Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent improvements in prediction of protein structure by global optimization of a potential energy function

Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.
Online Signature Verification Using Fourier Descriptors

We present a novel online signature verification system based on the Fast Fourier Transform. The advantage of using the Fourier domain is the ability to compactly represent an online signature using a fixed number of coefficients. The fixed-length representation leads to fast matching algorithms and is essential in certain applications. The challenge on the other hand is to find the right preprocessing steps and matching algorithm for this representation. We report on the effectiveness of the proposed method, along with the effects of individual preprocessing and normalization steps, based on comprehensive tests over two public signature databases. We also propose to use the pen-up duration information in identifying forgeries. The best results obtained on the SUSIG-Visual subcorpus and the MCYT-100 database are 6.2% and 12.1% error rate on skilled forgeries, respectively. The fusion of the proposed system with our state-of-the-art Dynamic Time Warping (DTW) system lowers the error rate of the DTW system by up to about 25%. While the current error rates are higher than state-of-the-art results for these databases, as an approach using global features, the system possesses many advantages. Considering also the suggested improvements, the FFT system shows promise both as a stand-alone system and especially in combination with approaches that are based on local features.
Key Insights into Hand Biomechanics: Human Grip Stiffness Can Be Decoupled from Force by Cocontraction and Predicted from Electromyography

We investigate the relation between grip force and grip stiffness for the human hand with and without voluntary cocontraction. Apart from gaining biomechanical insight, this issue is particularly relevant for variable-stiffness robotic systems, which can independently control the two parameters, but for which no clear methods exist to design or efficiently exploit them. Subjects were asked in one task to produce different levels of force, and stiffness was measured. As expected, this task reveals a linear coupling between force and stiffness. In a second task, subjects were then asked to additionally decouple stiffness from force at these force levels by using cocontraction. We measured the electromyogram from relevant groups of muscles and analyzed the possibility to predict stiffness and force. Optical tracking was used for avoiding wrist movements. We found that subjects were able to decouple grip stiffness from force when using cocontraction on average by about 20% of the maximum measured stiffness over all force levels, while this ability increased with the applied force. This result contradicts the force–stiffness behavior of most variable-stiffness actuators. Moreover, we found the thumb to be on average twice as stiff as the index finger and discovered that intrinsic hand muscles predominate our prediction of stiffness, but not of force. EMG activity and grip force allowed to explain 72 ± 12% of the measured variance in stiffness by simple linear regression, while only 33 ± 18% variance in force. Conclusively the high signal-to-noise ratio and the high correlation to stiffness of these muscles allow for a robust and reliable regression of stiffness, which can be used to continuously teleoperate compliance of modern robotic hands.
Fast Algorithms for Max Independent Set in Graphs of Small Average Degree

MAX INDEPENDENT SET is a paradigmatic problem in theoretical computer science and numerous studies tackle its resolution by exact algorithms with non-trivial worst-case complexity. The best such complexity is, to our knowledge, the O*(1.1889n) algorithm claimed by (J. M. Robson, Finding a maximum independent set in time O(2n/4), Technical Report 1251-01, LaBRI, Universite de Bordeaux I, 2001) in his unpublished technical report. We also quote the O*(1.2210n) algorithm by (F. V. Fomin, F. Grandoni and D. Kratsch, Measure and conquer: a simple O(20.288n) independent set algorithm, Proc. SODA'06, pages 18-25, 2006), that is the best published result about max independent set. In this paper we settle max independent set in (connected) graphs with "small" average degree, more precisely with average degree at most 3, 4, 5 and 6. Dealing with exact computation of max independent set in graphs of average degree at most 3, the best bound known is the recent O*(1.0977n) bound by (N. Bourgeois, B. Escoffier and V. Th. Paschos, An O*(1.0977n) exact algorithm for max independent set in sparse graphs, Proc. IWPEC'08, LNCS 5018, pages 55-65, 2008). Here we improve this result down to O*(1.0854n) by proposing finer and more powerful reduction rules. We then propose a generic method showing how improvement of the worst-case complexity for max independent set in graphs of average degree d entails improvement of it in any graph of average degree greater than d and, based upon it, we tackle max independent set in graphs of average degree 4, 5 and 6. For max independent set in graphs with average degree 4, we provide an upper complexity bound of O* (1.1571n), obviously still valid for graphs of maximum degree 4, that outperforms the best known bound of O*(1.1713n) by (R. Beigel, Finding maximum independent sets in sparse and general graphs, Proc. SODA'99, pages 856-857, 1999). For max independent set in graphs of average degree at most 5 and 6, we provide bounds of O*(1.1969n) and O*(1.2149n), respectively, that improve upon the corresponding bounds of O*(1.2023n) and O*(1.2172n) in graphs of maximum degree 5 and 6 by (Fomin et al., 2006). Let us remark that in the cases of graphs of average degree at most 3 and 4, our bounds outerperform the O*(1.1889n) claimed by (Robson, 2001).
Optimizing the directivity of piezoelectric matrix transducer elements mounted on an ASIC

