Miracle-dz/UniFAR-FTUs huggingface dataset:
Adherence to the Mediterranean diet and gastric cancer risk in Italy

We investigated gastric cancer risk in relation to the adherence to the Mediterranean diet using data from two case–control studies conducted in Italy between 1985 and 2007, including 999 incidents, histologically confirmed gastric cancers and 2,628 controls admitted to hospital for acute non‐neoplastic diseases. Adherence to the Mediterranean diet was assessed using the Mediterranean Diet Score (MDS) based on nine of the major characteristics of the Mediterranean diet in the overall dataset. The Mediterranean Dietary Pattern adherence index (MDP) and the Mediterranean Adequacy Index (MAI) were considered in the second study only. We estimated odds ratios (OR) and corresponding 95% confidence intervals (CI) of gastric cancer for categories of the three scores using multiple logistic regression models. We found a reduced risk of gastric cancer for increasing levels of the MDS: as compared to subjects in the lowest category of the MDS, the ORs were 0.78, 0.61 and 0.57 in subsequent levels of MDS, with a significant trend in risk. Risk estimates were consistent across strata of age, sex, education, smoking, body mass index, and family history of gastric cancer. We also observed a decreased risk of gastric cancer for the highest versus the lowest quintile for MDP and MAI, with OR of 0.58 and 0.71, respectively. Our study provides convincing evidence of a beneficial role of the Mediterranean diet on gastric cancer.
An image encryption system based on generalized discrete maps

This paper presents a simple encryption technique that uses different generalized discrete maps to achieve better performance. A summary of the generalized logistic, tent and sine maps is presented where one of the main advantages of the generalized maps is the extra parameters. Those extra parameters increase the system degrees of freedom, enrich the performance and expand the chaotic range. The presented three generalized maps have 13 parameters and initial conditions and can be used to construct an effective encryption key. Three different map combinations are investigated with the results of their security analysis, NIST test suite and sensitivity analysis.
A Genome-Wide Screen to Identify Transcription Factors Expressed in Pelvic Ganglia of the Lower Urinary Tract

Relative positions of neurons within mature murine pelvic ganglia based on expression of neurotransmitters have been described. However the spatial organization of developing innervation in the murine urogenital tract (UGT) and the gene networks that regulate specification and maturation of neurons within the pelvic ganglia of the lower urinary tract (LUT) are unknown. We used whole-mount immunohistochemistry and histochemical stains to localize neural elements in 15.5 days post coitus (dpc) fetal mice. To identify potential regulatory factors expressed in pelvic ganglia, we surveyed expression patterns for known or probable transcription factors (TF) annotated in the mouse genome by screening a whole-mount in situ hybridization library of fetal UGTs. Of the 155 genes detected in pelvic ganglia, 88 encode TFs based on the presence of predicted DNA-binding domains. Neural crest (NC)-derived progenitors within the LUT were labeled by Sox10, a well-known regulator of NC development. Genes identified were categorized based on patterns of restricted expression in pelvic ganglia, pelvic ganglia and urethral epithelium, or pelvic ganglia and urethral mesenchyme. Gene expression patterns and the distribution of Sox10+, Phox2b+, Hu+, and PGP9.5+ cells within developing ganglia suggest previously unrecognized regional segregation of Sox10+ progenitors and differentiating neurons in early development of pelvic ganglia. Reverse transcription-PCR of pelvic ganglia RNA from fetal and post-natal stages demonstrated that multiple TFs maintain post-natal expression, although Pax3 is extinguished before weaning. Our analysis identifies multiple potential regulatory genes including TFs that may participate in segregation of discrete lineages within pelvic ganglia. The genes identified here are attractive candidate disease genes that may now be further investigated for their roles in malformation syndromes or in LUT dysfunction.
Correlated Data Gathering With Double Trees in Wireless Sensor Networks

