Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxidative Stress Markers in Aqueous Humor of Patients with Senile Cataracts

Purpose: To investigate the levels of oxidative stress markers in human eyes with senile cataracts. Methods: We conducted a retrospective, case-controlled study of 57 patients with senile cataracts. To assess oxidative stress markers in the eye, we measured the enzymatic activities of superoxide dismutase (SOD) and catalase (CAT) as well as the total protein levels in aqueous humor. Results: In aqueous humor, SOD and CAT activity levels were 0.133 ± 0.020 and 1.223 ± 0.081 U/ml, respectively; protein levels were 2.372 ± 0.166 mg/ml (means ± SEM). We observed a significant increase in SOD activity and the protein level in progressed nuclear cataracts. No significant age-associated difference in antioxidant enzyme levels was detected. Conclusion: Significant increases in the levels of SOD activity and total protein correlated with the severity of the cataract but not with patient age, suggesting that progressed cataract is associated with molecules leaking from the lens capsule.
Roundup Ready Soybean Technology and Farm Production Costs

Roundup Ready soybean technology (RR) lowers adopters' costs by (a) allowing postemergence use of the inexpensive herbicide glyphosate, (b) saving on management costs because of simple use, and (c) cutting risk by widening the time window for postemergence spraying. RR lowers nonadopters' costs by (d) creating competition that lowers other herbicides' prices. Our empirical results suggest that for most farms (a) is insufficient to cover the RR seed price premium, so (b) and (c) must be substantial for many adopters. Preliminary results indicate that RR provides bigger cost savings in the western Corn Belt than the eastern. Oligopolistic RR suppliers have set its price premium higher than potential cost/risk savings on many farms. We conclude that RR will not be fully adopted soon.
Perceived communicative intent in gesture and language modulates the superior temporal sulcus

Behavioral evidence and theory suggest gesture and language processing may be part of a shared cognitive system for communication. While much research demonstrates both gesture and language recruit regions along perisylvian cortex, relatively less work has tested functional segregation within these regions on an individual level. Additionally, while most work has focused on a shared semantic network, less has examined shared regions for processing communicative intent. To address these questions, functional and structural MRI data were collected from 24 adult participants while viewing videos of an experimenter producing communicative, Participant‐Directed Gestures (PDG) (e.g., “Hello, come here”), noncommunicative Self‐adaptor Gestures (SG) (e.g., smoothing hair), and three written text conditions: (1) Participant‐Directed Sentences (PDS), matched in content to PDG, (2) Third‐person Sentences (3PS), describing a character's actions from a third‐person perspective, and (3) meaningless sentences, Jabberwocky (JW). Surface‐based conjunction and individual functional region of interest analyses identified shared neural activation between gesture (PDGvsSG) and language processing using two different language contrasts. Conjunction analyses of gesture (PDGvsSG) and Third‐person Sentences versus Jabberwocky revealed overlap within left anterior and posterior superior temporal sulcus (STS). Conjunction analyses of gesture and Participant‐Directed Sentences to Third‐person Sentences revealed regions sensitive to communicative intent, including the left middle and posterior STS and left inferior frontal gyrus. Further, parametric modulation using participants' ratings of stimuli revealed sensitivity of left posterior STS to individual perceptions of communicative intent in gesture. These data highlight an important role of the STS in processing participant‐directed communicative intent through gesture and language. Hum Brain Mapp 37:3444–3461, 2016. © 2016 Wiley Periodicals, Inc.
Investigating the occupational etiology of prostate cancer in Canadian men

Prostate cancer is one of the most commonly diagnosed cancers worldwide and the etiology of prostate cancer is poorly understood. Aside from non-modifiable factors, there is limited understanding of modifiable risk factors for prostate cancer, including occupation. In epidemiological studies, job titles are generally classified into occupational or more broadly industry groupings. Previous studies have reported inconsistent findings between occupation, industry, and prostate cancer, with weak associations for farming and agriculture, rubber manufacturing, and transportation. In Canada, there have been very few large population studies that include a range of occupation and industry groups, prostate cancer outcomes, and information on non-occupational factors. The purpose of this thesis was to further investigate the occupational etiology of prostate cancer in Canadian men. By identifying occupations and industries using multiple large Canadian population based datasets, we aimed to identify consistent patterns of the multi-faceted prostate cancer – job-industry relationships. Three population based studies and one meta-analysis were conducted. Significant associations between natural resource based (agriculture, forestry, logging, wood, paper), administrative, protective services (firefighters, police, and armed forces), construction, transportation, and prostate cancer risk were observed in the three population studies. Consistent evidence for increased prostate cancer incidence and mortality among firefighting and police work was observed in the meta-analysis. Non-occupational factors including lifestyle factors and screening behaviours were also potential confounders in the
STUDY OF EXPLANATORY FACTORS OF AUDIT QUALITY ASSURANCE: COMPARISON OF CANADA, FRANCE, JAPAN AND DENMARK CASES