Over the last decade, clinical studies show a strong interest in real-time 3D imaging. This calls for ultrasound probes with high-element-count 2D matrix transducer arrays. These may be interfaced to an imaging system using an in-probe Application Specific Integrated Circuit (ASIC) that takes care of signal amplification, element switching, sub-array beamforming, etc. Since the ASIC is made from silicon and is mounted directly behind the transducer elements, it can acoustically be regarded as a rigid plate that can sustain traveling lateral waves. These waves lead to acoustical cross-talk between the elements, and results in extra peaks in the directivity pattern. We propose two solutions to this problem, based on numerical simulations. One approach is to decrease the phase velocity in the silicon by reducing the silicon thickness and absorbing the energy using a proper backing material. Another solution is to disturb the waves inside the silicon plate by sub-dicing the back-side of the ASIC. We conclude that both solutions can be used to improve the directivity pattern.
Detection of Early-Stage Enterprise Infection by Mining Large-Scale Log Data

Recent years have seen the rise of sophisticated attacks including advanced persistent threats (APT) which pose severe risks to organizations and governments. Additionally, new malware strains appear at a higher rate than ever before. Since many of these malware evade existing security products, traditional defenses deployed by enterprises today often fail at detecting infections at an early stage. We address the problem of detecting early-stage APT infection by proposing a new framework based on belief propagation inspired from graph theory. We demonstrate that our techniques perform well on two large datasets. We achieve high accuracy on two months of DNS logs released by Los Alamos National Lab (LANL), which include APT infection attacks simulated by LANL domain experts. We also apply our algorithms to 38TB of web proxy logs collected at the border of a large enterprise and identify hundreds of malicious domains overlooked by state-of-the-art security products.
Personality Identification through Handwriting Analysis: A Review

Whenever we listen to or meet a new person we try to predict personality attributes of the person. Our behavior towards the person is hugely influenced by the predictions we make. Personality is made up of the characteristic patterns of thoughts, feelings and behaviors that make a person unique. Your personality affects your success in the role. Recognizing about yourself and reflecting on your personality can help you to understand how you might shape your future. Various approaches like personality prediction through speech, facial expression, video, and text are proposed in literature to recognize personality. Personality predictions can be made out of one's handwriting as well. The objective of this paper is to discuss methodology used to identify personality through handwriting analysis and present current state-of-art related to it.
Electrode degradation mechanisms studies by current distribution measurements

A technique is described for determining the source and degree of electrodes degradation in membrane electrode assemblies (MEAs) from proton exchange membrane fuel cells. This technique is nondestructive and provides spatial resolution across the MEA's active area. The degradation modes that are considered are the oxygen reduction activity loss through either electrochemically active area or mass activity loss, increased gas transport resistance from corrosion of the catalyst's carbon support, and the increased protonic transport loss through chemical degradation of the electrode layer's ion-conducting polymer. A current distribution tool is used with cyclic voltammetry and polarization curves to isolate each of the primary sources of voltage degradation. Results of new MEAs are presented first to demonstrate the approximate resolution of the test method. Then results are presented for MEAs that were aged in a model test to cause carbon corrosion in the cathode layer via localized anode starvation. These include follow-up materials characterization, where it is shown that the results of this electrochemical diagnostic correlate well with postmortem materials characterization. Finally, results are shown for a part aged in a model start-up/shutdown aging test and compared with modeling results to explain the spatial characteristics of the observed degradation. Keywords: degradation; durability; current distribution; electrode diagnostic; mass activity; gas transport; proton transport; carbon corrosion
The Endothelium and Its Role in Regulating Vascular Tone

The endothelium forms an important part of the vasculature and is involved in promoting an atheroprotective environment via the complementary actions of endothelial cell-derived vasoactive factors. Disruption of vascular homeostasis can lead to the development of endothelial dysfunction which in turn contributes to the early and late stages of atherosclerosis. In recent years an increasing number of non-invasive vascular tests have been developed to assess vascular structure and function in different clinical populations. The present review aims to provide an insight into the anatomy of the vasculature as well as the underlying endothelial cell physiology. In addition, an in-depth overview of the current methods used to assess vascular function and structure is provided as well as their link to certain clinical populations.
Multi-agent system security for mobile communication

