bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical activity types and risk of dementia in community-dwelling older people: the Three-City cohort.
Authors: Dupré Caroline , Bongue Bienvenue , Helmer Catherine , Dartigues Jean François , Hupin David , Roche Frédéric , Berr Claudine , Carriere Isabelle 
Published: March 2020

Abstract
Background Physical activity may decrease the risk of dementia; however, previous cohort studies seldom investigated the different types of physical activity and household activities. Our objective was to analyze the links between two physical activity types and dementia in older people. Methods The study used data from the prospective observational Three-city cohort and included 1550 community-dwelling individuals aged 72 to 87 without dementia at baseline. Physical activity was assessed with the Voorrips questionnaire. Two sub-scores were calculated to assess household/transportation activities and leisure/sport activities. Restricted cubic spline and proportional hazard Cox models were used to estimate the non-linear exposure-response curve for the dementia risk and the appropriate activity level thresholds. Models were adjusted for possible confounders, including socio-demographic variables, comorbidities, depressive symptoms and APOE genotype. Results The median age was 80 years, and 63.6% of participants were women. After a median follow-up of 4.6 years, dementia was diagnosed in 117 participants (7.6%). An inverse J-shaped association was found between household/transportation physical activity sub-score and dementia risk, which means that the risk is lowest for the moderately high values and then re-increases slightly for the highest values. The results remained significant when this sub-score was categorized in three classes (low, moderate, and high), with hazard ratios (95% confidence interval) of 0.55 (0.35-0.87) and 0.62 (0.38-1.01) for moderate and high activity levels, respectively. No significant effect was found for leisure/sport activities. Conclusions The 5-year risk of dementia was significantly and negatively associated with the household/transportation activity level, but not with the leisure and sport activity sub-score. This highlights the importance of considering all physical activity types in 72 years or older people.
Active and latent tuberculosis in refugees and asylum seekers: a systematic review and meta-analysis
Authors: Proenca Raquel , Souza Fernanda Mattos , Bastos Mayara Lisboa , Caetano Rosangela , Braga Jose Ueleres , Faerstein Eduardo , Trajman Anete 
Published: March 2020

Abstract
Background: In 2018, there were 70.8 million refugees, asylum seekers and persons displaced by wars and conflicts worldwide. Many of these individuals face a high risk for tuberculosis in their country of origin, which may be accentuated by adverse conditions endured during their journey. Objective: We summarised the prevalence of active and latent tuberculosis infection in refugees and asylum seekers through a systematic literature review and meta-analyses by country of origin and host continent. Methods: Articles published in Medline, EMBASE, Web of Science and LILACS from January 2000 to August 2017 were searched for, without language restriction. Two independent authors performed the study selection, data extraction and quality assessment. Random effect models were used to estimate average measures of active and latent tuberculosis prevalence. Sub-group meta-analyses were performed according to country of origin and host continent. Results: Sixty-seven out of 767 identified articles were included, of which 16 entered the meta-analyses. Average prevalence of active and latent tuberculosis was 1331 per 100 thousand inhabitants [95% confidence interval (CI) = 542-2384] and 37% (95% CI = 23-52%), respectively, both with high level of heterogeneity (variation in estimative attributable to heterogeneity [I 2 ] = 98.2% and 99.8%). Prevalence varied more according to countries of origin than host continent. Ninety-one per cent of studies reported routine screening of recently arrived immigrants in the host country; two-thirds confirmed tuberculosis bacteriologically. Many studies failed to provide relevant information. Conclusion: Tuberculosis is a major health problem among refugees and asylum seekers and should be given special attention in any host continent. To protect this vulnerable population, ensuring access to healthcare for early detection for prevention and treatment of the disease is essential.
Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low-parasitaemia samples
Authors: Shah Zalak , Adams Matthew , Moser Kara A , Shrestha Biraj , Stucke Emily M , Laufer Miriam K , Serre David , Silva Joana C , Takala-Harrison Shannon 
Published: March 2020

