Miracle-dz/UniFAR-FTUs huggingface dataset:
Mixture models for protein structure ensembles

MOTIVATION Protein structure ensembles provide important insight into the dynamics and function of a protein and contain information that is not captured with a single static structure. However, it is not clear a priori to what extent the variability within an ensemble is caused by internal structural changes. Additional variability results from overall translations and rotations of the molecule. And most experimental data do not provide information to relate the structures to a common reference frame. To report meaningful values of intrinsic dynamics, structural precision, conformational entropy, etc., it is therefore important to disentangle local from global conformational heterogeneity. RESULTS We consider the task of disentangling local from global heterogeneity as an inference problem. We use probabilistic methods to infer from the protein ensemble missing information on reference frames and stable conformational sub-states. To this end, we model a protein ensemble as a mixture of Gaussian probability distributions of either entire conformations or structural segments. We learn these models from a protein ensemble using the expectation-maximization algorithm. Our first model can be used to find multiple conformers in a structure ensemble. The second model partitions the protein chain into locally stable structural segments or core elements and less structured regions typically found in loops. Both models are simple to implement and contain only a single free parameter: the number of conformers or structural segments. Our models can be used to analyse experimental ensembles, molecular dynamics trajectories and conformational change in proteins. AVAILABILITY The Python source code for protein ensemble analysis is available from the authors upon request.
Adaptive Memory

Distinguishing between living (animate) and nonliving (inanimate) things is essential for survival and successful reproduction. Animacy is widely recognized as a foundational dimension, appearing early in development, but its role in remembering is currently unknown. We report two studies suggesting that animacy is a critical mnemonic dimension and is one of the most important item dimensions ultimately controlling retention. Both studies show that animate words are more likely to be recalled than inanimate words, even after the stimulus classes have been equated along other mnemonically relevant dimensions (e.g., imageability and meaningfulness). Mnemonic “tunings” for animacy are easily predicted a priori by a functional-evolutionary analysis.
Dynamic Binary Space Partitioning forHidden Surface

This paper describes a new technique for dynamic binary space partitioning with applications to the dynamic hidden surface removal problem of polygons. The dynamic hidden surface removal problem is to determine and maintain visible surfaces in 3-D set of polygons from a given viewpoint under changes to the scene and it allows for eecient insertions and deletions of polygons in a 3-D scene. The polygons are maintained in a space partitioning structure called the separating plane partition tree which is a variation of the traditional binary space partition (BSP) tree. In this structure , separating planes are the fundamental objects which are used to partition the space. The polygons are fragmented with each of the fragments being stored at the leaves. This allows for more easy access of polygon fragments for insertion and deletion. EEcient hidden surface removal of the polygons is then achieved by painting the fragments in an order obtained from the space partitioning tree.
Imitation of a VOT continuum by native speakers of English and Spanish: evidence for phonetic category formation.

This study examined imitation of a voice onset time (VOT) continuum ranging from/da/to/ta/by by subjects differing in age and/or linguistic experience. The subjects did not reproduce the incremental increases in VOT linearly, but instead showed abrupt shifts in VOT between two or three VOT response "modes. " The location of the response shifts occurred at the same location as phoneme boundaries obtained in a previous identification experiment. This supports the view that the stimuli were categorized before being imitated. Children and adults who spoke just Spanish generally produced only lead and short-lag VOT responses. English monolinguals tended to produce stops with only short-lag and long-lag VOT values. The native Spanish adults and children who spoke English, on the other hand, produced stops with VOT values falling into all three model VOT ranges. This was interpreted to mean that they had established a phonetic category [th] with which to implement the voiceless aspirated realizations of /t/ in English. Their inability to produce English /p,t,k/ with the same values as native speakers of English must therefore be attributed to the information specified in their new English phonetic categories (which might be incorrect as the result of exposure to Spanish-accented English), to partially formed phonetic realization rules, or both.
Large Scale Image Annotation via Deep Representation Learning and Tag Embedding Learning

In this paper, we focus on the issue of large scale image annotation, whereas most existing methods are devised for small datasets. A novel model based on deep representation learning and tag embedding learning is proposed. Specifically, the proposed model learns an unified latent space for image visual features and tag embeddings simultaneously. Furthermore, a metric matrix is introduced to estimate the relevance scores between images and tags. Finally, an objective function modeling triplet relationships (irrelevant tag, image, relevant tag) is proposed with maximum margin pursuit. The proposed model is easy to tackle new images and tags via online learning and has a relatively low test computation complexity. Experimental results on NUS-WIDE dataset demonstrate the effectiveness of the proposed model.
Structural Unfairness in 802.11-basedWireless Mesh Networks

