Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting class II MHC/peptide multi-level binding with an iterative stepwise discriminant analysis meta-algorithm

MOTIVATION Predicting peptides that bind to both Major Histocompatibility Complex (MHC) molecules and T cell receptors provides crucial information for vaccine development. An agretope is that portion of a peptide that interacts with an MHC molecule. The identification and prediction of agretopes is the first step towards vaccine design. RESULTS An iterative stepwise discriminant analysis meta-algorithm is utilized to derive a quantitative motif for classifying potential agretopes as high-, moderate- or non-binders for HLA-DR1, a class II MHC molecule. A large molecular online database provides the input for this data-driven algorithm. The model correctly classifies over 85% of the peptides in the database. AVAILABILITY Stepwise discriminant analysis software is available commercially in SPSS and BMDP statistical software packages. Peptides known to bind MHC molecules can be downloaded from http://wehih.wehi. edu.au/mhcpep/. Peptides known not to bind HLA-DR1 are available from the author upon request. CONTACT ronna@ucsfresno.edu.
Alterations in glycosyltransferase levels in mouse erythroleukemia cells during erythrodifferentiation and cell growth.

Mouse erythroleukemia (MEL) cells contained galactosyltransferase (GT), fucosyltransferase (FT), and N -acetylglucosaminyltransferase activities and only a small amount of sialyltransferase activity. Dimethyl sulfoxide-treated MEL cells, undergoing erythrodifferentiation, contained twice as much GT, 20 to 50% less FT, and approximately the same amount of N -acetylglucosaminyltransferase activities as did untreated cells. When log-phase MEL cells were used as the starting culture, GT activity remained constant during log phase but decreased to 30 to 60% of the log-phase level as the cells reached stationary phase. Under these conditions, FT activity increased more than two-fold as the cells reached stationary phase. When stationary-phase MEL cells were used as the starting culture, GT activity increased as the cells entered log phase and decreased as the cells returned to stationary phase. FT activity decreased initially and then increased as the cells reached stationary phase. Whether log-phase or stationary-phase MEL cells were used as the starting culture, cells maintained in dimethyl sulfoxide always contained more GT and less FT activity than did untreated cells. Since the changes in GT and FT activities were dependent on the concentration of dimethyl sulfoxide used and occurred prior to the onset of hemoglobin synthesis, it is possible that they are related to erythrodifferentiation in MEL cells.
p53-dependent regulation of autophagy protein LC3 supports cancer cell survival under prolonged starvation

The p53 tumor suppressor is mutated in a high percentage of human tumors. However, many other tumors retain wild-type (wt) p53 expression, raising the intriguing possibility that they actually benefit from it. Recent studies imply a role for p53 in regulation of autophagy, a catabolic pathway by which eukaryotic cells degrade and recycle macromolecules and organelles, particularly under conditions of nutrient deprivation. Here, we show that, in many cell types, p53 confers increased survival in the face of chronic starvation. We implicate regulation of autophagy in this effect. In HCT116 human colorectal cancer cells exposed to prolonged nutrient deprivation, the endogenous wt p53 posttranscriptionally down-regulates LC3, a pivotal component of the autophagic machinery. This enables reduced, yet sustainable autophagic flux. Loss of p53 impairs autophagic flux and causes excessive LC3 accumulation upon starvation, culminating in apoptosis. Thus, p53 increases cell fitness by maintaining better autophagic homeostasis, adjusting the rate of autophagy to changing circumstances. We propose that some cancer cells retain wt p53 to benefit from the resultant increased fitness under limited nutrient supply.
Perceptual Quality-Regulable Video Coding System With Region-Based Rate Control Scheme

