Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Dynamics of HIV-1 Envelope Gp120 Outer Domain with V3 Loop

Background The net charge of the hypervariable V3 loop on the HIV-1 envelope gp120 outer domain plays a key role in modulating viral phenotype. However, the molecular mechanisms underlying the modulation remain poorly understood. Methodology/Principal Findings By combining computational and experimental approaches, we examined how V3 net charge could influence the phenotype of the gp120 interaction surface. Molecular dynamics simulations of the identical gp120 outer domain, carrying a V3 loop with net charge of +3 or +7, showed that the V3 change alone could induce global changes in fluctuation and conformation of the loops involved in binding to CD4, coreceptor and antibodies. A neutralization study using the V3 recombinant HIV-1 infectious clones showed that the virus carrying the gp120 with +3 V3, but not with +7 V3, was resistant to neutralization by anti-CD4 binding site monoclonal antibodies. An information entropy study shows that otherwise variable surface of the gp120 outer domain, such as V3 and a region around the CD4 binding loop, are less heterogeneous in the gp120 subpopulation with +3 V3. Conclusions/Significance These results suggest that the HIV-1 gp120 V3 loop acts as an electrostatic modulator that influences the global structure and diversity of the interaction surface of the gp120 outer domain. Our findings will provide a novel structural basis to understand how HIV-1 adjusts relative replication fitness by V3 mutations.
Hypofractionated stereotactic radiosurgery with concurrent bevacizumab for recurrent malignant gliomas: the University of Alabama at Birmingham experience.

BACKGROUND Nearly all patients with malignant glioma will have disease recurrence. Our purpose was to define the treatment toxicity and efficacy of concurrent bevazicumab (BVZ) with hypofractionated stereotactic radiosurgery (SRS) of relatively larger targets for patients with recurrent MG. METHODS A retrospective review of 21 patients with recurrent malignant glioma (18 glioblastoma, 3 WHO grade III glioma), treated at initial diagnosis with surgery and standard chemoradiation, was performed. All patients had concurrent BVZ with hypofractionatedSRS, 30 Gy in 5 fractions, with or without concurrent chemotherapy (temozolomide or CCNU). RESULTS Median patient age was 54 years, median Karnofsky Performance Status was 80, and median target size was 4.3 cm (range, 3.4-7.5 cm). Eleven patients (52%) had previously failed BVZ. One patient had grade 3 toxicities (seizures, dysphasia), which resolved with inpatient admission and intravenous steroids/antiepileptics. Treatment-related toxicities were grade 3 (n = 1), grade 2 (n = 9), and grade 0-1 (n = 11). Kaplan-Meier median progression-free survival and overall survival estimates (calculated from start of SRS) for GBM patients (n = 18) were 11.0 and 12.5 months, respectively. Concurrent chemotherapy did not appear to show any statistically significant efficacy benefit or have any propensity for toxicity. CONCLUSION BVZ concurrent with hypofractionated SRS was well tolerated by this cohort of patients with relatively larger targets. Ongoing randomized trials with more moderate radiotherapy dosing may help establish the efficacy of this regimen, though intricacies of this approach, including patient selection, radiation target volume delineation/size, and optimal radiation dose, will need further evaluation.
A Study on Virtual Team Trust Mechanism and Its Construction Strategies

Trust is a critical success factor (CSF) of virtual team, and successful virtual team needs the support of trust construction and maintenance. Based on Theory of Reasoned Action (TRA), the connotation and conceptual model of trust are systematically analyzed, and virtual team trust construction mechanism is discussed by combining with its essential characteristics and its relationship to communication, collaboration, and team performance. The two essential characteristics of virtual team trust are pointed out, which are ldquoswift trustrdquo and ldquocognition-based trustrdquo. In virtual teams, trust can be swiftly developed, but it is very fragile. In virtual context, the cognitive element is more important than the affective element of trust. Finally, several management principles and specific strategies for trust construction and maintenance in virtual teams are presented.
Anxiety, coping skills and hypothalamus-pituitary-adrenal (HPA) axis in patients with endometriosis