The use of multi-hop wireless networks based on 802.11 technology is extensive and growing, owing to their ease of deployment and low cost. However, such networks exhibit poor fairness, starving nodes that are too many hops distant from the gateway. The best current solution to this problem is source rate limiting. While effective in many topologies, this fails to completely address the fairness problem. In this paper we investigate this problem of residual unfairness in multi-hop wireless networks that use source-rate limiting. We identify the five necessary conditions for its occurrence, showing that elimination of any of these conditions is sufficient to remove the remaining unfairness. For cases where the conditions are unavoidable, we present two simple changes that can ameliorate the problem, providing on average 30% improvement for the least-rate flow.
Les forums d'actionnaires individuels: un outil de réduction du risque ?

Les conclusions des travaux de Clark Murphy et Soutar (2004, 2005) et de Nagy et Obenberger (1994) demontrent que les investisseurs individuels ne font pas seulement un arbitrage entre la rentabilite et le risque associe aux titres mais qu’ils evaluent de nombreux criteres. L’etude des forums boursiers peut permettre de comprendre comment les actionnaires prennent leur decision et abordent la notion de risque. En finance, a priori, il est admis que les acteurs sont par nature individualistes. L’existence de forums boursiers dans lesquels les actionnaires individuels entrent en contact et echangent entre eux des informations contredit totalement cette idee. Il semble en effet surprenant que des actionnaires individuels decident de participer a un forum boursier sur Internet et choisissent d’y echanger des informations. Les forums d’actionnaires n’ont, a notre connaissance, pas encore ete etudies dans la litterature alors meme qu’ils semblent constituer un terrain de recherche tres riche. L’objet de cette recherche est d’essayer de dresser un cadre theorique afin d’observer ces forums, mieux connaitre les actionnaires individuels et proposer des voies de recherche potentielles.
Distributed Computing for Formation Flying Missions

There is a continuing trend in the space community to reduce costs involved in space missions. Miniaturization has been the primary method that was deployed for reducing space mission costs. This is now changing, due to the recent advancements in technology that enable advanced mission architectures namely, distributed spacecraft missions. Several spacecraft flying in close formations would collaboratively achieve the mission aims at lower costs and with enhanced reliability compared to larger single platform missions. Distributed algorithms have been proposed for use on-board these missions for coordination and control purposes. No work has been done to implement a distributed system at the lower levels of abstraction. This paper proposes the deployment of distributed computing on-board close formation flying missions. Two distributed computing paradigms namely, client-server and mobile agent, are analytically compared in view of close formation flying missions. As a result the mobile agent paradigm is proposed for the application in hand.
Varicella-Zoster Virus IE4 Protein Interacts with SR Proteins and Exports mRNAs through the TAP/NXF1 Pathway

Available data suggest that the Varicella-Zoster virus (VZV) IE4 protein acts as an important regulator on VZV and cellular genes expression and could exert its functions at post-transcriptional level. However, the molecular mechanisms supported by this protein are not yet fully characterized. In the present study, we have attempted to clarify this IE4-mediated gene regulation and identify some cellular partners of IE4. By yeast two-hybrid and immunoprecipitation analysis, we showed that IE4 interacts with three shuttling SR proteins, namely ASF/SF2, 9G8 and SRp20. We positioned the binding domain in the IE4 RbRc region and we showed that these interactions are not bridged by RNA. We demonstrated also that IE4 strongly interacts with the main SR protein kinase, SRPK1, and is phosphorylated in in vitro kinase assay on residue Ser-136 contained in the Rb domain. By Northwestern analysis, we showed that IE4 is able to bind RNA through its arginine-rich region and in immunoprecipitation experiments the presence of RNA stabilizes complexes containing IE4 and the cellular export factors TAP/NXF1 and Aly/REF since the interactions are RNase-sensitive. Finally, we determined that IE4 influences the export of reporter mRNAs and clearly showed, by TAP/NXF1 knockdown, that VZV infection requires the TAP/NXF1 export pathway to express some viral transcripts. We thus highlighted a new example of viral mRNA export factor and proposed a model of IE4-mediated viral mRNAs export.
Robust residual selection for fault detection

A number of residual generation methods have been developed for robust model-based fault detection and isolation (FDI). There have also been a number of offline (i.e., design-time) methods that focus on optimizing FDI performance (e.g., trading off detection performance versus cost). However, design-time algorithms are not tuned to optimize performance for different operating regions of system behavior. To do this, would need to define online measures of sensitivity and robustness, and use them to select the best residual set online as system behavior transitions between operating regions. In this paper we develop a quantitative measure of residual performance, called the detectability ratio that applies to additive and multiplicative uncertainties when determining the best residual set in different operating regions. We discuss this methodology and demonstrate its effectiveness using a case study.
Security Usability Studies : Risk , Roles and Ethics Position Paper for CHI 2007 Workshop on Security User Studies

