bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of key genes unique to the luminal A and basal-like breast cancer subtypes via bioinformatic analysis
Authors: Jia Rong , Li Zhongxian , Liang Wei , Ji Yucheng , Weng Yujie , Liang Ying , Ning Pengfei
Published: May 2020

Background Breast cancer subtypes are statistically associated with prognosis. The search for markers of breast tumor heterogeneity and the development of precision medicine for patients are the current focuses of the field. Methods We used a bioinformatic approach to identify key disease-causing genes unique to the luminal A and basal-like subtypes of breast cancer. First, we retrieved gene expression data for luminal A breast cancer, basal-like breast cancer, and normal breast tissue samples from The Cancer Genome Atlas database. The differentially expressed genes unique to the 2 breast cancer subtypes were identified and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. We constructed protein–protein interaction networks of the differentially expressed genes. Finally, we analyzed the key modules of the networks, which we combined with survival data to identify the unique cancer genes associated with each breast cancer subtype. Results We identified 1,114 differentially expressed genes in luminal A breast cancer and 1,042 differentially expressed genes in basal-like breast cancer, of which the subtypes shared 500. We observed 614 and 542 differentially expressed genes unique to luminal A and basal-like breast cancer, respectively. Through enrichment analyses, protein–protein interaction network analysis, and module mining, we identified 8 key differentially expressed genes unique to each subtype. Analysis of the gene expression data in the context of the survival data revealed that high expression of NMUR1 and NCAM1 in luminal A breast cancer statistically correlated with poor prognosis, whereas the low expression levels of CDC7 , KIF18A , STIL , and CKS2 in basal-like breast cancer statistically correlated with poor prognosis. Conclusions NMUR1 and NCAM1 are novel key disease-causing genes for luminal A breast cancer, and STIL is a novel key disease-causing gene for basal-like breast cancer. These genes are potential targets for clinical treatment.
Frailty is a useful predictive marker of postoperative complications after pancreaticoduodenectomy
Authors: NAKANO YUTAKA , Hirata Yuki , Shimogawara Tatsuya , Yamada Toru , Mihara Koki , Nishiyama Ryo , Nishiya Shin , Taniguchi Hideki , Egawa Tomohisa
Published: May 2020

BACKGROUND: Frailty results in a high risk for disability, hospitalization, and mortality. This study aimed to investigate perioperative details of frail patients who underwent pancreatectomy and whether frailty can be a predictive factor of postoperative complications, especially of clinically relevant postoperative pancreatic fistula (CR-POPF). METHODS: This retrospective study included patients who underwent pancreatectomy in our hospital between August 2016 and March 2019. The patients were divided into frail and pre-/non-frail groups. The diagnostic criteria were based on the Japanese version of the Cardiovascular Health Study. RESULTS: Of 93 patients, 11 (11.8%) and 82 (88.2%) were frail and pre-/non-frail patients, with median ages of 82 and 72 years, respectively (p=0.041). Postoperative complications (Clavien-Dindo ≧IIIa) were found in 8 and 32 patients (p=0.034), CR-POPF in 3 and 13 patients (p=0.346), and postoperative hospital stays were 21 and 17 days (p=0.041), respectively. On multivariate analysis, frailty was an independent predictive factor (odds ratio [OR] 5.604, 95.0% confidence interval [CI] 1.002-30.734; p=0.047) of postoperative complications (Clavien-Dindo ≧IIIa) after pancreaticoduodenectomy. On multivariate analysis, a soft pancreas (OR 5.696, 95.0% CI 1.142-28.149; p=0.034) was an independent and significant predictive factor of CR-POPF after pancreaticoduodenectomy. CONCLUSIONS: Frailty may be a useful predictive factor of postoperative complications in patients undergoing pancreaticoduodenectomy.
Angiopoietin-Tie2 and nitric oxide signaling of erythrocytes in response to surgical trauma in head and neck cancer
Authors: Wu Hsiang-Ling , Chu You-Hsiang , Tai Ying-Hsuan , Tsou Mei-Yung , Wu Cheng-Hsien , Lo Wen-Liang , Tai Shyh-Kuan , Yeh Chun-Chang , Lu Chih-Cherng
Published: May 2020

Background Angiopoietin-Tie2 and nitric oxide pathway is crucial in tumor angiogenesis and closely correlates with tumor development, growth, and metastasis. This study aimed to investigate the angiopoietin-Tie2 and nitric oxide signaling of erythrocyte membrane in response to surgical trauma in head and neck cancer.Methods We prospectively enrolled the patients with histology-proven head and neck squamous cell carcinoma undergoing surgical resection of primary tumors at the medical center between August and November 2019. We measured the preoperative and postoperative levels of angiopoietin-1, angiopoietin-2 in plasma using enzyme-linked immunosorbent assays, nitric oxide in plasma using nitrate/nitrite colorimetric assays, and Tie2 phosphorylation in erythrocyte membrane using Western blotting. Results The plasma angiopoietin-1 was down-regulated from median 971.3 pg/mL (interquartile range [IQR]: 532.1 – 1569.3) to 417.9 (IQR: 270.5 – 597.3) after tumor resection ( p =0.0020). Conversely, the plasma angiopoietin-2 was enhanced from 1173.6 pg/mL (IQR: 977.7 – 1450.2) to 2353.7 (IQR: 1352.4 – 2954.3) after surgery ( p =0.0021), with a concomitant increase in plasma nitric oxide level from 7.73 μM (IQR: 5.39 – 10.06) to 10.50 (IQR: 7.65 – 14.18) after surgical resection ( p =0.0093). Subgroup analyses further showed the angiopoietin-Tie2 and nitric oxide signaling was significant only in stage III and IV cancer.Conclusions The dynamic change of angiopoietin-Tie2 signaling in erythrocyte membrane along with the enhanced nitric oxide in plasma after tumor resection suggests erythrocytes play a significant role in modulating surgery-induced angiogenesis, which may provide a novel marker for cancer surveillance and control.
Prevalence of malnutrition and associated risk factors among under-five children in Amhara Region, Ethiopia: evidence from 2016 Ethiopian Demographic and Health Survey
Authors: Mengesha Damitie Kebede , Merkeb Yidnekachew
Published: May 2020

