over 18 years from 4 to 12 April 2020 in Mashhad, Khorasan-Razavi Province, as the second largest city of Iran. A systematic random sampling was carried out using fixed phone number lists provided by Telecommunication Company of Khorasan-Razavi Province. Phone interviews were carried out by four trained interviewers from the Iranian Students Polling Agency (ISPA) at various times of the day. The survey included sociodemographic questions, perceived social support scale (MSPSS) and questions about self-isolation. Statistical analysis included Chi-square test, Kruskal-Wallis and multivariate logistic regression.
Results
20.5% of participants reported poor compliance with self-isolation during the first two weeks of Nowruz. Clear social gradients were not found in people’s compliance with self-isolation. When controlling socio-demographic factors, perceived social support, interestingly, both fostered and hindered personal compliance with self-isolation, depending on the source of support from family members (OR = .875, 95% CI = .800, .957, p < .005), friends (OR = 1.147, 95% CI = 1.073, 1.223, p < .001) and a significant other person (OR = .916, 95% CI = .833, 1.007, p = .069).
Conclusions
Public health messaging may need to emphasize the role that friends and families can play in helping to protect those in their friendship/family groups by promoting compliance with social distancing. Further in-depth studies are recommended to evaluate how this kind of messaging can most effectively encourage people to engage in social distancing practices.
Determinants of student’s MVPA level in school and neighborhood environment changing with age: a 12-month follow-up study in Ningxia province
Authors: Huang Wei , Shi Xiangrong , Wang Yujie , Li Xiaoling , Gao Pengpeng , Lu Jieguo , Zhuang Jie
Published: August 2020

Background
The benefits of physical activity have been identified in children and adolescents. However, the prevalence of physical inactivity in school-aged children and adolescents was high in China. Most time of students spends in neighborhood and school, and these play an important role in student’s MVPA level. Therefore, we will investigate the impact of implementing the national health promotion policy on PA behavior in school-aged children and adolescents and the effects that influence the changes in PA behavior in this study.
Methods
This is a longitudinal study with a 12-month follow-up. The study sample came from 2016 and 2017 Physical Activity and Fitness in China—The Youth Study, total 1611 students (aged 7–18 years) from 31 primary, junior high, and high schools were included in this study. The physical and social environment in school and neighborhood were measured by questionnaire at baseline and after 12 months. Multiple logistic regression was used to examine the relationship of influential factors and moderate- and vigorous MVPA.
Results
There is no significant difference in MVPA level between 2016 and 2017. Student’s attitudes to PA, neighborhood facilities, and organizations were improved significantly after 12 months. The influential factors changed after 12 months. In 2016 the top three contributors were attitude to MVPA(OR 3.08 with 95% CL 1.22, 7.76), neighborhood PA facilities(OR 1.52, 95% CL 1.24, 1.86) and age(OR 1.38, 95% CL 1.13, 1.69), and in 2017 the top three factors were student’s attitude to PA(OR 4.28, 95%CL 1.788,10.245), school extra time for PA(OR 2.29, 95% CL 1.56, 3.36) and the frequency of sports events in neighborhood(OR 1.84, 95% CL 1.34, 2.53).
Conclusions
The single health policy is not effective for student’s MVPA promotion. There may be some factors mediate the relationship between neighborhood environment and MVPA level with age and grade increasing. In the future, more studies are needed to explore the change of influential factors and mediators with age. The findings of this study may provide some evidence for future policy-making.
Family function fully mediates the relationship between social support and depression among antenatal and postpartum women in rural Southwest China
Authors: Huang Yilin , Liu Yan , Wang Yu , Liu Danping
Published: August 2020

Background: Antenatal and postpartum depression is the most common complication of gestation and childbearing affecting women and their families, and good social support and family function are considered the protective and modifiable factors. This study aimed to investigate the depression status and to clarify the interrelationships between social support and depression considering the influence of family function among antenatal and postpartum women in rural areas of Southwest China.Methods: This is a cross-sectional study. Data were collected from a total of 490 rural antenatal (N=249) and postpartum(N=241) women (age: 28.17± 5.12). A structural equation modeling (SEM) was used to test the hypothesized relationships among the variables. The following instruments were used: the Edinburgh Postpartum Depression Scale (EPDS), the APGAR Family Care Index Scale, and the Social Support Rate Scale (SSRS).Results: We found that the prevalence of depression was 10.4%. Path analysis showed that family function had a direct negative correlation with depression (β =-0.251, 95%CI: (-0.382)– (-0.118)). Social support had a direct positive correlation with family function (β =0.293, 95%CI: (0.147– 0.434)) and had an indirect negative correlation with depression (β =-0.074, 95%CI: (-0.139)– (-0.032)), family function fully mediated the relationship between social support and depression. Conclusions: Findings of this study highlight that family function should be considered as the key target for interventions aiming to lower the prevalence of antenatal and postpartum depression. Family members interventions are critical to reduce depression among antenatal and postpartum women.
Indicators of early hospitalization decision to shorten emergency department length of stay of suicide attempters
Authors: Kim Hye Jin , Lee Duk Hee
Published: August 2020