Background Endometriosis is an inflammatory disease that is defined by growth of endometrial tissue outside the uterus, resulting in pain, infertility, and emotional distress. Previous studies have shown that the HPA axis is compromised in patients with chronic, painful diseases, including endometriosis. However, the underlying mechanisms and the physiological and emotional consequences of dysfunctions in the HPA axis in these patients are largely unknown. We aimed to understand whether diurnal circulating cortisol levels in women with endometriosis are affected and how this impacts their emotional and behavioral responses. Methods Thirty-two patients with endometriosis and 36 healthy control women provided saliva samples and completed a series of psychological questionnaires. Salivary cortisol levels were measured in duplicate using a colorimetric immunoassay. Results There were significant differences in average cortisol levels between endometriosis patients and controls. A negative correlation was found between cortisol levels and infertility and dyspareunia. Furthermore, incapacitating pain was found to be a strong predictor of hypocortisolism. Women with endometriosis reported higher levels of trait anxiety, but showed no differences in perceived stress or in coping styles compared to the control group. Conclusions This study supports previous reports of hypocortisolism as a biomarker of aberrant HPA responses in women with endometriosis. Moreover, it provides further insight into the link between HPA axis dysregulation, emotional responses, and the high comorbidity between endometriosis and other inflammatory conditions.
Complex Organic Materials in the Circumstellar Disk of HR 4796A

We combine HST NICMOS imaging photometry of the HR 4796A disk at previously unobserved wavelengths between 1.71-2.22 μm with reprocessed archival observations to produce a measure of the dust’s scattering efficiency as a function of wavelength. The spectrum of the dust, synthesized from the seven photometric measures, is characterized by a steep red slope increasing from 0.5 to 1.6 μm followed by a flattening of the spectrum at wavelengths >1.6 μm. We fit the spectrum with a model population of dust grains made of tholins, materials composed of complex organic materials seen throughout the outer parts of our solar system. The presence of organic material around a star that may be in the later stages of giant planet formation implies that the basic building blocks for life may be common in planetary systems.
Control of a Robotic Arm Using Low-Dimensional EMG and ECoG Biofeedback

In this dissertation we describe a system that uses a low dimensional input derived from electromyography and electrocorticography data to control a robot. The work involves creating a system that allows signals recorded directly from a human body to allow control of a small robot arm. We compare direct joystick control with electromyogram (EMG) input to determine if one input system is superior, or if the quality of control between them is comparable. We also verify the system that is used to record the electromyogram signals is adaptable to other forms of biosignal input; in particular, direct connection to a human brain via electrocorticography (ECoG). Because of the current limitations in sensing and interpreting biological signals, the dimensionality of the data available through these signals is low. Our system is designed to use these low dimensional data and map specific patterns to resulting actions of a robot arm.
Motion compensated lossy-to-lossless compression of 4-D medical images using integer wavelet transforms

This paper proposes a method for progressive lossy-to-lossless compression of four-dimensional (4-D) medical images (sequences of volumetric images over time) by using a combination of three-dimensional (3-D) integer wavelet transform (IWT) and 3-D motion compensation. A 3-D extension of the set-partitioning in hierarchical trees (SPIHT) algorithm is employed for coding the wavelet coefficients. To effectively exploit the redundancy between consecutive 3-D images, the concepts of key and residual frames from video coding is used. A fast 3-D cube matching algorithm is employed to do motion estimation. The key and the residual volumes are then coded using 3-D IWT and the modified 3-D SPIHT. The experimental results presented in this paper show that our proposed compression scheme achieves better lossy and lossless compression performance on 4-D medical images when compared with JPEG-2000 and volumetric compression based on 3-D SPIHT.
Fish shoal optimization for identification of the most suitable revetment stone for design of minimum cost earthen canals carrying sediment-laden flow