This thesis investigates security in multi-agent systems for mobile communication. Mobile as well as non-mobile agent technology is addressed. A general security analysis based on properties of agents and multi-agent systems is presented along with an overview of security measures applicable to multi-agent systems, and in particular to mobile agent systems. A security architecture, designed for deployment of agent technology in a mobile communication environment, is presented. The security architecture allows modelling of interactions at all levels within a mobile communication system. This architecture is used as the basis for describing security services and mechanisms for a multi-agent system. It is shown how security mechanisms can be used in an agent system, with emphasis on secure agent communication. Mobile agents are vulnerable to attacks from the hosts on which they are executing. Two methods for dealing with threats posed by malicious hosts to a trading agent are presented. The first approach uses a threshold scheme and multiple mobile agents to minimise the effect of malicious hosts. The second introduces trusted nodes into the infrastructure. Undetachable signatures have been proposed as a way to limit the damage a malicious host can do by misusing a signature key carried by a mobile agent. This thesis proposes an alternative scheme based on conventional signatures and public key certificates. Threshold signatures can be used in a mobile agent scenario to spread the risk between several agents and thereby overcome the threats posed by individual malicious hosts. An alternative to threshold signatures, based on conventional signatures, achieving comparable security guarantees with potential practical advantages compared to a threshold scheme is proposed in this thesis. Undetachable signatures and threshold signatures are both concepts applicable to mobile agents. This thesis proposes a technique combining the two schemes to achieve undetachable threshold signatures. This thesis defines the concept of certificate translation, which allows an agent to have one certificate translated into another format if so required, and thereby save storage space as well as being able to cope with a certificate format not foreseen at the time the agent was created.
Resolving Performance Interference in SR-IOV Setups with PCIe Quality-of-Service Extensions

PCI Express (PCIe) Single Root I/O Virtualization (SR-IOV) enables low latency and high performance virtualization of I/O devices. It has been embraced in cloud computing and is considered a promising foundation for sharing I/O in future multi-core embedded and mixed-criticality systems. Unfortunately, SR-IOV is vulnerable to Denial-of-Service (DoS) attacks, which cause performance interference. For cloud computing, an approach that mitigates ongoing attacks via software scheduling has been proposed. However, for embedded and mixed-criticality systems, solutions that go beyond mitigation are preferred. In this paper, we propose two integrated hardware architectures that completely prevent DoS attacks. As a foundation, we utilize optional Quality-of-Service (QoS) extensions from the PCIe specification. We determine which QoS extensions are needed, and show how virtualized multi-core CPUs need to implement and interface them (an aspect explicitly not covered in the PCIe specification) to enable DoS protection. The two proposed architectures are optimized for different goals, scheduling freedom or minimal hardware costs. As PCIe QoS is absent from current hardware, we evaluate our architectures with a QoS-enabled SystemC model of a real-world lab-setup. Results show that both architectures successfully prevent DoS attacks. To the best of our knowledge, we are the first to explore and evaluate feasibility of PCIe QoS for SR-IOV DoS prevention.
Characterization of bond formation in SiC and Si_3N_4 implanted with Ti, Fe, and Co

Ti, Fe, and Co ions were implanted in two ceramics, SiC and Si_3N_4, to reach concentrations on the order of 10% over a depth of about 50–60 nm. X-ray absorption spectroscopy was performed at the K edge of the implanted ions to identify their local environment at the end of the implantation process. Ti was found to form Ti–C and Ti–N bonds whereas Co and Fe precipitated and formed clusters in Si_3N_4. CoSi was detected in SiC whereas, in the same matrix, Fe clusters coexist with FeSi. A coherent interpretation of these results is given in terms of the heat of reaction for all possible systems. We also successfully interpret in the same way some results found in literature in the case of implanted oxides.
Effect of Liquid Hot Isostatic Pressing on Structure and Mechanical Properties of Aluminum Gravity Die Castings

Effect of liquid hot isostatic pressing (LHIP) on structure and mechanical properties of an A356.0 alloy was examined. Samples from this alloy were produced by gravity die castings. Part of these samples was subjected to homogenization annealing, and the other part was subjected to LHIP following homogenization annealing. All samples were water quenched from the temperature of prior homogenization annealing or LHIP and finally aged. It was shown that the LHIP processing leads to increase in yield stress, ultimate stress and total elongation. A significant increase in fatigue strength and decreased the scattering of fatigue data takes place too. This is caused by the fact that the fatigue crack initiation mostly occurs on lateral surfaces of the samples subjected to LHIP, whereas shrinkage voids in the non-hipped condition play a major role in crack initiation. In addition, crack propagation under fatigue occurs in samples subjected to LHIP in essentially ductile manner. Thus, LHIP eliminating shrinkage porosity enhances significantly mechanical properties and reliability of aluminum casting.
Suicidal ideation and suicide attempts among adults with psychotic experiences: data from the Collaborative Psychiatric Epidemiology Surveys.

