Miracle-dz/UniFAR-FTUs huggingface dataset:
Homing of a bacterial group II intron with an intron‐encoded protein lacking a recognizable endonuclease domain

RmInt1 is a functional group II intron found in Sinorhizobium meliloti where it interrupts a group of IS elements of the IS630‐Tc1 family. In contrast to many other group II introns, the intron‐encoded protein (IEP) of RmInt1 lacks the characteristic conserved part of the Zn domain associated with the IEP endonuclease activity. Nevertheless, in this study, we show that RmInt1 is capable of inserting into a vector containing the DNA spanning the RmInt1 target site from the genome of S. meliloti. Efficient homing was also observed in the absence of homologous recombination (RecA− strains). In addition, it is shown that RmInt1 is able to move to its target in a heterologous host (S. medicae). Homing of RmInt1 occurs very efficiently upon DNA target uptake (conjugation/electroporation) by the host cell resulting in a proportion of invaded target of 11–30%. Afterwards, the remaining intronless target DNA is protected from intron invasion.
Comparison of three sources of inocula for predicting apparent digestibility of ruminant feedstuffs

In the present study, gas production of three sources of inocula rumen liquor from fis- tulated sheep, rumen liquor from slaughtered cattle, and a suspension of sheep faeces, were evaluated to predict the apparent digestibility of ruminant feedstuffs. The highest gas production was obtained with rumen liquor from slaughtered cattle, and the lowest ( P 0.05). gas production / sources of inocula / in vivo digestibility / alternative methods
Game Analysis of Institutional Investors Participating in Corporate Governance

By building a game model between the institutional investors and the management, an analysis has been conducted to uncover the influential factors that are crucial to the role switching of institutional investors when confronting tunneling behaviors of the management: supervision cost, shareholding ratio, invisible income, fines and patience. In cases of lower supervision cost, higher shareholding ratios, less invisible income, larger amount of fines, more patience and pursuing long-term gains, institutional investors will tend to play an active role in corporate governance. They will act as an active supervisor to restrain the tunneling behavior of the management.
Perceptions of teachers and Students on the Social Behaviour of Secondary School Students whose Parents Abuse Alcohol in Elgeyo-Marakwet County, Kenya

Alcohol abuse is one of the social issues in today’s society. Parents and social institutions like schools have the responsibility of socializing the young people but they have also fallen victims of alcohol abuse. The need to carry out this research arose from the fact that alcohol consumption, especially illicit alcohol, had affected the society as a whole, the family included. The study was carried out in Keiyo North, Elgeyo-Marakwet County. The objective of this paper was to establish the perceptions of teachers and students on parental alcohol abuse and the social behavior of the secondary school students whose parents abused alcohol. The study was based on the theory of Social Cognitive Learning by Albert Bandura. The theory argues that through observation and the use of cognitive processes people have the potential to learn certain behaviours from their environments. Concurrent triangulation mixed method research design involving qualitative and quantitative approaches was used. The target population of this study comprised of all the public secondary schools in Keiyo North sub-County. The sample comprised of 49 participants sampled from seven public schools. Stratified random sampling and purposive sampling were used to select the schools and participants respectively. The study utilized questionnaires and interviews to collect data. Quantitative data was analyzed using descriptive statistics while qualitative data was analyzed thematically. The findings showed that parental alcohol abuse was perceived as a contributor to the antisocial behaviour of the students in various ways such as students wanting to fight, aggression, isolation, poor grooming, taking of alcohol and involvement in pre-marital sex.
Discovery of emerging design patterns in ontologies using tree mining

The research goal of this work is to investigate modeling patterns that recur in ontologies. Such patterns may originate from certain design solutions, and they may possibly indicate emerging ontology design patterns. We describe our tree-mining method for identifying the emerging design patterns. The method works in two steps: (1) we transform the ontology axioms in a tree shape in order to find axiom patterns; and then, (2) we use association analysis to mine co-occuring axiom patterns in order to extract emerging design patterns. We conduct an experimental study on a set of 331 ontologies from the BioPortal repository. We show that recurring axiom patterns appear across all individual ontologies, as well as across the whole set. In individual ontologies, we find frequent and non-trivial patterns with and without variables. Some of the former patterns have more than 300,000 occurrences. The longest pattern without a variable discovered from the whole ontology set has size 12, and it appears in 14 ontologies. To the best of our knowledge, this is the first method for automatic discovery of emerging design patterns in ontologies. Finally, we demonstrate that we are able to automatically detect patterns, for which we have manually confirmed that they are fragments of ontology design patterns described in the literature. Since our method is not specific to particular ontologies, we conclude that we should be able to discover new, emerging design patterns for arbitrary ontology sets.
MULTI-OBJECTIVE OPTIMIZATION OF AN SRF PHOTOINJECTOR FOR ERL AND UED APPLICATION