Abstract A novel variant of particle swarm optimization (PSO), referred to as Fish Shoal Optimization (FSO), is developed to add an additional capability to its ancestor PSO to handle concurrently three different types of stones for the design of minimum cost earthen canals whose side slopes are riprap riveted and bottom is unlined with the most suitable type of stone. Costs of land acquisition and freeboard provision (fixed magnitude and depth-dependent scenarios) for a non-symmetric canal carrying sediment-laden flow are accounted for. The FSO concurrently handled various types of riprap stones in a single program to portray its resemblance with the biological character of a fish shoal (aggregation of mixed species of fish in nature). It allowed interaction of dissimilar species of shoal – the social characteristic of PSO and stiff competition – a feature of Genetic Algorithms, among their own and other groups’ members to yield the minimum cost design of canals having symmetric shape and angular particles as the most suitable revetment stone. The FSO yielded not only the minimum cost canals but also hydraulically efficient designs with 1.32, 4.86, 4.42, 4.28, and 4.40% less costs than those obtained by PSO for five different freeboard scenarios, respectively.
Towards the development of a novel taxonomy of knowledge management systems from a learning perspective: an integrated approach to learning and knowledge infrastructures

Purpose – The paper aims to discuss the critical issue of learning and knowledge convergence in knowledge‐intensive organizations, and to provide practical guidelines for effective strategies.Design/methodology/approach – The paper brings together previous research in knowledge management and provides a critique for the lack of integration of previous studies with learning, a key process for efficient knowledge management. Stemming from this critique, an integrative framework for knowledge management support from a learning perspective is proposed.Findings – The major contribution is the framework for knowledge management support from a learning perspective, which can guide strategies of effective knowledge and learning management. This framework initiates an interesting discussion of technological issues that can enhance current knowledge management practices.Research limitations/implications – The taxonomy of knowledge management systems provides the basis for an extensive specification of knowledge man.
Parametric phase information based 2D Cepstrum PSF estimation method for blind de-convolution of ultrasound imaging

In the ultrasound imaging system, blurring which occurs after passing through ultrasound scanner system, represents point spread function (PSF) that describes the response of the ultrasound imaging system to a point source distribution. So, de-blurring can be achieved by de-convolving the ultrasound images with an estimated of corresponding PSF. However, it is hard to attain an accurate estimation of PSF due to the unknown properties of the tissues of the human body through the ultrasound signal propagates. In this paper, we present a new method for PSF estimation in the Fourier domain (FD) based on parametric minimum phase information, and simultaneously, it performs fast 2D de-convolution in the ultrasound imaging system. Although most of complex cepstrum methods [14], are obtained using complex 2D phase unwrapping [18] [19] in order to estimate the FD-phase information of PSF, our algorithm estimates the 2D PSF using 2D FD-phase information with the parametric weighting factor α and β. They affect the feature of PSF shapes.This makes the computations much simpler and the estimation more accurate. Our algorithm works on the beam-formed uncompressed radio-frequency data, with pre-measured and estimated 2D PSFs database from actual probe used. We have tested our algorithm with vera-sonic system and commercial ultrasound scanner (Philips C4-2), in known speed of sound phantoms and unknown speeds in vivo scans.
Pneumocystis Infection Enhances Antibody-Mediated Resistance to a Subsequent Influenza Infection1

In contrast to the detrimental outcomes most often associated with the resolution of coinfections, the model presented here involving a localized Pneumocystis infection of the lung, followed 2 wk later by an influenza virus infection, results in a significant beneficial outcome for the host. In the week following the influenza infection, immunocompetent coinfected animals exhibited an accelerated rate of virus clearance, an accelerated appearance of higher influenza-specific neutralizing Ab titers in their serum and bronchoalveolar lavage fluid (BALF), significantly reduced inflammatory cytokine levels in their BALF, and reduced levels of morbidity relative to animals infected only with influenza virus. The beneficial outcome observed in coinfected immunocompetent animals was dependent on the ongoing resolution of a viable Pneumocystis infection. No differences in viral clearance were detected between coinfected and influenza-only-infected μMT mice or likewise for SCID mice. The accelerated anti-influenza response did not appear to be associated with influenza-specific CD8 T cell-mediated responses or NK cell responses in the lung. Rather, the increased rate of viral clearance was due to the enhancement of the influenza-specific Ab response, which in turn was transiently dependent upon the resolution of the ongoing Pneumocystis infection.
OxiNet : A New Natural Language Processing Software

