Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of orthologous gene clusters among Aspergillus species

Orthologs or orthologous genes are clusters of genes in different species that originated by vertical descent from a single gene in the last common ancestor. To study the orthologous genes among different Aspergillus isolates we carried out whole genome sequencing of most aflatoxigenic A. flavus JAU2 and highly potent biocontrol atoxigenic A. flavus NRRL 21882. The protein gene FASTA file containing 14414 predicted protein sequences for AF JAU2 and 10154 for AF NRRL 21882 were used to predict the orthologous gene clusters among six species of Aspergillus viz A. oryzae, A. clavatus, A. flavus, A. niger, A. flavus JAU2 and A. flavus NRRL 21882. The analysis showed 12902 clusters based on the protein sequences from the 6 species. The numbers in the Venn diagram represent the number of orthologous clusters that AF JAU2 and AF NRRL 21882 shares with the four other species. All six species shared 5159 clusters and 210 clusters were found unique in all six species. The diagram showed that 5159 gene clusters were shared by all six species, suggesting their conservation in the lineage after speciation. The unique clusters were also found 41 in AF JAU2, two in AF NRRL 21882 and A. flavus, 115 in A. niger, 24 in A. clavatus and 21 in A. oryzae. So highest numbers of 115 unique genes were present in A. niger and only two unique gene clusters were present in AF NRRL 21882 and A. flavus. All A. flavus isolates viz. AF JAU2, AF NRRL 21882 and A. flavus shared 271 gene clusters whereas AF JAU2 and AF NRRL 21882 shared 109 orthologous genes.
Complexity as Integration: Pastoral Mobility and Community Building in Ancient Mongolia

The question of complex socio-political organization among pastoral nomadic groups has long posed a theoretical challenge for anthropologists, historians, and archaeologists alike. The problems arise from a disciplinary tendency to view pastoralists within a narrow economic and ecological framework but, in addition to this, the basic conception of ‘complexity’ has itself proven problematic. The definitions of complexity built originally upon systems theory and political economy place emphasis on organizational criteria derived primarily from sedentary societies with class stratification, intensive subsistence economies, and centralized administration. In this paper we argue that these classic definitions of complexity have not provided a good fit for analyzing the kinds of political organizations constructed by pastoral nomads of the Eurasian steppe zone. For that reason, we explore new ways of conceptualizing complex organization based on processes of integration, scale, and mobility. This approach offers a better explanation for material patterns documented across two neighboring valleys in northern Mongolia and provides substantial insight to the sub-regional polities preceding the rise of the Xiongnu state during the late first millennium BCE. Social Evolution & History / September 2019 56
Smoking and risk of sleep-related issues: a systematic review and meta-analysis of prospective studies

Objectives Smoking has many deleterious consequences on health, one of which can be sleep-related issues. Therefore, a meta-analysis was performed with the aim of pooling results from studies on the relationship between smoking and sleep-related issues. Methods The present study follows PRISMA guidelines. Databases were searched by both researchers to find the articles. The review was done up to December 2018. In order to analyze the results of the screened articles, statistical indexes were converted to logarithms and the studies were combined with each other. Finally, several analyses were conducted with respect to various subgroups. In the subgroup analysis, the pool index of the studies was determined and the degree of heterogeneity in each subgroup was presented. Meta-regression was also used. Results Smoking is associated with a risk of developing sleep-related issues. Risk ratio (1.47; 1.20–1.79) for smokers was higher than for non-smokers. Egger’s test and Begg’s test indicated publication bias. Conclusions Smoking is associated with sleep-related issues. Informing smokers about the effects of smoking on sleep issues can be effective in reducing and preventing its consequences. Objectifs Le tabagisme a de nombreuses conséquences délétères sur la santé, et les problèmes liés au sommeil peuvent en faire partie. Nous avons effectué une méta-analyse en vue de regrouper les résultats d’études sur la relation entre le tabagisme et les problèmes liés au sommeil. Méthode Notre étude suit les lignes directrices PRISMA. Les deux chercheurs ont interrogé des bases de données pour trouver les articles. La revue a été menée jusqu’en décembre 2018. Pour analyser les résultats des articles filtrés, des indices statistiques ont été convertis en logarithmes, et les études ont été combinées entre elles. Enfin, plusieurs analyses ont été effectuées pour divers sous-groupes. Dans les analyses des sous-groupes, nous avons déterminé l’indice des études regroupées et présenté le degré d’hétérogénéité dans chaque sous-groupe. Nous avons aussi utilisé la méta-régression. Résultats Le tabagisme est associé à un risque de contracter des problèmes liés au sommeil. Le risque relatif (1,47; 1,20-1,79) des fumeurs était supérieur à celui des non-fumeurs. Le test d’Egger et le test de Begg ont montré un biais de publication. Conclusions Le tabagisme est associé à des problèmes liés au sommeil. Informer les fumeurs des effets du tabagisme sur les problèmes de sommeil peut être un moyen efficace d’en réduire et d’en prévenir les conséquences.
Pediatric neurourology : Urodynamics II