The objective of this paper is on the one hand, to examine the differences of legal audit of four countries especially Canada, France, Japan and Denmark pertaining to four different judicial systems. In addition, to wonder about the factors which can influence audit quality assurance, particularly, those relating to judicial system of country, growth opportunities and ownership structure. The empirical results show, initially, that specificities of judicial system are positively associated with audit quality assurance appreciated by the size of audit firms. Then, growth opportunities influences partially the size of audit firms. Lastly, ownership structure does not seem to have a significant impact on the search for a high audit quality.
MicroRNA expression profiles and networks in CXCL12-stimulated human endometrial stromal cells

The chemokine stromal cell-derived factor-1 (C-X-C motif chemokine ligand 12; CXCL12) is important in the recruitment of leukocytes to the peritoneal cavity and the regulation of endometriotic tissue growth in endometriosis patients. However, the alterations in microRNA (miRNA) expression induced by CXCL12 remain to be fully elucidated. The present study evaluated key miRNAs in CXCL12-stimulated endometrial stromal cells (ESCs), and investigated the underlying cellular regulatory mechanisms of CXCL12 in endometriosis by building networks between miRNAs, genes and gene ontologies (GOs). Differential expression of miRNAs and mRNAs induced by CXCL12 stimulation in ESCs was measured using miRNA and gene chips, and it was observed that 35 miRNAs and 1,671 mRNAs were differentially expressed. Using potential target genes of the 35 miRNAs, intersections of these genes were examined and 63 intersection genes were identified. A total of 39 GOs were obtained for these intersection genes, based on information from GO databases, including immune cell chemoattractants, inflammatory and immune responses, and pathological processes of endometriotic lesions in endometriosis. In addition, miRNA-gene networks were built according to the GO and Kyoto Encyclopedia of Genes and Genomes databases. The present study, to the best of our knowledge, provides the most complete miRNAome and mRNAome profiles, and the most detailed investigation of the underlying cellular regulatory mechanisms, of the effects of CXCL12 in endometriosis. These results may facilitate the complete elucidation of the role of CXCL12 in endometriosis, and its underlying epigenetic mechanisms.
Cardiac Troponin I and Creatine Kinase Isoenzyme MB in Patients with Intradialytic Hypotension

Background: Intradialytic hypotension (IH) has been long recognized as a common complication during hemodialysis (HD) therapy, but few studies have discussed IH-related myocardial injuries and the long-term prognosis of patients prone to IH (HP). Methods: We conducted a prospective study on 70 chronic HD patients who had no recent occurrences of acute coronary artery syndrome. The patients were divided into two groups: HP (n = 29) and IH resistant (n = 41). While they underwent HD therapy, we monitored and evaluated their baseline data and their patterns of cardiac troponin I (cTnI), creatine kinase, and creatine kinase isoenzyme MB. Results: The HP and IH-resistant patients had similar baseline cardiac marker levels that did not seem to be influenced by uneventful HD therapy. However, if during HD therapy the patients experienced an episode of symptomatic IH, they were found to have significant increases in the creatine kinase MB activity at the end of HD therapy and in the cTnI levels 44 h following HD. After 12 months, the HP patients with baseline cTnI levels ≧0.20 ng/ml were more likely to experience cardiovascular events or death (adjusted odds ratio 15.0, p = 0.012). Conclusions: Our study showed that, after symptomatic IH episodes, the HP patients were more likely to suffer occult myocardial injuries. HP patients who have high cTnI levels should be closely monitored for cardiovascular diseases.
Recognition of peptide epitopes of the 16,000 MW antigen of Mycobacterium tuberculosis by murine T cells.

The T-cell repertoire to a prominent immunogen of Mycobacterium tuberculosis has been investigated on the assumption that differences in epitope specificity could influence the protective and pathogenic host reactions. Proliferative responses of lymph node and spleen cells to overlapping peptides, spanning the entire sequence of the 16,000 MW protein antigen were analysed in C57BL/10 and B10.BR mice. Following footpad priming and in vitro challenge with homologous peptide, 12 out of the 14 peptides tested were found to be immunogenic. However, only two peptides of residues 31-40 and 71-91 stimulated strong proliferative responses of T cells from mice which had been presensitized with either killed or live M. tuberculosis organisms; another three peptides were only weakly stimulatory. These epitopes have been immunodominant in both H-2b and H-2k mouse strains, indicating the genetically permissive nature of their recognition. Furthermore, both major immunodominant epitopes were found to be species specific for the M. tuberculosis complex and therefore potentially suitable for the early diagnosis of tuberculous infection.
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.