Background Childhood malnutrition is the most widely prevalent among under-five children in Amhara Region, Ethiopia. This study intended to explore the major determinants of malnutrition and its association with anemia among under-five children in Amhara Region, Ethiopia.Methods The data from the 2016 Ethiopian Demographic and Health Survey were used. A total of 977 under-five children were included in this analysis. A multivariable binary logistic regression analysis was used at a 5% level of significance to determine the individual- and community-level factors associated with childhood malnutrition. Results The prevalence of stunting, wasting, and underweight were 46.3%, 9.8%, and 28.4%, respectively. About 23.1% of children were both stunting and underweight, 7.3% were both underweight and wasting, and only 4.5% of children had all the three conditions. Among the factors considered in this study, Age of child in months, size of child at birth, mother highest education level, sex of household head, sources of drinking water, and type of toilet facility were significantly associated with malnutrition in Amhara Region. Conclusion Malnutrition among under-five children was one of the public health problems in the Amhara Region. The influence of these factors should be considered to develop strategies for reducing malnutrition in Amhara Region. Finally improving the living standards of the children is important to get better health care, to enhance the child’s nutritional status, and reduce child mortality.
Visceral adiposity index is closely associated with albuminuria in the Chinese population with prediabetes: results from the REACTION study
Authors: Wang Jie , Zhu Binruo , Jin Xinye , Chen Kang , Yan Wenhua , Wang Anping , Wang Weiqing , Gao Zhengnan , Tang Xulei , Yan Li , Wan Qin , Luo Zuojie , Qin Guijun , Chen Lulu , Mu Yiming
Published: May 2020

Background Visceral obesity is a major health issue and a risk factor for atherogenic state. It has been reported to be a crucial link between albuminuria and cardiovascular diseases (CVD). However, there is limited available data on the relationship between visceral obesity and albuminuria. Therefore, we aimed to explore the association between visceral obesity and albuminuria in the Chinses population with prediabetes. Methods This cross-sectional study included 24871 prediabetic participants aged over 40 years from seven centers across China. Visceral adiposity index (VAI), which has been confirmed as a simple and reliable indicator of visceral adiposity distribution and dysfunction, is determined based on the measurements of anthropometric indices and lipid parameters. Increased albuminuria was defined as urinary albumin-creatinine ratio (UACR)≥30 mg/g, indicating kidney damage. Propensity score matching was used to reduce the bias and multiple logistic regression model was performed to evaluate the association between visceral obesity and albuminuria in the population with prediabetes. Results Participants with increased UACR had increased VAI, age, blood pressure, triglycerides, poor glycemic control, and decreased estimated glomerular filtration rate (eGFR). The prevalence of CVD was higher in the increased UACR group. Multiple logistic regression analysis showed that VAI quartiles was positively associated with increased risk of albuminuria (Q2: odds rate (OR):1.10, 95% confidence intervals [CI]: 0.96-1.25; Q3: OR:1.16, 95%CI 1.01-1.32; Q4: OR:1.26, 95%CI 1.10-1.44, P for trend=0.001). Stratified analysis revealed that the association of VAI level with increased albuminuria risk was also observed in people who were young, women, overweight or obese, with poor control of blood pressure, and eGFR≥ 90 mL/min per 1.73 m 2 . Conclusions Visceral obesity assessed by VAI was significantly associated with increased albuminuria in the Chinese population with prediabetes.
The protection of LingqiHuangban Granule on human retinal endothelial cells against oxidative stress-induced injury by network pharmacology
Authors: Zhang Zhenzhen , Zhou Chuandi , Draga Deji , Thashi lhamo , Zheng Zhi , Qiu Qinghua
Published: May 2020