Abstract
Background
Owing to the large amount of host DNA in clinical samples, generation of high-quality Plasmodium falciparum whole genome sequencing (WGS) data requires enrichment for parasite DNA. Enrichment is often achieved by leukocyte depletion of infected blood prior to storage. However, leukocyte depletion is difficult in low-resource settings and limits analysis to prospectively-collected samples. As a result, approaches such as selective whole genome amplification (sWGA) are being used to enrich for parasite DNA. However, sWGA has had limited success in generating reliable sequencing data from low parasitaemia samples. In this study, enzymatic digestion with MspJI prior to sWGA and whole genome sequencing was evaluated to determine whether this approach improved genome coverage compared to sWGA alone. The potential of sWGA to cause amplification bias in polyclonal infections was also examined.
Methods
DNA extracted from laboratory-created dried blood spots was treated with a modification-dependent restriction endonuclease, MspJI, and filtered via vacuum filtration. Samples were then selectively amplified using a previously reported sWGA protocol and subjected to WGS. Genome coverage statistics were compared between the optimized sWGA approach and the previously reported sWGA approach performed in parallel. Differential amplification by sWGA was assessed by comparing WGS data generated from lab-created mixtures of parasite isolates, from the same geographical region, generated with or without sWGA.
Results
MspJI digestion did not enrich for parasite DNA. Samples that underwent vacuum filtration (without MspJI digestion) prior to sWGA had the highest parasite DNA concentration and displayed greater genome coverage compared to MspJI+sWGA and sWGA alone, particularly for low parasitaemia samples. The optimized sWGA (filtration + sWGA) approach was successfully used to generate WGS data from 218 non-leukocyte depleted field samples from Malawi. Sequences from lab-created mixtures of parasites did not show evidence of differential amplification of parasite strains compared to directly sequenced samples.
Conclusion
This optimized sWGA approach is a reliable method to obtain WGS data from non-leukocyte depleted, low parasitaemia samples. The absence of amplification bias in data generated from mixtures of isolates from the same geographic region suggests that this approach can be appropriately used for molecular epidemiological studies.
Keywords Plasmodium falciparum , malaria, whole genome sequencing, selective whole genome amplification, vacuum filtration
Integrative expression network analysis of microRNA and gene isoforms in sacred lotus
Authors: Zhang Yue , Rahmani Razgar Seyed , Yang Xingyu , Chen Jinming , Shi Tao 
Published: March 2020

Abstract
Background
Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus ( Nelumbo nucifera ), an economically important flowering plant.
Results
Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets, and tend to be tissue-specific. Further, our results showed that frequent interactions between miRNAs and hub gene isoforms highlight the critical roles of miRNAs in the gene network. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes.
Conclusions
Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.
Ethylene glycol and glycolic acid production from xylonic acid by Enterobacter cloacae
Authors: Zhang Zhongxi , Yang Yang , Wang Yike , Gu Jinjie , Lu Xiyang , Liao Xianyan , Shi Jiping , Kim Chulho , Lye Gary , Baganz Frank , Hao Jian 
Published: March 2020