Background Suicide attempters contribute to a significant public health problem. Individuals are estimated to make up to 20 suicide attempts before committing suicide. The emergency department (ED) is the first location where suicide attempters are brought. This study investigated the factors associated with early hospitalization decisions to determine the criteria for patient hospitalization rather than psychiatric ward admission and identify measures to shorten ED length of stay (LOS). Methods This study included suicide attempters (age ≥19 years) who visited the EDs at two tertiary teaching hospitals between March 2017 and April 2020. Results A total of 414 in the hospitalization and 1,346 in the discharge groups patients were included. The mean age was 50.3 ± 20.0 years and 40.7 ± 17.0 years in the hospitalization and discharge groups (p <0.001). The mean ED LOS was 4.2 ± 12.3 and 11.4 ± 18.8 h in the hospitalization and discharge groups, respectively. In the hospitalization group, the odds ratio and confidence interval for age (1.017, 1.008–1.026), sex (male) (1.787, 1.127–2.515), consciousness (2.330, 1.653–3.266), and the Risk-Rescue Ratio Scale (RRRS) (1.273, 1.242–1.304) were calculated. A receiver operating characteristics analysis of RRRS for the decision to hospitalize suicide attempters showed a cut-off value of 42, with sensitivity, specificity, and area under the curve of 85.7%, 85.5%, and 0.924, respectively.Conclusion For suicidal attempters in the ED, the decision on medical hospitalization rather than psychiatric admission should be based on their level of consciousness and the RRRS to reduce ED LOS and crowding.
MiR-142-3p May Be Involved in the Development of Solitary and Multiple Uterine Leiomyomasby Interacting with CTNNB1 and AXIN-2 Through Wnt Signaling Pathway
Authors: xue Luqi , Yang E , Gou Jinhai , Nie Dan , Yi Tao , Min Wenjiao , Li Zhengyu
Published: August 2020

Background

The pathogenesis and clinical behaviors between solitary uterine leiomyoma (SUL) and multiple uterine leiomyomas (MUL) vary, which lead to the difference in management for childbearing-aged patients. Herein, we aim to find the potential miRNAs involved in the development of SUL and MUL.
Results

The top 5 differentially expressed miRNAs, Wnt signalling pathway and its two central molecules APC and CTNNB1 were screened out according to microarray analysis and bioinformatics. MiR-142-3p was selected for further exploration. In validation of qRT-PCR, MiR-142-3p was significantly upregulated in SUL, while downregulated in MUL, CTNNB1 and sequencing target AXIN-2 were expressed at higher level in MUL than SUL. Overexpression of MiR-142-3p resulted in lower transcription level of CTNNB1 and AXIN-2, and lower cell proliferation level.
Conclusions

MiR-142-3p may be involved in the development of SUL and MUL by interacting with CTNNB1 and AXIN-2 through Wnt signaling pathway. MiR-142-3p could serve as a potential biomarker for individualized treatment between SUL and MUL in the future.
Complexity continuum within Ising formulation of NP problems
Authors: Kalinin Kirill , Berloff Natalia
Published: August 2020

A promising approach to achieve computational supremacy over the classical von Neumann architecture explores classical and quantum hardware as Ising machines. The minimisation of the Ising Hamiltonian is known to be NP-hard problem for certain interaction matrix classes, yet not all problem instances are equivalently hard to optimise. We propose to identify computationally simple instances with an `optimisation simplicity criterion'. Such optimisation simplicity can be found for a wide range of models from spin glasses to k-regular maximum cut problems. Many optical, photonic, and electronic systems are neuromorphic architectures that can naturally operate to optimise problems satisfying this criterion and, therefore, such problems are often chosen to illustrate the computational advantages of new Ising machines. We further probe an intermediate complexity for sparse and dense models by analysing circulant coupling matrices, that can be `rewired' to introduce greater complexity. A compelling approach for distinguishing easy and hard instances within the same NP-hard class of problems can be a starting point in developing a standardised procedure for the performance evaluation of emerging physical simulators and physics-inspired algorithms.
Research on the Cutoff Tumor Size of Omitting Radiotherapy after Breast Conserving Therapy in Women Aged 65 Years or Oder with Low-risk Invasive Breast Carcinoma: Results Based on the SEER Database
Authors: Yang Zejian , Li Kunlong , Wang Bin , Yan Yu , Feng Chen , Ren Yu , Meng Du , Li Yijun , Ma Yifei , Qiu Pei , Li Pingping , Zhou Can
Published: August 2020