IMPORTANCE Suicide is a leading cause of preventable death, especially among individuals with psychotic disorders, and may also be common among nonclinical populations of adults with subthreshold psychotic experiences. Understanding this association has the potential to critically bolster suicide prevention efforts. OBJECTIVES To examine the association between 12-month suicidality and 12-month psychotic experiences and to test the hypotheses that psychotic experiences are associated with increased prevalence of suicidal ideation and suicide attempts during the concurrent period and with greater severity of suicidal behavior. DESIGN, SETTING, AND PARTICIPANTS Cross-sectional survey data were drawn from a large general population-based sample of households in the United States identified through the Collaborative Psychiatric Epidemiology Surveys (2001-2003). Adult household residents (n = 11,716) were selected using a clustered multistage sampling design with oversampling of racial/ethnic minority groups. Logistic regression models were adjusted for potential demographic confounders and co-occurring DSM-IV mental health conditions. EXPOSURES Twelve-month psychotic experiences assessed with the Composite International Diagnostic Interview, version 3.0 psychosis screen. MAIN OUTCOMES AND MEASURES Twelve-month suicidal ideation and suicide attempts. RESULTS Respondents reporting psychotic experiences were more likely to report concurrent suicidal ideation (odds ratio [OR], 5.24; 95% CI, 2.85-9.62) and suicide attempts (OR, 9.48; 95% CI, 3.98-22.62). Most respondents with psychotic experiences (mean [SE], 65.2% [4.2%]) met criteria for a DSM-IV depressive, anxiety, or substance use disorder. Among respondents with suicidal ideation, those with psychotic experiences were likely to make an attempt during the concurrent 12-month period (OR, 3.49; 95% CI, 1.05-11.58) when adjusting for co-occurring psychiatric disorders. In contrast, depressive (OR, 1.67; 95% CI, 0.62-4.52), anxiety (OR, 1.57; 95% CI, 0.40-6.09), and substance use disorders (OR, 1.64; 95% CI, 0.24-11.17) did not reliably identify those at risk for attempts among respondents with suicidal ideation. The mean (SE) 12-month prevalence of suicide attempts among individuals reporting ideation and psychotic experiences and meeting criteria for any psychiatric disorder was 47.4% (10.9%) compared with 18.9% (4.8%) among those with just ideation and a disorder. Psychotic experiences were especially prevalent among individuals reporting severe attempts and may account for nearly one-third of attempts with intent to die (population attributable risk, 29.01%) in the United States annually. CONCLUSIONS AND RELEVANCE Assessment of psychotic experiences among individuals with suicidal ideation has potential clinical and public health utility in reducing the prevalence of suicide attempts, particularly attempts with intent to die.
The digital Michelangelo project: 3D scanning of large statues

We describe a hardware and software system for digitizing the shape and color of large fragile objects under non-laboratory conditions. Our system employs laser triangulation rangefinders, laser time-of-flight rangefinders, digital still cameras, and a suite of software for acquiring, aligning, merging, and viewing scanned data. As a demonstration of this system, we digitized 10 statues by Michelangelo, including the well-known figure of David, two building interiors, and all 1,163 extant fragments of the Forma Urbis Romae, a giant marble map of ancient Rome. Our largest single dataset is of the David - 2 billion polygons and 7,000 color images. In this paper, we discuss the challenges we faced in building this system, the solutions we employed, and the lessons we learned. We focus in particular on the unusual design of our laser triangulation scanner and on the algorithms and software we developed for handling very large scanned models.
Chlamydia Screening in Juvenile Corrections

The Centers for Disease Control and Prevention recommends chlamydia screening at intake for all females in juvenile detention facilities. Identifying factors predictive of chlamydia could enable targeted screening, reducing costs while still identifying most infections. This study used demographic, arrest, and health data to identify factors associated with chlamydia among females aged 12 to 18 years entering a juvenile detention facility in San Diego during January 2009 to June 2010. The study created different screening criteria based on combinations of factors associated with infection and calculated sensitivity and proportion screened for each criterion. Overall chlamydia prevalence was 10.3% and was 4.2% among females reporting no sexual risk factors. No acceptable targeted screening approach was identified. High prevalence, even among females without risk factors, supports universal screening at intake.