The problem of correlated data gathering in wireless sensor networks is studied in this paper. For the sake of efficiency, tree transmission structures are often used for data gathering. Previously, the problem of minimizing the total communication cost with a single-tree transmission structure was shown to be NP-hard. However, when the explicit communication approach is used, the total communication cost can be further reduced, provided a double-tree transmission structure is used and inverse links are allowed. This motivates us to devise a double-tree routing scheme in which two trees are used for data transmission, one carrying raw data and the other carrying encoded data. We show that with the double-tree routing scheme, the problem of minimizing the total communication cost remains NP-hard. A distributed algorithm for solving it is suggested. We show that under the simple correlation model, the algorithm has an approximation ratio of two. Extensive simulations are conducted to verify the effectiveness of the double-tree routing scheme.
Randomized trial of subfascial infusion of ropivacaine for early recovery in laparoscopic colorectal cancer surgery

Background There is a need for investigating the analgesic method as part of early recovery after surgery tailored for laparoscopic colorectal cancer (LCRC) surgery. In this randomized trial, we aimed to investigate the analgesic efficacy of an inverse ‘v’ shaped bilateral, subfascial ropivacaine continuous infusion in LCRC surgery. Methods Forty two patients undergoing elective LCRC surgery were randomly allocated to one of two groups to receive either 0.5% ropivacaine continuous infusion at the subfascial plane (n = 20, R group) or fentanyl intravenous patient controlled analgesia (IV PCA) (n = 22, F group) for postoperative 72 hours. The primary endpoint was the visual analogue scores (VAS) when coughing at postoperative 24 hours. Secondary end points were the VAS at 1, 6, 48, and 72 hours, time to first flatus, time to first rescue meperidine requirement, rescue meperidine consumption, length of hospital stay, postoperative nausea and vomiting, sedation, hypotension, dizziness, headache, and wound complications. Results The VAS at rest and when coughing were similar between the groups throughout the study. The time to first gas passage and time to first rescue meperidine at ward were significantly shorter in the R group compared to the F group (P = 0.010). Rescue meperidine was administered less in the R group; however, without statistical significance. Other study parameters were not different between the groups. Conclusions Ropivacaine continuous infusion with an inverse ‘v ’ shaped bilateral, subfascial catheter placement showed significantly enhanced bowel recovery and analgesic efficacy was not different from IV PCA in LCRC surgery.
COFFEE: an objective function for multiple sequence alignments

MOTIVATION In order to increase the accuracy of multiple sequence alignments, we designed a new strategy for optimizing multiple sequence alignments by genetic algorithm. We named it COFFEE (Consistency based Objective Function For alignmEnt Evaluation). The COFFEE score reflects the level of consistency between a multiple sequence alignment and a library containing pairwise alignments of the same sequences. RESULTS We show that multiple sequence alignments can be optimized for their COFFEE score with the genetic algorithm package SAGA. The COFFEE function is tested on 11 test cases made of structural alignments extracted from 3D_ali. These alignments are compared to those produced using five alternative methods. Results indicate that COFFEE outperforms the other methods when the level of identity between the sequences is low. Accuracy is evaluated by comparison with the structural alignments used as references. We also show that the COFFEE score can be used as a reliability index on multiple sequence alignments. Finally, we show that given a library of structure-based pairwise sequence alignments extracted from FSSP, SAGA can produce high-quality multiple sequence alignments. The main advantage of COFFEE is its flexibility. With COFFEE, any method suitable for making pairwise alignments can be extended to making multiple alignments. AVAILABILITY The package is available along with the test cases through the WWW: http://www. ebi.ac. uk/cedric CONTACT cedric.notredame@ebi.ac. uk
Processing of color- and noncolor-coded signals in the gourami retina. II. Amacrine cells.