Background

Radiotherapy (RT) after breast-conserving therapy (BCT) is not always necessary in older women staged T1N0M0 with low-risk invasive breast cancer, but few studies have concluded the detailed tumor size as a reference for avoiding RT. We aimed to explore and identify the cutoff tumor size for patients aged 65 or older with T1N0M0 stage and estrogen receptor positive (ER+), human epidermal growth factor receptor 2 positive (HER2-) breast cancer after BCT.
Methods

The study population was from the Surveillance, Epidemiology, and End Results (SEER) database in 2010 to 2016. Prognostic predictors associated with surgery were used by Kaplan–Meier analysis, X-tile analysis, competing risk model, Fine and Gray multivariable regression model, and propensity score matching (PSM) analysis.
Results

A total of 52049 women and 3846 deaths were included in the unmatched cohort, of which 11.93% (459/3846) were breast cancer-specific death (BCSD), and 88.07% (3387/3846) were other cause-specific death (OCSD), with a median follow-up of 34 months. Based on the cutoff value of 14 mm determined by X-tile analysis, the study population were divided into small tumor group (tumor ≤ 14 mm in diameter) and large tumor group (tumor ≥ 15 mm in diameter). Subjects in small tumor group and large tumor with RT (large tumor & RT) subgroup tended to have significantly lower cumulative BCSD (Gray’s test, P < 0.001) and OCSD (Gray’s test, P < 0.001) than those in large tumor with no RT (large tumor & non-RT) subgroup, regardless of before or after PSM analysis. In competing risk regression mode analysis, patients in the large tumor group had worse prognosis in BCSD (HR: 2.091, 95% CI 1.730–2.527, P < 0.001) than the small tumor group, even after the application of PSM (HR: 2.024, 95% CI 1.587–2.583, P < 0.001).
Conclusion

Our study demonstrated that small tumors (tumor ≤ 14 mm in diameter) were associated with better overall survival (OS), BCSD and OCSD, and radiotherapy might be omitted for patients aged 65 or older with T1N0M0 stage, ER + and HER2- small breast tumors after BCT.
A Randomized clinical trial of antioxidant therapy in patients with septic shock. Reference study to propose adjuvant therapy in patients with critical organic damage by COVID-19
Authors: Aisa-Alvarez Alfredo , Perez-Torres Israel , Camarena-Alejo Gilberto , Franco-Granillo Juvenal , Martínez-Rodríguez Enrique , Gamboa Ricardo , Guarner-Lans Veronica , Soto MariaElena
Published: August 2020

Background: Oxidative stress (OS) participates in the pathophysiology of patients with septic shock having multiple organ failure (MOF), ischemia-reperfusion injury and acute respiratory failure syndrome (ARDS). Antioxidants have been proposed in their therapy.Objective: To evaluate the effect of antioxidant treatment in patients with septic shock with MOF and levels OS after treatment.Research question: Will the administration of specific antioxidant therapy decrease deregulatory factors of oxidative stress and organ failure in patients with septic shock?Study design and Methods: Double-blind, placebo-controlled randomized clinical trial run in 2 ICU in Mexico City between May 2018 and January 2020. The random allocation sequence was generated using computer methods. Patients older than 18 years of either sex, with septic shock were included, were excluded when informed consent could not be obtained, they received chronic or recent use of steroids, statins, or antioxidants or if they had contraindications to the use of antioxidants. All antioxidants were administered by mouth or nasogastric tube during 5 days and were added to standard.Results: 97 patients were included with median age of 66 years. 20 were treated with MT and 18 with Vit C and they showed post-treatment decreased SOFA scores [p=0.007 and p<0.001 respectively]. Also, total antioxidant capacity (TAC) was improved by NAC. All patients had decreased basal levels of Vit C and patients that received Vit C had decreased levels of the NO3−/NO2− (p=0.02) and RCP levels [p=0.045]. Procalcitonin (PCT) levels were reduced by Vit E, [p=0.047], NAC; [p=0.001] and MT [p=0.045]. LPO was reduced in patients that received MT p=0.042 Conclusion: In septic shock, antioxidant therapy associated with standard intensive care unit therapy reduces MOF, the oxidative and inflammatory state. These results could be a reference to use adjuvant antioxidant therapy in patients with septic shock in COVID19.Trial Registration: ClinicalTrials.gov Identifier: NCT 03557229
A SWATH-MS analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome peripheral blood mononuclear cell proteomes reveals mitochondrial dysfunction
Authors: Sweetman Eiren , Kleffmann Torsten , Edgar Christina , de Lange Michel , Vallings Rosamund , Tate Warren
Published: August 2020

