Miracle-dz/UniFAR-FTUs huggingface dataset:
An new crossover operator for real-coded genetic algorithm with selective breeding based on difference between individuals

In this paper, we present an efficient crossover operator for real-coded genetic algorithm that breeds offspring based on difference between individuals. In the proposed crossover operator, offspring are generated following a promising direction with Laplace distribution based on the center of mass of parents. A set of 15 test problems available in the global optimization literature is used to evaluate the performance of proposed genetic algorithm. The comparative study shows that the proposed genetic algorithm performs quite well and outperforms other algorithms.
Effects of hypoxia on carotid body dopamine content and release in developing rabbits.

Hypoxia induces dopamine (DA) release from the carotid body (CB), but the role of DA during hypoxia in the postnatal maturation of carotid chemosensory discharge remains controversial. The aim of this study was to evaluate changes in CB content and release of DA evoked by hypoxia at different stages of development in the rabbit. Five groups of rabbits aged < or = 24 h (n = 9), 5 days (n = 27), 15 days (n = 18), 25 days (n = 16), and > or = 1 yr (n = 11) were studied. CBs were surgically removed and immediately incubated at 37 degrees C for 1 h in a surviving medium equilibrated with 100% O2 or 8% O2 in N2. The content of DA in the CB ([DA]CB) and the DA released in the surviving medium ([DA]r) were measured by high-performance liquid chromatography. [DA]CB was significantly larger in adults than in all pup groups in both 100% O2 [385.5 +/- 74.1 (SE) pmol/CB in adults and 43.6 +/- 6.0 pmol/CB in pups; P < 0.01] and hypoxia (518.1 +/- 99.9 pmol/CB in adults and 24.7 +/- 3.2 pmol/CB in pups; P < 0.01), presumably because of the larger CB mass. [DA]r was significantly larger in hypoxia than in 100% O2 only in 25-day-old rabbits (19.8 +/- 4.2 and 3.6 +/- 1.1 pmol/h, respectively; P < 0.01) and in adults (183.9 +/- 57.7 and 7.9 +/- 1.7 pmol/h, respectively; P < 0.01). The average ratio of [DA]r in hypoxia to [DA]r in 100% O2 ranged from 1.3 to 2.2 in the three younger age groups and was 5.5 and 23.3 in 25-day-old and adult rabbits, respectively. We conclude that the release of DA evoked by hypoxia is weak at birth and develops during the first weeks of life in rabbits.
Identification of AnkG107, a Muscle-specific Ankyrin-G Isoform*

We previously showed that alternatively spliced ankyrins-G, the Ank3 gene products, are expressed in skeletal muscle and localize to the postsynaptic folds and to the sarcoplasmic reticulum. Here we report the molecular cloning, tissue expression, and subcellular targeting of AnkG107, a novel ankyrin-G from rat skeletal muscle. AnkG107 lacks the entire ANK repeat domain and contains a 76-residue sequence near the COOH terminus. This sequence shares homology with COOH-terminal sequences of ankyrins-R and ankyrins-B, including the muscle-specific skAnk1. Despite widespread tissue expression of Ank3, the 76-residue sequence is predominantly detected in transcripts of skeletal muscle and heart, including both major 8- and 5.6-kb mRNAs of skeletal muscle. In 15-day-old rat skeletal muscle, antibodies against the 76-residue sequence localized to the sarcolemma and to the postsynaptic membrane and cross-reacted with three endogenous ankyrins-G, including one 130-kDa polypeptide that comigrated with in vitrotranslated AnkG107. In adult muscle, these polypeptides appeared significantly decreased, and immunofluorescence labeling was no more detectable. Green fluorescent protein-tagged AnkG107 transfected in primary cultures of rat myotubes was targeted to the plasma membrane. Deletion of the 76-residue insert resulted in additional cytoplasmic labeling suggestive of a reduced stability of AnkG107 at the membrane. Recruitment of the COOH-terminal domain to the membrane was much less efficient but still possible only in the presence of the 76-residue insert. We conclude that the 76-residue sequence contributes to the localization and is essential to the stabilization of AnkG107 at the membrane. These results suggest that tissue-dependent and developmentally regulated alternative processing of ankyrins generates isoforms with distinct sequences, potentially involved in specific protein-protein interactions during differentiation of the sarcolemma and, in particular, of the postsynaptic membrane.
Amifostine-Related Fever-Rash During Fractionated Radiotherapy: Diagnostic and Predictive Role of C-Reactive Protein

