Miracle-dz/UniFAR-FTUs huggingface dataset:
Synergistic Applications of MD and NMR for the Study of Biological Systems

Modern biological sciences are becoming more and more multidisciplinary. At the same time, theoretical and computational approaches gain in reliability and their field of application widens. In this short paper, we discuss recent advances in the areas of solution nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations that were made possible by the combination of both methods, that is, through their synergistic use. We present the main NMR observables and parameters that can be computed from simulations, and how they are used in a variety of complementary applications, including dynamics studies, model-free analysis, force field validation, and structural studies.
The occurrence of ochratoxin A in rice in six provinces of Iran

Three hundred and eight samples of rice purchased from retail markets in six different provinces in Iran from March 2012 to January 2013 were surveyed for the presence of ochratoxin A (OTA) using enzyme-linked immunosorbent assay. The recovery percentages of OTA from spiked rice samples at concentrations of 5 and 10 ng/g were found to be 85.3% and 86.7%, respectively. Analytical results showed a 9.4% frequency of contamination from total analyzed rice samples with a mean OTA level of 3.60 ± 2.66 ng/g. Concentrations of OTA in positive samples ranged from 0.84 ng/g to 11.37 ng/g, and in 17.3% of contaminated rice samples the concentrations exceeded the maximum tolerance limit set by European regulations for OTA in cereals (5 ng/g). Based on the results of this study, the estimated daily intake of OTA in rice was 0.62 ng/kg body weight/day for Iranian consumers.
In vitro regeneration and plant establishment of Tylophora indica (Burm. F.) Merrill: Petiole callus culture

SummaryA protocol has been developed for high-frequency shoot regeneration and plant establishment of Tylophora indica from petiole-derived callus. Optimal callus was developed from petiole explants on Murashige and Skoog basal medium supplemented with 10μM2,4-dichlorophenoxyacetic acid +2,5μM thidiazuron (TDZ). Adventitious shoot induction was achieved from the surface of the callus after transferring onto shoot induction medium. The highest rate (90%) of shoot multiplication was achieved on MS medium containing 2. 5μM TDZ. Individual elongated shoots were rooted best on halfstrength MS medium containing 0. 5μM indole-3-butyric acid (IBA). When the basal cut ends of the in vitro-regenerated shoots were dipped in 150μM IBA for 30 min followed by transplantation in plastic pots containing sterile vermiculite, a mean of 4.1 roots per shoot developed. The in vitro-raised plantlets with well-developed shoot and roots were successfully established in earthen pots containing garden soil and grown in a greenhouse with 100% survival. Four months after transfer to pots, the performance of in vitro-propagated plants of T. indica was evaluated on the basis of selected physiological parameters and compared with ex vitro plants of the same age.
AtSig 5 Is an Essential Nucleus-Encoded Arabidopsis-Like Factor 1

Transcription of chloroplast genes is subject to control by nucleus-encoded proteins. The chloroplast-encoded RNA polymerase (PEP) is a eubacterial-type RNA polymerase that is presumed to assemble with nucleus-encoded -factors mediating promoter recognition. Recently, families of -factor genes have been identified in several plants including Arabidopsis. One of these genes, Arabidopsis SIG5, encodes a -factor, AtSig5, which is phylogenetically distinct from the other family members. To investigate the role of this plant -factor, two different insertional alleles of the SIG5 gene were identified and characterized. Heterozygous mutant plants showed no visible leaf phenotype, but exhibited siliques containing aborted embryos and unfertilized ovules. Our inability to recover plants homozygous for a SIG5 gene disruption indicates that SIG5 is an essential gene. SIG5 transcripts accumulate in flower tissues, consistent with a role for AtSig5 protein in reproduction. Therefore, SIG5 encodes an essential member of the Arabidopsis -factor family that plays a role in plant reproduction in addition to its previously proposed role in leaf chloroplast gene expression.
Anti-angiogenic Activity Evaluation of Secondary Metabolites from Calycolpus Moritzianus Leaves

Angiogenesis is a crucial step in many pathological conditions like cancer, inflammation and metastasis formation; on these basis the search for antiangiogenic agents has widened. In order to identify new compounds able to interfere in the Vascular Endothelial Growth Factor Receptor-1 (VEGFR-1, also known as Flt-1) recognition by VEGFs family members, we screened Calycolpus moritzianus (O. Berg) Burret leaves extracts by a competitive ELISA-based assay. MeOH and CHCl3 extracts and several their fractions demonstrated to be able to prevent VEGF or PlGF interaction with Flt-1, with an inhibition about 50% at concentration of 100 μg/mL. Phytochemical and pharmacological investigation of the active fractions led to the isolation of flavonoids, and terpenes.
Use of substance abuse treatment services by persons with mental health and substance use problems.