The idea of giving computers the ability to process human language is as old as the idea of computer themselves [1]. Nowadays, designing computer systems with full human intelligence capabilities has been the conspicuous focus of Artificial Intelligence researchers. They have made tremendous amount of efforts in designing programs that understand with deep knowledge of the semantic meaning of texts. In this paper, I am going to introduce an art called Natural Language Processing that makes all the Artificial Intelligence researchers to reach their goal. Through this paper, I will introduce the most important Natural Language Processing typical examples (UNO, Rule based, Statistical, Finite state machine, Logic programming etc.). Moreover, I will give a brief overview on the important tools used in the implementation of NLP applications. These tools include Lexicons such as Wordnet and syntactic parsers such as the Link Grammar. Finally I will provide a design schema that illustrates how lexicons and parsers are used in order to implement a simple NLP application. The application will take a userdefined sentence as input and it detects the main verb and outputs all the possible synonyms corresponding to that verb. This work presents a new Wordnet model called, Optimized Lexicon Wordnet (OxiNet) that is able to detect anomalies in sentences and words of a given text with close to 80% accuracy.
Towards the characterization of realistic models: evaluation of multidisciplinary graph metrics

Custom generators of graph-based models are used in MDE for many purposes such as functional testing and performance benchmarking of modeling environments to ensure the correctness and scalability of tools. However, while existing generators may generate large models in increasing size, these models are claimed to be simple and synthetic, which hinders their credibility for industrial and research benchmarking purposes. But how to characterize a realistic model used in software and systems engineering? This question is investigated in the paper by collecting over 17 different widely used graph metrics taken from other disciplines (e.g. network theory) and evaluating them on 83 instance models originating from six modeling domains. Our preliminary results show that certain metrics are similar within a domain, but differ greatly between domains, which makes them suitable input for future instance model generators to derive more realistic models.
Spring Migration Phenology of Wheatear Species in Southern Turkey

Millions of birds migrate between breeding and wintering areas every year. Turkey has many important areas for migratory birds as stopover or wintering. The coastal line of the southern Turkey provides safety resting areas and rich opportunity for refueling. Bogazkent is one of the important area just coast line of the Mediterranean Sea and we studied the migration phenology and stopover durations of three Wheatear species: Northern wheatear ( Oenanthe oenanthe ), Isabelline wheatear ( Oenanthe isabellina ) and Black-eared wheatear ( Oenanthe hispanica ). In the study, with this wheatear species Desert wheatear ( Oenanthe deserti ) and Finsch’s wheatear ( Oenanthe finschii ) also were captured. Birds were captured by using spring traps baited with mealworms, Tenebrio molitor , throughout the daylight period from the 1 st of March to the 31 st May both in 2009 and 2010. More northern wheatears use this site to stopover. As the spring migration of the Northern wheatear at study site takes two months, Isabelline wheatear and Black-eared wheatear have almost one-month migrations in southern Turkey after passing the Mediterranean Sea. On the other hand, timing of spring migration has differences between wheatear species.
An edge-oriented spatial interpolation for consecutive block error concealment