Background: LingqiHuangban Granule(LQHBG) is a famous traditional Chinese medicine formula used to manage retinal diseases, as an effective holistic treatment through warming Yang to exert tonifying effects on kidney and invigorating spleen to remove dampness to nourish essence of effect. The study examined protection of LQHBG on oxidative stress-induced injury in human retinal endothelial cells(HRECs) in vitro, determined the potential molecular targets of LQHBG using network pharmacology.Methods: The potential targets of active ingredients in LQHBG were predicted using pharmmapper. Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analyses were carried out using Molecule Annotation System. The protein-protein interaction networks were constructed using Cytoscape. LQHBG was administered to rabbits to prepare medicated serum. The apoptosis of HRECs was evaluated by TUNEL and Flow Cytometry(FCM). MDA, SOD, LDH, GSH-Px, and T-AOC were detected. The mRNA expressions of Nrf2, NF-κB and HO-1 were detected, protein expression levels of Nrf2, Bcl-2, NF-κB, HO-1 and caspase-3 were analyzed.Results: TUNEL demonstrated the numbers of apoptotic cells in low-and high-dose LQHBG groups was obviously less than model group(P<0.05). FCM analysis revealed apoptotic rates of HRECs in low-and high-dose LQHBG groups were obviously reduced in a dose-dependent manner(P<0.05). The potential mechanism of LQHBG was the NF-κB pathway identified using PharmMapper. LQHBG significantly decreased MDA, LDH levels and enhanced SOD, GSH-Px and T-AOC generation. LQHBG inhibited upregulation of NF-κB, caspase-3 and enhanced Bcl-2, Nrf2, and HO-1 expression.Conclusion: LQHBG protected HRECs against oxidative-stress via suppression of apoptosis and elevation of antioxidant ability, which may involve activation of Nrf2/ARE/HO-1 pathway and inhibition of NF-κB pathway.
Economic Dependency and Opportunity Cost of Childbearing: Implications for fertility control in sub-Sahara Africa
Authors: ADEYEMI OLUWAGBEMIGA , Adedokun Olaide Aderonke , Adeniyi Bolajoko Florence , Olowe Kolawole Samuel
Published: May 2020

The dynamics in the household income within the marital unions especially with the emergence of female breadwinners in the last decade is gradually changing the demand for children and the need for child spacing. It is in line with this that this study examines the impact of changing spousal roles on the cost of bearing children in three sub-Saharan African countries. Demographic and Health Surveys data were analyzed using three levels of statistical analysis, while at multivariate level, five models were constructed to test the formulated hypotheses. The study identified significant relationship between economic dependency and the control variables (use of modern contraceptives and fertility timing) in the three countries (Pvalue < .0001). The study also affirmed a positive significant relationship between economic dependency and labour force participation of women except in Lesotho (Pvalue < .0001). In addition, higher significant differential was ascertained between labour force participation and fertility in the study area. The three countries also indicate high significant correlation of the effect of women economic dependency on fertility. The study concludes that empowering women and allowing them to involve in paid activities will not only reduce fertility but significantly contribute to poverty reduction in Africa.
Studies on Trueperella Pyogenes Isolated from an Okapi (Okapia johnstoni) and A Royal Python (Python Regius)
Authors: Ahmed Marwa F.E. , Alssahen Mazen , Lämmler Christoph , Eisenberg Tobias , Plötz Madeleine , Abdulmawjood Amir
Published: May 2020

Background The present study was designed to characterize phenotypically and genotypically two Trueperella pyogenes strains isolated from an okapi (Okapia johnstoni) and a royal python (Python regius), respectively.Results The species identity could be confirmed by phenotypic properties, by MALDI-TOF MS analysis and by detection of T. pyogenes chaperonin-encoding gene cpn60 with a previously developed loop-mediated isothermal amplification (LAMP) assay. Furthermore, sequencing of the 16S ribosomal RNA (rRNA) gene, the 16S-23S rDNA intergenic spacer region (ISR), the target genes rpoB encoding the β-subunit of bacterial RNA polymerase, tuf encoding elongation factor tu and plo encoding the putative virulence factor pyolysin allowed the identification of both T. pyogenes isolates at species level.Conclosion Both strains could be clearly identified as T. pyogenes. The T. pyogenes strain isolated in high number from the vaginal discharge of an okapi seems to be of importance for the infectious process; the T. pyogenes strain from the royal python could be isolated from an apparently non-infectious process. However, both strains represent the first isolation of T. pyogenes from these animal species.
The associations of SNF5 with prognosis and immune responses in bladder cancer
Authors: Ding Hua , Zhang Jingqi , Liu Sha , Wang Liwei , Shi Jiazhong , Huang Yaqin , Zhou Xiaozhou , Yang Jin , Chen Zhiwen
Published: May 2020

Background

Bladder cancer (BC) is the second most common malignancy in the urinary system. Improving survival has been hampered by high heterogeneity and drug resistance. SNF5, a subunit of the SWI/SNF chromatin-remodeling complex, is commonly lost or inactivated in multiple malignancies. The role of SNF5 in bladder cancer has not yet been elucidated. This is the first exploration into the associations of SNF5 with prognosis and its functions in BC.
Methods

Using datasets from The Cancer Genome Atlas projects and our institution, we investigated the predictive value of SNF5 in bladder cancer, as well as the relationships with clinical characteristics. The differential genes expression analysis, gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene set enrichment analyses (GSEA) were performed to investigate the functions of SNF5. The Immune Cell Abundance Identifier (ImmuCellAI) algorithm was used to infer the fractions of tumor-infiltrating lymphocytes (TILs). Next, we conducted gene set variation analysis (GSVA) and Tumor Immune Dysfunction and Exclusion (TIDE) algorithm to assess the effects of SNF5 on antitumor response and sensitivity to immune checkpoint blockade (ICB).
Results

SNF5 had the potential to predict bladder cancer and a negative correlation with survival. SNF5 was involved in immune response. Low expression of SNF5 promoted infiltration of immune cells into tumor, enhanced the abilities to process and present antigens by activating the MHC-T cell receptor activation pathway. Moreover, decreased SNF5 activated CTLA-4 pathway, upregulating CTLA-4 expression, but SNF5 did not modify the expression of PD-1 or PD-L1. A higher TIDE score was generated in the low-expression group, which indicated that patients with low expression might derive greater benefit from ICB.
Conclusions