Introduction: Fever/rash is a side-effect of amifostine that demands immediate interruption of the drug. Here, we focus on the role of C-reactive protein (CRP) as a putative marker linked with amifostine fever/rash. Materials and Methods: The CRP serum values were analyzed in 496 patients receiving radiotherapy supported with amifostine (500–1000 mg/d). CRP levels were recorded before the onset of radiotherapy (day 0), on day 15 and when the fever/rash appeared. For 121 out of 496 patients, CRP values on day 7 were also available. About 79 patients (15.9%) developed fever/rash symptoms. Results: The CRP levels before the onset of therapy were 0 to 20.7 mg/dL (normal, ≤0.5 mg/dL). For patients who did not develop fever/rash, the CRP levels increased from a median of 0.30 to 0.50 on day 15; P = 0.001. Patients who developed fever/rash showed a more than 7-fold increase of the median CRP levels (median, 3.50; P < 0.0001). This sharp CRP rise was specific for amifostine-related fever/rash. Initially abnormal CRP levels were linked with a 2-fold risk for fever/rash (P = 0.01), while abnormal levels on day 7 were linked with a 3-fold higher risk (P = 0.08). The occurrence of fever/rash was independent of the amifostine dose level. Conclusions: Sharp rise of CRP levels on the day after the fever/rash development suggest amifostine-related etiology of fever/rash. Abnormal initial CRP levels and/or high CRP levels on day 7 should be considered as an alert signal as the probability to develop fever/rash reaches the 30%.
Predicting breast cancer survivability using fuzzy decision trees for personalized healthcare

Data analysis systems, intended to assist a physician, are highly desirable to be accurate, human interpretable and balanced, with a degree of confidence associated with final decision. In cancer prognosis, such systems estimate recurrence of disease and predict survival of patient; hence resulting in improved patient management. To develop such a prognostic system, this paper proposes to investigate a hybrid scheme based on fuzzy decision trees, as an efficient alternative to crisp classifiers that are applied independently. Experiments were performed using different combinations of: number of decision tree rules, types of fuzzy membership functions and inference techniques. For this purpose, SEER breast cancer data set (1973–2003), the most comprehensible source of information on cancer incidence in United States, is considered. Performance comparisons suggest that, for cancer prognosis, hybrid fuzzy decision tree classification is more robust and balanced than independently applied crisp classification; moreover it has a potential to adapt for significant performance enhancement.
Joint Transcriptional Control of xpsR, the Unusual Signal Integrator of the Ralstonia solanacearum Virulence Gene Regulatory Network, by a Response Regulator and a LysR-Type Transcriptional Activator

ABSTRACT Ralstonia (Pseudomonas)solanacearum is a soil-borne phytopathogen that causes a wilting disease of many important crops. It makes large amounts of the exopolysaccharide EPS I, which it requires for efficient colonization, wilting, and killing of plants. Transcription of the epsoperon, encoding biosynthetic enzymes for EPS I, is controlled by a unique and complex sensory network that responds to multiple environmental signals. This network is comprised of the novel transcriptional activator XpsR, three distinct two-component regulatory systems (VsrAD, VsrBC, and PhcSR), and the LysR-type regulator PhcA, which is under the control of PhcSR. Here we show that thexpsR promoter (PxpsR) is simultaneously controlled by PhcA and VsrD, permitting XpsR to act like a signal integrator, simultaneously coordinating signal input into theeps promoter from both VsrAD and PhcSR. Additionally, we used in vivo expression analysis and in vitro DNA binding assays with substitution and deletion mutants of PxpsR to show the following. (i) PhcA primarily interacts with a typical 14-bp LysR-type consensus sequence around position −77, causing a sixfold activation of PxpsR; a weaker, less-defined binding site between −183 and −239 likely enhances PhcA binding and activation via the −77 site another twofold. (ii) Full 70-fold activation of PxpsR requires the additional interaction of the VsrD response regulator (or its surrogate) with a 14-bp dyadic sequence centered around −315 where it enhances activation (and possibly binding) by PhcA; however, VsrD alone cannot activate PxpsR. (iii) Increasing the distance between the putative VsrD binding site from that of PhcA by up to 232 bp did not dramatically affect PxpsR activation or regulation.
Assembly of Trp1 in a Signaling Complex Associated with Caveolin-Scaffolding Lipid Raft Domains*

