Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water.

To establish a framework for extrapolating the helix-forming properties of peptides from TFE/H2O mixtures (TFE = 2,2, 2-trifluoroethanol) back to water, the thermal unfolding curves have been measured by circular dichroism for four repeating-sequence peptides, with chain lengths from 7 to 22 residues. The unfolding curves were measured between 0 and 50 volume percent TFE and were fitted to the modified Lifson-Roig theory. A single set of helix-coil parameters fits the results for the four peptides at each TFE concentration; only two of the basic helix-coil parameters, , the mean helix propagation parameter of residues in the sequence repeat, and DeltaH, the enthalpy change per residue on unfolding the helix, are allowed to vary with TFE molarity. The success in fitting these curves over a wide range of experimental variables shows that helix formation is basically the same in TFE/H2O mixtures as in water. Moreover, a simple model based on a linear dependence of ln and DeltaH on TFE molarity can be used to extrapolate the results from 25% TFE (approximately 4 M) back to water. The results also give curves of helix formation induced by TFE at constant temperature, and the properties of these helix induction curves explain some of the puzzling results shown by other peptides in the literature. The average helix propensity increases regularly from 0 to 25% TFE but levels off at higher TFE concentrations, which explains why the extent of helix formation levels off in this range. The change in the apparent cooperativity of thermal unfolding curves in concentrated TFE solutions results from the decrease of the enthalpy change for helix unfolding at higher TFE concentrations. The rapid decrease in the plateau values of apparent helix content with increasing temperature results mainly from the strong temperature dependence of the ellipticity of the complete helix. To determine whether the helix-stabilizing effect of TFE arises from strengthening the hydrogen bonds in the helix backbone, the strength of the hydrogen bond in a model compound, salicylic acid, has been measured in TFE/H2O mixtures from the pKa difference between salicylic acid and a similar compound which cannot form the hydrogen bond. The curve of hydrogen bond strength versus increasing TFE concentration matches both in shape and magnitude the increase in average helix propensity in TFE/H2O mixtures.
A Review of the Potential and Versatility of Colloidal Gold Cytochemical Labeling for Molecular Morphology

In the present article we review several postembedding cytochemical techniques using the colloidal gold marker. Owing to the high atomic number of gold, the colloidal gold particles are electron dense. They are spherical in shape and can be prepared in sizes from 1 to 25 nm, which renders this marker among the best for electron microscopy. In addition, because it can be bound to several molecules, this marker has the advantage of being extremely versatile. Combined to immunoglobulins or immunoglobulin-binding proteins (protein A), it has been applied successfully in immunocytochemistry. Colloidal gold particles 5–15 nm in size are excellent for postembedding cytochemistry. Particles of smaller size, such as 1 nm, must be silver enhanced to be visualized by transmission electron microscopy. We have elected to review the superiority of indirect immunocytochemical approaches using IgG-gold or protein A-gold (protein G-gold and protein AG-gold). Lectins or enzymes can be tagged with colloidal gold particles, and the corresponding lectin-gold and enzyme-gold techniques have specific advantages and great potential. Using an indirect digoxigenin-tagged nucleotide and an antidigoxigenin probe, colloidal gold technology can also be used for in situ hybridization at the electron microscope level. Affinity characteristics lie behind all cytochemical techniques and several molecules displaying high affinity properties can also be beneficial for colloidal gold electron microscopy cytochemistry. All of these techniques can be combined in various ways to produce multiple labelings of several binding sites on the same tissue section. Colloidal gold is particulate and can easily be counted; thus the cytochemical signal can be evaluated quantitatively, introducing further advantages to the use of the colloidal gold marker. Finally, several combinations and multiple step procedures have been designed to amplify the final signal which renders the techniques more sensitive. The approaches reviewed here have been applied successfully in different fields of cell and molecular biology, cell pathology, plant biology and pathology, microbiology and virology. The potential of the approaches is emphasized in addition to different ways to assess specificity, sensitivity and accuracy of results.
Elk with a long incubation prion disease phenotype have a unique PrPd profile

The transmissible spongiform encephalopathies (TSEs) invariably result in fatal neurodegeneration and accumulation of PrPd, an abnormal form of the host prion protein PrPc, encoded by the PRNP gene. A naturally occurring polymorphism (methionine/valine) at PRNP codon 129 is associated with variation in relative disease susceptibility, incubation time, clinical presentation, neuropathology, and/or PrPd biochemical characteristics in a range of human TSEs. A methionine/leucine polymorphism at the corresponding site in the Rocky Mountain elk PRNP gene is associated with variation in relative susceptibility and incubation time in the cervid TSE chronic wasting disease. We now report that elk lacking the predisposing 132-methionine allele develop chronic wasting disease after a long incubation period and display a novel PrPd folding pattern.
The relationship of changes in leptin, neuropeptide Y and reproductive hormones to antipsychotic induced weight gain