Our findings indicated that SNF5 was not only a good biomarker for diagnosis and prognosis of BC, but a potential new target in the immunotherapy for BC.
The tumor environment immune phenotype of LUSC by genome-wide analysis
Authors: Zheng Yuansheng , Bi Guoshu , Bian Yunyi , Li Ming , Huang Yiwei , Zhao Mengnan , Chen Zhencong , Zhan Cheng , Jiang Wei
Published: May 2020

Background

To compare the landscape of tumor microenvironment (TME) of lung squamous carcinoma (LUSC) in different immune pattern and explore potential factors on immune therapy and prognosis
Method and Materials:

We have obtained the LUSC data from TCGA, GEO, and our department and classified them into 2 TME clusters by random forest model based on the infiltration pattern of 24 immune cell populations. Then we systemically compared the genomic significance, clinical characteristic and immune infiltration pattern in 2 TME clusters.
Results

Samples were divided into 2 TME clusters based on the relative abundance of 24 immune cells and a random forest classifier model was constructed. TME cluster B was a higher immune infiltration group with lower mutation load, richer co-infiltrate immune cells, up-regulated immune-related cytokines including immune checkpoint molecules, and higher active immune cells. TME cluster was also an independent predictor in prognosis (B vs A, p < 0.05) in patients from TCGA, GEO and our department.
Conclusions

Our study has described the microenvironment landscape of LUSC in different immune infiltration patterns and systemically analyzed genomic and clinical characteristics with distinct immunophenotypes, thus partly revealed the interaction between tumors and immune microenvironment, which may guide a more precise and personalized immune therapeutic strategy for LUSC patients.
Women’s Status and Empowerment within the Household as a Determinant of Adequate Antenatal Care Visits in Malawi. A Population-Based Study
Authors: Ntenda Peter Austin Morton
Published: May 2020

Background Research has linked women status and empowerment to an improved health status of the general population. However, there is a deficiency of pragmatic data to support how females’ position within the household may impact adequate antenatal care (ANC) visits in Malawi. Therefore, this study explored whether the women’s status and empowerment influence adequate ANC visits in Malawi.Methods The current study sampled and analyzed ever-married women of reproductive age from the 2010 and 2015–16 Malawi Demographic and Health Surveys (MDHS). The two-level multilevel multivariable analyses were performed by means of the generalized linear mixed models (GLMMs) to investigate the relationships between the women’s status and empowerment within the household and adequate ANC visits while controlling for covariates.Results About 46% and slightly over 50% of participants had adequate ANC visits in 2010 and 2015–16 respectively. The GLMMs shows that women with no formal education (adjusted odds ratio [aOR]: 0.71; 95% confidence interval [CI]: 0.54–0.94) and primary education (aOR: 0.65; 95% CI: 0.53–0.80) had reduced odds of achieving adequate ANC visits. Additionally, younger women, women from the poorest households, women who did not have access to media and women who resided in the northern region had reduced odds of achieving adequate ANC visits. The GLMMs also revealed variations in the communities with respect to the odds of achieving adequate ANC visits.Conclusion The association of women’s education on adequate ANC visits underscores the need for policymakers’ to think through incorporating education sector in ANC settings to increase health-related knowledge among women of reproductive age in order to inform them of the importance of achieving adequate ANC visits.
Investigation of the effect of Delayed Auditory Feedback and transcranial Direct Current Stimulation (DAF-tDCS) treatment for the enhancement of speech fluency in adults who stutter: a Randomized Controlled Trial
Authors: Moein Narges , Mohamadi Reyhane , Rostami Reza , Nitsche Michael , Zomorrodi Reza , Ostadi Amir , Keshtkar Abbasali
Published: May 2020

Background: With a population prevalence of one percent, stuttering is among the main speech pathology-related topics of research. Adults who stutter may benefit from transcranial direct current stimulation (tDCS) as an adjunctive intervention for enhancing speech fluency. In this study, Delayed Auditory Feedback (DAF) was combined with tDCS applied over the superior temporal gyrus. It was anticipated that intervention caused improvements of speech fluency become more stable.Methods: A randomized, double-blind, sham-controlled clinical trial was conducted to investigate the effectiveness of intervention in enhancing speech fluency. Fifty participants were randomly allocated the intervention or control group. In the intervention group, participants received DAF combined with anodal tDCS, while the control group was exposed to sham tDCS simultaneously with DAF. Each subject participated in six intervention sessions. Speech fluency was assessed before intervention as baseline, as well as immediately, one week and six weeks after intervention.Results: In the intervention group, the percentage of stuttered syllables was significantly reduced immediately, one week and six weeks after the intervention, as compared with the control group. The scores of the Stuttering Severity Instrument, also showed a significant reduction in the intervention group compared with the control group. No significant difference was found in the Overall Assessment of the Speaker’s Experience of Stuttering questionnaire scores between the two patient two groups after intervention.Conclusion: The results of this study propose anodal tDCS as an adjunctive method to increase speech fluency in stuttering for a prolonged time course after intervention, when combined with fluency therapy.Trial registration: This trial was registered in ClinicalTrial.gov before recruiting the subjects. The registration number is NCT03990168 and the date of registration is June 18, 2019. https://clinicaltrials.gov/ct2/show/NCT03990168
The effects of sex disparities on clinicopathological characteristics and prognosis of 3937 Chinese patients with gastric cancer
Authors: Zhang Xiaoxu , Chen Zhiqiang , Chen Ping , Zhang Qinghua , Yu Jia , Cao Juan , Wang Wenfan , Zhao Dan , Zhang Qian , Wu Jing , Ruan Jigang , Yang Wenjun
Published: May 2020