Abstract
Background: Biological routes for ethylene glycol production have been developed in recent years by constructing the synthesis pathways in different microorganisms. However, no microorganisms have been reported yet to produce ethylene glycol naturally. Results: Xylonic acid utilizing microorganisms were screened from natural environments, and an Enterobacter cloacae strain was isolated. The major metabolites of this strain were ethylene glycol and glycolic acid. However, the metabolites were switched to 2,3-butanediol, acetoin or acetic acid when this strain was cultured with other carbon sources. The metabolic pathway of ethylene glycol and glycolic acid synthesis from xylonic acid in this bacterium was identified. Xylonic acid was converted to 2-dehydro-3-deoxy-D-pentonate catalyzed by D-xylonic acid dehydratase. 2-Dehydro-3-deoxy-D-pentonate was converted to form pyruvate and glycolaldehyde, and this reaction was catalyzed by an aldolase. D-xylonic acid dehydratase and 2-dehydro-3-deoxy-D-pentonate aldolase were encoded by yjhG and yjhH, respectively. The two genes are part of the same operon and are located adjacent on the chromosome. Besides yjhG and yjhH, this operon contains four other genes. However, individually inactivation of these four genes had no effect on either ethylene glycol or glycolic acid production; both formed from glycolaldehyde. YqhD exhibits ethylene glycol dehydrogenase activity in vitro. However, a low level of ethylene glycol was still synthesized by E. cloacae ΔyqhD. Fermentation parameters for ethylene glycol and glycolic acid production by the E. cloacae strain were optimized, and aerobic cultivation at neutral pH were found to be optimal. In fed batch culture, 34 g/L of ethylene glycol and 13 g/L of glycolic acid were produced in 46 hours, with a total conversion ratio of 0.99 mol/mol xylonic acid.Conclusions: A novel route of xylose biorefinery via xylonic acid as an intermediate has been established.
No evidence for amyloid pathology as a key mediator of neurodegeneration post-stroke - a seven year follow-up study
Authors: Hagberg Guri , Ihle-Hansen Hege , Fure Brynjar , Thommessen Bente , Ihle-Hansen Håkon , Øksengård Anne Rita , Beyer Mona K. , Wyller  , Müller Ebba Gløersen , Pendlebury Sarah T. , Selnes Per 
Published: March 2020

Abstract
Background Cognitive impairment (CI) with mixed vascular and neurodegenerative pathologies after stroke is common. The role of amyloid pathology in post-stroke CI is unclear. We hypothesize that amyloid deposition, measured with Flutemetamol ( 18 F-Flut) positron emission tomography (PET), is common in 7-year stroke survivors diagnosed with CI and, further, that quantitatively assessed 18 F-Flut-PET uptake after seven years correlates with amyloid-β peptide (Aβ 42 ) levels in cerebrospinal fluid (CSF) at one year, and with measures of neurodegeneration and cognition at seven years post-stroke. Methods 208 patients with first-ever stroke or TIA without pre-existing CI were included during 2007 and 2008. At one- and seven-years post-stroke, cognitive status was assessed, and categorized into dementia, mild cognitive impairment or none. Etiologic sub-classification was based on magnetic resonance imaging (MRI) findings, CSF biomarkers and clinical cognitive profile. At seven years, patients were offered 18 F-Flut-PET, and amyloid-positivity was assessed visually and semi-quantitatively. The associations between 18 F-Flut-PET standardized uptake value ratios (SUVr) and measures of neurodegeneration (medial temporal lobe atrophy (MTLA), global cortical atrophy (GCA)) and cognition (Mini-Mental State Exam (MMSE), Trail-making test A (TMT-A)) and CSF Aβ 42 levels were assessed using linear regression. Results In all, 111 patients completed 7-year follow-up, and 26 patients agreed to PET imaging, of whom 13 had CSF biomarkers from one year. Thirteen out of 26 patients were diagnosed with CI seven years post-stroke, but only one had visually assessed amyloid positivity. CSF Aβ 42 levels at one year, MTA grade, GCA scale, MMSE score or TMT-A at seven years did not correlate with 18 F-Flut-PET SUVr in this cohort. Conclusions Amyloid binding were not common in 7-year stroke survivors diagnosed with CI. Quantitatively assessed amyloid did not correlate with other measures related to neurodegeneration and cognition. Therefore amyloid pathology may not be a key mediator of neurodegeneration seven years post-stroke.
Expression of VEGF-C and its association with clinicopathological features among patients with gastric cancer undergoing gastric surgery at Tongji medical hospital, China.
Authors: MAWALLA BRIAN , Luo Xiaoxiao , Xianglin Yuan 
Published: March 2020

