Miracle-dz/UniFAR-FTUs huggingface dataset:
MUTATIONS IN THE RPOB GENE OF RIFAMPIN RESISTANT MYCOBACTERIUM TUBERCULOSIS ISOLATED IN ISFAHAN BY PCR-SSCP

Rifampin interacts with the beta-subunit of RNA Polymerase (rpoB), thereby hindering transcription. Mutations in the rpoB locus confer conformational changes leading to defective binding of the drug to rpoB and consequently resistance. Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and direct sequencing have been established as a rapid screening test for the detection of mutation in rpoB gene, which is responsible for rifampin resistance of Mycobacterium tuberculosis species. In this study, a total of 37 strains of M. tuberculosis, 16 sensitive and 15 resistant of Isfahan isolates, and 6 resistant strains obtained from Pasteur institute of Iran, were used. They were confirmed as M. tuberculosis by conventional methods and amplification of DR gene a region that belongs to M. tuberculosis complex group. Their sensitivity or resistance to Rifampin was initially determined by proportion method. The 193-bp region of the rpoB gene was then amplified and PCR-SSCP patterns of rifampin resistance (RIFr) and rifampin susceptible (RIFs) strains were determined by electrophoresis on 10% acrylamide gels and silver staining. Also 8 samples of 193-bp rpoB amplicons with different PCRSSCP patterns from Rifr and one from Rifs were sequenced. By PCR-SSCP analysis, 7 PCR-SSCP distinguishable patterns were recognized in the Isfahan RIFr strains. Although 6 of these patterns were different from sensitive strain, one pattern was identical to sensitive standard strain H37Rv. Six resistant strains from Pasteur institute of Iran demonstrated two patterns that one of them was alike to pattern 4 of Isfahan RIFr but other was different. 15 out of 16 RIFs isolates demonstrated PCR-SSCP banding patterns similar to that of sensitive standard strain H37Rv. However, one of the sensitive isolates demonstrated different pattern. After determinations the rpoB sequences of the resistance strains, different mutations were seen in codon 523(GGG/GGT), 526(CAC/TAC), 531(TCG/TTG) and 511(CTG/TTG). This study demonstrated the high specificity (93.8%) and sensitivity (95.2%) of PCR-SSCP method. Presence of different PCR-SSCP banding patterns that were observed in this study is in accordance with the results of similar studies in other parts of the world. The two most prevalent mutations were missense mutations at the positions Ser-531 (TCG/ TTG: Ser/Leu) and His-526 (CAC/TAC: His/Tyr). This finding is comparable to the results of early studies demonstrating the rpoB mutation frequencies in isolates from other parts of the world.
The Phenolic Potential of Wines from French Grape Varieties Cabernet Sauvignon, Merlot and Syrah Cultivated in the Region of Thessaloniki (Northern Greece) and Its Evolution during Aging

The aim of this work is mainly to determine the effect of the pedoclimatic conditions (“terroir”) on the phenolic composition of wine originated from three French red grape varieties Cabernet Sauvignon, Merlot and Syrah, cultivated in the region of Thessaloniki (Northern Greece); simultaneously a study of its evolution during aging in a stainless steel tank, in oak barrels of different origin and in bottles is conducted. Additionally, in this work, we try to compare the evolution of phenolic composition of wines during aging in French medium toast oak barrel and in American heavy toast oak barrel. For this reason, 20 red wine samples originated from this area were analyzed. The color markers were measured by UV-spectrometry, while the phenolic acids and catechin content of the wine samples and their evolution during aging were determine by UVis-High performance liquid chromatography. Significant differences detected among the three grape varieties regarding color parameters, total anthocyanins and some phenolic acids. The increase of the extraction time during vinification affected the amounts of phenolic acids, catechin, total phenolic index (TPI) and tannin content. Gallic acid and catechin were the most abundant phenolic compounds and their amounts, as well as the concentrations of several phenolic acids were significantly affected during the storage period. Finally, the phenolic composition and the amounts of phenolic acids did not appear to be affected by the origin of oak barrels.
Modelling bilberry and cowberry yields in Finland: different approaches to develop models for forest planning calculations