Background: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a serious and complex physical illness that affects all body systems with a multiplicity of symptoms, but key hallmarks of the disease are pervasive fatigue and ‘post-exertional malaise’, exacerbation after physical and/or mental activity of the intrinsic fatigue and other symptoms that can be highly debilitating and last from days to months. Although the disease can vary widely between individuals, common symptoms also include pain, cognitive deficits, sleep dysfunction, as well as immune, neurological and autonomic symptoms. Typically, it is a very isolating illness socially, carrying a stigma because of the lack of understanding of the cause and pathophysiology.Methods: To gain insight into the pathophysiology of ME/CFS, we examined the proteomes of peripheral blood mononuclear cells (PBMCs) by SWATH-MS analysis in a small well-characterised group of patients and matched controls. A principal component analysis (PCA) was used to stratify groups based on protein abundance patterns, which clearly segregated the majority of the ME/CFS patients (9/11) from the controls. This majority subgroup of ME/CFS patients was then further compared to the control group. Results: A total of 60 proteins in the ME/CFS patients were differentially expressed (P < 0.01, Log10 (Fold Change) > 0.2 and < -0.2). Comparison of the PCA selected subgroup of ME/CFS patients (9/11) with controls increased the number of proteins differentially expressed to 99. Of particular relevance to the core symptoms of fatigue and post-exertional malaise experienced in ME/CFS, a proportion of the identified proteins in the ME/CFS groups were involved in mitochondrial function, oxidative phosphorylation, electron transport chain complexes, and redox regulation. A significant number were also involved in previously implicated disturbances in ME/CFS, such as the immune inflammatory response, DNA methylation, apoptosis and proteasome activation. Conclusions: The results from this study support a model of deficient ATP production in ME/CFS, compensated for by upregulation of immediate pathways upstream of Complex V that would suggest an elevation of oxidative stress. This study and others have found evidence of a distinct pathology in ME/CFS that holds promise for developing diagnostic biomarkers.
Prevalence of Incretin-mimetic and Sodium-Glucose-Transporter-2-Inhibitor Therapy in Hospitalized Type-2-Diabetics following Myocardial Revascularization: an Observational Study
Authors: Pliquett Rainer U. , Golle Linda , Wienke Andreas , Girndt Matthias
Published: August 2020

Background:
We hypothesized that the recommended incretin-mimetic therapy associates with a better outcome (1-year mortality after discharge, rehospitalizations within 12 months) and with less hypoglycemic events in type − 2 diabetics following myocardial revascularization.
Methods:
Hospitalized type-2 diabetics of the Departments of Cardiology and Cardiothoracic Surgery (University Hospital Halle), who had percutaneous coronary intervention (29.4%) or coronary artery bypass graft (70.6%) in 2016, were included in this observational study: Group 1 (incretin-mimetic therapy), Group 2 (insulin therapy without incretin mimetics) or Group 3 (oral diabetes medication without incretins or insulin). They were asked to mail in a questionnaire on medical therapy, number of hypoglycemic episodes and rehospitalizations 2 years following discharge. In non-responders, the vital status was obtained by local registries 2.4 years after discharge.
Results:
204 patients were recruited in this prospective observational study. At discharge, only 3.9% of all type-2 diabetics had an incretin mimetic, 39.7% were on insulin, and 56.4% on oral medication. In all patient groups together, the prevalence of incretin-mimetic therapy did not change (3.9% at discharge, 2.9% at follow-up). The prevalence of sodium glucose transporter-2–inhibitor therapy slightly increased from 6.8% at discharge to 9.2% at follow-up. However, 85 out of 173 patients (49.1%) did not provide follow-up questionnaires. In hospital mortality (Group 1: 0%, Group 2: 0%, Group 3: 5.2%; p = 0.092), 1-year mortality after discharge ( Group 1: 12.5%, Group 2: 13.6%, Group 3: 11.9%; p = 0.944), and number of rehospitalizations within 12 months after discharge (Group 1: 1.0 per capita, Group 2: 1.0, Group 3: 1.1; p = 0.697) were similar among groups. Hypoglycemic events 6 months prior to follow-up were highest in Group 2 (0.9 ± 2.3) in comparison to Group 1 (0 ± 0) and Group 3 (0.1 ± 0.3; p = 0.017).
Conclusion:
Even after adjusting for surviving patients not sending back questionnaires, the adherence to the recommendations regarding incretin-mimetic and sodium-glucose transporter-2–inhibitor therapy was poor. With the limitation of a low patient number, both 1-year mortality after discharge and rehospitalizations were similar among groups. Self-reported hypoglycemic events occurred more often in insulin-treated diabetics than in the ones without.
Characterization of the Gut DNA and RNA Viromes in A Cohort of Chinese Residents and Visiting Pakistanis
Authors: Yan Qiulong , Wang Yu , Chen Xiuli , Jin Hao , Wang Guangyang , Guan Kuiqing , Zhang Yue , Zhang Pan , Ayaz Taj , Liang Yanshan , Wang Junyi , Cui Guangyi , Sun Yuanyuan , Xiao Manchun , Kang Jian , Zhang Wei , Zhang Aiqin , Li Peng , Liu Xueyang , Ma Yufang , Li Shenghui , Ma Tonghui
Published: August 2020