Abstract
Objectives: Gastric cancer shows epidemiological variability according to geographic locations, these differences have been demonstrated both regionally and within countries. There is no baseline protocol regarding using VEGF-C as tumor marker in local setting therefore it was necessary to conduct this study, the current study conducted to analyze the correlation exists between VEGF-C and clinicopathological parameters in patients with gastric cancer undergoing a surgical procedure at Tongji medical hospital. Results: 161samples analyzed were from Chinese patients who had undergone either palliative or curative surgical procedure between October 2015 and September 2017 at Tongji medical hospital. I mmunohistochemistry was method was used to analyses presence of VEGF-C in tissues. Among 161 gastric cancer patients, 101 (62.7%) gastric samples showed strong VEGF-C expression and 60 (37.3%) gastric samples showed weak VEGF-C expression. Using multivariate logistic regression analysis, tumor grade, invasion of lymph nodes and TNM staging were statistically significantly found to associate with strong expression of VEGF-C. VEGF-C strong expression was significantly seen more in adenocarcinoma of gastric cancer, and Therefore, VEGF-C may be used as a biological marker for assessing the biological characteristics of gastric.
Unraveling the Molecular Heterogeneity in type 2 Diabetes: A Potential Subtype Discovery Study Followed by Metabolic Modeling
Authors: Khoshnejat Maryam , Kavousi Kaveh , Moghaddam Ali Mohammad Banaei , Moosavi-Movahedi Ali Akbar 
Published: March 2020

Abstract
Background: Type 2 diabetes mellitus (T2DM) is a complex multifactorial disease with a high prevalence in the world. Insulin resistance and impaired insulin secretion are the two major abnormalities in the pathogenesis of T2DM. Skeletal muscle is responsible for over 75% of the glucose uptake thus plays a critical role in T2DM. Here, we attempt to provide a better understanding of abnormalities in this tissue. Methods: We have explored the muscle gene expression pattern in healthy and newly-diagnosed T2DM individuals using supervised and unsupervised classification along with the discovery of potential subtypes of type 2 diabetes. Results: A machine-learning technique applied to identify a pattern of gene expression that could potentially discriminates between normoglycemic and diabetic groups. A gene set comprises of 26 genes identified which was able to discriminate healthy from diabetic individuals with the 94% accuracy after 10-fold stratified cross-validation. In addition, three distinct potential subtypes with different dysregulated genes and metabolic pathways identified in diabetic patients. Conclusion: This study implies that it seems the disease has triggered through different cellular/molecular mechanisms. Therefore, subtyping of T2DM patients in combination with real clinical profiles of patients will provide a better understanding of abnormalities in each group and lead to the recommendation of the appropriate precision therapy for each subtype in the future.
Hospitalization and Definitive Radiotherapy in Lung Cancer: Incidence, Risk Factors and Survival Impact
Authors: Hazell Sarah Z. , Mai Nicholas , Fu Wei , Hu Chen , Friedes Cole , Negron Alex , Voong Khinh Ranh , Feliciano Josephine L. , Han Peijin , Myers Samantha , McNutt Todd R. , Hales Russell K. 
Published: March 2020

Abstract
Background: Unplanned hospitalization during cancer treatment is costly, can disrupt treatment, and affect patient quality of life. However, incidence and risks factors for hospitalization during lung cancer radiotherapy are not well characterized. Methods: Patients treated with definitive intent radiation (≥45 Gy) for lung cancer between 2008 and 2018 at a tertiary academic institution were identified. In addition to patient, tumor, and treatment related characteristics, specific baseline frailty markers (Charlson comorbidity index, ECOG, patient reported weight loss, BMI, hemoglobin, creatinine, albumin) were recorded. All cancer-related hospitalizations during or within 30 days of completing radiation were identified. Associations between baseline variables and any hospitalization, number of hospitalizations, and overall survival were identified using multivariable linear regression and multivariable Cox proportional-hazards models, respectively. Results: Of 270 patients included: median age was 66.6 years (31-88), 50.4% of patients were male (n=136), 62% were Caucasian (n=168). Cancer-related hospitalization incidence was 17% (n=47), of which 21% of patients hospitalized (n=10/47) had >1 hospitalization. On multivariable analysis, each 1 g/dL baseline drop in albumin was associated with a 2.4 times higher risk of any hospitalization (95% confidence interval (CI) 1.2-5.0, P =0.01), and baseline hemoglobin ≤10 was associated with, on average, 2.7 more hospitalizations than having pre-treatment hemoglobin >10 (95% CI 1.3-5.4, P =0.01). After controlling for baseline variables, cancer-related hospitalization was associated with 1.8 times increased risk of all-cause death (95% CI: 1.02-3.1, P =0.04).Conclusions: Our data show baseline factors can predict those who may be at increased risk for hospitalization, which was independently associated with increased mortality. Taken together, these data support the need for developing further studies aimed at early and aggressive interventions to decrease hospitalizations during treatment.
Effect of the Short-Segment Internal Fixation with Intermediate Inclined-Angle polyaxial Screw at the Fractured Vertebrae on the Treatment of Denis type B Thoracolumbar Fracture
Authors: Xiong Chengjie , Huang Biwang , Wei Tanjun , Kang Hui , Xu Feng 
Published: March 2020