The aim of this research was to create yield models for the two most significant wild berry species in Finland, namely, the bilberry and the cowberry. In particular, the aim was to develop models applicable to multi-objective forest planning calculations. The models were developed using approaches based on both expertise and empirical measurements. In expert-knowledge-based studies, different methods of data collection were used: experts evaluated berry production of different forest stands (i) from slides, (ii) visually in the field and (iii) using a questionnaire. Data for empirical studies were also collected using different methods: measurements (i) of systematically placed sample plots and (ii) of forest stands found to be advantageous with respect to berry production. Statistical analyses of data and modelling techniques varied from study to study. Thus, another aim was to test different methods of data collection and different modelling techniques and also assess their usability. According to the results, the best bilberry yield can be found in a mature stand which is not too dense and is located on a mineral soil site of medium or rather poor fertility. It is also obvious that pine-dominated heath forests of rather poor or poorer fertility have the highest cowberry yields. A stand suitable for cowberry picking should not be dense. These results are very much in line with previous studies on the effects of site and stand characteristics on berry production. However, it is concluded that there is still a need to for further research to explore the dependence of cowberry crops on stand characteristics on poor mineral soil sites. Comparisons of the results of this thesis with empirical berry yield studies and also with earlier berry models indicate that modelling expertise is a reasonable way to create production functions for different wild berry species. This finding encourages the utilization of expertise in other applications for the development of models for different non-wood forest products. In particular, the method based on visual assessments conducted in the field was found to be a promising one.
Coupled interaction between unsteady flame dynamics and acoustic field in a turbulent combustor.

Thermoacoustic instability is a result of the positive feedback between the acoustic pressure and the unsteady heat release rate fluctuations in a combustor. We apply the framework of the synchronization theory to study the coupled behavior of these oscillations during the transition to thermoacoustic instability in a turbulent bluff-body stabilized gas-fired combustor. Furthermore, we characterize this complex behavior using recurrence plots and recurrence networks. We mainly found that the correlation of probability of recurrence ( C P R ), the joint probability of recurrence ( J P R ), the determinism ( D E T ), and the recurrence rate ( R R ) of the joint recurrence matrix aid in detecting the synchronization transitions in this thermoacoustic system. We noticed that C P R and D E T can uncover the occurrence of phase synchronization state, whereas J P R and R R can be used as indices to identify the occurrence of generalized synchronization (GS) state in the system. We applied measures derived from joint and cross recurrence networks and observed that the joint recurrence network measures, transitivity ratio, and joint transitivity are useful to detect GS. Furthermore, we use the directional property of the network measure, namely, cross transitivity to analyze the type of coupling existing between the acoustic field ( p ' ) and the heat release rate ( q ˙ ' ) fluctuations. We discover a possible asymmetric bidirectional coupling between q ˙ ' and p ' , wherein q ˙ ' is observed to exert a stronger influence on p ' than vice versa.
Influence of medium range transport of particles from nucleation burst on particle number concentration within the urban airshed

Abstract. An elevated particle number concentration (PNC) observed during nucleation events could play a significant contribution to the total particle load and therefore to the air pollution in the urban environments. Therefore, a field measurement study of PNC was commenced to investigate the temporal and spatial variations of PNC within the urban airshed of Brisbane, Australia. PNC was monitored at urban (QUT), roadside (WOO) and semi-urban (ROC) areas around the Brisbane region during 2009. During the morning traffic peak period, the highest relative fraction of PNC reached about 5% at QUT and WOO on weekdays. PNC peaks were observed around noon, which correlated with the highest solar radiation levels at all three stations, thus suggesting that high PNC levels were likely to be associated with new particle formation caused by photochemical reactions. Wind rose plots showed relatively higher PNC for the NE direction, which was associated with industrial pollution, accounting for 12%, 9% and 14% of overall PNC at QUT, WOO and ROC, respectively. Although there was no significant correlation between PNC at each station, the variation of PNC was well correlated among three stations during regional nucleation events. In addition, PNC at ROC was significantly influenced by upwind urban pollution during the nucleation burst events, with the average enrichment factor of 15.4. This study provides an insight into the influence of regional nucleation events on PNC in the Brisbane region and it the first study to quantify the effect of urban pollution on semi-urban PNC through the nucleation events.
Coherence Lengths of the Interplanetary Electric Field: Solar Cycle Maximum Conditions