Children with voiding disturbances and neuropathic bladders present challenges to the practicing urologist. The clinical and radiologic evaluation of these patients occasionally can be difficult and the indications for urodynamic investigation are often perplexing. This article describes the clinical and radiologic evaluation of the child with abnormal bladder function and discusses contemporary urodynamic studies used in children.
Medical and Surgical Management of Pediatric Pneumonia

The participant will be able to: • describe diagnostic evaluation and admission criteria for infants and children presenting with clinical features of pneumonia • describe antibiotic strategies to treat community and nosocomial pneumonias in children • describe the various operative approaches in the management of empyema • list the indications for tube thoracostomy in children presenting with empyema • discuss the indication for fibrinolytic therapy and at least one suggested treatment algorithm • describe clinical significant and measureable treatment outcomes in this patient population Case Study
Pathogenic mechanisms in microvillus inclusion disease

Eten is de gewoonste zaak van de wereld. Dit geldt niet voor kinderen met microvillusinclusieziekte (afgekort met MVID). MVID is een zeer zeldzame en ernstige aangeboren darmafwijking waardoor opname van voeding via de darmen onmogelijk is en wat leidt tot aanhoudende diarree en uitdroging. Zonder behandeling sterven de kinderen kort na de geboorte. De prognose is afhankelijk van levenslange intraveneuze voeding en uiteindelijke darmtransplantatie. Recent zijn mutaties in het MYO5B gen geidentificeerd als onderliggende genetische oorzaak van MVID. Ieder kind/ familie met MVID heeft unieke MYO5B mutaties. Ondanks de identificatie van het defecte gen is het onbekend hoe het genetisch defect leidt tot de ziekte en is er nog geen genezing mogelijk. In dit promotieonderzoek wordt in detail het cellulaire en moleculaire mechanisme ontrafeld via welk het verlies van MYO5B functie leidt tot afwijkingen in de opbouw van de cellen in de darmwand. Het door het MYO5B gen gecodeerde eiwit myosine Vb blijkt een sleutelrol te spelen in het organiseren van de infrastructuur binnen de darmcel. De ontregelde infrastructuur in de darmcellen van kinderen met MVID leidt tot een afname van het beschikbare celoppervlak waar voedingsstoffen worden opgenomen, en voorkomt dat de in de darmcel aangemaakte enzymen die voor de vertering van voedingsstoffen nodig zijn het celoppervlak kunnen bereiken. Deze nieuwe inzichten in de ontstaanswijze van MVID, tesamen met het opgerichtte internationale online MVID patientenregister en database van MYO5B gen mutaties, is een belangrijke stap op weg naar effectievere behandelingen voor deze ernstige ziekte
Detection of embB Gene Mutations in EMB-Resistant Mycobacterium tuberculosis Isolates From Isfahan Province by PCR-SSCP and Direct Sequencing