Background: Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated. Results: Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa.Conclusions: we systematically described the baseline gut virome in a well-characterized cohort of Chinese and visiting Pakistanis and demonstrated that the national background contributed a primary variation to gut virome. The mechanisms underlying the difference between two cohorts remain unclear, but the ethnic factor must be proposed and considered in designing future studies of the virome.
Nomogram for predicting the overall survival of cervical cancer patients with nonsurgical treatment
Authors: Ji Xiaoyu , Song Kejuan , Lv Teng , Diao Yuchao , Xia Nannan , Yao Qin
Published: August 2020

Background: Surgery is an important treatment for cervical cancer, but some patients choose not to operate on the primary site. The purpose of this study was to establish nomogram for predicting overall survival (OS) in nonsurgical cervical cancer on the primary site(NSCC) patients by using cases in the public database.Methods: All patients diagnosed between 2004 and 2015 were randomly divided into training (n=4283) or validation (n=1832) cohort. Cox regression analysis was used on the training cohort to select independent prognostic factors to construct nomogram for predicting 3- and 5-year OS. In two cohorts, receiver operating characteristic curve (ROC), Harrell’s concordance index (C-index), calibration curves and decision curve analysis (DCA) were used to evaluate the accuracy and the reliability of the model. We made a risk stratification system based on the model and performed Kaplan-Meier survival analysis on the risk level.Results: In the training set, ten clinicopathological factors were significantly correlated with survival outcomes and were included in the nomogram. In the training cohort and validation cohort, the C-index, ROC and calibration plots exhibited an excellent consistency between actual OS and model predictions. DCA indicated great clinical benefit. Compared with FIGO staging, nomogram's evaluation effect is superior.Conclusions: Age, histological type, grade, tumor size, extension, lymph node involvement, distant metastasis, lymph node removed, chemotherapy and radiotherapy were independent prognostic factors for OS in NSCC patients. The model showed more satisfactory accuracy and clinical practicability than FIGO staging system, and may provide integration and improvement for therapeutic decisions.
Evaluation of D-TACE combined with endovascular brachytherapy for HCC with MPVTT
Authors: Wu Zhiyuan , Gong Ju , Huang Wei , Wang Qingbing , Wang Ziyin , Liu Qin , Liu Jingjing , Gu Junwei , Ding Xiaoyi , Wang Zhongmin
Published: August 2020

BackgroundThe goal of this study was to compare the clinical results of conventional transcatheter arterial chemoembolization (C-TACE) and doxorubicin-eluting bead transcatheter arterial chemoembolization (D-TACE) combined with endovascular stent implantation with an iodine-125 seed strand in hepatocellular carcinoma (HCC) patients with main portal vein tumor thrombus (MPVTT).MethodsThis study was a prospective controlled study with follow-up dates spanning from Mar 2015 to Feb 2020. Patients with both HCC and MPVTT were randomly divided into two groups. Portal vein stents with iodine-125 seed strands were implanted first; then, C-TACE or D-TACE was administered to all patients. Objective response rates were assessed. The time to disease progression and survival rate were compared between the two groups.ResultsA total of 26 patients were enrolled, with 13 in each group. During follow-up, the portal stent patency times were 112.3 ± 98.2 days in the C-TACE group and 101.7 ± 90.4 days in the D-TACE group. The time to disease progression was 42 days in the C-TACE group and 120 days in the D-TACE group (p = 0.03). The overall survival time from the first intervention procedure was 216 days in the C-TACE group and 239 days in the D-TACE group (p = 0.047). The D-TACE group was superior to the C-TACE group in terms of progression-free survival (PFS) and overall survival (OS) times.ConclusionEndovascular implantation of a stent with an iodine-125 seed strand combined with TACE is safe and effective in HCC patients with MPVTT. Compared to C-TACE, D-TACE achieves more benefits regarding PFS and OS.Trial registrationThis study was a cohort study, no health-related interventions to evaluate the effects on health outcomes. This study wasn’t a clinical trial.
Variation of HLA-DPB1 Gene in Hepatitis B Infection
Authors: Ou Guo-Jin , Liu Xiao , Xu Haixia , Ji Xin , Liu Xiaojuan , Wang Jue
Published: August 2020