In this paper, we discuss a region-based perceptual quality-regulable H.264 video encoder system that we developed. The ability to adjust the quality of specific regions of a source video to a predefined level of quality is an essential technique for region-based video applications. We use the structural similarity index as the quality metric for distortion-quantization modeling and develop a bit allocation and rate control scheme for enhancing regional perceptual quality. Exploiting the relationship between the reconstructed macroblock and the best predicted macroblock from mode decision, a novel quantization parameter prediction method is built and used to achieve the target video quality of the processed macroblock. Experimental results show that the system model has only 0.013 quality error in average. Moreover, the proposed region-based rate control system can encode video well under a bitrate constraint with a 0.1% bitrate error in average. For the situation of the low bitrate constraint, the proposed system can encode video with a 0.5% bit error rate in average and enhance the quality of the target regions.
On the Diversity-Multiplexing Tradeoff for Frequency-Selective MIMO Channels

We have previously (ISIT'05) introduced the optimal diversity versus multiplexing tradeoff (DMT) for a FIR frequency-selective i.i. d. Rayleigh MIMO channel. This tradeoff is the same as for a frequency-flat MIMO channel with the larger of the number of receive or transmit antennas being multiplied by the delay spread. In this paper we provide alternative proofs and insights into this result. In particular, we consider the ordered LDU decomposition instead of the usual eigen decomposition of the channel Gram matrix. Popular approaches for frequency-selective channels use OFDM techniques in order to exploit the diversity gain due to frequency selectivity. We show that the minimum number of subcarriers that need to be involved in space-frequency coding to allow achieving the optimal tradeoff is the delay spread times the smaller of the number of transmit or receive antennas, thus answering a question that was open hitherto. Although the no-CSIT/full- CSIR case is considered here, we propose an alterative DMT interpretation based on negligible CSIT. This CSIT allows to exploit the ordered LDU decomposition.
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data

Nematode.net (http://nematode.net) has been a publicly available resource for studying nematodes for over a decade. In the past 3 years, we reorganized Nematode.net to provide more user-friendly navigation through the site, a necessity due to the explosion of data from next-generation sequencing platforms. Organism-centric portals containing dynamically generated data are available for over 56 different nematode species. Next-generation data has been added to the various data-mining portals hosted, including NemaBLAST and NemaBrowse. The NemaPath metabolic pathway viewer builds associations using KOs, rather than ECs to provide more accurate and fine-grained descriptions of proteins. Two new features for data analysis and comparative genomics have been added to the site. NemaSNP enables the user to perform population genetics studies in various nematode populations using next-generation sequencing data. HelmCoP (Helminth Control and Prevention) as an independent component of Nematode.net provides an integrated resource for storage, annotation and comparative genomics of helminth genomes to aid in learning more about nematode genomes, as well as drug, pesticide, vaccine and drug target discovery. With this update, Nematode.net will continue to realize its original goal to disseminate diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner.
Shape Recognition with Spectral Distances

Recent works have shown the use of diffusion geometry for various pattern recognition applications, including nonrigid shape analysis. In this paper, we introduce spectral shape distance as a general framework for distribution-based shape similarity and show that two recent methods for shape similarity due to Rustamov and Mahmoudi and Sapiro are particular cases thereof.
A Imputed Neighborhood based Collaborative Filtering System for Web Personalization

Recommender system is the most important technology in Ecommerce . It is used to suggest valuable products for the customer and improve their business intelligence. Collaborative filtering is a technique which is used to suggest information from similar kinds of users. Scalability is the biggest challenge in collaborative filtering recommender system. When more number of users is increasing in the site the system should provide accurate recommendations for the super user. We use Imputed divisive hierarchical clustering approach to overcome this scalability issue when more number of users increases in terms of neighborhood size.
Learning multi-goal dialogue strategies using reinforcement learning with reduced state-action spaces