Background: Ethambutol (EMB) is the ﬁrst-line drug used for the treatment of tuberculosis. Recent reports on the EMB-resistant isolatesof Mycobacteriumtuberculosis indiﬀerentgeographicalregionsof theworldhaverevealedtheEMBresistancepatternsof M. tuberculosis and mutations in the embB gene. Objectives: In this study, we determined the emb locus in sensitive and resistant Iranian M. tuberculosis isolates using two eﬀective methods for the detection of point mutation, i.e., single-strand conformational polymorphism (SSCP) and direct sequencing. Methods: Thirty-two M.tuberculosis isolatesfromthe Isfahantuberculosiscenterwerecharacterizedby conventionalmethodsand speciﬁc ampliﬁcation of the regions of diﬀerence ( rd ) gene and internal transcribed spacer ( its ) gene. Observing standard opera-tionalprocedures, EMBsusceptibilitytestswereperformedontheLJmediumusingtheproportionmethodwith2, 5, and10 µ g/mL concentrations. PCR-SSCP and direct sequencing were used to detect diﬀerent kinds of mutation in the embB gene with precision. Results: In a total of 32 isolates, two isolates (6.25%) were found to be resistant to EMB in 2, 5, and 10 µ g/mL concentrations. Single-strand conformational polymorphism showed altered mobility with triple bands in the resistant isolates and double bands in the sensitive isolates. In the two EMB-resistant cases, mutation was found to occur codons 309and 299. Conclusions: We concluded from the results that the frequency of EMB-resistant M. tuberculosis cases in Iran is lower than that of many other regions. The PCR-SSCP technique can separate resistant isolates from sensitive isolates. The sequencing results of this study showed mutation in codons 309 and 299 of the embB gene. In none of the resistant isolates, mutation was observed in codon 306. FurtherstudiesarerequiredtodetermineotherpointmutationsandanalyzeothergeneticlociassociatedwithEMBresistance in M. tuberculosis isolates in Iran.
TRAFFIC SIGN RECOGNITION AND CLASSIFICATION USING CONVOLUTIONAL NEURAL NETWORKS

: The traffic signs engraved on the roads these days enhance traffic safety by informing the driver of speed limits or any further possible dangers such as deep curvy roads, imminent repair road works or any pedestrian crossings. This paper covers three-stage the real-time Traffic Sign Recognition and classification system, which consists of image segmentation, detecting the traffic sign and a classification phase based on the input image. To extract red regions in the image the colour enhancement technique is used. The detection, classification and recognition are performed using Convolutional Neural Networks (CNN) to identify the content of the traffic signs found.
SOME CARDIOPROTECTIVE EFFECTS OF AQUEOUS EXTRACT OF GINGER AGAINST MONOSODIUM GLUTAMATE INDUCED TOXICITY IN THE HEART OF ADULT WISTAR RATS

Research findings have indicated cardiovascular disease (CVD) to be the major morbidity and mortality in adult man.The protective effect of ginger extract against Monosodium Glutamateinduced cardiotoxicity was evaluated in 48 wistar rats (weighing 150-250 g) classified into 6 groups (8 rats per group). The rats in control group (Group A) received distilled water for 21 successive days. The rats in treated (Group B) were treated with 4g/kg/day of MSG orally for 21 successive days, rats in treated group (Group C) were treated with 1g/kg/day of ginger extract orally for 21 successive days, rats in treated group (Group D) received 2g/kg/day of ginger extract orally for 21 successive days, rats in treated group (Group E) received 4g/kg/day of MSG and 1g/kg/day of ginger extract orally for 21 successive days, rats in treated group (Group F) received 4g/kg/day of MSG and 2g/kg/day of ginger extract orally for 21 successive days. Results show that MSG administration resulted in changes in body weight, significant increase in the levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP) and distortions to cardiac tissue as compared to rats treated with ginger extract. The cardiac tissues of the aqueous Gingertreated rats showed preserved tissue compared with distorted cardiac in MSG –treated rats. Ginger extract improves the histological changes by induced by MSG in the cardiac muscle cells in comparison with the control. The study concluded that, ginger extract when used concomitantly with MSG protects the heart against the toxicity induced by this flavour enhancer.
Harnessing Advances in Rice Genetics and Genomics For Unraveling Genes and QTLs Governing Yield and Yield Components For Developing Designer Rice