Background: Hepatitis B virus (HBV) affects approximately 68 million people in China. 10-15% of adult infected with HBV will develop to chronic HBV, liver cirrhosis (LC), liver failure and hepatocellular carcinoma (HCC). The human leukocyte antigen HLA-DPB1 gene polymorphism and expression were identified to be associated with HBV susceptible and spontaneous clearance. We evaluated the role of HLA-DPB1 gene polymorphism in HBV infection.Methods: In this study, HLA-DPB1, rs9277535 polymorphisms were investigated in 259 HBV infection patients (CHB) and 442 healthy controls (HC) by using a sequence based typing. The mRNA of HLA-DPB1 were measured by real-time polymerase chain reaction (RT-PCR). Results: The results shown that DPB1 gene, rs9277535 were all associated with HBV infection in the Sichuan Han population. Rs9277535A, DPB1*04:02 play a protected role in HBV infection, Rs9277535G, DPB1*05:01 prone to susceptible to HBV infection. rs9277535GG have significantly higher HLA-DPB1 mRNA expression in HBV group compared that in HC group. DPB1*05:01 and DPB1*21:01 have a significantly lower HLA-DPB1 mRNA expression in HBV infection group compared than HC group. The meta-analysis revealed that HLA-DPB1*02:01, DPB1*02:02, DPB1*04:01 and DPB1*04:02 protected against HBV infection, while DPB1*05:01, DPB1*09:01, and DPB1*13:01 were risk factors for HBV infection susceptibility. DPB1*02:01 and DPB1*04:01 were prone to HBV spontaneous clearance, while DPB1*05:01 and DPB1*13:01 were associated with chronic HBV infection.Conclusions: DPB1 alleles and rs9277535 have a major effect on the risk of HBV infection, HBV infection associated with lower HLA-DPB1 expression. DPB1 alleles have important role in HBV susceptible and spontaneous clearance.
Per1 has the capacity to serve as a diagnostic biomarker for cholangiocarcinoma patient
Authors: Wang Ning , Li Yanni , Zheng Yanfang , Chen Huoming , Wen Xiaolong , Li Zhaoxia
Published: August 2020

Background

Period 1 (Per1) had been reported to be involved in the tumorigenesis and progression of human cancers. However, the clinical significance of Per1 in cholangiocarcinoma (CCA) was unclear. The purpose of this study was to explore the diagnostic value of serum Per1 in CCA patients.
Methods

Serum levels of Per1 in CCA patients and healthy individuals were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Chi-square test was used to evaluate the relationship between Per1 expression and clinical characteristics of patients. The diagnostic value of Per1 in CCA was estimated by establishing a receiver operating characteristic (ROC) curve.
Results

Serum Per1 level was significantly down-regulated in CCA patients compared to that in healthy controls (P < 0.001). Moreover, the decreased expression of Per1 was closely associated with poor histological differentiation (P = 0.040), advanced TNM stage (P = 0.035) and positive lymph node metastasis (P = 0.007). ROC curve indicated that the area under the curve (AUC) was 0.863 with a sensitivity of 88.1% and a specificity of 72.1%, revealing the high diagnostic value of serum Per1 in CCA.
Conclusions

Per1 is down-regulated in CCA and negatively correlated with tumor progression. Serum Per1 may be a potential biomarker for early screening of CCA.
SOX9 stands for a bio-marker for prostate cancer detection
Authors: Zi Hao , Tao Wen-Lin , Gao Lei , Yu Zhao-Hua , Bai Xiao-Dong , Li Xiao-Dong
Published: August 2020

Background

Prostate cancer is one of common cancers around the world, and in our country the incidence and mortality of PCa are both increasing. More and more reports have revealed that SOX9 is involved in various human cancers. In this study, we aimed to explore the relationship between SOX9 expression and diagnostic value of PCa patients.
Methods

In this study, quantitative real-time PCR (qRT-PCR) was performed to determine the expression of SOX9 of the 131 PCa patients and 74 healthy volunteers. And receiver operating characteristic (ROC) curve was used to determine the diagnostic value of SOX9 for PCa patients.
Results