It is increasingly being realized that by affecting geoeffective scale lengths the interplanetary electric field (IEF) is a key quantity in space weather discussions. In this work we derive and analyze statistically IEF coherence lengths in year 2000, i.e., near maximum of solar cycle 23, working in a much used formulation for the IEF. We focus on the frequency domain. We use magnetic field and plasma data sets acquired by Wind and ACE. During year 2000, ACE‐Wind separations were very variable and, in particular, Wind’s first dayside distant prograde orbit resulted in a Y‐separation comparable to the X‐separation (∼220 RE). We find IEF coherence lengths of 200–250 RE (X) and 50–100 RE (Y). The coherence is mainly carried by the low frequency components (f < 0.01 min−1).
TDP‐43 accelerates deadenylation of target mRNAs by recruiting Caf1 deadenylase

TAR DNA‐binding protein 43 (TDP‐43) is an RNA‐binding protein, whose loss‐of‐function mutation causes amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. Recent studies demonstrated that TDP‐43 binds to the 3′ untranslated region (UTR) of target mRNAs to promote mRNA instability. Here, we show that TDP‐43 recruits Caf1 deadenylase to mRNA targets and accelerates their deadenylation. Tethering TDP‐43 to the mRNA 3′UTR recapitulates destabilization of the mRNA, and TDP‐43 accelerates their deadenylation. This accelerated deadenylation is inhibited by a dominant negative mutant of Caf1. We find that TDP‐43 physically interacts with Caf1. In addition, we provide evidence that TDP‐43 regulates poly(A) tail length of endogenous Progranulin (GRN) mRNA. These results may shed light on the link between dysregulation of TDP‐43‐mediated mRNA deadenylation and pathogenesis of neurodegenerative diseases.
Dating and Digging Stratified Archaeology in Circumpolar North America: A View from Nunalleq, Southwestern Alaska

Through the case study of the Thule-era village site of Nunalleq (GDN-248), this paper presents 14C dating results and perspectives on the issues associated with radiocarbon dating stratified archaeological sites in circumpolar North America. The objective was to investigate relative variation in the 14C age of ecofacts with the aim of establishing a hierarchy of dating suitability for Nunalleq that could more widely inform 14C sample selection on archaeological sites across the North American sub-Arctic and Arctic and Greenland. Owing to the complexities associated with interpreting and establishing the relative chronology of the deeply stratified sod deposits at Nunalleq, we adopted open-area excavation and single-context recording methods. This approach, we suggest, allowed us to eliminate stratigraphic complexity as a source of variation in 14C measurements and to assess the taphonomic issues associated with dating different ecofacts. In total, 16 samples were submitted for dating, comprising two sets of eight different ecofacts, one from each of two stratigraphically contemporary but spatially discrete contexts. In most instances, the 14C ages of ecofacts were statistically indistinguishable between the two contexts and support the relative chronological relationships established by excavation. Only Elymus arenarius (grass) manufactures and Heleomyzidae (fly) puparia produced different ages in the two contexts, variations that suggest that these items are unreliable dating materials. As noted in previous studies, Phoca sp. (seal) and Oncorhynchus sp. (salmon) bone collagen demonstrated a strong marine reservoir effect (c. 700 14C yr.). Picea sp. (wood chips) were marginally older than seeds from edible berries ( Rubus chamaemorus and Empetrum nigrum ) and caribou ( Rangifer tarandus ) bone collagen, which provided the most consistent ages.
Stylometric analysis of classical Arabic texts for genre detection

