Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Structures and Motions of Loops in Protein Molecules

Authors to whom correspondence should be addressed; E-Mails: amarda@gmu.edu (A.S.);kavraki@rice.edu (L.E.K.); Tel. : +1-703-993-4135 (A.S.); Fax: +1-703-993-1710 (A.S.);Tel. : +1-713-348-5737 (L.E.K.); Fax: +1-713-348-5930 (L.E.K.)Received: 26 December 2011; in revised form: 10 January 2012 / Accepted: 3 February 2012 /Published: 13 February 2012Abstract: Unlike the secondary structure elements that connect in protein structures, loopfragments in protein chains are often highly mobile even in generally stable proteins. Thestructural variability of loops is often at the center of a protein’s stability, folding, and evenbiological function. Loops are found to mediate important biological processes, such assignaling, protein-ligand binding, and protein-protein interactions. Modeling conformationsof a loop under physiological conditions remains an open problem in computational biology.This article reviews computational research in loop modeling, highlighting progress andchallenges. Important insight is obtained on potential directions for future research.Keywords: loop modeling; conformational ensemble; equilibrium ﬂuctuations; native state;structural analysis of proteins; structural bioinformatics
Smartphone and self-extension: Functionally, anthropomorphically, and ontologically extending self via the smartphone

This paper focuses on the blurring boundary between the “human self” and the smartphone, using interviews with 60 heavy smartphone users. The interview responses reveal three types of self-extension via the smartphone—functional extension, anthropomorphic extension, and ontological extension. Smartphone users assert that their phone has become an indispensable part of their self and thus influences their identity and sense of being in both positive and negative ways.
Performance analysis of protein structure clustering techniques and CUDA implementation of RMSD computation

Knowledge of the 3-dimensional structure of proteins is an important aspect in the field of structure based drug design. Structure prediction algorithms generally operate by computationally generating a large number of protein structures known as decoys and selecting the best candidates from among them. This is done by clustering the decoy set to identify the best models. RMSD (Root Mean Square Deviation) is the metric used for measuring similarity between protein structures. As the number of decoys becomes larger, the huge computational time of RMSD calculation affects the overall performance. This paper is about the performance analysis done on clustering techniques of SPICKER, Calibur and Hierarchical Ward's clustering and also describes 2 methods for parallelizing RMSD computation.
Construction of low cost virtual backbone for sensor networks

Virtual backbone formation is a popular approach to reduce the routing overhead and increase the network scalability in the wireless ad hoc networks. Most of the centralized and distributed algorithms aim at minimizing the size of the virtual backbone. However, if every node of the network has a cost for handling the additional responsibilities as backbone node, goal of the backbone construction algorithm should be the minimization of the total cost. In this paper, we propose a distributed low cost backbone construction algorithm with the message complexity of O(n). Simulation results show that the proposed algorithm is cost and message efficient.
Regional Intellectual Capital Integration Performance Evaluation Based on Two-Phase Model

Intellectual capital integration is important to regional innovation system realizing technology innovation, and advancing intellectual capital integration performance makes sense for exalting regional innovative ability. Based on defining the connotation of regional intellectual capital integration and its performance evaluation, the intellectual capital integration performance is divided into intellectual capital integration ability and intellectual capital integration efficiency, and then a two-phase model is constructed to evaluate regional intellectual capital conformty performance. Then, the evaluation index systems of regional intellectual capital integration ability and efficiency are constructed, and the empirical analysis of evaluating thirty-one provinces's intellectual capital performances is done by TOPSIS and Across DEA method. Finally, the thirty-one provinces are sorted into four classes by evaluation resluts, and some suggestions are put forward for them.
Discriminant Features Extraction by Predictive Neural Networks