OBJECTIVES This study provided population estimates of mental syndromes and substance use problems and examined whether the co-occurrence of mental health and substance use problems was associated with the use of substance abuse treatment services. METHODS Study data were drawn from the 1997 National Household Survey on Drug Abuse. RESULTS Of the total sample of 16,661 adults, 2 percent reported using services for alcohol or drug use problems in the previous year. Among the 3,474 (17 percent) who reported at least one alcohol or drug use problem, 6 percent used substance abuse services. Only 4 percent of persons who reported substance use problems alone received any substance abuse treatment service in the previous year. Only 3 percent of persons who reported alcohol use problems alone received such services. Among persons with one or more substance use problems, the prevalence of service use was 11 percent among persons who reported one co-occurring mental syndrome and 18 percent among those who reported two or more mental syndromes. Multiple logistic regression analyses identified a number of subgroups who might have needed substance abuse services but did not receive them, including women, Asians and Pacific Islanders, college graduates, persons employed full-time, persons who abused alcohol only, and persons with substance use problems who reported no coexisting mental syndromes. CONCLUSIONS The rate of help seeking among persons with alcohol use problems is low, which is a public health concern.
The Tricarballylate Utilization (tcuRABC) Genes of Salmonella enterica Serovar Typhimurium LT2

ABSTRACT The genes of Salmonella enterica serovar Typhimurium LT2 encoding functions needed for the utilization of tricarballylate as a carbon and energy source were identified and their locations in the chromosome were established. Three of the tricarballylate utilization (tcu) genes, tcuABC, are organized as an operon; a fourth gene, tcuR, is located immediately 5′ to the tcuABC operon. The tcuABC operon and tcuR gene share the same direction of transcription but are independently transcribed. The tcuRABC genes are missing in the Escherichia coli K-12 chromosome. The tcuR gene is proposed to encode a regulatory protein needed for the expression of tcuABC. The tcuC gene is proposed to encode an integral membrane protein whose role is to transport tricarballylate across the cell membrane. tcuC function was sufficient to allow E. coli K-12 to grow on citrate (a tricarballylate analog) but not to allow growth of this bacterium on tricarballylate. E. coli K-12 carrying a plasmid with wild-type alleles of tcuABC grew on tricarballylate, suggesting that the functions of the TcuABC proteins were the only ones unique to S. enterica needed to catabolize tricarballylate. Analyses of the predicted amino acid sequences of the TcuAB proteins suggest that TcuA is a flavoprotein, and TcuB is likely anchored to the cell membrane and probably contains one or more Fe-S centers. The TcuB protein is proposed to work in concert with TcuA to oxidize tricarballylate to cis-aconitate, which is further catabolized via the Krebs cycle. The glyoxylate shunt is not required for growth of S. enterica on tricarballylate. A model for tricarballylate catabolism in S. enterica is proposed.
Avoidance of Model Re-Induction in SVM-Based Feature Selection for Text Categorization

Searching the feature space for a subset yielding optimum performance tends to be expensive, especially in applications where the cardinality of the feature space is high (e.g., text categorization). This is particularly true for massive datasets and learning algorithms with worse than linear scaling factors. Linear Support Vector Machines (SVMs) are among the top performers in the text classification domain and often work best with very rich feature representations. Even they however benefit from reducing the number of features, sometimes to a large extent. In this work we propose alternatives to exact re-induction of SVM models during the search for the optimum feature subset. The approximations offer substantial benefits in terms of computational efficiency. We are able to demonstrate that no significant compromises in terms of model quality are made and, moreover, in some cases gains in accuracy can be achieved.
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. The major human pathogen Streptococcus pneumoniae represents the first bacterial organism for which densely enough sampled population data became available for such an analysis. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. Genome data from over three thousand pneumococcal isolates identified 5,199 putative epistatic interactions between 1,936 sites. Over three-quarters of the links were between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of which are critical in determining non-susceptibility to beta-lactam antibiotics. A network-based analysis found these genes were also coupled to that encoding dihydrofolate reductase, changes to which underlie trimethoprim resistance. Distinct from these resistance genes, a large network component of 384 protein coding sequences encompassed many genes critical in basic cellular functions, while another distinct component included genes associated with virulence. These results have the potential both to identify previously unsuspected protein-protein interactions, as well as genes making independent contributions to the same phenotype. This approach greatly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for experimental work. Author Summary Epistatic interactions between polymorphisms in DNA are recognized as important drivers of evolution in numerous organisms. Study of epistasis in bacteria has been hampered by the lack of both densely sampled population genomic data, suitable statistical models and powerful inference algorithms for extremely high-dimensional parameter spaces. We introduce the first model-based method for genome-wide epistasis analysis and use the largest available bacterial population genome data set on Streptococcus pneumoniae (the pneumococcus) to demonstrate its potential for biological discovery. Our approach reveals interacting networks of resistance, virulence and core machinery genes in the pneumococcus, which highlights putative candidates for novel drug targets. Our method significantly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for experimental work.
Early results for treatment of two- and three-part fractures of the proximal humerus using Contours PHP (proximal humeral plate)