The same set of stimuli and analytic methods that was used to study the dynamics of horizontal cells () was applied to a study of the response dynamics and signal processing in amacrine cells in the retina of the kissing gourami, Helostoma rudolfi. The retina contains two major classes of amacrine cells that could be identified from their morphology: C and N amacrine cells. C amacrine cells had a two-layered dendritic field, whereas N cells had a monolayered dendritic field. Both types of amacrine cell were tracer-coupled but coupling was more extensive in the N amacrine cells. Responses from C amacrine cells lacked a DC component and had a small linear component that was <10% in terms of mean square error (MSE); the second-order component often accounted for >50% of the modulation response. The C amacrine cells did not show any characteristic color coding under any stimulus condition. Most responses of N cells to a pulsatile stimulus consisted of a series of depolarizing transient potentials and steady illumination did not generate any DC potential in these cells. The response to a white-noise modulated input was composed of well-defined first- and second-order components and, possibly, higher-order components. The response evoked by a red or green white-noise-modulated stimulus given alone was not color coded. Modulated red illumination in the presence of a green illumination elicited a color-coded response from >70% of N amacrine cells. Color information was carried not only by the polarity but also by the dynamics of the first-order component. No convincing evidence was obtained to indicate that the second-order component might be involved in color processing. Some N amacrine cells produced a well-defined (second-order) interaction kernel to show that the temporal sequence of red and green stimuli was a parameter to be considered. In a complex cell such as an amacrine cell, responses evoked by a pulsatile stimulus given in darkness and by modulation of a mean luminance could be very different in terms of their characteristics. It was not always possible to predict the response evoked by one stimulus from observing the cell's response to another stimulus. This is because, in N cells, a flash-evoked (nonsteady state) response is composed largely of nonlinear components whereas a modulation (steady state) response is composed of linear as well as nonlinear components.
Response of Simian Virus 40-Transformed Cell Lines and Cell Hybrids to Superinfection with Simian Virus 40 and Its Deoxyribonucleic Acid

Whereas normal human and monkey cells were susceptible both to intact simian virus 40 (SV40) and to SV40 deoxyribonucleic acid (DNA), human and monkey cells transformed by SV40 were incapable of producing infectious virus after exposure to SV40, but displayed susceptibility to SV40 DNA. On the other hand, mouse and hamster cells, either normal or SV40-transformed, were resistant both to the virus and to SV40 DNA. Hybrids between permissive and nonpermissive parental cells revealed a complex response: whereas most hybrids tested were resistant, three of them produced a small amount of infectious virus upon challenge with SV40 DNA. All were resistant to whole virus challenge. The persistence of infectious SV40 DNA in permissive and nonpermissive cells up to 96 hr after infection was ascertained by cell fusion. The decay kinetics proved to be quite different in permissive and nonpermissive cells. Adsorption of SV40 varied widely among the different cell lines. Very low adsorption of SV40 was detected in nonsusceptible cells with the exception of the mKS-BU100 cell line. A strong increase in SV40 adsorption was produced by pretreating cells with polyoma virus. In spite of this increased adsorption, the resistance displayed by SV40-transformed cells to superinfection with the virus was maintained.
Modeling and Testing of a Micro-Tubular Low-Temperature Fuel Cell for use in a Micro Air Vehicle

Micro air vehicles (MAVs) are small remote controlled aircraft used by military personnel for reconnaissance and are currently powered by batteries. The MAVs rely on the battery for propulsion, navigation, and reconnaissance equipment. The thrust of this research is to develop a fuel cell system capable of higher energy densities, higher energy to weight ratios, and increased overall energy output than the batteries in use today. To this end, a feasibility study is first conducted to determine if fuel cells could be used to replace batteries as the MAV energy source and what fuel cell configurations would show the best performance. Hydrogen, methanol, and formic acid fuel cells are considered, using a conventional flat-plate design and a novel micro-tubular design. Several micro-tubular fuel cells (MTFCs) are tested to show that these cells are a possibility for energy production in MAVs. Those tested are developed and improved in collaboration between Luna Innovations, Inc. and the Center for Energy Systems Research at Virginia Tech and then manufactured by Luna Innovations, Inc. Also, an isothermal, lumped-parameter (LP) model for MTFCs is developed to predict behavior. The use of this LP model aids in understanding the dominant losses of the cell and ways of improving cell performance. Results from the feasibility study indicate that by using methanol powered MTFCs a 50% increase in overall energy output is possible, while also decreasing the mass of the power production system. Through testing and an iterative design process, an increase of three orders of magnitude of the maximum power production of the MTFCs constructed by Luna Innovations, Inc., has been realized. Results of the LP MTFC model are compared with the experimental results from the MTFC testing and tubular cells from the literature.
Association of ZEB1 and TCF4 rs613872 changes with late onset Fuchs endothelial corneal dystrophy in patients from northern India