Superconducting radio frequency (SRF) photoinjectors, running in continuous-wave (cw) mode, are able to generate electron beams of high average brightness and ultrashort bunches. Therefore, they satisfy the requirements of future accelerator facilities, such as energy recovery linacs (ERL). Further, SRF guns are able to provide relativistic probe beams for ultrafast electron diffraction (UED). Choosing suitable values for the drive laser, cavity and solenoid settings poses a great challenge for the injector commissioning and operation. Using multi-objective optimization based on an evolutionary algorithm, optimum gun parameter settings are extracted from Paretooptimum solutions. The development of a universal multiobjective optimization algorithm for SRF photoinjectors as well as first Pareto-optimum results for an ERL and UED application of GunLab, the compact SRF gun test facility at Helmholtz-Zentrum Berlin, are presented.
O-GlcNAcase Uses Substrate-assisted Catalysis

The post-translational modification of serine and threonine residues of nucleocytoplasmic proteins with 2-acetamido-2-deoxy-d-glucopyranose (GlcNAc) is a reversible process implicated in multiple cellular processes. The enzyme O-GlcNAcase catalyzes the cleavage of β-O-linked GlcNAc (O-GlcNAc) from modified proteins and is a member of the family 84 glycoside hydrolases. The family 20 β-hexosaminidases bear no apparent sequence similarity yet are functionally related to O-GlcNAcase because both enzymes cleave terminal GlcNAc residues from glycoconjugates. Lysosomal β-hexosaminidase is known to use substrate-assisted catalysis involving the 2-acetamido group of the substrate; however, the catalytic mechanism of human O-GlcNAcase is unknown. By using a series of 4-methylumbelliferyl 2-deoxy-2-N-fluoroacetyl-β-d-glucopyranoside substrates, Taft-like linear free energy analyses of these enzymes indicates that O-GlcNAcase uses a catalytic mechanism involving anchimeric assistance. Consistent with this proposal, 1,2-dideoxy-2′-methyl-α-d-glucopyranoso-[2,1-d]-Δ2′-thiazoline, an inhibitor that mimics the oxazoline intermediate proposed in the catalytic mechanism of family 20 glycoside hydrolases, is shown to act as a potent competitive inhibitor of both O-GlcNAcase (KII = 0.070 μm) and β-hexosaminidase (K = 0.070 μm). A series of 1,2-dideoxy-2′-methyl-α-d-glucopyranoso-[2,1-d]-Δ2′-thiazoline analogues were prepared, and one inhibitor demonstrated a remarkable 1500-fold selectivity for O-GlcNAcase (KI = 0.230 μm) over β-hexosaminidase (KI = 340 μm). These inhibitors are cell permeable and modulate the activity of O-GlcNAcase in tissue culture. Because both enzymes have vital roles in organismal health, these potent and selective inhibitors of O-GlcNAcase should prove useful in studying the role of this enzyme at the organismal level without generating a complex chemical phenotype stemming from concomitant inhibition of β-hexosaminidase.
A functional carbohydrate chip platform for analysis of carbohydrate–protein interaction

A carbohydrate chip based on glass or other transparent surfaces has been suggested as a potential tool for high-throughput analysis of carbohydrate–protein interactions. Here we proposed a facile, efficient, and cost-effective method whereby diverse carbohydrate types are modified in a single step and directly immobilized onto a glass surface, with retention of functional orientation. We modified various types of carbohydrates by reductive amination, in which reducing sugar groups were coupled with 4-(2-aminoethyl)aniline, which has di-amine groups at both ends. The modified carbohydrates were covalently attached to an amino-reactive NHS-activated glass surface by formation of stable amide bonds. This proposed method was applied for efficient construction of a carbohydrate microarray to analyze carbohydrate–protein interactions. The carbohydrate chip prepared using our method can be successfully used in diverse biomimetic studies of carbohydrates, including carbohydrate–biomolecule interactions, and carbohydrate sensor chip or microarray development for diagnosis and screening.
Indoor Air Quality in Portuguese Children Day Care Centers - ENVIRH Project