Weight gain is an important side effect of antipsychotic (AP) treatment. Weight is regulated by multiple systems, including leptin, neuropeptide Y (NPY) and gonadal steroids. The aim was to investigate whether AP‐induced weight gain was related to leptin and NPY abnormalities and whether these were associated with a disruption of gonadal steroid production.
Learning Statistical and Geometric Models from Microarray Gene Expression Data

Analysis of microarray gene expression data is important for disease study at the molecular and genomic level. Computational data modeling and analysis are essential for extracting meaningful and specific information from noisy, high-throughput, and large-scale microarray gene expression data. In this dissertation, we propose and develop innovative data modeling and analysis methods for learning statistical and geometric models from gene expression data and subsequently discover data structure and information associated with disease mechanisms. To provide a high-level overview of gene expression data for easy and insightful understanding of data structure relevant to the physiological event of interest, we propose a novel statistical data clustering and visualization algorithm that is comprehensive and effective for multiple clustering tasks and that overcomes some of the major limitations associated with existing clustering methods. The proposed clustering and visualization algorithm performs progressive, divisive hierarchical clustering and visualization, supported by hierarchical statistical modeling, supervised/unsupervised informative gene/feature selection, supervised/unsupervised data visualization, and user/prior knowledge guidance through humandata interactions, to discover cluster structure within complex, high-dimensional gene expression data. Applications to muscular dystrophy, muscle regeneration, and cancer data demonstrated its abilities to identify functionally enriched (co-regulated) gene groups, detect/validate disease types/subtypes, and discover the pathological relationship among multiple disease types reflected by gene expression profiles. For the purpose of selecting suitable clustering algorithm(s) for gene expression data analysis and validating the advantage of our proposed clustering algorithm, we design an
Draft Genome Sequence of the Dimorphic Yeast Yarrowia lipolytica Strain W29

ABSTRACT Here, we present the draft genome sequence of the dimorphic ascomycete yeast Yarrowia lipolytica strain W29 (ATCC 20460). Y. lipolytica is a commonly employed model for the industrial production of lipases, small molecules, and more recently for its ability to accumulate lipids.
Web Based Tools for Signals and Systems Course

In this paper we present web-based tools that visualize standard concepts (convolution of analog and discrete signals, pole-zero diagram, Fourier series, sampling and reconstruction) in a classical Signal and Systems course. The tools can be used by a teacher as a teaching aid to explain basic concepts in Signal and Systems course. They can also be used by students as a learning aid. They are easy for use and can be used in different locations using different operating systems.
Vapor: Virtual Machine Based Parallel Program Profiling Framework

It is hard to execute parallel program efficiently on man-core platform because we could not divide program into appropriate granularity executed simultaneously. Based on virtual machine and binary translation technologies the article proposes the vapor profiling framework that uses SBIRP instruction in-place replacement method to collect program’s run-time control flow and data flow information precisely. Moreover, it explains how to create control flow and data flow dependency graphs. Experiment results prove that vapor has better performance than traditional methods.
Examining document model residuals to provide feedback during Information Retrieval evaluation

Evaluation of document models for text based Information retrieval is crucial for developing document models that are appropriate for speciﬁc domains. Unfortunately, current document model evaluation methods for text retrieval provide no feedback, except for an evaluation score. To improve a model, we must use trial and error. In this article, we examine how we can provide feedback in the document model evaluation process, by providing a method of computing relevance score residuals and document model residuals for a given document-query set. Document model residuals provide us with an indication of where the document model is accurate and where it is not. We derive a simple method of computing the document model residuals using ridge regression. We also provide an analysis of the residuals of two document models, and show how we can use the correlation of document statistics to the residuals to provide statistically signiﬁcant improvements to the precision of the model.
Trans-acting regulatory mutations that alter transcription of Saccharomyces cerevisiae histone genes

Using a Saccharomyces cerevisiae strain containing an integrated copy of an H2A-lacZ fusion gene, we screened for mutants which overexpressed beta-galactosidase as a way to identify genes which regulate transcription of the histone genes. Five recessive mutants with this phenotype were shown to contain altered regulatory genes because they had lost repression of HTA1 transcription which occurs upon inhibition of chromosome replication (D. E. Lycan, M. A. Osley, and L. Hereford, Mol. Cell. Biol. 7:614-621, 1987). Periodic transcription was affected in the mutants as well, since the HTA1 gene was transcribed during the G1 and G2 phases of the cell cycle, periods in the cell cycle when this gene is normally not expressed. A similar loss of cell cycle-dependent transcription was noted for two of the three remaining histone loci, while the HO and CDC9 genes continued to be expressed periodically. Using isolated promoter elements inserted into a heterologous cycl-lacZ fusion gene, we demonstrated that the mutations fell in genes which acted through a negative site in the TRT1 H2A-H2B promoter.
Nanoparticles and their interactions with the dermal barrier