Purpose In the context of information retrieval, text genre is as important as its content, and knowledge of the text genre enhances the search engine features by providing customized retrieval. The purpose of this study is to explore and evaluate the use of stylometric analysis, a quantitative analysis for the linguistics features of text, to support the task of automated text genre detection for Classical Arabic text. Design/methodology/approach Unsupervised clustering and supervised classification were applied on the King Saud University Corpus of Classical Arabic texts (KSUCCA) using the most frequent words in the corpus (MFWs) as stylometric features. Four popular distance measures established in stylometric research are evaluated for the genre detection task. Findings The results of the experiments show that stylometry-based genre clustering and classification align well with human-defined genre. The evidence suggests that genre style signals exist for Classical Arabic and can be used to support the task of automated genre detection. Originality/value This work targets the task of genre detection in Classical Arabic text using stylometric features, an approach that has only been previously applied to Arabic authorship attribution. The study also provides a comparison of four distance measures used in stylomtreic analysis on the KSUCCA, a corpus with over 50 million words of Classical Arabic using clustering and classification.
Metabolic effects of breastfeed in women with prior gestational diabetes mellitus: A systematic review and meta‐analysis

This study was undertaken to provide comprehensive analyses of current research developments in the field of breastfeed (BF) and metabolic‐related outcomes among women with prior gestational diabetes mellitus (GDM). Database PubMed, Embase, BIOSIS Previews, Web of Science, and Cochrane Library were searched through December 3, 2017. Odds ratio (OR) and weighted mean difference (WMD) with 95% confidence interval (CI) were pooled by random‐effects model using Stata version 12.0. Twenty‐three observational studies were included in quantitative synthesis. Reduced possibility of progression to type 2 diabetes mellitus (T2DM; OR = 0.79; 95% CI, 0.68‐0.92) and pre‐DM (OR = 0.66; 95% CI, 0.51‐0.86) were found among women with longer BF of any intensity after GDM pregnancy. The positive effect of longer BF on progression to T2DM gradually became prominent with the extension of follow‐up period. Compared with women with shorter BF, those with longer BF manifested more favourable metabolic parameters, including significant lower body mass index, fasting glucose, triglyceride, and higher insulin sensitivity index. The findings support that BF may play an important role in protection against the development of T2DM‐related outcomes in midlife of women with prior GDM. However, further studies are needed to reveal the etiological mechanism.
A hybrid generalised linear and Levenberg–Marquardt artificial neural network approach for downscaling future rainfall in North Western England

This paper describes a novel technique for downscaling daily rainfall which uses a combination of a generalised linear model (GLM) and artificial neural network (ANN) to downscale rainfall. A two-stage process is applied, an occurrence process which uses the GLM model and an amount process which uses an ANN model trained with a Levenberg–Marquardt approach. The GLM-ANN was compared with other three downscaling models, the traditional neural network (ANN), multiple linear regression (MLR) and Poisson regression (PR). The models are applied for downscaling daily rainfall at three locations in the North West of England during the winter and summer. Model performances with respect to reproduction of various statistics such as correlation coefficient, autocorrelation, root mean square errors (RMSE), standard deviation and the mean rainfall are examined. It is found that the GLM-ANN model performs better than the other three models in reproducing most daily rainfall statistics, with slight difficulties in predicting extremes rainfall event in summer. The GLM-ANN model is then used to project future rainfall at the three locations employing three different general circulation models (GCMs) for SRES scenarios A2 and B2. The study projects significant increases in mean daily rainfall at most locations for winter and decreases in summer.
Patterns of cognitive deficits in persons with spinal cord injury as compared with both age-matched and older individuals without spinal cord injury