In this article we propose an extension of the Neural Predictive Coder (NPC) called NPC-2 applied to speech phonemes recognition; This model is an extension to the non linear area of adaptative coding systems used in speech processing. We show that it is possible with NPC-2 to take into account class membership informations of the phonemes from the stage of coding. In order to evaluate the NPC-2 coder, a study of Darpa-Timit phonemes recognition is done. Presented simulations put in obviousness an improvement of the classification, relatively to currently used coding methods. Key-Words: Phoneme Recognition, Neural Networks, Neural Predictive Coding.
Utilization of an IEEE 1588 Timing Reference Source in the iNET RF Transceiver

Synchronization of the iNET communication link is essential for implementing the TDMA channel access control functions within the transceiver MAC transport layer, and providing coherent signal demodulation timing at the transceiver PHY layer. In the following implementation, the 1588 timing reference source is the GPS receiver. Because it is being used in the Ground Station Segment and Test Article Segment, it becomes feasible to utilize the 1588 timing reference for cross-layer (MAC+PHY) iNET transceiver synchronization. In this paper, we propose an unified iNET transceiver synchronization architecture to improve iNET transceiver performance. The results of the synchronization performance analysis are given.
Entropy Principle and Recent Results in Non-Equilibrium Theories

We present the state of the art on the modern mathematical methods of exploiting the entropy principle in thermomechanics of continuous media. A survey of recent results and conceptual discussions of this topic in some well-known non-equilibrium theories (Classical irreversible thermodynamics CIT, Rational thermodynamics RT, Thermodynamics of irreversible processes TIP, Extended irreversible thermodynamics EIT, Rational Extended thermodynamics RET) is also summarized.
On-Line Modelling Based on Genetic Programming

Genetic Programming, a heuristic optimization technique based on the theory of Genetic Algorithms, is a method successfully used to identify nonlinear model structures by analyzing a system’s measured signals. Mostly, it is used as an offline tool which means that structural analysis is done after collecting all available identification data. In this paper, we propose an enhanced on-line GP approach that is able to adapt its behaviour to new observations while the GP process is executed. Furthermore, an approach using GP for on-line fault diagnosis is described, and finally test results using measurement data of NOx emissions of a BMW diesel engine are discussed.
CFTR dysfunction induces vascular endothelial growth factor synthesis in airway epithelium

Peribronchial angiogenesis may occur in cystic fibrosis and vascular endothelial growth factor (VEGF)-A regulates angiogenesis in airways. Peribronchial vascularity and VEGF-A expression were examined using immunocytochemistry and morphometric analysis in lung sections obtained in 10 cystic fibrosis patients at transplantation versus 10 control nonsmokers, and in two strains of Cftr-deficient mice versus wild-type littermates. Airway epithelial NCI-H292 cells and primary cultures of noncystic fibrosis human airway epithelial cells were treated with cystic fibrosis transmembrane conductance regulator (CFTR) inhibitors (CFTR-inh172 or PPQ-102) or transfected with a CFTR small interfering (si)RNA with or without a selective epidermal growth factor receptor tyrosine kinase inhibitor. Concentrations of VEGF-A and phosphorylated epidermal growth factor receptor were measured by ELISA. Peribronchial vascularity was increased in cystic fibrosis patients, but not in Cftr-deficient mice. VEGF-A immunostaining was localised to airway epithelium and was increased in cystic fibrosis patients and in Cftr-deficient mice. In cultured airway epithelial cells, treatment with CFTR inhibitors or transfection with CFTR siRNA induced a twofold increase in VEGF-A production. CFTR inhibitors triggered epidermal growth factor receptor phosphorylation that was required for VEGF-A synthesis. Cystic fibrosis airways at transplantation showed increased peribronchial vascularity and epithelial VEGF-A expression. CFTR dysfunction triggered epithelial synthesis of VEGF-A, which may contribute to vascular remodelling. CFTR dysfunction triggers epithelial synthesis of VEGF-A, which may contribute to vascular remodelling http://ow.ly/p7ebY
Reducing the Number of Canonical Form Tests for Frequent Subgraph Mining