Learning dialogue strategies using the reinforcement learning framework is problematic due to its expensive computational cost. In this paper we propose an algorithm that reduces a state-action space to one which includes only valid state-actions. We performed experiments on full and reduced spaces using three systems (with 5, 9 and 20 slots) in the travel domain using a simulated environment. The task was to learn multi-goal dialogue strategies optimizing single and multiple confirmations. Average results using strategies learnt on reduced spaces reveal the following benefits against full spaces: 1) less computer memory (94% reduction), 2) faster learning (93% faster convergence) and better performance (8.4% less time steps and 7.7% higher reward). Index Terms: reinforcement learning, spoken dialogue systems.
Visual analysis of uncertainties in ocean forecasts for planning and operation of off-shore structures

We present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations used in ocean forecasting, i.e, simulations of sea surface elevation. Our system enables the interactive planning of both the placement and operation of off-shore structures. We illustrate this using a real-world simulation of the Gulf of Mexico. Off-shore structures, such as those used for oil exploration, are vulnerable to hazards caused by strong loop currents. The oil and gas industry therefore relies on accurate ocean forecasting systems for planning their operations. Nowadays, these forecasts are based on multiple spatio-temporal simulations resulting in multidimensional, multivariate and multivalued data, so-called ensemble data. Changes in sea surface elevation are a good indicator for the movement of loop current eddies, and our visualization approach enables their interactive exploration and analysis. We enable analysis of the spatial domain, for planning the placement of structures, as well as detailed exploration of the temporal evolution at any chosen position, for the prediction of critical ocean states that require the shutdown of rig operations.
MPEG-4 Structured Audio Systems

The MPEG-4 standard has been proposed to provide high quality audio and video content over the Internet. This content is represented in the form of audiovisual objects. However, different parts of the audiovisual scene are encoded seperately depending on the nature of the data to be encoded. The standard calls for aggresive coding techniques which ensure reception of high quality audio and video at low bit rates. One such encoding scheme for audio, generally applied to synthetic audio and sound effects, is known as Structured Audio. This paper presents a survey on the structured representation of sound and the ways it can be decoded and synthesized at the receiving terminal. All the different components of the audio scene are decoded seperately (Structured Audio is one of the components). The different decoded streams are then composed into one coherent sound signal and presented to the user. This audio composition in MPEG-4 is accomplished by the AudioBIFS layer in the MPEG-4 decoder. The nodes in this layer compose the different sounds together and also provide some abstract effects and virtual reality effects post-processing on the entire audio scene. Some of the post-processing can also be represented in the structured audio format that is used for synthetic sound encoding. This project focuses on the working of the AudioBIFS layer, specifically the nodes in this layer which rely use a structured representation encode postprocessing of audio effects, such as reverbrations.
Adaptation in automated user-interface design

Design problems involve issues of stylistic preference and flexible standards of success; human designers often proceed by intuition and are unaware of following any strict rule-based procedures. These features make design tasks especially difficult to automate. Adaptation is proposed as a means to overcome these challenges. We describe a system that applies an adaptive algorithm to automated user interface design within the framework of the MOBI-D (Model-Based Interface Designer) interface development environment. Preliminary experiments indicate that adaptation improves the performance of the automated user interface design system.
The moving parts of voltage-gated ion channels

