Miracle-dz/UniFAR-FTUs huggingface dataset:
VEGFA, FLT1, KDR and colorectal cancer: Assessment of disease risk, tumor molecular phenotype, and survival

Angiogenesis is essential for tumor progression. Vascular endothelial growth factor (VEGFA) and its receptors 1 (FLT1) and 2 (KDR), have been identified as major mediators of this process. We hypothesized that genetic variation in FLT1 (38 SNPs), KDR (22 SNPS), and VEGFA (11 SNPs) would be associated with colon and rectal cancer development and survival. Data from a case–control study of 1555 colon cancer cases and 1956 controls and 754 rectal cancer cases and 959 controls were used. An adaptive rank truncation product (ARTP), based on 10 000 permutations, was used to determine the statistical significance of the candidate genes and angiogenesis pathway. Based on ARTP results, FLT1 was significantly associated with risk of colon cancer (PARTP = 0.045) and VEGFA was significantly associated with rectal cancer (PARTP = 0.036). After stratifying by tumor molecular subtype, SNP associations observed for colon cancer were: VEGFA rs2010963 with CIMP+ colon tumors; FLT1 rs4771249 and rs7987649 with TP53; FLT1 rs3751397, rs7337610, rs7987649, and rs9513008 and KDR rs10020464, rs11941492, and rs12498529 with MSI+ and CIMP+/KRAS2‐mutated tumors. FLT1 rs2296189 and rs600640 were associated with CIMP+ rectal tumors and FLT1 rs7983774 was associated with TP53‐mutated rectal tumors. Four SNPs in FLT1 were associated with colon cancer survival while three SNPs in KDR were associated with survival after diagnosis with rectal cancer. Aspirin/NSAID use, smoking cigarettes, and BMI modified the associations. These findings suggest the importance of inflammation and angiogenesis in the etiology of colorectal cancer and that genetic and lifestyle factors may be targets for modulating disease risk. © 2013 Wiley Periodicals, Inc.
Improving the performance of skin segmentation in quasi-skin regions via multiple classifier system

This paper presents a skin segmentation method based on multiple classifier system strategy in order to improve the performance of classification especially in quasi-skin regions. Quasi-skin regions in digital images are non-skin patches which have characteristics like the human skin and are known as a basic origin of misclassification error in skin segmentation. To cope with this problem, we have designed an algorithmic architecture by combining four prominent classifiers to construct a synergy to conceal their weaknesses and amplify their strengths. Participant classifiers in our approach include cellular learning automaton, likelihood, Gaussian and Support Vector Machines in which decision making performs via a conditional voting step. The accuracy and specificity were employed to evaluate the performance. Experiments on a collected test-set database including 142 challenging images demonstrate that the proposed skin detector is able to improve the accuracy and specificity up to 1.92% and 0.83%, respectively, than the best of individual classifier.
A novel approach for feature quantization using one-dimensional histogram

A new approach for quantizing feature vectors of interest points is proposed in this study. The method utilizes the histograms which work as a dimensionality reduction algorithm for quantizing the local and global features. The performance of activity recognition is generally depend upon the quantity of significant features but with proper feature quantization one can delivered the same performance with less number of features. The basic characteristics of algorithm are discussed and demonstrated by experiment. It is scalable in nature and work efficiently under varying conditions. In an experiment section, we show that our novel feature quantization approach takes less number of features in compared to standard quantization, while delivering the same performance.
Lectins : An Analysis

Introduction: The study of lectins began with the work of Hermann Stillmark in the year 1888. Lectins are carbohydratebinding proteins of nonimmune origin and find application in diagnostic pathology. Objectives: Recent research work shows a remarkable development in lectin science. This comprehensive review tries to emphasize the historical aspects, biological sources, classification, applications, and recent advances of lectins. Materials and methods: Electronic database searches for published literature were performed. The following electronic databases with no language and publication date restrictions were searched: MEDLINE (via Ovid and PubMed), EMBASE (via Ovid), the Cochrane Oral Health Group’s Trials Register, and CENTRAL. Results: Lectins have been proven to be effective in in vitro trials for combating many medical conditions like cancer, autoimmune disorders, etc. Conclusion: Lectins could be the next generation therapy if efficient research work is contributed to the understanding of their behavior.
Proctographic features of anismus.