Frequent connected subgraph (FCS) mining is an interesting problem with wide applications in real life. Most of the FCS mining algorithms have been focused on detecting duplicate candidates using canonical form tests. Canonical form tests have high computational complexity, and therefore, they affect the efficiency of graph miners. In this paper, we introduce novel properties to reduce the number of canonical form tests in FCS mining. Based on these properties, a new algorithm for FCS mining called gRed is presented. The experimentation on real world datasets shows the impact of the proposed properties on the efficiency of gRed reducing the number of canonical form tests regarding gSpan. Besides, the performance of our algorithm is compared against gSpan and other state-of-the-art algorithms.
The Physical Therapy Assessment and Management of Infants with Congenital Muscular Torticollis. A Survey and a Suggested Assessment Protocol for CMT

Background: Infants with congenital muscular torticollis(CMT) are treated with physical therapy, however the knowledge about type of assessment and treatment in current clinical practice is not clear. Aim: This study aimed to investigate the management of infants with CMT within a network of physical therapists. Settings/population: Physical therapists from a network for CMT participated in the study. Method: With permission a questionnaire from New Zealand was used. Subsequently an expert group of physical therapists developed a draft assessment protocol. Result: In general there was a high degree of consensus between the respondents in the current survey. For the assessment visual estimates were most commonly used and an evaluation of cervical muscle strength of the neck was always/often conducted. The most effective form of intervention as perceived by the respondents in the management of CMT was passive stretching, handling advice, facilitation with strengthening exercises of the neck muscle and facilitation of active cervical range of motion. There were big discrepancies in assessment of hand- and hip asymmetry. Conclusion: There seems to be a need to develop international guidelines for CMT to improve the evidence practice of assessment and treatment.
From Maximum Entropy to Maximum Entropy Production: A New Approach

Evidence from climate science suggests that a principle of maximum thermodynamic entropy production can be used to make predictions about some physical systems. I discuss the general form of this principle and an inherent problem with it, currently unsolved by theoretical approaches: how to determine which system it should be applied to. I suggest a new way to derive the principle from statistical mechanics, and present a tentative solution to the system boundary problem. I discuss the need for experimental validation of the principle, and its impact on the way we see the relationship between thermodynamics and kinetics.
Development and Characterization of Recombinant Antibody Fragments That Recognize and Neutralize In Vitro Stx2 Toxin from Shiga Toxin-Producing Escherichia coli

Background Stx toxin is a member of the AB5 family of bacterial toxins: the active A subunit has N-glycosidase activity against 28S rRNA, resulting in inhibition of protein synthesis in eukaryotic cells, and the pentamer ligand B subunits (StxB) bind to globotria(tetra)osylceramide receptors (Gb3/Gb4) on the cell membrane. Shiga toxin-producing Escherichia coli strains (STEC) may produce Stx1 and/or Stx2 and variants. Strains carrying Stx2 are considered more virulent and related to the majority of outbreaks, besides being usually associated with hemolytic uremic syndrome in humans. The development of tools for the detection and/or neutralization of these toxins is a turning point for early diagnosis and therapeutics. Antibodies are an excellent paradigm for the design of high-affinity, protein-based binding reagents used for these purposes. Methods and Findings In this work, we developed two recombinant antibodies; scFv fragments from mouse hybridomas and Fab fragments by phage display technology using a human synthetic antibody library. Both fragments showed high binding affinity to Stx2, and they were able to bind specifically to the GKIEFSKYNEDDTF region of the Stx2 B subunit and to neutralize in vitro the cytotoxicity of the toxin up to 80%. Furthermore, the scFv fragments showed 79% sensitivity and 100% specificity in detecting STEC strains by ELISA. Conclusion In this work, we developed and characterized two recombinant antibodies against Stx2, as promising tools to be used in diagnosis or therapeutic approaches against STEC, and for the first time, we showed a human monovalent molecule, produced in bacteria, able to neutralize the cytotoxicity of Stx2 in vitro.
- 1-Feature-Based Cluster Segmentation of Image Sequences