Trp1 has been proposed as a component of the store-operated Ca2+ entry (SOC) channel. However, neither the molecular mechanism of SOC nor the role of Trp in this process is yet understood. We have examined possible molecular interactions involved in the regulation of SOC and Trp1 and report here for the first time that Trp1 is assembled in signaling complex associated with caveolin-scaffolding lipid raft domains. Endogenous hTrp1 and caveolin-1 were present in low density fractions of Triton X-100-extracted human submandibular gland cell membranes. Depletion of plasma membrane cholesterol increased Triton X-100 solubility of Trp1 and inhibited carbachol-stimulated Ca2+ signaling. Importantly, thapsigargin stimulated Ca2+ influx, but not internal Ca2+ release, and inositol 1,4,5-triphosphate (IP3)-stimulated I soc were also attenuated. Furthermore, both anti-Trp1 and anti-caveolin-1 antibodies co-immunoprecipitated hTrp1, caveolin-1, Gαq/11, and IP3 receptor-type 3 (IP3R3). These results demonstrate that caveolar microdomains provide a scaffold for (i) assembly of key Ca2+ signaling proteins into a complex and (ii) coordination of the molecular interactions leading to the activation of SOC. Importantly, we have shown that Trp1 is also localized in this microdomain where it interacts with one or more components of this complex, including IP3R3. This finding is potentially important in elucidating the physiological function of Trp.
Bacillus subtilis MreB paralogues have different filament architectures and lead to shape remodelling of a heterologous cell system

Like many bacteria, Bacillus subtilis cells contain three actin‐like MreB proteins. We show that the three paralogues, MreB, Mbl and MreBH, have different filament architectures in a heterologous cell system, and form straight filaments, helices or ring structures, different from the regular helical arrangement in B. subtilis cells. However, when coexpressed, they colocalize into a single filamentous helical structure, showing that the paralogues influence each other's filament architecture. Ring‐like MreBH structures can be converted into MreB‐like helical filaments by a single point mutation affecting subunit contacts, showing that MreB paralogues feature flexible filament arrangements. Time‐lapse and FRAP experiments show that filaments can extend as well as shrink at both ends, and also show internal rearrangement, suggesting that filaments consist of overlapping bundles of shorter filaments that continuously turn over. Upon induction in Escherichia coli cells, B. subtilis MreB (BsMreB) filaments push the cells into strikingly altered cell morphology, showing that MreB filaments can change cell shape. E. coli cells with a weakened cell wall were ruptured upon induction of BsMreB filaments, suggesting that the bacterial actin orthologue may exert force against the cell membrane and envelope, and thus possibly plays an additional mechanical role in bacteria.
Case-Control Study of Dietary Patterns and Endometrial Cancer Risk

Dietary patterns, rather than intakes of specific foods or nutrients, may influence risk of endometrial cancer (EC). This population-based case-control study in Canada (2002–2006) included incident EC cases (n = 506) from the Alberta Cancer Registry and controls frequency age-matched to cases (n = 981). Past-year dietary patterns were defined using factor analysis of food frequency questionnaire data. Logistic regression was used to estimate EC risk within quartiles of dietary patterns. Three patterns (sweets, meat, plants) explained 23% of the variance in the dietary data. In multivariable models, EC risk was significantly reduced by 30% for women in the highest quartile of the healthier plants pattern (OR = 0.70, 95% CI 0.50–0.98, P trend = 0.02). When stratified by body mass index (BMI; kg/m2), risk was further reduced among overweight or obese women with a BMI ≥25 (OR = 0.57, 95% CI 0.39–0.83; P trend = 0.004). EC was not associated with the less healthy sweets and meat patterns. However, risk was modestly, but not significantly, elevated for higher intakes of the meat pattern among overweight or obese women. A mostly plant-based dietary pattern may reduce EC risk. Recommendations for risk reduction should focus on maintaining a healthy weight and the role of diet should be studied further.
The molecular classification of the clinical manifestations of Crohn's disease.