Objective: To investigate the effects of sex disparities on clinicopathological characteristics and prognosis of 3937 Chinese gastric cancer (GC) patients.Materials and methods: A total of 3937 Chinese patients, including 3098 males (78.7%) and 839 females (21.3%), diagnosed with GC at the General Hospital of Ningxia Medical University of China were selected through inclusion and exclusion criteria, and the prognosis of the patients was followed up. Clinicopathological features were assessed, and univariate and multivariate survival analyses were performed.Results: The ratio of male to female was approximately 3.7:1. Compared to females, male patients were relatively older and had more cigarette smoking and alcohol consumption history, higher percentage of late-stage GC, more proximal tumors, and better differentiation of cancer (p<0.05). There was no significant difference between the male and female patient groups in terms of the cumulative overall survival rate (62.1% vs. 64.8%), 1-year survival rate (69.7% vs. 71.6%), 3-year survival rate (46.6% vs. 48.5%)and 5-year survival rate (20.8% vs. 15.8%). Female patients with cigarette smoking history and male patients in stage IV or without treatment had a poorer prognosis (p<0.05). Age, clinical differentiation, pathologic T stage, pathologic N stage, clinical stage, and surgery type were significantly independent prognostic factors (p<0.05).Conclusion: Sex disparities play an important role in clinicopathological features and prognosis of GC. Considering that the effect of sexual dimorphism in the development and prognosis of GC is complex, further research is warranted.
Is Novel Corona Virus Truly a Trigger for Kawasaki Disease in Infants?– Reporting the First Asian Case 
Authors: Acharyya Bhaswati C , Acharyya Saumyabrata , Das Dhritabrata
Published: May 2020

SARSCov2 pandemic has hit the world this year with alarming consequences in most of the continents. There are relatively few reported cases of COVID-19 infection in children, compared to the total number of cases in the general population. Children are battling the infection more positively unless they have pre-existing morbidity. Interestingly an inflammatory condition is being reported from western world in this COVID 19 era with increased risk of mortality. We report the first Asian infant with florid features of Kawasaki Disease who eventually tested positive for Novel Corona virus.
Expression, purification and characterization of α-synuclein fibrillar specific scFv from inclusion bodies
Authors: Gupta Vijay , Sudhakaran Indulekha P. , Islam Zeyaul , Vaikath Nishant N. , Hmila Issam , Lukacsovich Tamas , Kolatkar Prasanna R. , El-Agnaf Omar
Published: May 2020

Background: Aggregation of α-synuclein (α-syn) has been implicated in multiple neurodegenerative disorders including Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), collectively grouped as synucleinopathies. Recently, recombinant antibody fragments (Fab, scFvs and diabodies) against α-syn have emerged as an alternative to the traditional full-length antibody in immunotherapeutic approaches owing to their advantages including smaller size and higher stability, specificity and affinity. However, most of the recombinant antibody fragments tend to be expressed as inclusion bodies (IBs) making its purification extremely challenging.
Results: In the current study, a single-chain variable fragment (scFv-F) antibody, targeting the pathogenic α-syn fibrils, was engineered and expressed in E.coli. Majority of the expressed scFv-F accumulated in insoluble aggregates as IBs. A variety of mild and harsh solubilizing conditions were tested to solubilize IBs containing scFv-F to obtain the active protein. To preserve secondary structure and bioactivity, a mild solubilizing protocol involving 100 mM Tris, pH 12.5 with 2 M urea was chosen to dissolve IBs. Slow on-column refolding method was employed to subsequently remove urea and obtain active scFv-F. A three-dimensional (3D) model was built using homology modeling and subjected to molecular docking with the known α-syn structure. Structural alignment was performed to delineate the potential binding pocket.
Conclusion: The scFv-F thus purified demonstrated high specificity towards α-syn fibrils compared to monomers. Molecular modeling studies suggest that scFv-F shares the same structural topology with other known scFvs. We present evidence through structural docking and alignment that scFv-F binds to α-syn C-terminal region. In conclusion, mild solubilization followed by slow on-column refolding can be utilized as a generalized and efficient method for hard to purify disease relevant insoluble proteins and/or antibody molecules from IBs.
 A Simulation Approach to Predict the Transmission of COVID-19in Bangladesh  
Authors: Muka Abul Mukid Md. , Sannyal Mridul
Published: May 2020

The coronavirus disease (COVID-19) was first identiﬁed in Wuhan, China, in December 2019. Since then, it has been affecting 212 countries and territories around the world. First detected on March 8, 2020, as of April 30, there are 7,667 confirmed COVID-19 cases in Bangladesh, including 130 patients who have recovered and 168 related deaths. We identify the facts of COVID-19 and government’s preventive actions taken in Bangladesh and examine the transmission parameters, infection rate, fatality rate, and recovered rate using the publicly available data until April 30. We estimated the transmission parameters using the susceptible-exposed-infected-cured-dead (SEICD) model and linear regression. Based on these parameters, we then predicted the growth of the infection, cure, and deaths and compared them with reported data. The number of patients infected as of April 30 in Bangladesh closely follows an exponential trend. If this trend continues for fewer weeks, there will be around 50,000 infected patients if necessary steps are not seriously taken by the government. There is now breakneck concern regarding the capacity to respond to needs of infected patients effectively and to prevent this pandemic from further spreading in Bangladesh, one of the densest countries in the world. Health authorities might assimilate this analysis into their disease prevention and control decision-making process.
An adapted ODE model to study the Dynamics of SARS-Cov-2 Infection (COVID-19): different scenarios for Brazil and other countries
Authors: González Ramón E. R. , M. Miguel A. Zorro , Estupiñán-López C. , Morales Carlos Andrés Collazos
Published: May 2020