Abstract
Backgroud Short-segment internal fixation with straight-forward monoaxial screw (SSIF-SFM) and long-segment internal fixation (LSIF) are two major surgical options for thoracolumbar (TL) fracture, however, limitations of both surgical options l are obvious. SSIF with inclined-angle polyxial screw (SSIF-IAP) have been developed to take advantage of their benefits and minimize their adverse effects . Methods 69 consecutive patients (47 males and 22 females; average 34.5 years ) who met the criteria for inclusion were enrolled in this study . Sagittal Cobb’s angle (SCA), anterior vertebral body height (AVBH), vertebral body index (VBI) and spinal canal encroachment (SCE) were measured and assessed . Functional recovery Visual Analogue Scale (VAS) and Oswestry disability index (ODI) were also evaluated. Results The value of incision length, mean blood loss, duration of operation and hospital stay in the SSIF–IAP group and SSIF-SFM group were significantly lower than those in the LSIF group. The AVBH and VBI in the SSIF–IA P group and LSIF group were significantly more improved than those in the SSIF–SFM group at 6 months and the latest follow-ups (p < 0.05). The correction losses of AVBH and VBI ( calculated by the reduction of AVBH and VBI) in the SSIF-IAP group and LSIF group were also significantly lower than those in the SSIF–SFM group at 6 months and the latest follow-ups (P<0.05). There was no significant difference of SCE among three groups. The VAS and ODI in the SSIF–IAP group and SSIF-SFM group were significantly lower than those in the LSIF group at 6 months and the latest follow-ups (P<0.05). Conclusion SSIF-IAP can achieve comparable treatment outcomes compared with LSIF, but it was less invasive compared with LSIF . The SSIF–IA was an effective and reliable operative technique for patients with Denis type B TL fracture.
Combined ANN/ EVOP Factorial Design Approach for Media Screening for Cost-effective Production of Alkaline Proteases from Rhizopus oryzae (SN5) / NCIM-1447 under SSF
Authors: Negi Sangeeta , Jain Sapna , Kumar Anand 
Published: March 2020

Abstract
In order to achieve high yield of fungal protease in a very cost effective way and to meet its increased market demand, current study deals with the screening of various agro-wastes as carbon source for the production of protease from Rhizopus oryzae (SN5) / NCIM-1447 under solid state fermentation. Substrates and culture parameters such as wheat bran, soybean meal, black-gram husk, rice husk, mixture of wheat bran, soybean meal, nitrogen sources, pH, temperature and incubation time were first optimized with one factor at time strategy and then EVOP factorial and yield of alkaline protease was achieved 412.8 U/gds at 28 o C and pH=6 after 72 hours of fermentation taking wheat bran and soybean as a substrate in 4:1 ratio. Further Artificial Neural Networks (ANN), was trained with data of EVOP and yield of protease was enhanced up to 422.6 U/gds with wheat bran: soyabean in ratio of 70:30, pH 6.2 at 30°C. The evolved process and Rhizopus oryzae (SN5)/ NCIM-1447 strain would be promising for protease production at industrial scale at low cost.