One of the crucial points in object segmentation within image sequences is the interdependence of different features that classify some area as an object. This paper introduces a concept of cluster segmentation, which acquires different features on a pixel basis. Weighting of these features based on predefined rules is applied, in order to judge the evidence of each particular feature for the final classification. To determine the various clusters, we use a procedure which is similar to vector quantization. This allows the tracking of classification results over time, because cluster labels change only gradually from frame to frame. Furthermore, a technique for local feature analysis is applied for segment merging after global classification. The most common features used for object separation in image sequences are color and motion. The results indicate that reliable segmentation and tracking of objects can be accomplished, using this low-complexity technique.
Collective Information Maximization for Self-Organizing Maps

The present paper shows that a self-organizing process can be realized by maximizing information between input patterns and competitive units. We have already shown that information maximization corresponds to competitive processes. Thus, if cooperation processes can be incorporated in information maximization, self-organizing maps can naturally be realized by information maximization. By using the weighted sum of distances among neurons or collected distance, we successfully incorporate cooperation processes in the main mechanism of information maximization. For comparing our method with the standard SOM, we applied the method to the well-known artificial data and show that clear feature maps can be obtained by maximizing information
Beyond verification: Leveraging formal for debugging

The latest advancements in the commercial formal model checkers have enabled the integration of formal property verification with the conventional testbench based methods in the overall verification plan. This has led to significant verification productivity across the entire design flow (from architectural verification to post-silicon debugging). As verification productivity is improved, debugging efficiency has become more important than before. In this paper, we discuss how formal technology can be leveraged to bring efficiency in the debugging process. In particular, we discuss how ldquobehavioral indexingrdquo enables a top-down view of the counter-example and facilitates debugging by overlaying a higher abstraction view on the bit-level counter-example. We also discuss how formal technology can be leveraged to do ldquowhat-ifrdquo analysis to localize the root cause of the bug. We also discuss how formal technology supports the even more challenging task of traceless debugging (the process of debugging the ldquoabsence of witness/counter-examplerdquo).
Improving Precision of BLE-based Indoor Positioning by Using Multiple Wearable Devices

Many kinds of smart (wearable) devices like smartphones are penetrating into our life. With these devices, indoor positioning techniques have been extensively researched. However, the positioning precision, using a single Wi-Fi or BLE (Bluetooth Low Energy) device, is usually limited to several meters. To improve positioning precision, we propose an approach of fingerprinting using multiple wearable BLE devices. In the initial experiments, we noticed that body obstruction leads to different signal strengths when a person with a wearable device turns around. On this basis, we further build directional maps for fingerprinting and study the potential combination of multiple devices in positioning. The experimental results in two indoor scenarios confirm that using multiple devices and directional maps help to greatly improve positioning precision to the decimeter level (more specifically 0.07m). The impact of BLE beacon density is also investigated.
Interference management via capacity-achieving codes for the deterministic broadcast channel

We motivate the consideration of deterministic broadcast channel coding as an interference management technique in wireless scenarios. We address practical coding strategies for such channels and discuss two approaches. The first relies upon enumerative source coding and can be applied for any deterministic broadcast channel problem as the first step in pipelined encoding for vertex rates. The second approach addresses a wireless interference management scenario and is a complete, practical, capacity-achieving strategy that dualizes the Luby transform code construction and encoding/decoding algorithms. This results in the first practical, nontrivial, capacity achieving code construction for the deterministic broadcast channel.
Multi-View Pose and Facial Expression Recognition