A mathematical model to calculate the transmissibility of SARS-Cov-2 in Wuhan City was developed and published recently by Tian-Mu Chen et al. The present work generalizes this model to study the effect of different scenarios that include actions to contain the pandemic, such as the isolation and quarantine of infected and at-risk people. Comparisons made between the different scenarios show that the progress of the infection depends heavily on the measures taken in each case. The particular case of some countries, was studied, showing the dynamics of infection in comparison with the different scenarios contained in the model. Real data from different countries, such as Brazil, was used for the validation of the model. This study shows that the model reproduce adequately the dynamic of infection for all studied countries. The relative evolution of the number of new infections and reported cases was used to estimate a pandemic containment date. The progression of the epidemic was analyzed using the system’s phase diagram, which shows the "path" followed by the epidemic in each scenario. Finally, the basic values of the number of reproduction R0 were estimated for each scenario, ranging from 4.04 to 1.12.
Circulating Inflammatory Markers are Inversely Associated with Heart Rate Variability Measures in type 1 Diabetes
Authors: Wegeberg Anne-Marie Langmach , Okdahl Tina , Fløyel Tina , Brock Christina , Ejskjaer Niels , Riahi Sam , Pociot Flemming , Størling Joachim , Brock Birgitte
Published: May 2020

Background A neuro-immune communication exists, and compiling evidence suggests that diabetic neuropathy and systemic inflammation are linked. Our aims were 1) to investigate biomarkers of the ongoing inflammation processes including cytokines, adhesion molecules and chemokines, and 2) to associate the findings with cardiovascular autonomic neuropathy in type 1 diabetes by measuring heart rate variability and cardiac vagal tone.Methods We included 104 adults with type 1 diabetes. Heart rate variability, time- and frequency domains, were calculated from a 24-hour Holter electrocardiogram, while cardiac vagal tone was determined from a 5-minute electrocardiogram. Cytokines (interleukin (IL)-1α, IL-4, IL-12p70, IL-13, IL-17 and tumor necrosis factor (TNF)-α), adhesion molecules (E-selectin, P-selectin and intercellular adhesion molecule (ICAM)-1) and chemokines (chemokine (C-C motif) ligand (CCL)2, CCL3, CCL4 and C-X-C motif chemokine (CXCL)10) were assessed using a Luminex multiplexing technology. Associations between concentrations of inflammatory biomarkers and continuous variables of heart rate variability and cardiac vagal tone were estimated using multivariable linear regression adjusting for age, sex, disease duration and smoking.Results Participants with the presence of cardiovascular autonomic neuropathy had higher systemic levels of IL-1α, IL-4, CCL2 and E-selectin, than those without cardiovascular autonomic neuropathy. IL-1α, IL-4, IL-12, TNF-α and E-selectin were inversely associated with both sympathetic and parasympathetic heart rate variability measures (p>0.01).Conclusion Our results show that several pro- and anti-inflammatory factors, believed to be involved in the progression of diabetic polyneuropathy are associated with cardiovascular autonomic neuropathy, suggesting that these factors may also contribute to the pathogenesis of cardiovascular autonomic neuropathy. Our findings emphasize the importance of the neuro-immune regulatory system in the pathogenesis of neuropathy in type 1 diabetes.Trial registration: The study was approved by the North Denmark Regional Committee on Health Research Ethics (N2013-0077 and N2017-0045) and registered in public databases (Eudra CT 2013-004375-12 and clinicaltrials.gov NCT02138045.
Altered Metabolism of Mothers of Young Children with Autism Spectrum Disorder: A Case Control Study
Authors: Hollowood-Jones Kathryn , Adams James B. , Coleman Devon M. , Ramamoorthy Sivapriya , Melnyk Stephan , James S. Jill , Woodruff Bryan K. , Pollard Elena L. , Snozek Christine L. , Kruger Uwe , Chuah Joshua , Hahn Juergen
Published: May 2020

Background: Previous research studies have demonstrated abnormalities in the metabolism of mothers of young children with autism. Method: Metabolic analysis was performed on blood samples from 30 mothers of young children with Autism Spectrum Disorder (ASD-M) and from 29 mothers of young typically-developing children (TD-M). Targeted metabolic analysis focusing on the folate one-carbon metabolism (FOCM) and the transsulfuration pathway (TS) as well as broad metabolic analysis were performed. Statistical analysis of the data involved both univariate and multivariate statistical methods. Results: Univariate analysis revealed significant differences in 5 metabolites from the folate one-carbon metabolism and the transsulfuration pathway and differences in an additional 48 metabolites identified by broad metabolic analysis, including lower levels of many carnitine-conjugated molecules. Multivariate analysis with leave one-out cross validation allowed classification of samples as belonging to one of the two groups with 93% sensitivity and 97% specificity with five metabolites. Furthermore, each of these five metabolites correlated with 8-15 other metabolites indicating that there are five clusters of correlated metabolites. In fact, all but 5 of the 50 metabolites with the highest area under the receiver operating characteristic curve were associated with the five identified groups. Many of the abnormalities appear linked to low levels of folate, vitamin B12, and carnitine-conjugated molecules. Conclusions: Mothers of children with ASD have many significantly different metabolite levels compared to mothers of typically developing children at 2-5 years after birth.
Ayurveda botanicals in COVID-19 management: An in silico- multitarget approach
Authors: Borse Swapnil , Joshi Manali , Saggam Akash , Bhat Vedika , Walia Safal , Sagar Sneha , Chavan-Gautam Preeti , Tillu Girish
Published: May 2020