We conducted a study to evaluate website authentication measures that are designed to protect users from man-inthe-middle, ‘phishing’, and other site forgery attacks [1]. We also investigated how a study’s design affects participant behavior: we asked some participants to play a role and others to use their own accounts and passwords. We also presented some participants with security-focused instructions.
HYDRA: A Novel Framework for Making High-Performance Computing Offload Capable

The proliferation of programmable peripheral devices for computer systems opens new possibilities for academic research that will influence system designs in the near future. Programmability is a key feature that enables application-specific extensions to improve performance and offer new features. Increasing transistor density and decreasing cost provide excess computational power in devices such as disk controllers, network interfaces and video cards. This paper proposes an innovative programming model and runtime support that enables utilization of such devices by providing a generic code offloading framework. The framework enables an application developer to design the offloading aspects of the application by specifying an "offloading layout", which is enforced by the runtime during application deployment. The framework also provides the necessary development tools and programming constructs for developing such applications. We test our framework by implementing a packet generator on a programmable network card for network testing. The offloaded application produces traffic at five times the rate, and with inter-packet variability that is many orders of magnitude smaller than the non-offloaded version
Experimental verification of friction and dynamic models of a parallel kinematic machine

The Gantry-Tau is a parallel kinematic manipulator (PKM) that overcomes the workspace limitations of typical PKMs, while retaining PKM benefits such as small moving masses and high stiffness. An experimental verification of the dynamics of the Gantry-Tau is presented for the first time in this paper. A new friction model based on axial forces in the links of the 3-DOF Gantry-Tau combined with a recent inverse dynamics model for parallel kinematic machines is also presented and verified experimentally. The inverse dynamics model combining the friction model and the Jacobians shows a good match to the measured linear actuator forces from a full-scale prototype machine.
Rnd3 Regulates Lung Cancer Cell Proliferation through Notch Signaling

Rnd3/RhoE is a small Rho GTPase involved in the regulation of different cell behaviors. Dysregulation of Rnd3 has been linked to tumorigenesis and metastasis. Lung cancers are the leading cause of cancer-related death in the West and around the world. The expression of Rnd3 and its ectopic role in non-small cell lung cancer (NSCLC) remain to be explored. Here, we reported that Rnd3 was down-regulated in three NSCLC cell lines: H358, H520 and A549. The down-regulation of Rnd3 led to hyper-activation of Rho Kinase and Notch signaling. The reintroduction of Rnd3 or selective inhibition of Notch signaling, but not Rho Kinase signaling, blocked the proliferation of H358 and H520 cells. Mechanistically, Notch intracellular domain (NICD) protein abundance in H358 cells was regulated by Rnd3-mediated NICD proteasome degradation. Rnd3 regulated H358 and H520 cell proliferation through a Notch1/NICD/Hes1 signaling axis independent of Rho Kinase.
Asymptotic evaluation of distance measure on high dimensional vector spaces in text mining

This paper discusses the document classification problems in text mining from the viewpoint of asymptotic statistical analysis. In the problem of text mining, the several heuristics are applied to practical analysis because of its experimental effectiveness in many case studies. The theoretical explanation about the performance of text mining techniques is required and such thinking will give us very clear idea. In this paper, the performances of distance measures used to classify the documents are analyzed from the new viewpoint of asymptotic analysis. We also discuss the asymptotic performance of IDF measure used in the information retrieval field.
Stereo-olfaction with a sniffing neuromorphic robot using spiking neurons

This paper presents a neuromorphic robot using stereo-olfaction and a sniffing system based on nonselective chemosensors that mimic the animal behavior of tracking a specific odor. In order to be able to go toward an odor source, two tasks must be performed : 1) estimation of the gas-concentration gradient and 2) gas recognition independent of the intensity. It is shown how these two tasks can be implemented with artificial spiking neurons in a biologically inspired approach.
The moderating role of organizational culture on the effect of organizational justice on organizational citizenship behavior

The main objective of this study is to examine the effect of distributive justice and procedural justice on organizational citizenship behavior (OCB) with organizational culture as a moderating variable. The data in this study were collected from questionnaires distributed to 94 permanent employees of PT Telekomunikasi Indonesia (Telkom) Tbk. Regional Division IV. Hypotheses testing shows that distributive and procedural justice positively affects OCB. Organizational culture is also found to be the moderator on the effect of procedural justice on OCB. However, our prediction that organizational culture could be the moderator on the effect of distributive justice on OCB is not supported. Further results and discussion are explained.
Small population effects and hybridization