PURPOSE To document the proctographic features of anismus at evacuation proctography and determine the optimum radiologic measurements for diagnosis. MATERIALS AND METHODS Twenty-four patients with anismus according to clinical and multiple physiologic criteria were examined with evacuation proctography. Structural and functional measurements were compared with those of a group of 20 asymptomatic subjects. RESULTS No significant difference between patients and control subjects was found with respect to pelvic descent, rectocele, or any anorectal angle measurement. In patients with anismus, initiation of evacuation was prolonged (median, 9 vs 3 seconds for control subjects; P < .0001) and anal canal width was reduced (median, 0.6 vs 1.2 cm; P = .0075). Evacuation time was increased (median, 50 vs 10 seconds; P < .0001), and the percentage of contrast material evacuated was decreased (median, 60% vs 100%; P < .0001). Only four patients were able to evacuate more than 66% of the contrast material within 30 seconds, whereas all control subjects were able to do so. CONCLUSION Measurement of the anorectal angle to diagnose anismus should be abandoned. Patients with anismus demonstrate delayed initiation of evacuation, which is also prolonged and incomplete. Incomplete evacuation after 30 seconds is highly suggestive of anismus.
Contribution of relative sea‐level rise to historical hurricane flooding in New York City

Flooding during hurricanes is a hazard for New York City. Flood height is determined by storm surge characteristics, timing (high or low tide) and relative sea‐level (RSL) change. The contribution from these factors is estimated for seven historical hurricanes (1788–2012) that caused flooding in New York City. Measurements from The Battery tide gauge and historical accounts are supplemented with a RSL reconstruction from Barnegat Bay, New Jersey. RSL was reconstructed from foraminifera preserved in salt‐marsh sediment that was dated using marker horizons of lead and copper pollution and 137Cs activity. Between the 1788 hurricane and Hurricane Sandy in 2012, RSL rose by 56 cm, including 15 cm from glacio‐isostatic adjustment. Storm surge characteristics and timing with respect to astronomical tides remain the dominant factors in determining flood height. However, RSL rise will raise the base level for flood heights in New York City and exacerbate flooding caused by future hurricanes. Copyright © 2013 John Wiley & Sons, Ltd.
Assessment of Knowledge and Perception Towards Modern Contraceptives Use Among Women of Reproductive Age in Mtwivila, Tanzania

This study was conducted in 2014 in Mtwivila, Tanzania. The objective of the study was to assess knowledge, perception and factors associated with use of modern contraceptive use among women. Simple random sampling technique was used to select a representative sample of 96 women aged 15-49 years. Data were collected through interviews, focus group discussions and documentary reviews. Findings show that knowledge of modern FP was almost universal (100% percent), although 79 (82.3 percent) claimed to have been using modern contraceptives methods. Much smaller proportion (17.7 percent) reported not to be using modern contraceptives during the time of interview. Most of the respondents (96%) had positive attitude on modern contraceptive use as 96 of all interviewed women stated contraceptives were effective for birth control and that they would recommend to a friend or a relative the use of modern contraceptive. However, 28% women reported having stopped using modern contraceptive of which 25% due to side effects. Chi-square confirmed the association of education, sources of information about contraceptives, occupation, household income, distance from the health center and husband's involvement with the use of contraceptives among women. It is concluded that there is a good level of knowledge and a positive perception towards contraceptive use among women of reproductive age. Men involvement during sensitization on family planning would be an effective strategy toward sexual and reproductive health promotion.
Differences in the secretome of cartilage explants and cultured chondrocytes unveiled by SILAC technology