The comprehensive inventory of functional elements in 44 human genomic regions carried out by the ENCODE Project Consortium enables for the first time a global analysis of the genomic distribution of transcriptional regulatory elements. In this study we developed an intuitive and yet powerful approach to analyze the distribution of regulatory elements found in many different ChIP-chip experiments on a 10 approximately 100-kb scale. First, we focus on the overall chromosomal distribution of regulatory elements in the ENCODE regions and show that it is highly nonuniform. We demonstrate, in fact, that regulatory elements are associated with the location of known genes. Further examination on a local, single-gene scale shows an enrichment of regulatory elements near both transcription start and end sites. Our results indicate that overall these elements are clustered into regulatory rich "islands" and poor "deserts. " Next, we examine how consistent the nonuniform distribution is between different transcription factors. We perform on all the factors a multivariate analysis in the framework of a biplot, which enhances biological signals in the experiments. This groups transcription factors into sequence-specific and sequence-nonspecific clusters. Moreover, with experimental variation carefully controlled, detailed correlations show that the distribution of sites was generally reproducible for a specific factor between different laboratories and microarray platforms. Data sets associated with histone modifications have particularly strong correlations. Finally, we show how the correlations between factors change when only regulatory elements far from the transcription start sites are considered.
Enhancement of Cellulase (CMCase) production from marine actinomycetes Streptomyces sp. Bse 7-9: Optimization of fermentation medium by Response Surface Methodology

Optimization of fermentation conditions is important in the development of bioprocesses. Here, we used the Taguchi experimental design and Response Surface Methodology to optimize fermentation medium for enhancing carboxymethyl cellulase (CMCase) production by marine actinomycetes Streptomyces sp. Bse 7-9. Optimization using the Taguchi experimental design we found that bagasse has a significant effect on other factors. The Central Composite Design was used to determine the interaction between the factors selected in the fermentation medium to obtain the optimal concentration of ingredients. The experimental results demonstrated that bagasse as a carbon source plays as the key component for the production of CMCase by marine actinomycetes Streptomyces sp. Bse 7-9. In conclusion, the optimal fermentation medium for maximum cellulase production by marine actinomycete Streptomyces sp. Bse 7-9 was as follows: bagasse concentration (1.84 % w/v), yeast extract (0.5 % w/v) and CaSO4 (0.02 % w/v). The maximum activity of CMCase at this optimum medium was 4.496 U mL−1.
Correct Timing of dnaA Transcription and Initiation of DNA Replication Requires trans Translation

ABSTRACT The trans translation pathway for protein tagging and ribosome release has been found in all bacteria and is required for proliferation and differentiation in many systems. Caulobacter crescentus mutants that lack the trans translation pathway have a defect in the cell cycle and do not initiate DNA replication at the correct time. To determine the molecular basis for this phenotype, effects on events known to be important for initiation of DNA replication were investigated. In the absence of trans translation, transcription from the dnaA promoter and an origin-proximal promoter involved in replication initiation is delayed. Characterization of the dnaA promoter revealed two cis-acting elements that have dramatic effects on dnaA gene expression. A 5′ leader sequence in dnaA mRNA represses gene expression by >15-fold but does not affect the timing of dnaA expression. The second cis-acting element, a sequence upstream of the −35 region, affects both the amount of dnaA transcription and the timing of transcription in response to trans translation. Mutations in this promoter element eliminate the transcription delay and partially suppress the DNA replication phenotype in mutants lacking trans translation activity. These results suggest that the trans translation capacity of the cell is sensed through the dnaA promoter to control the timing of DNA replication initiation.
gag as well as myc sequences contribute to the transforming phenotype of the avian retrovirus FH3

The avian retrovirus FH3, like MC29 and CMII, encodes a Gag-Myc fusion protein. However, the FH3-encoded protein is larger, about 145 kDa, and contains almost the entire retroviral gag gene. In contrast to the other gag-myc avian retroviruses, FH3 fails to transform fibroblasts in vitro, although macrophages are transformed both in vitro and in vivo (C. Chen, B. J. Biegalke, R. N. Eisenman, and M. L. Linial, J. Virol. 63:5092-5100, 1989). We have used the polymerase chain reaction technique to obtain a molecular clone of FH3. Sequence analysis of the FH3 myc oncogene revealed a single proline----histidine change (position 223) relative to c-myc. However, substitution of the FH3 myc sequence with the chicken c-myc sequence did not alter the transformation potential of the virus. Hence, overexpression of the proto-oncogene as a Gag-Myc retroviral protein is sufficient for macrophage, but not fibroblast, transformation. After passage of FH3 in fibroblast cultures, a virus (FH3L) that is capable of rapidly transforming fibroblasts appears. The Gag-Myc protein encoded by FH3L is smaller (ca. 130 kDa) than that encoded by the original viral stock (FH3E). Sequencing of an FH3L molecular clone revealed a 212-amino-acid deletion within the Gag portion. Using FH3E/FH3L recombinants, we have demonstrated that the ability of encoded viruses to transform fibroblasts directly correlates with the presence of this deletion. Moreover, the addition of the Gag sequence deleted from FH3L to the MC29 oncoprotein significantly reduces its transforming activity as measured by focus assay. These data suggest that the C-terminal segment of Gag attenuates the oncogenic potential of Gag-Myc fusion proteins.
A Probabilistic Framework for Real-time 3D Segmentation using Spatial, Temporal, and Semantic Cues