Context/Objective: Cognitive deficits can impact as many as 60% of individuals with spinal cord injury (SCI). In an effort to identify the nature of cognitive deficits in SCI, we examined neuropsychological test performance in individuals with SCI, age matched healthy controls and older healthy controls. Design: Participants completed a motor-free neuropsychological test battery assessing attention, working memory, information processing speed, new learning /memory and executive control. Setting: Outpatient rehabilitation research facility. Participants: Participants included 60 individuals with chronic spinal cord injury [SCI; 32 with paraplegia (T2-T12) and 28 with tetraplegia (C3-T1)], 30 age-matched healthy controls (AMHC; 30–40 years old) and 20 older healthy controls (OHC; 50–60 years old). Outcome Measures: Wechsler Intelligence Scale – 3rd edition (WAIS-III) Digit Span and Letter-Number Sequencing; Symbol Digit Modalities Test (SDMT) – oral version; California Verbal Learning Test-II; Paced Auditory Serial Addition Test (PASAT); Wechsler Abbreviated Scale of Intelligence (WASI); Delis-Kaplan Executive Function System; Verbal Fluency subtest. Results: Significant differences were noted between the SCI and AMHC groups on measures of information processing speed, new learning and memory, and verbal fluency. No significant differences were noted between the groups on tests of attention or working memory. Conclusion: The current study documented differences in specific realms of cognitive functioning between a chronic SCI sample and AMHC. Implications for cognitive rehabilitation and overall quality of life are discussed. Additional research is needed utilizing a more comprehensive battery of motor-free neuropsychological tests that avoid the confound of upper limb motor limitations on cognitive performance.
Children's Perspectives on Economic Adversity: A review of the literature

This paper reviews some of the recent qualitative literature on children's perspectives on economic disadvantage. The idea of asking people who experience disadvantage about their own situations is still a relatively new one in the social sciences, and the idea of asking children about their own perceptions of economic and social disadvantage is even more recent. Nine analyses, all published since 1998, and all of them involving in-depth interviews or group work with children aged between 5 and 17, are examined in detail. Most of these studies develop frameworks based on the 'new sociology of childhood', which emphasises the social construction of childhood and children's agency in the context of child-adult relations. The nine studies cover a number of issues related to economic disadvantage, including exclusion from activities and peer groups at school and in the community; perceptions of 'poor' and 'affluent' children; participation in organized activities outside of school hours; methods of coping with financial hardship; support for parents in coping and in seeking and keeping employment, and aspirations for future careers and lives.
Working Paper Series 606 ( ISSN 1211-3298 ) Generalized Disappointment Aversion , Learning , and Asset Prices

This paper provides a generalized disappointment aversion (GDA) interpretation of the variance and skew risk premia in equity returns and the volatility skew in equity index options. The key ingredients are Bayesian learning about a hidden consumption growth rate and the investor’s tail aversion induced by GDA preferences which amplify the impact of consumption shocks. This model with disappointment risk reproduces salient properties of the variance and skew risk premia and generates a realistic volatility skew implied by index options, while simultaneously matching the mean and volatility of risk-free rate and equity returns, and the level of the price-dividend ratio. Additionally, the time-varying probability of disappointment events generates a wide range of dynamic asset pricing phenomena.
Nutrient Digestibility and Growth of Five Breeds of Sheep under Different Levels of Undegradable Protein

A study was conducted to evaluate the effect of feeding different levels of rumen undegradable protein (UDP) in concentrate on performance of five breeds of sheep. Namely: Compass Agrinak (CA); Garut Composite breed (KG); Barbados Cross breed (BC); St Croix breed (SC); and Local Garut (GL) breed. Ten heads of sheep were used from each breed, in which each breed was grouped into 5 groups according to their body weight, and each sheep in each group was assigned to one of two treatments diet. The diet treatment consisted of concentrate containing different levels of undegradable protein (UDP). The levels of undegradable protein were 4.5% and 7.5%. Concentrate were formulated in iso nitrogen (CP content 16.7%) and iso energy (ME content 2.5 Mcal/kg). During feeding trial the sheep were kept in individual pen for three months. Study was conducted in randomized complete block design in factorial 5 x 2 arrangement, 5 levels of breeds sheep and 2 levels of UDP content. Results shows that there was no interaction effect of breed and levels UDP on feed consumption, average daily gain and feed conversion. These variables were significantly (P 0.05) by interaction between breed of sheep and UDP levels in the diet except for OM digestibility. While breed of sheep did not affect nutrient digestibility and UDP levels only affected NDF digestibility. From this study, it is concluded that increasing UDP in the diet did not improve growth performance of sheep. At similar quality of feed the growth performance was affected by breed of sheep in which KG and GL sheep had similar average daily gain (86.01 vs 82.38 g/day).