The main goal of our study was to analyze and compare the profiles of secreted proteins from adult human articular chondrocytes in monolayers, and cartilage explants in culture, using a de novo protein labeling approach. Stable isotope labeling of proteins in culture was used to differentiate between chondrocyte‐derived proteins and other preexisting matrix‐derived components, or proteins coming from serum or synovial fluids. Proteins in culture supernatants were resolved by one‐dimensional SDS‐PAGE electrophoresis, and analyzed in tandem with LC/MS‐MS (liquid chromatography/double mass spectrometry). Results from stable isotope labeling with amino acids in cell culture (SILAC) were validated by specific immunoblotting of four relevant proteins identified in the secretion media. After 8–10 days of culture, over 90% of proteins secreted during monolayer growth contained 13C6‐Arg and 13C6‐Lys. Nonlabeled proteins corresponded mostly to plasma‐associated proteins, indicating background contamination of medium with serum remnants. The majority of the secreted proteins in 2D cultures were extracellular matrix components and matrix regulators, along with some inflammatory agents and metabolic enzymes. In explants, only 25%–30% of proteins were labeled with heavy amino acids, corresponding to matrix regulators and carrier molecules. Nonlabeled proteins corresponded primarily to structural matrix components. In qualitative terms, all labeled proteins coming from cartilage explants were also found in chondrocytes supernatants. In summary, our results show differences in the labeling pattern of proteins found in supernatants from explants and monolayers. Most proteins found in the media of explants were subproducts of matrix turnover rather than newly synthesized. To our knowledge, this study is the first one so far applying SILAC technology in the context of cartilage and chondrocytes physiology. © 2010 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 28:1040–1049, 2010
ANTIOXIDATIVE PROPERTIES OF Plantago lanceolata L . EXTRACTS EVALUATED BY CHEMILUMINESCENCE METHOD

Plantago lanceolata L. is used as astringent, anti-inflammatory, immunoregulatory, antispasmodic, expectorant, emollient, topical anodyne, antibacterial for cuts, bruises and abscesses. These pharmacological properties are due to its complex chemical composition: iridoid glycosides, polysaccharides (plantaglucide, glucomannon), terpenoids, coumarins, lignans, caffeic acid derivatives, polysaccharides, flavonoids, flavone glycosides and other constituents, like allantoin. In this paper, antioxidant activity, qualitative and quantitative determination of some active components (flavonoids, polyphenols, and polyphenols carboxylic acids) are evaluated, taking into account the biological properties. Antioxidant properties were evaluated by chemiluminescence (CL) technique in system generator based at 5-amino-2.3dihydrophthalazine-1.4-dione and hydrogen peroxide, in alkaline medium and DPPH (2.2-diphenyl-1-picrylhydrazyl) method. The total flavonoids, polyphenols content and polyphenol carboxylic acids was spectrophotometrically determined according to Romanian Pharmacopoeia (FR). In addition, the qualitative biochemical fingerprint was investigated by mass spectrometry LC-ESI-MS. The mass spectral data and amount of active components (flavonoids, polyphenols, polyphenols carboxylic acids) demonstrated the chemical structural complexity. The results of the chemiluminescence in vitro tests revealed that the Plantago lanceolata L. extracts exhibit high antioxidant activity (84-96%), being in accordance with the value provided by DPPH free radical scavenging assay. Also is established a dependence directly proportional to the content of polyphenolic compounds found in herbal extracts with level of antioxidant activity.
Facilitating effects of exercise on information processing