BACKGROUND & AIMS Crohn's disease is a common inflammatory disorder of the gut characterized by variation in both location and behavior. Chromosome 16 and the HLA region on chromosome 6 have been implicated in susceptibility to disease. Mutations in the NOD2/CARD15 gene, recently identified on chromosome 16, have been associated with disease overall but are found in only 25% of patients. No data regarding their contribution to specific disease subtypes exist. Here we report a detailed genotype-phenotype analysis of 244 accurately characterized patients. METHODS A total of 244 white patients with Crohn's disease recruited from a single center in the United Kingdom were studied. All patients were rigorously phenotyped and followed-up for a median time of 16 years. By using linkage disequilibrium mapping we studied 340 polymorphisms in 24 HLA genes and 3 NOD2/CARD15 polymorphisms. RESULTS We show that NOD2/CARD15 mutations determine ileal disease only. We confirm that alleles on specific long-range HLA haplotypes determine overall susceptibility and describe novel genetic associations with susceptibility, location, and behavior of Crohn's disease. CONCLUSIONS The clinical pattern of Crohn's disease may be defined by specific genotypes. This study may provide the basis for a future molecular classification of disease.
GRid-INdependent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors.

Traditional methods for performing 3D-QSAR rely upon an alignment step that is often time-consuming and can introduce user bias, the resultant model being dependent upon and sensitive to the alignment used. There are several methods which overcome this problem, but in general the necessary transformations prevent a simple interpretation of the resultant models in the original descriptor space (i.e. 3D molecular coordinates). Here we present a novel class of molecular descriptors which we have termed GRid-INdependent Descriptors (GRIND). They are derived in such a way as to be highly relevant for describing biological properties of compounds while being alignment-independent, chemically interpretable, and easy to compute. GRIND are obtained starting from a set of molecular interaction fields, computed by the program GRID or by other programs. The procedure for computing the descriptors involves a first step, in which the fields are simplified, and a second step, in which the results are encoded into alignment-independent variables using a particular type of autocorrelation transform. The molecular descriptors so obtained can be used to obtain graphical diagrams called "correlograms" and can be used in different chemometric analyses, such as principal component analysis or partial least-squares. An important feature of GRIND is that, with the use of appropriate software, the original descriptors (molecular interaction fields) can be regenerated from the autocorrelation transform and, thus, the results of the analysis represented graphically, together with the original molecular structures, in 3D plots. In this respect, the article introduces the program ALMOND, a software package developed in our group for the computation, analysis, and interpretation of GRIND. The use of the methodology is illustrated using some examples from the field of 3D-QSAR. Highly predictive and interpretable models are obtained showing the promising potential of the novel descriptors in drug design.
FOCUS ISSUE: DRUG-ELUTING STENTS: TAXUS-IV Outcomes With the Polymer-Based Paclitaxel-Eluting TAXUS Stent in Patients With Diabetes Mellitus The TAXUS-IV Trial

OBJECTIVES We sought to determine the safety and efﬁcacy of polymer-regulated site-speciﬁc delivery ofpaclitaxel in patients with diabetes mellitus undergoing stent implantation.BACKGROUND Percutaneous coronary intervention in patients with diabetes is associated with high rates ofrestenosis and repeat revascularization due to excessive neointimal proliferation, a process thatmay be blunted with the site-speciﬁc delivery of paclitaxel.METHODS In the TAXUS-IV trial, 1,314 patients were prospectively randomized to the slow rate-releasepolymer-based paclitaxel-eluting TAXUS stent or the bare-metal EXPRESS stent (BostonScientiﬁc Corp., Natick, Massachusetts). Medically treated diabetes was present in 318patients (24%), 105 of whom required insulin.RESULTS Among patients with diabetes, the TAXUS stent, compared to the bare-metal stent, reducedthe rate of 9-month binary angiographic restenosis by 81% (6.4% vs. 34.5%, p 0.0001), andreduced the 12-month rates of target lesion revascularization by 65% (7.4% vs. 20.9%, p 0.0008), target vessel revascularization by 53% (11.3% vs. 24%, p 0.004), and compositemajor adverse cardiac events by 44% (15.6% vs. 27.7%, p 0.01). The one-year rates ofcardiac death (1.9% vs. 2.5%), myocardial infarction (3.2% vs. 6.4%), and subacute thrombosis(0.6% vs. 1.2%) were comparable between the paclitaxel-eluting and control stents, respec-tively. In the insulin-requiring subgroup, the TAXUS stent reduced angiographic restenosisby 82% (7.7% vs. 42.9%, p 0.0065), and reduced the one-year rate of target lesionrevascularization by 68% (6.2% vs. 19.4%, p 0.07), a relative reduction similar to patientswithout diabetes.CONCLUSIONS The site-speciﬁc delivery of paclitaxel after coronary stent implantation is highly effective inreducing clinical and angiographic restenosis in patients with diabetes mellitus. (J Am CollCardiol 2005;45:1172–9) © 2005 by the American College of Cardiology Foundation
A Spread Spectrum Clock Generator Using Digital Tracking Scheme