The dermal application of drugs is promising due to the ease of application. In this context nano-scale carrier systems were already evaluated in several studies with respect to the skin interaction and the impact on drug penetration. At the same time the upcoming production of engineered nano-scale materials requires a thorough safety evaluation. Drug delivery as well as risk assessment depends crucially on the ability of such carriers to overcome the skin barrier and reach deeper tissue layers. Therefore, the interaction of nanoparticles with skin and especially skin models is an intriguing field. However, the data obtained do not show a clear image on the effect of nano-carriers. Especially the penetration of such particles is an open and controversially discussed topic. The literature reports different results mainly on pig or murine skin showing strong penetration (pig and mouse) or the opposite. Looking only at the sizes of the particles also no conclusive picture can be obtained. Nevertheless, size is regarded to play an important role for skin penetration. Furthermore, the state of the skin influences penetration (hydration) and the mechanical stress is of outmost importance.
Reward‐Based Decision Making and Electrodermal Responding by Young Children with Autism Spectrum Disorders during a Gambling Task

In this study, we explore reward‐based decision making and electrodermal responding (EDR) among children with autism spectrum disorder (ASD) during a children's gambling task. In addition, we examine whether individual behavioral and EDR responses predict social communication, repetitive symptoms, parent reports of executive function, and behavioral challenges. The ability to form advantageous strategies for long‐term gain is of interest for children with ASD, who exhibit both difficulty with executive function and atypical responses to reward. Twenty‐one children ages 6–7 years with ASD and no intellectual disability, and 21 age‐ and IQ‐matched typically developing children participated. Both groups exhibited a similar pattern of gambling selections, but children with ASD showed less knowledge of the reward contingencies of the decks after playing. In addition, although EDR was similar between groups in anticipation of selections, children with ASD exhibited greater EDR during feedback about rewards as the task progressed. Children with ASD who exhibited the greatest increases in EDR were more likely to exhibit repetitive symptoms, particularly rituals and the need for sameness, as well as internalizing behaviors and reduced executive function in other settings. Autism Res 2013, 6: 494–505. © 2013 International Society for Autism Research, Wiley Periodicals, Inc.
Preventive maintenance scheduling for a multi-component system with non-negligible replacement time

When maintenance models are developed for complex continuous operating systems, with large production losses, it is important to take into account the maintenance duration, in order to provide an effective maintenance program. In this work, a preventive maintenance model is presented in order to coordinate the component replacements in a multi-component system. The model is based on the partial periodic renewal policy. At each partial renewal, a group of components to be replaced is defined. When all components are replaced simultaneously, we consider that the system undergoes an overhaul which resets it to the new state. Moreover, the model takes into account for non-negligible replacement times, where different assumptions are considered. The relevant effect of maintenance times on the optimal policy is clearly shown by the numerical results, provided by the application in an oil refinery.
Cisplatin-Modified De Gramont in Second-Line Therapy for Pancreatic Adenocarcinoma

Objectives In Belgium, combination chemotherapy of cisplatin and 5-fluorouracil + leucovorin (CFL) according to the modified de Gramont schedule is the treatment of choice in second line for metastatic pancreatic cancer. We retrospectively analyzed survival data in 2 Belgian centers in a nonselected population. Methods Between January 2004 and October 2011, 48 patients with histologically proven recurrent or unresectable pancreatic adenocarcinoma who had received CFL as second-line treatment were identified. We retrospectively analyzed the following parameters: progression-free survival (PFS1 and PFS2) for each line (after the start of first and second line), overall survival (OS), and growth modulation index. Results The median PFS1 was 5.4 months (95% confidence interval [CI], 4.1–6.6). The median PFS2 was 3.6 months (95% CI, 2–5.2). The median OS was 12 months (95% CI, 9.3–14.7). Twenty-three percent of patients had a growth modulation index >1.33. Conclusion We show an OS of 12 months with gemcitabine in first-line and CFL in second-line therapy for pancreatic cancer. Sequential therapy with good OS and good quality of life may be preferred to strong upfront therapy in an incurable disease such as pancreatic cancer.
Statistical Control Process: A Historical Perspective