Rice (Oryza sativa L.) accounts for over 21 per cent of global calorie intake and in order feed the projected population of 9 billion people in 2050, rice yields have to be increased by 50%. Traditional breeding methods including exploitation of plant type concept and heterosis have been successful in recombining genes or alleles and exploiting their interactions which have contributed to yield gains to achieve food sufficiency in the present world. But rice researchers face a Herculean challenge of improving rice yields per unit area in view of the constraints imposed by changing climate, shrinking land and water resources. Grain yield in rice is a polygenic trait which is highly influenced by environmental factors as well and therefore, rice research over the decades have focused on gaining an understanding on the basis of yield and yield components. The availability of the high quality genome sequence coupled with advances in technological tools, enormous genetic and genomic resources have been made available in rice to accelerate the isolation of agronomically important QTLs or genes governing complex traits such as yield. The present paper focuses on the progress made in mapping QTLs for yield and yield component traits in rice through the development of an array of different mapping populations employing conventional linkage mapping strategy and discusses novel approaches for discovery of new genes and QTLs for yield, mining favourable alleles and designing rice with higher per unit productivity through integration of next generation high throughput genomics and phenomics technologies with rice breeding.
Non-Financial Performance Indicators and Operational Efficiency of Deposit Money Banks in Nigeria

This study examined the effect of non-financial performance indicators, based on balanced scorecard model, on operational efficiency of Deposit Money Banks (DMBs) in Nigeria with a view of evaluating the impact of the drivers of operational efficiency. Emphasis, from prior studies, on measuring operational efficiency have been on financial performance indicators with little or no consideration for the contributions of non-financial performance indicators (NFPIs) that drive the financial indicators. The study adopted a descriptive survey research design and a structured questionnaire was administered on sampled employees of the DMBs. Data collected were analysed with the mean of descriptive and inferential statistics. The study found out that internal control and business process, customer satisfaction and learning and growth of employees individually have significant effect on operational efficiency of DMBs in Nigeria. The study concluded that NFPIs have positive relationship with, have significant effect on operational efficiency of DMBs in Nigeria and explain about 56.9% variations in operational efficiency. The study contributed to literature on significance of NFPIs and recommended that DMBs should develop objective matrices to measure individual non-financial performance indicators that tend to contribute to their operational efficiency. KeywordsBalanced scorecard; Financial performance indicators; Internal control and business process; Customer satisfaction; Learning and growth of employees
Simulation of the Interlocking Capacity of the Modified Hip Implant Surface

During hip replacement procedure femoral head is removed and instead of it implant is inserted into the hollow femur. When an implant is inserted into the fractured bone the healing process starts to happen, which means that the newly formed bone interlocks with the inserted implant. Interlocking capacity is commonly analyzed using in vivo experiments, and only several papers have information on numerical approach. The goal of this study was to use the numerical approach to analyze the interlocking capacity of the modified hip implant surface. Numerical approach included implementation of the finite element method (FEM) for simulation of the interlocking capacity of modified surface topographies in the titanium alloys (Ti-6Al-4V) implants. Analyzed topographies were produced by the electron beam (EB) technique on the surface of the titanium alloy. The structures were analyzed by infinite focus microscopy and exported as a 3D profile for the application of the finite element method. The biggest advantage of this approach is that it can provide information about different types of topographies under a wide range of loading conditions before needing to insert an implant into an animal.
Antibacterial activity of newly synthesized endodontic nanomaterial based on calcium aluminate

Introduction Materials used for root canal obturation and root perforation are expected to have, in addition to preventing apical, lateral and coronary leakage, antimicrobial effects on microorganisms that are not accessible to chemomechanical instrumentation and intra-canal medications. The aim of this study was to evaluate the antimicrobial effect of a novel calcium aluminate-based endodontic nanostructured biomaterial (ALBO-MCCA) using agar diffusion test. Material and methods the two materials were tested in the study. The nanostructured calcium aluminate was synthesized by the hydrothermal sol-gel method from individual components of calcium aluminate (CaOxAl2 O3 ), calcite (CaCO3 ) and barium sulfate (BaSO4 ) as radiocontrast agent in the ratio of 2:2:1 according to V. Jokanovic's recipe. The other used material was calcium silicate MTA Angelus (Londrina, Brazil). The antimicrobial effect was assessed using agar diffusion test. Standard strains of Enterococcus faecalis, Escherichia coli, Staphylococcus aureus, cultured on blood Mueller-Hinton agar and Candida albicans cultivated on Sabouraud Dextrose Agar, were used as test microorganisms. Results the best antimicrobial effect after 24 h both materials showed against S. aureus. The mean values of the growth inhibition zone for ALBO MCCA were 5.7 ± 0.25 mm and MTA 6.2 ± 0.4 mm. The ALBO MCCA material showed slightly stronger antibacterial effect against E. coli compared to MTA (p < 0.05), whereas none of the materials showed antibacterial effect against E. faecalis. Conclusion the ALBO MCCA material showed certain antibacterial effect on Escherichia coli, Staphylococcus aureus and Candida albicans that was comparable to antibacterial effect of MTA.
Arterial Hypertension in Children with Chronic Kidney Diseases