Background and aim of the work: The management of displaced 2- and 3-part fractures of the proximal humerus is controversial, both in younger and in elderly patients. The purpose of this paper is to evaluate the functional results of the Contours Proximal Humerus Plate (OrthofixR, Bussolengo,Verona, Italy), for the treatment of displaced 2- and 3-part fractures of the proximal humerus. Methods: We retrospectively reviewed 55 patients with proximal humerus fractures, who underwent osteosynthesis with Contours Proximal Humerus Plate from December 2011 to March 2015. We had 21 patients with 2-part fractures and with an average age of 67.1 years and 34 patients with 3-part fractures, with average age of 63.6 years. Results: The average union time was 3 months. The mean Constant score was 67 for 2-part fracture group and 64.9 for 3-part fracture group. The difference was not statistically significant (p = 0.18). The overall complication rate was 14.5 %. Six patients underwent additional surgery (10.9%). Conclusions: The most frequent major complication was secondary loss of reduction following varus collapse of the fracture (2 cases). In these patients, there was loss of medial hinge integrity due to impaction and osteoporosis. The placement of the main locking screw in the calcar area to provide inferomedial support is the rational of the Contours Proximal Humerus Plate. Osteosynthesis with Contours Proximal Humerus Plate is a safe system for treating displaced 2- and 3-part fractures of the proximal humerus, with good functional results and complication rates comparable to those reported in the literature. (www.actabiomedica.it)
Effects of physical activity on life expectancy with cardiovascular disease.

BACKGROUND Physical inactivity is a modifiable risk factor for cardiovascular disease. However, little is known about the effects of physical activity on life expectancy with and without cardiovascular disease. Our objective was to calculate the consequences of different physical activity levels after age 50 years on total life expectancy and life expectancy with and without cardiovascular disease. METHODS We constructed multistate life tables using data from the Framingham Heart Study to calculate the effects of 3 levels of physical activity (low, moderate, and high) among populations older than 50 years. For the life table calculations, we used hazard ratios for 3 transitions (healthy to death, healthy to disease, and disease to death) by levels of physical activity and adjusted for age, sex, smoking, any comorbidity (cancer, left ventricular hypertrophy, arthritis, diabetes, ankle edema, or pulmonary disease), and examination at start of follow-up period. RESULTS Moderate and high physical activity levels led to 1.3 and 3.7 years more in total life expectancy and 1.1 and 3.2 more years lived without cardiovascular disease, respectively, for men aged 50 years or older compared with those who maintained a low physical activity level. For women the differences were 1.5 and 3.5 years in total life expectancy and 1.3 and 3.3 more years lived free of cardiovascular disease, respectively. CONCLUSIONS Avoiding a sedentary lifestyle during adulthood not only prevents cardiovascular disease independently of other risk factors but also substantially expands the total life expectancy and the cardiovascular disease-free life expectancy for men and women. This effect is already seen at moderate levels of physical activity, and the gains in cardiovascular disease-free life expectancy are twice as large at higher activity levels.
Air Pollution and Hospital Admissions for Pneumonia in A Tropical City: Kaohsiung, Taiwan

This study was undertaken to determine whether there was an association between air pollutant levels and hospital admissions for pneumonia in Kaohsiung, Taiwan. Hospital admissions for pneumonia and ambient air pollution data for Kaohsiung were obtained for the period of 1996–2004. The relative risk of hospital admission was estimated using a case-crossover approach, controlling for weather variables, day of the week, seasonality, and long-term time trends. In the single-pollutant models, on warm days (=25°C) statistically significant positive associations were found for all pollutants. On cool days (<25°C), all pollutants were also significantly associated with number of pneumonia admissions. For the two-pollutant model, O3 and CO were significant in combination with each of the other four pollutants on warm days. On cool days, PM10 and NO2 remained statistically significant in all the two-pollutant models. This study provides evidence that higher levels of ambient air pollutants increase the risk of hospital admissions for pneumonia. The effects of air pollutants on hospital admissions for pneumonia were temperature dependent.
Domain Adaptation for Statistical Machine Translation

Statistical machine translation (SMT) systems perform poorly when it is applied to new target domains. Our goal is to explore domain adaptation approaches and techniques for improving the translation quality of domain-specific SMT systems. However, translating texts from a specific domain (e.g., medicine) is full of challenges. The first challenge is ambiguity. Words or phrases contain different meanings in different contexts. The second one is language style due to the fact that texts from different genres are always presented in different syntax, length and structural organization. The third one is the out-of-vocabulary words (OOVs) problem. In-domain training data are often scarce with low terminology coverage. In this thesis, we explore the state-of-the-art domain adaptation approaches and propose effective solutions to address those problems.
Comparative Geno-Plasticity Analysis of Mycoplasma bovis HB0801 (Chinese Isolate)