1 Instituto Nacional de Saude Dr. Ricardo Jorge IP, DSA, Portugal 2 Laboratorio Nacional de Engenharia Civil, Lisboa, Portugal 3 Departamento de Bioestatistica e Informatica, FCM UNL, CEAUL, Lisboa, Portugal 4 Centro de Investigacao do Centro Hospitalar de Lisboa Central, EPE, Lisboa, Portugal 5 Servico de Imunoalergologia, Hospital de Dona Estefânia, CHLC, EPE, Lisboa, Portugal 6 Centro de Estudos de Doencas Cronicas – CEDOC, Lisboa, Portugal 7 Departamento de Fisiopatologia, Faculdade de Ciencias Medicas da Universidade Nova de Lisboa, Portugal 8 Departamento de Microbiologia, Faculdade de Ciencias Medicas da Universidade Nova de Lisboa, Lisboa, Portugal 9 Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Lisboa, Portugal 10 Hospital da Luz, Lisboa, Portugal
Effect of celecoxib on experimental liver fibrosis in rat

Abstract: Background/Aim: Cyclooxygenase‐2 (COX‐2), an inducible enzyme that catalyzes prostaglandin synthesis, has been implicated in a number of hepatic stellate cell (HSC) functions. In the current study, we assessed the in vivo effect of celecoxib, a COX‐2‐selective inhibitor, in experimental liver fibrosis in rats.
Effects of B-Myb on Gene Transcription

The transcription factor B-Myb is a cell-cycle regulated phosphoprotein involved in cell cycle progression through the transcriptional regulation of many genes. In this study, we show that the promoter of the fibroblast growth factor-4(FGF-4) gene is strongly activated by B-Myb in HeLa cells and it can serve as a novel diagnostic tool for assessing B-Myb activity. Specifically, B-Myb deletion mutants were examined and domains of B-Myb required for activation of the FGF-4promoter were identified. Using phosphorylation-deficient mutant forms of B-Myb, we also show that phosphorylation is essential for B-Myb activity. Moreover, a mutant form of B-Myb, which lacks all identified phosphorylation sites and which has little activity, can function as a dominant-negative and suppress wild-type B-Myb activity. Acetylation is another post-translational modification known to affect the activity of other Myb family members. We show that B-Myb is acetylated by the co-activator p300. We also show that the bromo and histone acetyltransferase domains of p300 are sufficient to interact with and acetylate B-Myb. These data indicate that phosphorylation of B-Myb is an essential modification for activity and that acetylation of B-Myb may play a role in B-Myb activity.
Changes in soil phosphorus and its influencing factors following afforestation in Northern China

Changes in soil carbon (C) and nitrogen (N) stocks following afforestation have been widely studied at different scales. However, soil phosphorus (P) dynamics following afforestation are poorly understood, especially at the regional scale. This paper studied the effects of prior land use (cropland, grassland, and barren land), tree species (conifer, broadleaf, shrub, and mixed), plantation age (young, middle, and old), and climate on soil total phosphorus and available phosphorus stocks change in the top 20 cm following afforestation based on a synthesis of 50 recent publications in northern China. We also considered possible confounding effects between these factors. The results showed that, overall, soil total phosphorus and available phosphorus stocks significantly decreased by 7.3% and significantly increased by 8.8%, respectively, following afforestation. Prior land use was found to be the most important driver in determining changes in soil P stocks. Compared with a significant decrease in P of afforestation of former cropland and grassland, afforestation of barren land caused no clear decrease in P. Tree species was found to have a limited effect on changes in soil P after afforestation, and broadleaf afforestation has a lower P demand than coniferous forests in the studied region. Plantation age did not affect the dynamics of P stocks. Our results showed confounding effects of precipitation, prior land use, and tree species, which impacted the estimates of the drivers of changes in P stocks. These results highlighted the importance of tree species selection and replication across sites that receive different amounts of precipitation.
Detection and phylogenetic analysis of human pegivirus (GBV‐C) among blood donors and patients infected with hepatitis B virus (HBV) in Qatar