The coding scheme is currently the most commonly used process of compressing image data. However, this process often results in very serious distortion in the decoded image if the bit-stream suffers from damages. In order to address this drawback, this letter aims to develop a new error concealment technique based on edge-oriented interpolation for still image or intra-frame correction. The first step involves finding the edge direction of a lost block by using one-dimensional matching techniques from two boundaries of neighboring blocks. Then, the error pixels are recovered by weighting linear interpolation along the estimated edge direction. Afterwards, the median filter is used to recover residual damaged-pixels. Simulations demonstrate that the important edge information can be significantly recovered, and also prove that this method performs better compared to other methods that use both subjective and objective measures.
Microwave large-signal effects on the low-frequency noise characteristics of GaInP/GaAs HBTs

This paper addresses both experimentally and through simulations the effects of a microwave tone on the low-frequency noise properties of GaInP/GaAs heterojunction bipolar transistors. The aim is to contribute to the still unsolved controversy on which modulation strategy should be adopted for the low-frequency noise sources when they should face large signal conditions, as in the cases of oscillators and mixers. An approach similar but not equal to the modulated stationary noise model has been adopted for three different kinds of noise source modulation strategy in the frame of a bias-dependent compact low-frequency noise model
On-line Adaptation of Neural Networks with Evolvable Hardware

This paper describes an evolvable hardware (EHW) system for generalized neural network learning. We have developed an ASIC VLSI chip, which is a building block to congure a scalable neural network hardware system. In our system, both the topology and the hidden layer node functions of a neural network mapped on the chips are dynamically changed using a genetic algorithm. Thus, the most desirable network topology and choice of node function (e.g. Gaussian or sigmoid) for a given application can be determined adaptively. This approach is particularly suited to applications requiring ability to cope with time-varying problems and realtime timing constraints. The chip consists of 15 Digital Signal Processors (DSPs), whose functions and interconnections are recon gured dynamically according to the chromosomes of the genetic algorithm. Incorporation of local learning hardware increases the learning speed signi cantly. Simulation results on the prediction of chaotic data and adaptive equalization in digital mobile communication are also given. Our system is two orders of magnitude faster than a Sun SS20 on the corresponding problem.
What You See Is What You Meant: direct knowledge editing with natural language feedback

Many kinds of knowledge-based system would be easier to develop and maintain if domain experts (as opposed to knowledge engineers) were in a position to define and edit the knowledge. From the viewpoint of domain experts, the best medium for defining the knowledge would be a text in natural language; however, natural lan- guage input cannot be decoded reliably unless written in controlled languages, which are difficult for domain experts to learn and use. WYSIWYM editing is an alternative solution in which the texts em- ployed to view and edit the knowledge are generated not by the user but by the system. The user can add knowledge by clicking on 'an- chors' in the text and choosing from a list of semantic alternatives; each choice directly updates the knowledge base, from which a new text is then generated.
Identification and Characterization of a Novel Human Aldose Reductase-like Gene*

We have identified a novel human protein that is highly homologous to aldose reductase (AR). This protein, which we called ARL-1, consists of 316 amino acids, the same size as AR, and its amino acid sequence is 71% identical to that of AR. It is more closely related to the AR-like proteins such as mouse vas deferens protein, fibroblast growth factor-regulated protein, and Chinese hamster ovary reductase, with 81, 82, and 83%, respectively, of its amino acid sequence identical to the amino acid sequence of these proteins. The cDNA of ARL-1 was expressed in Escherichia coli to obtain recombinant protein for characterization of its enzymatic activities. For comparison, the cDNA of human AR was also expressed in E. coli and analyzed in parallel. These two enzymes differ in their pH optima and salt requirement, but they act on a similar spectrum of substrates. Similar to AR, ARL-1 can efficiently reduce aliphatic and aromatic aldehydes, and it is less active on hexoses. While AR mRNA is found in most tissues studied,ARL-1 is primarily expressed in the small intestines and in the colon, with a low level of its mRNA in the liver. The ability of ARL-1 to reduce various aldehydes and the locations of expression of this gene suggest that it may be responsible for detoxification of reactive aldehydes in the digested food before the nutrients are passed on to other organs. Interestingly, ARL-1 and ARare overexpressed in some liver cancers, but it is not clear if they contribute to the pathogenesis of this disease.