Arrterial hypertension (HTN) is one of the most common sequelae of chronic kidney disease (CKD) in children. In children with chronic kidney disease (CKD) HTN is several times higher than in the general pediatric population. With progression of CKD, HTN increases, reaching 45-60% in dialysis patients. The regulation of hypertension in children is mandatory in the treatment of CKD due to the fact that hypertension is often goes unrecognized, insufficiently controlled and often masked. The etiology of hypertension is different depending on the age of diagnosis. In newborns and young children, hypertension occurs due to renovascular diseases such as renal venous thrombosis, renal artery stenosis and other renal parenchymal diseases. HTN is considered a marker for disease severity in CKD and is a risk factor for accelerated deterioration of kidney function as well as for cardiovascular disease. Activation of the renin–angiotensin–aldosterone system plays a pivotal role in renal hypertension. Оbesity and hyperuricemia are the risk factors for HTN in CKD in children and lead to the progression of CKD. HTN-induced target organ damage (TOD) manifests as microalbuminuria/proteinuria, retinopathy, increase in intima media thickness, atherosclerosis, reduced arterial compliance, cognitive impairment, and left ventricular hypertrophy (LVH). In adults and children with CKD, ABPM has been found to be superior than causal blood pressure to diagnose hypertension and to monitor adequacy of treatment. The main drug therapy used in children with HTN and CKD consists of ACE inhibitors. Strict BP control and limitation of proteinuria with ACE inhibitors and angiotensin receptor blockers (ARB) can slow the progression of CKD.
University of Birmingham Tumour hypoxia causes DNA hypermethylation by reducing TET activity

Citation for published version (Harvard): Thienpont, B, Steinbacher, J, Zhao, H, D'Anna, F, Kuchnio, A, Ploumakis, A, Ghesquière, B, Van Dyck, L, Boeckx, B, Schoonjans, L, Hermans, E, Amant, F, Kristensen, VN, Koh, KP, Mazzone, M, Coleman, ML, Carell, T, Carmeliet, P & Lambrechts, D 2016, 'Tumour hypoxia causes DNA hypermethylation by reducing TET activity', Nature, vol. 537, no. 7618, pp. 63-68. https://doi.org/10.1038/nature19081
Prediction of probable impact of miR-34a and miR-215 on differentiation of naive CD4+ T cells to Th17 cells in multiple sclerosis

Background and aims: miRNAs, as a class of non-coding RNAs, take part in different cellular processes. Dysregulation of different miRNAs has been reported in numerous disorders to date. Multiple sclerosis (MS) is an autoimmune disease with high prevalence in Iran and Th17 cells play an important role in its pathogenesis. In the current study, we aimed to predict the possible role of miR-34a and miR-215 in the process of controlling Th17 differentiation, and hence, their possible impact on the onset and progression of MS. Methods: We investigated probable interactions of miRNAs and genes that participate in Th17 cells differentiation using miRwalk database as an integrative one which utilizes 10 different algorithms to predict miRNA-mRNA interaction. Results: Based on our findings, miR-34a and miR-215 were predicted to have a potential role in the induction of Th17 cells differentiation. Conclusion: Conclusively, miR-34a and miR-215 may up-regulate Th17 cells of MS patients. Since bioinformatics data have shown that these miRNAs suppress negative regulatory genes in Th17 cells differentiation, we suppose that down-regulation of these miRNAs could ameliorate MS symptoms. Therefore, several therapeutic approaches may be considered for these miRNAs besides their application as valuable prognostic/diagnostic biomarkers in detection of various stages of MS.