Ion channels, like many other proteins, have moving parts that perform useful functions. The channel proteins contain an aqueous, ion-selective pore that crosses the plasma membrane, and they use a number of distinct ‘gating’ mechanisms to open and close this pore in response to biological stimuli such as the binding of a ligand or a change in the transmembrane voltage. This review is written at a watershed in our understanding of ion channels. 1. INTRODUCTION 240 1.1 Basic structure of voltage-activated channels 241 1.2 What are the physical motions of the channel protein during gating? 243 1.3 Gating involves several distinct mechanisms of activation and inactivation 246 2. ACTIVATION GATING 246 2.1 Early evidence for an activation gate at the intracellular mouth 247 2.1.1 Open channel blockade 247 2.1.2 The ‘ foot-in-the-door’ effect 249 2.1.3 Trapping of blockers behind closed activation gates 249 2.2 Site-directed mutagenesis and the difficulty of inferring structural roles from functional effects 250 2.3 State-dependent cysteine modification as a reporter of position and motion 251 2.4 Localization of activation gating 254 2.4.1 The trapping cavity 254 2.4.2 The activation gate 255 2.4.3 Is there more than one site of activation gating? 258 3. INACTIVATION GATING 259 3.1 Ball-and-chain (N-type) inactivation 261 3.1.1 Nature of the ‘ball’ – a tethered blocking particle 262 3.1.2 The ball receptor 263 3.1.3 The chain 264 3.1. 4 Variations on the N-type inactivation theme: multiple balls, foreign balls, anti-balls 265 3.2 C-type inactivation 266 3.2.1 C-type inactivation and the outer mouth of the K+ channel 266 3.2.2 The selectivity filter participates in C-type inactivation 267 3.2.3 A consistent structural picture of C-type inactivation 269 3.3 By what mechanism do other voltage-gated channels inactivate? 272 4. THE VOLTAGE SENSOR 273 4.1 Quantitative principles of voltage-dependent gating 276 4.2 S4 (and its neighbours) as the principal voltage sensor 277 4.2.1 Mutational effects on voltage-dependence and charge movement 277 4.2.2 Evidence for the translocation of S4 279 4.2.3 Real-time monitoring of S4 motion by fluorescence 282 4.3 Coupling between the voltage sensor and gating 283 5. CONCLUSION 284 6. ACKNOWLEDGEMENTS 287 7. REFERENCES 287
A Unified Threat Model for Assessing Threat in Web Applications

This paper presents a unified threat model for assessing threat in web applications. We extend the threat tree model with more semantic and context information about threat to form the new model which is used to analyze and evaluate threat in the software design stage. We utilize historical statistical information contained in this model to design threat mitigation schemes. The threat assessing results and mitigation schemes can be used to direct secure coding and testing. This makes it possible to design threat-resistant web applications by means of detecting and mitigating threat in the early software design stage.
Nonverbal expressions of positive emotions

Positive emotions affect the tone of our voice, the ways in which we move our body, and the expressions on our face. In this chapter, we review research on the production and comprehension of nonverbal signals of positive emotions. We take a lifespan approach, considering research on infants and children, as well as adults. We first review the literature on the production and perception of positive emotions in the voice, the body, and the face, and provide a summary of its conclusions and limitations. We end the chapter with a general discussion and proposals for future research. The vast majority of studies on emotional communication do not differentiate among positive emotions. The difficulty with this approach has been recognized for some time, with one theorist noting that “a comparison of results from different studies is virtually impossible if it is unclear whether . ‘happiness’ refers to quiet bliss or bubbling elation” (Scherer, 1986, p. 163; see also Ekman, 1992, for a similar point). Nevertheless, most contemporary studies still treat positive emotion as a unitary category. Increasingly, however, researchers are starting to go beyond a single positive emotion to examine a range of diverse positive states and expressions. That work is the focus of this chapter.
Sharp beveled tip hollow microneedle arrays fabricated by LIGA and 3D soft lithography with polyvinyl alcohol

This paper describes a fabrication process of hollow microneedle arrays with a sharp beveled tip for transdermal drug delivery. A master is fabricated through a double deep x-ray lithography process. First, a polymethylmethacrylate (PMMA) sheet is exposed to produce single PMMA parts with a sawtooth profile. The tip angle of each tooth determines the final tip angle of the microneedles. The PMMA parts are assembled and glued on a conductive substrate and then exposed through a second x-ray mask containing an array of hollow triangles as absorbing structures. A metal layer is then electrodeposited around the needles in order to form the future base of the array. A polyvinyl alcohol (PVA) solution is cast on top of the master to form a negative mold of the microneedle array after a low temperature curing and peel-off steps. A liquid PMMA solution is cast on top of the PVA negative mold and after the full PMMA polymerization the PVA is dissolved in water. This fabrication method can be performed in a non-clean room environment and requires little instrumentation. It is therefore compatible with a low-cost mass-fabrication scheme.
Calcium-sensing receptor is a physiologic multimodal chemosensor regulating gastric G-cell growth and gastrin secretion