The results of qRT-PCR showed that the expression of serum SOX9 in PCa patients was higher than that in healthy controls (P < 0.05). And the expression of SOX9 was significantly associated with PSA (P = 0.001), differentiation (P = 0.000), and lymph node metastasis (P = 0.000). Besides, the area under the ROC curve (AUC) was 0.966 with the sensitivity of 93.2% and specificity of 87.8% respectively. The optimal cutoff value of SOX9 was 2.34.
Conclusions

Our results found that SOX9 is a novel oncogene for PCa, and may be a novel and effective biomarker for the diagnosis of patients with PCa.
Comprehensive Analysis of Non Redundant Protein Database
Authors: Bagheri Hamid , Dyer Robert , Severin Andrew , Rajan Hridesh
Published: August 2020

Background: Scientists around the world use NCBI’s non-redundant (NR) database to identify the taxonomic origin and functional annotation of their favorite protein sequences using BLAST. Unfortunately, due to the exponential growth of this database, many scientists do not have a good understanding of the contents of the NR database. There is a need for tools to explore the contents of large biological datasets, such as NR, to better understand the assumptions and limitations of the data they contain. Results: Protein sequence data, protein functional annotation, and taxonomic assignment from NCBI’s NR database were placed into a BoaG database, a domain-specific language and shared data science infrastructure for genomics, along with a CD-HIT clustering of all these protein sequences at different sequence similarity levels. We show that BoaG can efficiently perform queries on this large dataset to determine the average length of protein sequences and identify the most common taxonomic assignments and functional annotations. Using the clustering information, we also show that the non-redundant (NR) database has a considerable amount of annotation redundancy at the 95% similarity level. Conclusions: We implemented BoaG and provided a web-based interface to BoaG’s infrastructure that will help researchers to explore the dataset further. Researchers can submit queries and download the results or share them with others. Availability and implementation: The web-interface of the BoaG infrastructure can be accessed here: http://boa.cs.iastate.edu/boag. Please use user = boag and password = boag to login. Source code and other documentation are also provided as a GitHub repository: https://github.com/boalang/NR_Dataset.
Breastfeeding Practice Among Teenage Mothers And The Nutritional Status Of Their 0-6 Month Old Infants
Authors: Sholichah Farohatus , Muis S. Fatimah , Margawati Ani
Published: August 2020

Background: The percentage of early marriage in Indonesia is the second highest in ASEAN after Kamboja. The purpose of this study is to analyze breastfeeding practise among teenage mothers and the nutritional status of their 0-6 months infants. Methods: The study was conducted on 16 teenage mothers. The qualitative method with in-depth interview and observation were used to obtain breastfeeding data. Quantitative method was used for obtaining data of infants’ food intake (recall 2x24 hours) and anthropometry. Content analysis was used for the qualitative data, while the descriptive analysis was used for the quantitative data. Results: The majority (87.5%) provided non-exclusive breastfeeding and 12.5% stopped breastfeeding. The majority (93.75%) during one month of study was exposed to infectious disease (fever, cough, runny nose, diarrhea). Conclusions: All infants stayed well nourished, but the score of nutritional status decreased (62.5%).
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs.
Authors: Flossmann Gabriele , Wurmser Christine , Pausch Hubert , Tenghe Amabel , Dodenhoff Jörg , Dahinten Günther , Götz Kay-Uwe , Russ Ingolf , Fries Ruedi
Published: August 2020

Background: Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means for identifying chromosomal regions harboring deleterious DNA-variants causing such phenotypes. We performed a GWAS to unravel the causes of incidental cases of atypically small vulvae in German Landrace gilts.Results: A case-control GWAS involving Illumina porcine SNP60 BeadChip-called genotypes of 17 gilts with atypically small vulvae and 1,818 control animals (fertile German Landrace sows) identified a significantly associated region on the X-chromosome (P = 8.81 × 10− 43). Inspection of whole-genome sequencing data in the critical area allowed us to pinpoint a likely causal variant in the form of a nonsense mutation of bone morphogenetic protein-15 (Sscrofa11.1_X:g.44618787C > T, BMP15:p.R212X). The mutant allele occurs at a frequency of 6.2% in the German Landrace breeding population. Homozygous gilts exhibit underdeveloped, most likely not functional ovaries and are not fertile. Male carriers do not seem to manifest defects. Heterozygous sows produce 0.41 ± 0.02 (P = 4.5 × 10− 83) piglets more than wildtype animals. However, the mutant allele’s positive effect on litter size accompanies a negative impact on lean meat growth.Conclusion: Our results provide an example for the power of GWAS in identifying the genetic causes of a fuzzy phenotype and add to the list of natural deleterious BMP15 mutations that affect fertility in a dosage-dependent manner, the first time in a poly-ovulatory species. We advise eradicating the mutant allele from the German Landrace breeding population since the adverse effects on the lean meat growth outweigh the larger litter size in heterozygous sows.
Serum interleukin-6 is an indicator for severity in 901 patients with SARS-CoV-2 infection: A cohort study
Authors: Zhang Jing , Hao Yiqun , Ou Wuling , Ming Fei , Liang Gai , Qian Yu , Cai Qian , Dong Shuang , Hu Sheng , Wang Weida , Wei Shaozhong
Published: August 2020