The aim of this study was to examine the facilitating effects of moderate physical exercise on the reaction process to gain a better understanding of the interaction between physiological and cognitive processes. Sixteen participants with specific expertise in decision-making sports performed a double task consisting of choice reaction time while cycling. Signal quality, stimulus–response compatibility and time uncertainty were manipulated. Participants were tested at rest and while cycling at 20% and at 50% of their maximal aerobic power. A mood assessment questionnaire and a critical flicker fusion test were administered before and after the choice reaction time task. The results showed that moderate-intensity exercise (50% maximal aerobic power) improves cognitive performance and that low-intensity exercise (20% maximal aerobic power) enables participants to compensate the negative dual-task effect.
Biofilm Susceptibility to Antimicrobials

Microbial biofilms, where organisms are intimately associated with each other and a solid substratum through binding and inclusion within an exopolymer matrix, are widely distributed in nature and disease. In the mouth, multispecies biofilms are associated not only with dental plaque and tooth decay but also with soft tissues of the buccal cavity and with most forms of periodontal disease. Organization of micro-organisms within biofilms confers, on the component species, properties which are not evident with the individual species grown independently or as planktonic populations in liquid media. While many of these properties relate to the establishment of functional, mixed-species consortia within the exopolymeric matrices, others relate to the establishment of physico-chemical gradients, within the biofilm, that modify the metabolism of the component cells. A consequence of biofilm growth that has profound implications for their control in the environment and in medicine is a markedly enhanced resistance to chemical antimicrobial agents and antibiotics. Mechanisms associated with such resistance in biofilms will form the substance of the present review. While some aspects of biofilm resistance are yet only poorly understood, the dominant mechanisms are thought to be related to: (i) modified nutrient environments and suppression of growth rate within the biofilm; (ii) direct interactions between the exopolymer matrices, and their constituents, and antimicrobials, affecting diffusion and availability; and (iii) the development of biofilm/attachmentspecific phenotypes.
Analysis of zinc‐ligand bond lengths in metalloproteins: Trends and patterns

Zinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X‐ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Neural mechanism of cognitive control impairment in patients with hepatic cirrhosis: a functional magnetic resonance imaging study

Background: Many studies have claimed the existence of attention alterations in cirrhotic patients without overt hepatic encephalopathy (HE). No functional magnetic resonance imaging (fMRI) study in this respect has been published. Purpose: To investigate the neural basis of cognitive control deficiency in cirrhotic patients using fMRI. Material and Methods: 14 patients with hepatic cirrhosis and 14 healthy volunteers were included in the study. A modified Stroop task with Chinese characters was used as the target stimulus, and block-design fMRI was used to acquire resource data, including four stimulus blocks and five control blocks, each presented alternatively. Image analysis was performed using statistical parametric mapping 99. After fMRI examinations were complete, behavior tests of Stroop interference were performed for all subjects. Overall reaction time and error numbers were recorded. Results: Both healthy volunteers and patients with hepatic cirrhosis had Stroop interference effects. Patients with hepatic cirrhosis had more errors and longer reaction time in performing an incongruous color-naming task than healthy volunteers (P<0.001); there was no significant difference in performing an incongruous word-reading task (P = 0.066). Compared with controls, patients with hepatic cirrhosis had greater activation of the bilateral prefrontal cortex and parietal cortex when performing the incongruous word-reading task. With increased conflict, activation of the anterior cingulate cortex (ACC), bilateral prefrontal cortex (PFC), parietal lobe, and temporal fusiform gyrus (TFG) was decreased when patients with hepatic cirrhosis performed the incongruous color-naming task. Conclusion: This study demonstrates that patients with hepatic cirrhostic have cognitive control deficiency. The abnormal brain network of the ACC–PFC–parietal lobe–TFG is the neural basis of cognitive control impairment in cirrhotic patients.
Endotoxin induced cellular communication in the liver: Murine models for clarification of the role of LPS‐responsive macrophages in the pathogenesis of liver diseases