Purpose Fuchs endothelial corneal dystrophy (FECD) results in loss of vision associated with progressive corneal edema and loss of corneal transparency. The aim of the study was to evaluate changes in ZEB1, COL8A2, SLC4A11, and TCF4 rs613872 and correlate them with clinical findings. Methods Eighty-two patients with clinically diagnosed FECD and 143 controls were recruited during the period 2007–2012. Clinical details, pedigree information up to three generations, and 5 ml of blood samples were collected. Histopathological and transmission electron microscopy studies were performed on host corneal buttons from patients who underwent keratoplasty. Genomic DNA from blood was processed for PCR amplification followed by direct sequencing to screen genetic changes in the candidate genes. The pathogenic nature of the genetic variants was assessed using Sorting Intolerant From Tolerant (SIFT) and MutationTaster. Results The mean age at the onset of symptoms was 59.14±1.41years, the male to female ratio was 1:1.5, and the mean specular count (endothelial cell density) was 1629±93.62 cells/mm2 with a mean central corneal thickness (CCT) of 617.30±15.73 µm. ZEB1 showed a novel variant IVS2+276 C/T in 14% of the cases, a novel nonsense p.Leu947stop mutation in one patient, two novel missense mutations (p.Glu733Lys, p.Ala818Val) in one patient each, and one novel synonymous variation (p.Ser234Ser) in two patients. Reported mutation p.Gln840Pro and five polymorphisms were also identified. The TCF4 single nucleotide polymorphism (SNP) rs613872 was significantly higher in patients with FECD. Conclusions This is the first report of genetic variations in ZEB1 and TCF4 SNP rs613872 in patients with FECD from northern India that suggests a possible role in disease pathogenesis and the regulation of endothelial cell density.
Immunocytochemical Method for Early Laboratory Diagnosis of Tuberculous Meningitis

ABSTRACT A simple immunocytochemical method was standardized for the direct demonstration of mycobacterial antigen in cerebrospinal fluid (CSF) specimens of patients with tuberculous meningitis (TBM). CSF-cytospin smears were prepared from 22 patients with a clinical diagnosis of TBM and also from an equal number of patients with nontuberculous neurological diseases (disease control). Immunocytological demonstration of mycobacterial antigens in the cytoplasm of monocytoid cells was attempted, by using rabbit immunoglobulin G to Mycobacterium tuberculosis as the primary antibody. Of the 22 CSF-cytospin smears from TBM patients, 16 showed positive immunostaining, while all of the CSF-cytospin smears from the disease control showed negative immunostaining for mycobacterial antigen. The technical aspects of this immunocytological method for the demonstration of mycobacterial antigens are simple, rapid, and reproducible, as well as specific, and therefore can be applied for the early diagnosis of TBM, particularly in patients in whom bacteriological methods did not demonstrate the presence of M. tuberculosis in the CSF.
Complete and optimal visibility-based pursuit-evasion

This paper computes a minimum-length pursuer trajectory that solves a visibility-based pursuit-evasion problem in which a single pursuer moving through a simply-connected polygonal environment seeks to locate an evader which may move arbitrarily fast, using an omni-directional field-of-view that extends to the environment boundary. We present a complete algorithm that computes a minimum-cost pursuer trajectory that ensures that the evader is captured, or reports in finite time that no such trajectory exists. This result improves upon the known algorithm of Guibas, Latombe, LaValle, Lin, and Motwani, which is complete but makes no guarantees about the quality of the solution. Our algorithm employs a branch-and-bound forward search that considers pursuer trajectories that could potentially lead to an optimal pursuer strategy. The search is performed on an exponential graph that can generate an infinite number of unique pursuer trajectories, so we must conduct meticulous pruning during the search to quickly discard pursuer trajectories that are demonstrably suboptimal. We describe an implementation of the algorithm, along with experiments that measure its performance in several environments with a variety of pruning operations.
Low-frequency component of the heart rate variability spectrum: a poor marker of sympathetic activity.