In order to track dynamic objects in a robot’s environment, one must first segment the scene into a collection of separate objects. Most real-time robotic vision systems today rely on simple spatial relations to segment the scene into separate objects. However, such methods fail under a variety of realworld situations such as occlusions or crowds of closely-packed objects. We propose a probabilistic 3D segmentation method that combines spatial, temporal, and semantic information to make better-informed decisions about how to segment a scene. We begin with a coarse initial segmentation. We then compute the probability that a given segment should be split into multiple segments or that multiple segments should be merged into a single segment, using spatial, semantic, and temporal cues. Our probabilistic segmentation framework enables us to significantly reduce both undersegmentations and oversegmentations on the KITTI dataset [3, 4, 5] while still running in real-time. By combining spatial, temporal, and semantic information, we are able to create a more robust 3D segmentation system that leads to better overall perception in crowded dynamic environments.
Mapping protein energy landscapes with amide hydrogen exchange and mass spectrometry: I. A generalized model for a two‐state protein and comparison with experiment

Protein amide hydrogen exchange (HDX) is a convoluted process, whose kinetics is determined by both dynamics of the protein and the intrinsic exchange rate of labile hydrogen atoms fully exposed to solvent. Both processes are influenced by a variety of intrinsic and extrinsic factors. A mathematical formalism initially developed to rationalize exchange kinetics of individual amide hydrogen atoms is now often used to interpret global exchange kinetics (e.g., as measured in HDX MS experiments). One particularly important advantage of HDX MS is direct visualization of various protein states by observing distinct protein ion populations with different levels of isotope labeling under conditions favoring correlated exchange (the so‐called EX1 exchange mechanism). However, mildly denaturing conditions often lead to a situation where the overall HDX kinetics cannot be clearly classified as either EX1 or EX2. The goal of this work is to develop a framework for a generalized exchange model that takes into account multiple processes leading to amide hydrogen exchange, and does not require that the exchange proceed strictly via EX1 or EX2 kinetics. To achieve this goal, we use a probabilistic approach that assigns a transition probability and a residual protection to each equilibrium state of the protein. When applied to a small protein chymotrypsin inhibitor 2, the algorithm allows complex HDX patterns observed experimentally to be modeled with remarkably good fidelity. On the basis of the model we are now in a position to begin to extract quantitative dynamic information from convoluted exchange kinetics.
Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions.
Conditional Utility, Utility Independence, and Utility Networks

We introduce a new interpretation of two related notions - conditional utility and utility independence. Unlike the traditional interpretation, the new interpretation renders the notions the direct analogues of their probabilistic counterparts. To capture these notions formally, we appeal to the notion of utility distribution, introduced in previous paper. We show that utility distributions, which have a structure that is identical to that of probability distributions, can be viewed as a special case of an additive multiattribute utility functions, and show how this special case permits us to capture the novel senses of conditional utility and utility independence. Finally, we present the notion of utility networks, which do for utilities what Bayesian networks do for probabilities. Specifically, utility networks exploit the new interpretation of conditional utility and utility independence to compactly represent a utility distribution.
Accurate Approach in the Treatment of Oral Bisphosphonate–Related Jaw Osteonecrosis

AbstractBisphosphonate-related osteonecrosis of the jaw (BRONJ) is not completely understood and difficult to treat. Even though the occurrence of BRONJ is mainly related to the therapy with intravenous bisphosphonates (BPs), this article reports a case of long-term oral BP use and BRONJ occurrence. In addition, a literature review provides some additional information about BPs, BRONJ, and also a guideline for the prevention and treatment of BRONJ stages. A 79-year-old patient presented intense and persistent pain, purulent secretion, and exposed bone at the right side of the lower jaw. Thus, she was submitted to anamnesis, radiologic and tomographic examinations, and bacterial culture and sensitivity tests. These procedures were followed by surgical debridement of the bone and surrounding tissues/cyst and antibiotic prescription and histopathologic analysis of the fragments. Together, the examinations performed showed the occurrence of stage 2 BRONJ. Moreover, the antibiotic prescription, discontinuation of oral BP, and surgical procedures ensure that the patient had no more symptoms. Therefore, considering the presented case, we believe that an accurate approach is promising to diagnose and treat stage 2 BRONJ and other associated pathologic findings.