The Coronavirus disease (COVID-19) caused by the virus SARS-CoV-2 has become a global pandemic in a very short time span. Currently, there is no specific treatment or vaccine to counter this highly contagiousdisease. Presently, existing anti-virals and disease-modifying agents are being repurposed to manage COVID-19. There is an urgent need to find a specific cure for the disease and global efforts are directed at developing SARS-CoV-2 specific anti-viralsand immunomodulators.The objective of this study is to explore the immunomodulatory and anti-SARS-CoV-2 potential of key phytoconstituents from Ayurveda based Rasayana drugs, Withania somnifera (Ashwagandha), Tinospora cordifolia (Guduchi) and Asparagus racemosus (Shatavari) using in silico approaches like network pharmacology, and molecular docking. The SWISS-ADME tool was used to predict the pharmacokinetic and pharmacodynamic (PK-PD) interactions and drug likeliness potential. Using these approaches we propose a library of phytomolecules with potential to be developed as phytopharmaceuticals for COVID 19 management.The plant extracts were prepared as per Ayurvedic procedures and a total of 31 phytoconstituents were identified using HPLC and MS studies. The network pharmacology model shows that these phytoconstituents possess the potential to modulate several immune pathways. Amongst the three botanicalsWithania somnifera was found to be the most potent immunomodulator through its potential to modulate T cell differentiation, NK cell cytotoxicity as well as T cell, B cell and NOD-like receptor signalling pathways.Molecular docking studies showed thatseveral phytoconstituents possess good affinity for the Spike protein, Main Protease and RNA dependent RNA polymerase of SARS-CoV-2 suggesting their application for the termination of viral life cycle. Further, predictive tools indicate that there would beneficial herb-drug pharmacokinetic-pharmacodynamic interactions with concomitantly administered drug therapy. We thus make a compelling case to evaluate the potential of these Rasayana botanicals in the management of COVID-19 following rigorous experimental validation.
Transmissibility of SARS-CoV-2 during incubation period: Epidemiologic evidence from 178 confirmed clusters in China
Authors: Wu Yuyan , Liu Shelan , Sun Jimin , Gong Zhenyu , Ling Feng , Chen Zhiping , Chan Ta-Chien , Lin Junfen , Pan Jinren , Chen Enfu
Published: May 2020

An outbreak of novel coronavirus (SARS-CoV-2) was identified in China in December 2019, and has spread rapidly to more than 200 countries and areas in four months. A few studies have reported that transmissibility exists during the late incubation period based on one single infection cluster caused by SARS-CoV-2. Here based on 178 SARS-CoV-2 clusters confirmed in Zhejiang Province, we analyzed the epidemic link between all 212 secondary cases with their previous cases, and found 49 secondary cases (from 26 clusters), which were 23.11% (49/212) of the total secondary cases infected from previous cases during the latter’s incubation period. The median days from the last exposure of secondary cases to the onset of previous cases was 2.0 days (IQR: 1.00~5.00 days, 90th percentile: 9.00 days) .This study has shown transmission of the SARS-CoV-2 during the incubation period and indicated that some cases might be infectious soon after they were exposed to a prior transmitter. The results highlight the importance of extending the contact group for medical observation and isolation to those in contact with the index case nine (90th percentile) or more days before the latter’s illness onset, when medical resources were sufficient.
Composition and Production of Essential Oil during Eremothecium ashbyi and Eremothecium gossypii Submerged Cultivation
Authors: Presniakova V.S. , Kurakov A.V. , Bezrukova E.I.
Published: May 2020

The dependence of essential oil accumulation by Eremothecium ashbyi Guilliermond 1935 and Eremothecium gossypii Kurtzman 1995 strains on various endogenous factors has been studied. It was found that the level of the Eremothecium oil synthesis correlated with the culture final pH at the end of fermentation. The quantity of monoterpene alcohols and the ratio of geraniol to other alcohols depended on the strain. It was shown that E. ashbyi ВКПМ F-1320 strain is the most promising in terms of essential oil production level and its composition.

Eremothecium, accumulation of phenylethanol and monoterpene alcohols, essential oil
CHARACTER IMAGE SEGMENTATION OF JAVANESE SCRIPT USING CONNECTED COMPONENT METHOD
Authors: Sugianela Yuna , Suciati Nanik
Published: May 2020

Automation of Javanese script translation is needed to make it easier for people to understand the meaning of ancient Javanese script. By using Javanese script image as input, the translation system generally consists of character segmentation, character recognition, and combining the recognized characters as a meaningful word. The segmentation which obtains region of interest of each character, is an important process in the translation system. In the previous research, segmentation using projection profile method can separate each character well. The method can overcome characters overlapping, but it still produces truncated characters. In this study, we proposed a new segmentation to reduce the truncated character. The first step of the proposed method is pre-processing that consists of converting input into binary image and cleaning noises. The next step is to determine the connected component labels, which further perform as candidate of characters. Some of the candidates are still represented by more than one labels, so that we need a process to merge the connected component labels that have centroid distance less than threshold. We evaluate the proposed method using Intersection over Union (IoU). The evaluation shows the best accuracy 93,26%.
APPLICATION OF THE FORWARD CHAINING METHOD IN DOWN SYNDROME PATIENTS
Authors: . Kurniati
Published: May 2020