This paper examines the confluence of two lines of research that seek to improve the performance of evolutionary computation systems through management of information flow. The first is hybridization; the second is using small population effects. Hybridization consists of restarting evolutionary algorithms with copies of best-of-population individuals drawn from many populations. Small population effects occur when an evolutionary algorithmpsilas performance, either speed or probability of premature convergence, is improved by use of a very small population. This paper presents a structure for evolutionary computation called a blender which performs hybridization of many small populations. The blender algorithm is tested on the PORS and Tartarus tasks. Substantial and significant effects result from varying the size of the small populations used and from varying the frequency with which hybridization is performed. The major effect results from changing the frequency of hybridization; the impact of population size is more modest. The parameter settings which yield best performance of the blender algorithm are remarkably consistent across all seven sets of experiments performed. Blender performance is found to be superior to other algorithms for six cases of the PORS problem. For Tartarus, blender performs well, but not as well as the previous hybridization experiments that motivated its development.
A heterogeneous memory organization with minimum energy consumption in 3D chip-multiprocessors

Main memories play an important role in overall energy consumption of embedded systems. Using conventional memory technologies in future designs in nanoscale era cause a drastic increase in leakage power consumption and temperature-related problems. Emerging non-volatile memory (NVM) technologies offer many desirable characteristics such as near-zero leakage power, high density and non-volatility. They can significantly mitigate the issue of memory leakage power in future embedded chip-multiprocessor (eCMP) systems. However, they suffer from challenges such as limited write endurance and high write energy consumption which restrict them for adoption in modern memory systems. In this article, we propose a stacked hybrid memory system for 3D chip-multiprocessors to take advantages of both traditional and non-volatile memory technologies. For reaching this target, we present a convex optimization-based model that minimizes the system energy consumption while satisfy endurance constraint in order to design a reliable memory system. Experimental results show that the proposed method improves energy-delay product (EDP) and performance by about 44.8% and 13.8% on average respectively compared with the traditional memory design where single technology is used.
Closed loop time invariant control of 3D underactuated underwater vehicles

A novel strategy to design time invariant motion controllers for underactuated mobile systems is applied to the position and attitude control of an underactuated 3D vehicle. The idea consists in defining a velocity vector field such that an ideal, fully actuated system would exponentially achieve the control objective by simply following such field. Then a steering law for the given underactuated system is designed such that it is exponentially stabilized parallel to the above mentioned velocity vector field. For the particular problem here addressed, due to the use of polar like coordinates, this method yields a discontinuous control law. Both the design process and the resulting solution have a most clear physical interpretation. Important practical requirements as approaching the target on a null curvature path, avoiding cusps in the whole path and moving in only one given forward direction are easily satisfied within this framework.
Amplitude integrated EEG 3 and 6 hours after birth in full term neonates with hypoxic–ischaemic encephalopathy

AIM To assess the prognostic value of amplitude integrated EEG (aEEG) 3 and 6 hours after birth. METHODS Seventy three term, asphyxiated infants were studied (from two different centres), using the Cerebral Function Monitor (CFM Lectromed). The different aEEG tracings were compared using pattern recognition (flat tracing mainly isoelectric (FT); continuous extremely low voltage (CLV); burst–suppression (BS); discontinuous normal voltage (DNV); continuous normal voltage (CNV)) with subsequent outcome. RESULTS Sixty eight infants were followed up for more than 12 months (range 12 months to 6 years). Twenty one out of 68 infants (31%) showed a change in pattern from 3 to 6 hours, but this was only significant in five cases (24%). In three this changed from BS to CNV with a normal outcome. One infant showed a change in pattern from CNV to FT and had a major handicap at follow up. Another infant showed a change in pattern from DNV to BS, and developed a major handicap at follow up. The other 16 infants did not have any significant changes in pattern: 11 infants had CLV, BS, or FT at 3 and 6 hours and died (n = 9) in the neonatal period or developed a major handicap (n = 2). Five infants had a CNV or DNV pattern at 3 and 6 hours, with a normal outcome. The sensitivity and specificity of BS, together with FT and CLV, for poor outcome at 3 hours was 0.85 and 0.77, respectively; at 6 hours 0.91 and 0.86, respectively. The positive predictive value (PPV) was 78% and the negative predictive value (NPV) 84% 3 hours after birth. At 6 hours the PPV was 86% and the NPV was 91%. CONCLUSION aEEG could be very useful for selecting those infants who might benefit from intervention after birth asphyxia.