Human Pegivirus (HPgV), formerly GB virus‐C/Hepatitis G virus (GBV‐C/HGV), collectively known as GBV‐C, is widely spread and has been reported to be associated with non‐A–E hepatitis. To our knowledge, no previous study was conducted about HPgV in Qatar. Thus, the objectives of this study were as follows: (i) to determine the rates of HPgV infection in Qatar among healthy blood donors and HBV‐infected patients, and (ii) to determine the most predominant HPgV genotype in Qatar. A total of 714 blood plasma samples from healthy donors (612) and HBV‐infected patients (102) were collected. RNA was extracted, reversed transcribed, and then subjected for HPgV detection by two round‐nested PCR using primers amplifying a 208 bp of 5′‐UTR of the HPgV. For genotyping, the 5′‐UTR PCR products (from 25 randomly picked samples) were cloned and sequenced. The overall infection rate of HPgV in Qatar was 13.3%. There was no significant difference (P = 0.41) in the infection rates between healthy donor (13.7%) and in HBV‐infected patients (10.7%). Moreover, we did not find any significant association between HPgV infection rates and nationality, sex, or age (P > 0.05). Sequence analysis of 40 5′‐UTR PCR amplicons yielded the European genotype 2 as most predominant in Qatar, although other genotypes (5 and7) were also present. Our results indicate that there is no strong correlation between HPgV infection rate, condition, nationality, age, and sex, and genotype 2 is most predominant in Qatar. J. Med. Virol. 87:2074–2081, 2015. © 2015 Wiley Periodicals, Inc.
CD147 in Ovarian and Other Cancers

Ovarian cancer, a gynecological malignancy, is the most common cause of death in older women worldwide. The overall 5-year survival of ovarian cancer patients is only 20% because of late diagnosis, as well as distant metastasis and multidrug resistance. Therefore, predictive and prognostic markers are urgently required for the early diagnosis of ovarian cancer. CD147, an extracellular matrix metalloproteinase inducer, is overexpressed in ovarian cancers. Current knowledge suggests that CD147 is associated with the survival and progression of ovarian cancer, and is considered as a biomarker of poor outcome. Here, we specifically review the roles of CD147 in ovarian cancer progression and discuss the diagnostic and prognostic value of CD147 in patients with ovarian cancer. CD147 promotes ovarian cancer progression by its involvement in every facet of malignancy, including invasion, metastasis, survival, angiogenesis, and drug resistance. Although it is not fully confirmed, the combination of CD147 with other biomarkers might be of diagnostic value.
Analysis of Feature Generated of Marathi Word

continuous segmentation approach is used to get the isolated letters or pseudo character from the handwritten word for feature extraction. The preprocessing is done using morphological operation to remove noise, compress and provide smoother way for Feature extraction. To get better results Invariant moments (IM) are applied for feature extraction once preprocessing and segmentation is over because invariant moments are insensitive to translation, scale change, mirroring, and rotation. After segmentation it is often necessary to evaluate the quality of the image for that objective quality measure like mean and standard deviation are used and to see the relevance of our features for post- processing, correlation between the average of the group of similar pseudo-unit and sample of the similar pseudo-unit is calculated. Keywordsextraction, segmentation, moments
Application of machine learning algorithms to predict coronary artery calcification with a sibship‐based design