One of the most powerful tools in thestatistical quality process is the statisticalmethods.First developed in the 1920’s byWalter Shewhart, the control chart found widespread use during World War II and has been employed, with various modifications, ever since. There are many processes in which thesimultaneous monitoring or control of two ormore quality characteristics is necessary. Reviewing statistical process control tools and providing a description about necessity of using these tools for improving the production process and providing some applications of statistical process control.This study covers both the motivation for statistical quality process and a discussion of some of the techniques currently available. The emphasis focuses primarily on the developments occurring since the mid-980’s
Vpu-induced degradation of CD4: requirement for specific amino acid residues in the cytoplasmic domain of CD4

Two functions have been attributed to the product of the human immunodeficiency virus type 1 vpu open reading frame: it increases virion release from infected cells and induces rapid degradation of CD4 shortly after its synthesis. In the absence of Vpu, newly synthesized gp160 and CD4 associate in the endoplasmic reticulum (ER), forming a complex whose further maturation is blocked and which is eventually degraded. In studies using NL4-3-based expression vectors, it has been previously shown that Vpu induces the release of gp160 from the complex that it forms with CD4 in the ER. This release, which appears to be due to the rapid degradation of CD4 induced by Vpu, allows gp160 to transit to the Golgi, where it matures further. We investigated which regions of CD4 are important for its susceptibility to Vpu-induced degradation by transfecting HeLa cells with isogenic vpu-positive and vpu-negative proviruses and vectors expressing various truncated or mutated CD4 molecules. The results suggested that the cytoplasmic domain of CD4 contains a determinant lying within amino acids 418 to 425 that is critical for susceptibility to Vpu-induced degradation. Neither the phosphorylation sites in the cytoplasmic domain nor the Lck interaction region was required for the effect. Vpu-induced degradation was specific for CD4, since CD8, even when retained in the ER, was not degraded. In addition, under conditions of high-level Vpu expression, CD4 degradation could be observed in the absence of gp160 or other means of retaining CD4 in the ER.
Psychological and physiological effects of intravenous pervitin.

1. The physiological and psychological effects of i. v. pervitin, sodium amytal, and benzedrine were studied in 75 psychiatric cases. 2. Pervitin has cephalotropic and sympathecotropic effects. It is a more potent cephalotropic and less potent sympathecotropic drug than benzedrine. 3. Pervitin produces an emotionally charged free flow of material, which may include painful memories, traumatic experiences, intimate personal phantasies, and delusional ideas. Most patients experience a dramatic relief of tension and feeling of relaxation. Mild depressions are often delayed. The psychologically rich response evoked by pervitin is helpful both diagnostically and therapeutically. 4. The physiological effects of pervitin include evaluation of blood pressure for 24-36 hours, alteration of pulse rate, dryness of the mouth with thirst, loss of appetite, tightness in the chest, increased awareness of the environment and of sensory stimuli, elimination of fatigue, and wakefulness. The EKG is not significantly altered.
Improving the Automatic Identification of Malicious Android Apps in Unofficial Stores through Logo Analysis

The wide diffusion of mobile devices and the ability of users to customize their experience through applications (Apps) is opening to new problems related to privacy, security and data integrity for the mobile ecosystem. Smartphones, in general, and Android devices, in particular, are rapidly becoming emerging threat vectors of cybercrime activities. Unofficial Android markets, especially those with weak controls on published Apps, are the places where frauds may easily start and spread. Hence, the ability to identify and quickly shut down deceptive Apps is of paramount importance in the protection of users, services and infrastructures. Traditional approaches that aim at mitigating the presence of malicious Apps in unofficial markets, are based on crawlers for scanning stores and checking the words used in Apps’ description. These methods works very well when the App’s title, keywords and description match specific patterns that identify services to protect and the application owner or App’s signature do not match expected ones. Unluckily, the performance of such methods reduce sharply when the store adopts a language that is not supported by the recognition system or the App publisher uses misleading words in the App’s description. Nevertheless, App publishers always use a logo which is familiar to the user in order to highlight the application and increase the probability that the users install it. In this paper we presents a system that overcomes the limitation of traditional approaches including logo analysis in the process of App recognition. Our contribution is the definition and evaluation of a logo-based complementary system to be used in conjunction with traditional approaches based on word lists checking. The system and the performance of the proposed solution are presented and analyzed in the paper.
Structural Health Monitoring of Tall Buildings with Numerical Integrator and Convex-Concave Hull Classification

An important objective of health monitoring systems for tall buildings is to diagnose the state of the building and to evaluate its possible damage. In this paper, we use our prototype to evaluate our data-mining approach for the fault monitoring. The offset cancellation and high-pass filtering techniques are combined effectively to solve common problems in numerical integration of acceleration signals in real-time applications. The integration accuracy is improved compared with other numerical integrators. Then we introduce a novel method for support vector machine (SVM) classification, called convex-concave hull. We use the Jarvis march method to decide the concave (nonconvex) hull for the inseparable points. Finally the vertices of the convex-concave hull are applied for SVM training.