Background
Interleukin-6 (IL-6) was proposed to be associated with the severity of coronavirus disease 2019 (COVID-19). The present study aimed to explore the kinetics of IL-6 levels, validate this association in COVID-19 patients, and report preliminary data on the efficacy of IL-6 receptor blockade.
Methods
We conducted a retrospective single-institutional study of 901 consecutive confirmed cases. Serum IL-6 concentrations were tested on admission and/or during hospital stay. Tocilizumab was given to 16 patients with elevated IL-6 concentration.
Results
366 patients were defined as common cases, 411 patients as severe, and 124 patients as critical according to the Chinese guideline on diagnosis and treatment of COVID-19. The median concentration of IL-6 was < 1.5 pg/ml (IQR < 1.50–2.15), 1.85 pg/ml (IQR < 1.50–5.21), and 21.55 pg/ml (IQR 6.47–94.66) for the common, severe, and critical groups respectively (P༜0.001). The follow-up kinetics revealed serum IL-6 remained high in critical patients even when cured. An IL-6 concentration higher than 37.65 pg/ml was predictive of in-hospital death (AUC 0.97 [95%CI 0.95–0.99], P < 0.001) with a sensitivity of 91.7% and a specificity of 95.7%. In the 16 patients who received tocilizumab, IL-6 concentrations were significantly increased after administration, and survival outcome was not significantly different from that of propensity-score matched counterparts (n = 53, P = 0.12).
Conclusion
Serum IL-6 should be included in diagnostic work-up to stratify disease severity, but the benefit of tocilizumab needs further confirmation.
Trial registration:
retrospectively registered.
A Nexus between Corporate Social Responsibility Disclosure and its Determinants in Energy Enterprises
Authors: AHMED RAHIL , Zhao GuoHao
Published: August 2020

The authors have requested that this preprint be removed from Research Square.
Comparative analysis of patients with upper urinary tract urothelial carcinoma in black-foot disease endemic and non-endemic area
Authors: Chang Che-Wei , Ou Chien-Hui , Yu Chih-Chin , Lo Chi-Wen , Tsai Chung-You , Cheng Pai-Yu , Chen Yung-Tai , Huang Hsu-Che , Wu Chia-Chang , Wu Wen-Jeng , Li Ching-Chia , Li Wei-Ming , Ke Hung-Lung , Lee Hsiang-Ying
Published: August 2020

Objective

High incidence of upper urinary tract urothelial carcinoma has been reported in South- Western area of Taiwan, where arsenic water contamination was considered to be the main cause. However, there is no definite proof to show the correlation between the arsenic water contamination and upper urinary tract urothelial carcinoma. To investigate the clinical and epidemiological features of the patients with upper urinary tract urothelial carcinoma between arsenic water endemic and non-endemic areas, we analyzed patients in terms of characteristics, stratified overall survival, disease-free survival and cancer-specific survival

Method

The records of a total 1194 patients diagnosed with upper urinary tract urothelial carcinoma were retrospectively reviewed. Clinical data and current medical status were collected from medical records. Statistical analyses were performed to determine the clinical variables and stratified survival curves between endemic and non-endemic groups.

Results

Female predominance was revealed in both endemic and non-endemic groups (Male:Female=1:1.2- 1.4). No statistical differences were found in histological types, staging and tumor size among two groups. Nonetheless, patients with characteristics of aging and having end stage renal disease outnumbered in non-endemic group while higher prevalence of previous bladder tumor and more ureteral tumor were found in endemic group. Adjusted stratified cumulative survival curves suggested poorer prognosis fashion in endemic patients, especially in disease free survival of early stage disease.

Conclusions

Higher mortality rate with more previous bladder cancer history and ureteral tumor were seen in patients with upper urinary tract urothelial carcinoma residing in arsenic water contamination area. This may attribute to the long-term carcinogenesis effect of arsenic underground water.