The low-frequency component of the heart rate variability spectrum (0.06-0.10 Hz) is often used as an accurate reflection of sympathetic activity. Therefore, interventions that enhance cardiac sympathetic drive, e.g., exercise and myocardial ischemia, should elicit increases in the low-frequency power. Furthermore, because an enhanced sympathetic activation has been linked to an increased propensity for malignant arrhythmias, one might also predict a greater low-frequency power in animals that are susceptible to ventricular fibrillation than in resistant animals. To test these hypotheses, a 2-min coronary occlusion was made during the last minute of exercise in 71 dogs with healed myocardial infarctions: 43 had ventricular fibrillation (susceptible) and 28 did not experience arrhythmias (resistant). Exercise or ischemia alone provoked significant heart rate increases in both groups of animals, with the largest increase in the susceptible animals. These heart rate increases were attenuated by β-adrenergic receptor blockade. Despite the sympathetically mediated increases in heart rate, the low-frequency power decreased, rather than increased, in both groups, with the largest decrease again in the susceptible animals: 4.0 ± 0.2 (susceptible) vs. 4.1 ± 0.2 ln ms2 (resistant) in preexercise control and 2.2 ± 0.2 (susceptible) vs. 2.9 ± 0.2 ln ms2 (resistant) at highest exercise level. In a similar manner the parasympathetic antagonist atropine sulfate elicited significant reductions in the low-frequency power. Although sympathetic nerve activity was not directly recorded, these data suggest that the low-frequency component of the heart rate power spectrum probably results from an interaction of the sympathetic and parasympathetic nervous systems and, as such, does not accurately reflect changes in the sympathetic activity.
Edinburgh Research Explorer Susceptibility to apoptosis is differentially regulated by c-myc and mutated Ha-ras oncogenes and is associated with endonuclease availability

Summary Oncogenes and oncosuppressors can derugulate cell replication in tumours, and recently have been shown to influence the probability of apoptosis. The effects of human c-myc and mutated (T24) Ha-ras oncogenes on susceptibility to apoptosis were investigated by introducting them into immortalised rat fibroblasts. The resulting family of transfectants showed closely similar measures of proliferation, but widely divergent rates of apoptosis, differing by up to fifteen-fold, that correlated inversely with population expansion rates in vitro. T24-ras transfectants with moderate or high p2lras expression showed reduced apoptosis, and this was reversed by pharmacological inhibition of membrane localisation of p2l's by mevinolin. In contrast, c-myc stimulated apoptosis, and this was further enhanced by serum deprivation. Inducibility of effector proteins represents one possible mechanism of genetic control of the susceptibility to apoptosis, and its investigation showed that c-myc was associated with expression by viable cells of latent calcium/magnesium sensitive endonuclease activity characteristic of apoptosis. In contrast, endonuclease activity was not detected in viable cells of a T24-ras transfectant expressing high levels of p2lras. Thus, there appeared to be differential regulation of susceptibility to apoptosis, positively by c-myc and negatively by activated ras, and this was associated with availability of endonuclease activity. Genetic modulation of apoptosis in human neoplasms is likely to influence net growth rate, retention of cells acquiring new mutations and response to certain chemotherapeutic agents.
The presence of sboA and spaS genes and antimicrobial peptides subtilosin A and subtilin among Bacillus strains of the Amazon basin

This report demonstrates the usefulness of PCR for the genes spaS and sboA as a means of identifying Bacillus strains with a potential to produce subtilin and subtilosin A. One collection strain and five Bacillus spp. isolated from aquatic environments in the Amazon basin were screened by PCR using primers for sboA and spaS designed specifically for this study. The sequences of the PCR products showed elevated homology with previously described spaS and sboA genes. Antimicrobial peptides were isolated from culture supernatants and analyzed by mass spectrometry. For all samples, the mass spectra revealed clusters with peaks at m/z 3300–3500 Da, corresponding to subtilosin A, subtilin and isoforms of these peptides. These results suggest that the antimicrobial activity of these strains may be associated with the production of subtilosin A and/or subtilin. The PCR used here was efficient in identifying novel Bacillus strains with the essential genes for producing subtilosin A and subtilin.