A Spread Spectrum Clock Generator (SSCG) using Digital Tracking scheme (DT-SSCG) is described. Using digital tracking control outside a PLL, DT-SSCG can realize stable modulation characteristic independent of the PLL constants. Moreover, DT-SSCG can apply to various modulation profiles easily by brief change of the digital tracking parameters. A test chip has realized the fitting of 5000 ppm downspread with 6.02 dB and 8.02 dB spectrum peak reduction for triangle and Non-Linear modulation.
Hollow-Core FRP–Concrete–Steel Bridge Columns under Torsional Loading

This paper presents the behavior of hollow-core fiber-reinforced polymer–concrete–steel (HC-FCS) columns under cyclic torsional loading combined with constant axial load. The HC-FCS consists of an outer fiber-reinforced polymer (FRP) tube and an inner steel tube, with a concrete shell sandwiched between the two tubes. The FRP tube was stopped at the surface of the footing, and provided confinement to the concrete shell from the outer direction. The steel tube was embedded into the footing to a length of 1.8 times the diameter of the steel tube. The longitudinal and transversal reinforcements of the column were provided by the steel tube only. A large-scale HC-FCS column with a diameter of 24 in. (610 mm) and applied load height of 96 in. (2438 mm) with an aspect ratio of four was investigated during this study. The study revealed that the torsional behavior of the HC-FCS column mainly depended on the stiffness of the steel tube and the interactions among the column components (concrete shell, steel tube, and FRP tube). A brief comparison of torsional behavior was made between the conventional reinforced concrete columns and the HC-FCS column. The comparison illustrated that both column types showed high initial stiffness under torsional loading. However, the HC-FCS column maintained the torsion strength until a high twist angle, while the conventional reinforced concrete column did not.
Tyrosine Phosphatase SHP-2 Is Involved in Regulation of Platelet-derived Growth Factor-induced Migration*

SHP-2 is a ubiquitously expressed Src homology-2-containing cytosolic tyrosine phosphatase that binds to and becomes tyrosine-phosphorylated by the activated platelet-derived growth factor receptor-β (PDGFR-β). Removal of the binding site on the receptor, by mutation of Tyr1009 to Phe1009 (denoted Y1009F), led to loss of PDGF-stimulated phosphatase activity in cells expressing the mutated receptor, and these cells failed to form membrane edge ruffles and to migrate toward PDGF. Furthermore, treatment with phosphatase inhibitors phenylarsine oxide (PAO) and orthovanadate led to loss of PDGF-stimulated phosphatase activity and attenuated PDGF-stimulated migration of wild type PDGFR-β cells. Treatment of wild type PDGFR-β cells with combinations of PAO or orthovanadate and phosphatidylinositol 3-kinase inhibitors wortmannin or LY294002 resulted in a synergistic inhibition of PDGFR-β-mediated cell migration. PDGF stimulation of wild type PDGFR-β cells led to induction of p125 focal adhesion kinase (FAK) activity at low concentrations of the growth factor and a decrease at higher concentrations. In the mutant Y1009F cells and in wild type PDGFR-β cells treated with PAO and orthovanadate, FAK activity was not increased in response to PDGF. These results suggest that SHP-2 activity is involved in regulation of FAK activity and thereby of cell migration through PDGFR-β, independently of phosphatidylinositol 3-kinase.
Performance Evaluation of Some Distributed Averaging Algorithms for Sensor Networks

Though capillary sensor networks have the advantage of reporting punctual estimations of their sensed quantity, it is often useful for the nodes to know the overall average value of the same quantity. This is required, for example, when the network can make autonomous decisions. Several algorithms exist for solving the averaging problem in a distributed manner. Their efficiency can be measured by the number of iterations needed to converge to the average sensed value. In this paper, we consider two point-to-point and one point-to-multipoint distributed averaging algorithms that can be seen as variants of the same averaging solution. We define a set of analytical tools to evaluate the performance of these algorithms and to optimize their parameters in such a way to accelerate convergence. We also provide a performance assessment, based on numerical simulations, aimed at verifying the results of the analytical treatment and at comparing the considered schemes.