The calcium-sensing receptor (CaR) is the major sensor and regulator of extracellular Ca2+, whose activity is allosterically regulated by amino acids and pH. Recently, CaR has been identified in the stomach and intestinal tract, where it has been proposed to function in a non-Ca2+ homeostatic capacity. Luminal nutrients, such as Ca2+ and amino acids, have been recognized for decades as potent stimulants for gastrin and acid secretion, although the molecular basis for their recognition remains unknown. The expression of CaR on gastrin-secreting G cells in the stomach and their shared activation by Ca2+, amino acids, and elevated pH suggest that CaR may function as the elusive physiologic sensor regulating gastrin and acid secretion. The genetic and pharmacologic studies presented here comparing CaR-null mice and wild-type littermates support this hypothesis. Gavage of Ca2+, peptone, phenylalanine, Hepes buffer (pH 7.4), and CaR-specific calcimimetic, cinacalcet, stimulated gastrin and acid secretion, whereas the calcilytic, NPS 2143, inhibited secretion only in the wild-type mouse. Consistent with known growth and developmental functions of CaR, G-cell number was progressively reduced between 30 and 90 d of age by more than 65% in CaR-null mice. These studies of nutrient-regulated G-cell gastrin secretion and growth provide definitive evidence that CaR functions as a physiologically relevant multimodal sensor. Medicinals targeting diseases of Ca2+ homeostasis should be reviewed for effects outside traditional Ca2+-regulating tissues in view of the broader distribution and function of CaR.
The Biochemistry of Gene Therapy for AIDS

Abstract Gene therapy has enormous potential and could in the near future involve the clinical biochemist in monitoring its efficacy. The involvement of clinical biochemists in this field could be not only in evaluating the impact of a gene-based strategy on disease progression, but also in measuring the expression of the products of therapeutic genes in treated individuals. Indeed, gene therapy presents new possibilities for the treatment of many diseases and, in particular, merits consideration in the treatment of a fatal disease like AIDS. The aim of this paper is to review the biochemical basis and clinical relevance of the gene therapy approaches directed towards the inhibition of human immunodeficiency virus type-1. We discuss the goals which have been achieved, the problems which have occurred and the efforts that are being made to solve them. In this regard, particular attention is paid to new strategies targeting ‘therapeutic’ enzymes to human immunodeficiency virus type-1 nucleic acids.
A green single-step procedure to synthesize Ag-containing nanocomposite coatings with low cytotoxicity and efficient antibacterial properties

Implant-associated infections still pose a serious threat leading to several complications. This study reported an environmentally benign Ag-containing nanocomposite coating with efficient antibacterial property fabricated on the metal implant via electrophoretic deposition (EPD). In such coatings, Ag2O/AgCl mixed with chitosan/gelatin (CS/G) polymers work together to exert the antibacterial property which could act as an alternative to traditional Ag nanoparticles. Scanning electron microscopy images showed the shuttle fiber-like morphology distributed lamellarly and some nanoparticles carved uniformly into the cross section. Transmission electron microscopy results revealed a core–shell-like structure of the released nanoparticles in experimental groups. The Ag-containing coatings exhibited strong antibacterial properties against Staphylococcus aureus strains and Escherichia coli strains. Meanwhile, the CCK-8 tests showed that after assembling with chitosan and gelatin polymers, the cytotoxicity of Ag was largely decreased. In addition, such coatings also exhibited strong bond strength with metal substrates and good degradable properties. Therefore, such Ag-containing CS/G coatings fabricated via EPD may be a promising candidate to be administrated in controlling the implant-associated infections.