According to WHO data, the incidence of Down syndrome is 1 in 1,000 live births in the world. Down syndrome is a backward condition in the physical and mental development of children that results from abnormal chromosome development. However, these conditions are often too late to be realized by the parents of the sufferer. By conducting this study using the forward chaining method aims to help parents to do early detection of the level of retardation of Down syndrome. So, with the existence of this application, it is very petrifying for parents to carry out treatment from an early age in the right way. Thus, sufferers of dwon syndrome get maximum support and attention from the people closest and nearby so that children with dwon syndrome can grow happily and have a decent life like other normal children even though this dwon syndrome cannot be cured.
Group Decision Support System based on AHP-TOPSIS for Culinary Recommendation System
Authors: Dewi Ratih kartika
Published: May 2020

This paper proposes the integration of AHP and TOPSIS to generate the ranking results of culinary recommendation for a group of users to provide better recommendation results. Formerly, Group Decision Support System (GDSS) for culinary recommendations has been developed with the TOPSIS method. TOPSIS has low algorithm complexity, so it is suitable to be applied in mobile devices. However, GDSS with TOPSIS has its disadvantages, TOPSIS have not been able to facilitate the preferences of each user inside a group so the recommendation result always consist only on dominant user. TOPSIS method produces unchanging rankings, because this method recommends a food menu based on the 1 dominant user so that the ranking is always consistent. Meanwhile, this study aims to integrate AHP for weighting criteria from each user and TOPSIS for ranking culinary recommendations. Based on rank consistency testing results that conducted in 6 different user groups, unlike the previous research, AHP-TOPSIS shows inconsistency ranking, which means that changes in user preferences affect the recommendation results that are generated by application. The AHP-TOPSIS method proved can be accommodated the computation of various preferences of each user in GDSS culinary recommendation
LEARNING WORD RELATEDNESS OVER TIME FOR TEMPORAL RANKING
Authors: Sigmawaty Dinda , Adriani Mirna
Published: May 2020

Queries and ranking with temporal aspects gain significant attention in field of Information Retrieval. While searching for articles published over time, the relevant documents usually occur in certain temporal patterns. Given a query that is implicitly time sensitive, we develop a temporal ranking using the important times of query by drawing from the distribution of query trend relatedness over time. We also combine the model with Dual Embedding Space Model (DESM) in the temporal model according to document timestamp. We apply our model using three temporal word embeddings algorithms to learn relatedness of words from news archive in Bahasa Indonesia: (1) QT-W2V-Rank using Word2Vec (2) QT-OW2V-Rank using OrthoTrans-Word2Vec (3) QT-DBE-Rank using Dynamic Bernoulli Embeddings. The highest score was achieved with static word embeddings learned separately over time, called QT-W2V-Rank, which is 66% in average precision and 68% in early precision. Furthermore, studies of different characteristics of temporal topics showed that QT-W2V-Rank is also more effective in capturing temporal patterns such as spikes, periodicity, and seasonality than the baselines.
MULTI-CLASS REGION MERGING FOR INTERACTIVE IMAGE SEGMENTATION USING HIERARCHICAL CLUSTERING ANALYSIS
Authors: Aisyah Khairiyyah Nur , Anggraini Syadza , Putriwijaya Novi Nur , Arifin Agus Zainal , Indraswari Rarasmaya , Navastara Dini Adni
Published: May 2020

In interactive image segmentation, distance calculation between regions and sequence of region merging is being an important thing that needs to be considered to obtain accurate segmentation results. Region merging without regard to label in Hierarchical Clustering Analysis causes the possibility of two different labels merged into a cluster and resulting errors in segmentation. This study proposes a new multi-class region merging strategy for interactive image segmentation using the Hierarchical Clustering Analysis. Marking is given to regions that are considered as objects and background, which are then referred as classes. A different label for each class is given to prevent any classes with different label merged into a cluster. Based on experiment, the mean value of ME and RAE for the results of segmentation using the proposed method are 0.035 and 0.083, respectively. Experimental results show that giving the label on each class is effectively used in multi-class region merging.
Irregular Grid Interpolation using Radial Basis Function for Large Cylindrical Volume
Authors: Iryanto Syam Budi , Muttaqien Furqon Hensan , Sadikin Rifki
Published: May 2020

Irregular grid interpolation is one of the numerical functions that often used to approximate value on an arbitrary location in the area closed by non-regular grid pivot points. In this paper, we propose method for achieving efficient computation time of radial basis function-based non-regular grid interpolation on a cylindrical coordinate. Our method consist of two stages. The first stage is the computation of weights from solving linear RBF systems constructed by known pivot points. We divide the volume into many subvolumes. At second stages, interpolation on an arbitrary point could be done using weights calculated on the first stage. At first, we find the nearest point with the query point by structuring pivot points in a K-D tree structure. After that, using the closest pivot point, we could compute the interpolated value with RBF functions. We present the performance of our method based on computation time on two stages and its precision by calculating the mean square error between the interpolated values and analytic functions. Based on the performance evaluation, our method is acceptable.