Multi-view facial expression recognition is important in many scenarios, as frontal view images are not always available. In this paper, we investigate facial expression recognition from frontal to profile view. Few works have investigated this issue on live captured data. A recent database, multi-pie, allows empirical investigation of facial expression recognition for different yaw angles. Experiments are carried out on 100 subjects over 7 poses for 6 facial expressions ( neutral, smile, surprise, squint, disgust and scream). Opencv frontal and profile face detectors are used to locate the face region. Head pose classifiers and pose dependent facial expression classifiers are trained using multi-class support vector machines (SVM). We investigate multi-scale local binary patterns (LBPms) as well as local gabor binary patterns (LGBP) as texture descriptors.
Implied Ocean Heat Transports in the Standard and Superparameterized Community Atmospheric Models

Abstract Implied ocean heat transport (To) based on net surface energy budgets is computed for two versions of the Community Atmospheric Model (CAM, version 3.0) general circulation model (GCM). The first version is the standard CAM with parameterized convection. The second is the multiscale modeling framework (MMF), in which parameterized convection is replaced with a two-dimensional cloud-resolving model in each GCM grid column. Although global-mean net surface energy totals are similar for both models, differences in the geographic distributions of the component errors lead to distinctly different To for each model, with CAM’s To generally agreeing with observationally based To estimates, and the MMF’s To producing northward transport at all latitudes north of ∼50°S. Analysis of component error sources in the To calculation identifies needed improvements in the MMF. Net surface shortwave radiation and latent heat fluxes over the oceans are the primary causes of To errors in the MMF. Surface shortwave r.
Depression bei Erwachsenen mit Autismus-Spektrum-Störung

Zusammenfassung Gegenstand und Ziel: Depressionen zählen zu den häufigsten Komorbiditäten von Autismus im Erwachsenenalter und gehen insbesondere bei Erwachsenen mit hochfunktionalem Autismus (HFA) mit einer hohen Suizidrate einher. Welche Risikofaktoren hierbei relevant sind, ist unklar. Material und Methoden: In einer Stichprobe von 186 autistischen Erwachsenen aus der Ambulanz bzw. Tagklinik für Störungen der sozialen Interaktion des Max-Planck-Instituts für Psychiatrie wurden epidemiologische, psychometrische und psychosoziale Daten mit Einverständnis der Patienten wissenschaftlich ausgewertet. Ergebnisse: 50% der Patienten litten neben einer ASS an einer depressiven Episode. Als Risikofaktoren für eine depressive Erkrankung wurden das Alter der Patienten sowie Arbeitslosigkeit identifiziert. Schlussfolgerungen und klinische Relevanz: Aufgrund der hohen Rate von Depressionen und Suiziden bei Erwachsenen mit ASS ist eine sorgfältige Exploration dahingehend mit Abklärung von Suizidalität zu empfehlen. Weiterhin besteht ein großer Bedarf bei der Weiterentwicklung von störungsspezifischen Behandlungsmaßnahmen sowie Unterstützungsmöglichkeiten bei der beruflichen Integration. Hier liegen für spätdiagnostizierte Personen mit HFA erste psychotherapeutische und teilstationäre Behandlungskonzepte vor. Summary Objective: Depressions are among the most frequent comorbidities in adults suffering from ASD, in particular in those patients who fulfill the criteria for high-functioning autism (HFA) depressive disorders are combined with high suicidal rates. The exact risk factors remain unclear. Material and methods: For this study a sample of 186 adult patients with ASD, who had visited the outpatients or day clinic for disorders of social interaction, was included. With the patients’ consents, their clinical data sets were analyzed for epidemiological, psychometric and psycho-social research. Results: 50 % of the autistic patients suffered from a depressive episode. The patients’ age and the status of unemployment at the time of admission were found to contribute to the development of a comorbid depression. Conclusions and clinical relevance: Due to the high rates of depression and suicides in adult patients with ASD, a thorough medical assessment including the clarification of suicidality is highly recommended at every patient contact. Further developments of disorder specific therapies and professional support networks for patients with ASD are still urgently required. First approaches on therapeutic and outpatient basis have been realized for patients with latediagnosed HFA.