Mycoplasma bovis pneumonia in cattle has been epidemic in China since 2008. To investigate M. bovis pathogenesis, we completed genome sequencing of strain HB0801 isolated from a lesioned bovine lung from Hubei, China. The genomic plasticity was determined by comparing HB0801 with M. bovis strain ATCC® 25523™/PG45 from cow mastitis milk, Chinese strain Hubei-1 from lesioned lung tissue, and 16 other Mycoplasmas species. Compared to PG45, the genome size of HB0801 was reduced by 11.7 kb. Furthermore, a large chromosome inversion (580 kb) was confirmed in all Chinese isolates including HB0801, HB1007, a strain from cow mastitis milk, and Hubei-1. In addition, the variable surface lipoproteins (vsp) gene cluster existed in HB0801, but contained less than half of the genes, and had poor identity to that in PG45, but they had conserved structures. Further inter-strain comparisons revealed other mechanisms of gene acquisition and loss in HB0801 that primarily involved insertion sequence (IS) elements, integrative conjugative element, restriction and modification systems, and some lipoproteins and transmembrane proteins. Subsequently, PG45 and HB0801 virulence in cattle was compared. Results indicated that both strains were pathogenic to cattle. The scores of gross pathological assessment for the control group, and the PG45- and HB0801-infected groups were 3, 13 and 9, respectively. Meanwhile the scores of lung lesion for these three groups were 36, 70, and 69, respectively. In addition, immunohistochemistry detection demonstrated that both strains were similarly distributed in lungs and lymph nodes. Although PG45 showed slightly higher virulence in calves than HB0801, there was no statistical difference between the strains (P>0.05). Compared to Hubei-1, a total of 122 SNP loci were disclosed in HB0801. In conclusion, although genomic plasticity was thought to be an evolutionary advantage, it did not apparently affect virulence of M. bovis strains in cattle.
An integrated monitoring and data analysis system to evaluate the effects of lightning activity on distribution networks

Overhead power distribution lines have significant power quality variations (voltage transients) during thunderstorms. Lightning strokes, whether direct or indirect, are among the main causes of such power quality disturbances. In order to assist the analysis of lightning effects on power quality indices, we present in this paper a monitoring network and an integrated database analysis, including voltage waveform recorders, local electric field measurement, information from Lightning Location Systems, and utility databases. The idea is to present a general procedure to indicate the correlation between lightning and power quality events (mainly short-circuits) in the monitored distribution network. Also, we present an automatic waveform analysis that allows the automatic segmentation and classification of transients in a waveform and a simulation procedure that assists the correlation process. Finally, we present an initial case study addressing the advantages and relevant correlations that can be obtained from the proposed approach.
Improving M-SBL for Joint Sparse Recovery Using a Subspace Penalty

A multiple measurement vector problem (MMV) is a generalization of the compressed sensing problem that addresses the recovery of a set of jointly sparse signal vectors. One of the important contributions of this paper is to show that the seemingly least related state-of-the-art MMV joint sparse recovery algorithms - the M-SBL (multiple sparse Bayesian learning) and subspace-based hybrid greedy algorithms - have a very important link. More specifically, we show that replacing the log det(·) term in the M-SBL by a rank surrogate that exploits the spark reduction property discovered in the subspace-based joint sparse recovery algorithms provides significant improvements. In particular, if we use the Schatten-p quasi-norm as the corresponding rank surrogate, the global minimizer of the cost function in the proposed algorithm becomes identical to the true solution as p → 0. Furthermore, under regularity conditions, we show that convergence to a local minimizer is guaranteed using an alternating minimization algorithm that has closed form expressions for each of the minimization steps, which are convex. Numerical simulations under a variety of scenarios in terms of SNR and the condition number of the signal amplitude matrix show that the proposed algorithm consistently outperformed the M-SBL and other state-of-the art algorithms.
2016 Ieee International Conference on Big Data (big Data) Predicting the Shape and Peak Time of News Article Views

—Predicting the popularity of news articles— whether measured via retweets, clicks, or views—is an important problem for editors, journalists, and readers alike. In this paper, we introduce a new model to predict the shape of news article views, and use this model to determine when an article will likely reach its maximum number of views. Although volume prediction for news articles has been extensively studied predicting when a burst of views will happen, in what shape, and by how much, remains an open problem. We engineer several classes of features (metadata, contextual or content-based, temporal, and social), develop models to classify shape of views, with particular attention paid to performing online, time-updated, prediction, i.e., using data before and during the early stages of article prediction to predict its eventual peak views and update earlier predictions. The system presented here is an emerging application being developed at The Washington Post and can be used to support article placement, updating, and promotion strategies.