In several experimental models, lipopolysaccharide (LPS) plays an important role in the pathogenesis of liver diseases. Murine models of C3H/HeN and C3H/HeJ mice have been used to elucidate the role of LPS and its responsive‐macrophages in vivo, as C3H/HeN strain mice are known to be LPS‐responsive, while C3H/HeJ strain mice are LPS‐resistant. Furthermore, release of several kinds of biologically active mediators such as interleukin‐1, tumour necrosis factor‐α, colony stimulating factor and reactive oxygen radical is not enhanced in C3H/HeJ mice even after stimulation with LPS. Thus, these murine models could be suitable for clarification of endotoxin induced cellular communication in the liver.
Report printing as a Homing Mechanism in Pacific Salmon

Nathan F. Putman,1,* Kenneth J. Lohmann,2 Emily M. Putman,3 Thomas P. Quinn,4 A. Peter Klimley,5 and David L.G. Noakes1,6 1Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, OR 97331, USA 2Department of Biology, CB #3280, University of North Carolina, Chapel Hill, NC 27599, USA 3519 NW 14th Street, Corvallis, OR 97330, USA 4School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA 5Department of Wildlife, Fisheries, and Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA 6Oregon Hatchery Research Center, 2418 Fall Creek Road, Alsea, OR 97324, USA
Average-Voice-Based Speech Synthesis Using HSMM-Based Speaker Adaptation and Adaptive Training

In speaker adaptation for speech synthesis, it is desirable to convert both voice characteristics and prosodic features such as F0 and phone duration. For simultaneous adaptation of spectrum, F0 and phone duration within the HMM framework, we need to transform not only the state output distributions corresponding to spectrum and F0 but also the duration distributions corresponding to phone duration. However, it is not straightforward to adapt the state duration because the original HMM does not have explicit duration distributions. Therefore, we utilize the framework of the hidden semi-Markov model (HSMM), which is an HMM having explicit state duration distributions, and we apply an HSMM-based model adaptation algorithm to simultaneously transform both the state output and state duration distributions. Furthermore, we propose an HSMM-based adaptive training algorithm to simultaneously normalize the state output and state duration distributions of the average voice model. We incorporate these techniques into our HSMM-based speech synthesis system, and show their effectiveness from the results of subjective and objective evaluation tests.
Use of cooled radiofrequency lateral branch neurotomy for the treatment of sacroiliac joint-mediated low back pain: a large case series.

BACKGROUND. : The sacroiliac joint (SIJ) complex has been identified as a common source of chronic low back pain. Radiofrequency (RF) neurotomy has been investigated in recent years as a minimally invasive treatment option for SIJ-mediated low back pain. A number of RF neurotomy methodologies have been investigated, including the use of cooled RF. OBJECTIVE. : To retrospectively evaluate the use of cooled RF lateral branch neurotomy (LBN) to treat chronic SIJ-mediated low back pain in a large European study population. STUDY DESIGN. : The electronic records of 126 patients with chronic low back pain who underwent treatment with cooled RF LBN were identified. Subjects were selected for treatment based on physical examination and positive response (≥50% pain relief) to an intra-articular SIJ block. Cooled RF LBN involved lesioning the L5 dorsal ramus and lateral to the S1, S2, and S3 posterior sacral foraminal apertures. Visual analog scale (VAS) pain scores, quality of life, medication usage, and satisfaction were collected before the procedure, at 3-4 weeks postprocedure (N = 97), and once again between 4 and 20 months postprocedure (N = 105). RESULTS. : When stratified by time to final follow-up (4-6, 6-12, and >12 months, respectively): 86%, 71%, and 48% of subjects experienced ≥50% reduction in VAS pain scores, 96%, 93%, and 85% reported their quality of life as much improved or improved, and 100%, 62%, and 67% of opioid users stopped or decreased use of opioids. CONCLUSIONS. : The current results show promising, durable improvements in pain, quality of life, and medication usage in a large European study population, with benefits persisting in some subjects at 20 months after treatment. These results are consistent with previous study findings on the use of cooled RF to treat SIJ-mediated low back pain.