As part of the Genetic Epidemiology Network of Arteriopathy study, hypertensive non‐Hispanic White sibships were screened using 471 single nucleotide polymorphisms (SNPs) to identify genes influencing coronary artery calcification (CAC) measured by computed tomography. Individuals with detectable CAC and CAC quantity ≥70th age‐ and sex‐specific percentile were classified as having a high CAC burden and compared to individuals with CAC quantity <70th percentile. Two sibs from each sibship were randomly chosen and divided into two data sets, each with 360 unrelated individuals. Within each data set, we applied two machine learning algorithms, Random Forests and RuleFit, to identify the best predictors of having high CAC burden among 17 risk factors and 471 SNPs. Using five‐fold cross‐validation, both methods had ∼70% sensitivity and ∼60% specificity. Prediction accuracies were significantly different from random predictions (P‐value<0.001) based on 1,000 permutation tests. Predictability of using 287 tagSNPs was as good as using all 471 SNPs. For Random Forests, among the top 50 predictors, the same eight tagSNPs and 15 risk factors were found in both data sets while eight tagSNPs and 12 risk factors were found in both data sets for RuleFit. Replicable effects of two tagSNPs (in genes GPR35 and NOS3) and 12 risk factors (age, body mass index, sex, serum glucose, high‐density lipoprotein cholesterol, systolic blood pressure, cholesterol, homocysteine, triglycerides, fibrinogen, Lp(a) and low‐density lipoprotein particle size) were identified by both methods. This study illustrates how machine learning methods can be used in sibships to identify important, replicable predictors of subclinical coronary atherosclerosis. Genet. Epidemiol. 2008. © 2008 Wiley‐Liss, Inc.
Prevalence of drug resistance and importance of viral load measurements in Honduran HIV‐infected patients failing antiretroviral treatment

The Honduran HIV/AIDS Program began to scale up access to HIV therapy in 2002. Up to May 2008, more than 6000 patients received combination antiretroviral therapy (cART). As HIV drug resistance is the major obstacle for effective treatment, the purpose of this study was to assess the prevalence of antiretroviral drug resistance in Honduran HIV‐1‐infected individuals.
CAC : un algorithme de colonies de fourmis pour la classification automatique

Les methodes de classification automatique souffren t encore de plusieurs insuffisances et necessitent so uvent l’initialisation de plusieurs parametres comme le nombre de classes ou l’initialisation des groupes. Paradoxalement, ces derniers sont a decouvrir par l a methode de partitionnement elle-meme. Alternativeme nt, le monde du vivant nous inspire encore et permet de proposer des methodes de resolution de problemes qu i s’inspirent de ses mecanismes. Les fourmis en sont des exemples qui presentent un interet grandissant pou r la resolution de problemes complexes. La classificatio n automatique fait partie des problemes pour lesquels les fourmis suggerent des heuristiques tres interessant es. Malheureusement, la plupart des methodes proposees a cet effet, n’exploitent pas toutes les proprietes biologiques des fourmis reelles et notamment les fo rmes de communications qu’elles utilisent. Dans ce trava il, nous proposons une nouvelle adaptation des methodes de colonies de fourmis pour une tâche de classifica tion automatique. Les fourmis artificielles resolvent collectivement le probleme en disposant chacune d’u ne representation locale et partielle du probleme et a yant la capacite de communiquer avec les autres fourmis. Ce ci est une tentative d’adaptation des proprietes de communication sonores chez les fourmis reelles.
A clustering Bayesian approach for multivariate non-ordered circular data

This article presents a Bayesian model for the clustering of non-ordered multivariate directional or circular data. The particular trait of our data is that each single observation is made up of k ≥ 2 non-ordered points on the circle. We introduce a hierarchical model that combines a symmetrization technique, projected normal distributions and a Dirichlet process. One parameter is introduced to model the non-ordered trait and another one to control the variability of the angles on the circle. An informative prior on the relative locations of the k angles is also provided. The gain of the symmetrization is highlighted by a theoretical study. The parameters of the model are then inferred using a Metropolis–Hastings-within-Gibbs algorithm. Simulated datasets are analysed to study the sensitivity to hyperparameters. Then, the benefits of our approach are illustrated by clustering real data made up of the positions of five separate radiotherapy X-ray beams on a circle.
RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region

The endoribonuclease RNase E in a range of bacteria has a conserved N-terminal catalytic domain and a less well-conserved C-terminal tail. While the role of the C-terminal tail in the formation of the degradosome, including the interaction with the polynucleotide phosphorylase PNPase, has been studied extensively in Escherichia coli, less is known about RNase E in other bacteria. In this study, Zhang and colleagues characterize RNase E in Anabaena and Synechocystis and find that, despite having C-termini that are very different from E. coli and contain an unusual RRRRRRSSA motif, the cyanobacterial enzymes also bind PNPase.