Miracle-dz/UniFAR-FTUs huggingface dataset:
High-throughput modeling and analysis of protein structural dynamics

Protein function is a dynamic property closely related to the conformational mechanisms of protein structure in its physiological environment. To understand and control the function of target proteins, it becomes increasingly important to develop methods and tools for predicting collective motions at the molecular level. In this article, we review computational methods for predicting conformational dynamics and discuss software tools for data analysis. In particular, we discuss a high-throughput, web-based system called iGNM for protein structural dynamics. iGNM contains a database of protein motions for more than 20 000 PDB structures and supports online calculations for newly deposited PDB structures or user-modified structures. iGNM allows dynamics analysis of protein structures ranging from enzymes to large complexes and assemblies, and enables the exploration of protein sequence-structure-dynamics-function relations.
Dynamics of abducens nucleus neuron discharges during disjunctive saccades.

In this report, we provide the first characterization of abducens nucleus neuron (ABN) discharge dynamics during horizontal disjunctive saccades. These movements function to rapidly transfer the visual axes between targets located at different eccentricities and depths. Our primary objective was to determine whether the signals carried by ABNs during these movements are appropriate to drive the motion of the eye to which they project. We also asked whether ABNs encode eye movements similarly during disjunctive saccades and disjunctive fixation. To address the first objective we 1) assessed whether we could predict the discharge dynamics of individual neurons during disjunctive saccades based on their discharge properties during conjugate saccades and 2) directly estimated the sensitivity of individual neurons to either the ipsilateral/contralateral eye or the conjugate/vergence position and velocity using bootstrap statistics. Our main finding was that during disjunctive saccades in the direction ipsilateral to the recording site (ON-direction), the majority of ABNs preferentially encoded the velocity and the position of the ipsilateral eye. The remaining neurons predominantly encoded the conjugate motion of the eyes (i.e., were equally sensitive to the motion of both eyes). Generally, ipsilateral/contralateral eye based models better described neuronal discharges than conjugate/vergence based models, yet both model structures yielded similar conclusions. Moreover, the preferred eye of individual neurons based on their position and velocity sensitivities were generally well matched. We also found that for saccades in the OFF-direction, the pausing behavior of ABNs was similar during conjugate and disjunctive saccades, with the exception that for movements of small amplitudes, more ABNs paused during conjugate saccades. Finally, we found that putative motoneurons and internuclear neurons encoded ON- and OFF-direction disjunctive saccades in a similar manner. To address our second objective, we compared the discharge properties of individual ABNs during disjunctive saccades and disjunctive fixation. Good coherence was observed between the preferred eye of individual ABNs during the two behaviors. Taken together, our results indicate that although individual ABNs can encode the motion of both eyes to various degrees, the population drive of ABNs accounts for most of the movement of the ipsilateral eye during disjunctive saccades and disjunctive fixation.
Role Semantics for Better Models of Implicit Discourse Relations

Predicting the structure of a discourse is challenging because relations between discourse segments are often implicit and thus hard to distinguish computationally. I extend previous work to classify implicit discourse relations by introducing a novel set of features on the level of semantic roles. My results demonstrate that such features are helpful, yielding results competitive with other feature-rich approaches on the PDTB. My main contribution is an analysis of improvements that can be traced back to role-based features, providing insights into why and when role semantics is helpful.
Why Simple Shrinkage Is Still Relevant for Redundant Representations?

Shrinkage is a well known and appealing denoising technique, introduced originally by Donoho and Johnstone in 1994. The use of shrinkage for denoising is known to be optimal for Gaussian white noise, provided that the sparsity on the signal's representation is enforced using a unitary transform. Still, shrinkage is also practiced with nonunitary, and even redundant representations, typically leading to very satisfactory results. In this correspondence we shed some light on this behavior. The main argument in this work is that such simple shrinkage could be interpreted as the first iteration of an algorithm that solves the basis pursuit denoising (BPDN) problem. While the desired solution of BPDN is hard to obtain in general, we develop a simple iterative procedure for the BPDN minimization that amounts to stepwise shrinkage. We demonstrate how the simple shrinkage emerges as the first iteration of this novel algorithm. Furthermore, we show how shrinkage can be iterated, turning into an effective algorithm that minimizes the BPDN via simple shrinkage steps, in order to further strengthen the denoising effect
A photonic technique for microwave frequency measurement employing tunable dispersive medium

We propose a novel photonic technique for microwave frequency measurement by employing an optical group delay line. The 7-bit optical delay line composed of several magneto-optical switches and 1.6km single-mode fiber (SMF) is designed as a tunable dispersive medium (TDM) in the measurement system. In our scheme, the measurable frequency range of 1–20GHz with a measurement error less than ± 40MHz is demonstrated experimentally. Also, we have studied the dynamic range of the measurement system.
Fathering, Feminism(s), Gender, and Sexualities: Connections, Tensions, and New Pathways

This article provides a critical overview of selected intersections of feminist theories and gender theories within fathering research and looks at a variety of theoretical and methodological approaches to a diversity of fathering experiences, including differences of class, ethnicity, race, sexuality, and family forms. Although there are many overlaps between feminist theories and gender theories, and most scholars who write about gender are feminist or profeminist scholars, there is one important distinction. Gender theories attend to multiple dimensions of gendered narratives, lives, practices, identities, and institutions. Feminism and feminist theories share all of these concerns; however, feminism and feminist theories are also directly connected to the promotion of social change for diverse groups of women, especially disadvantaged women. This point is important because it can lead to potential conflicts between feminist concerns and fathering.
Improving multi-channel operations in VANETs by leveraging stopped vehicles

Multiple channels have been allocated in the 5 GHz spectrum for vehicular communications in USA and in Europe. Due to the limited spectrum, simultaneous communications may occur over nearby channels and be affected by adjacent channel interference (ACI). To protect safety messages delivered on the control channel (CCH), the most likely approach is to prevent the use of adjacent channels with the consequence of spectrum resources wasting. In this paper we identify temporarily stopped vehicles (e.g., at the gas station for refuelling) as users that are potentially allowed to transmit on a channel that is adjacent to the CCH. A simulation study has been conducted to evaluate the viability of our proposal. Achieved results show that the two conflicting objectives of improving spectrum utilization and not penalizing safety messages can be successfully met, provided that the transmission power on the adjacent channel is adequately tuned and the stopped vehicle is at a sufficient distance from the vehicle that is using the CCH.
Flood Detection in Urban Areas Using TerraSAR-X

Flooding is a major hazard in both rural and urban areas worldwide, but it is in urban areas that the impacts are most severe. An investigation of the ability of high-resolution TerraSAR-X synthetic aperture radar (SAR) data to detect flooded regions in urban areas is described. The study uses a TerraSAR-X image of a one-in-150-year flood near Tewkesbury, U.K., in 2007, for which contemporaneous aerial photography exists for validation. The German Aerospace Center (DLR) SAR end-to-end simulator (SETES) was used in conjunction with airborne scanning laser altimetry (LiDAR) data to estimate regions of the image in which water would not be visible due to shadow or layover caused by buildings and taller vegetation. A semiautomatic algorithm for the detection of floodwater in urban areas is described, together with its validation using aerial photographs. Of the urban water pixels that are visible to TerraSAR-X, 76% were correctly detected, with an associated false positive rate of 25%. If all the urban water pixels were considered, including those in shadow and layover regions, these figures fell to 58% and 19%, respectively. The algorithm is aimed at producing urban flood extents with which to calibrate and validate urban flood inundation models, and these findings indicate that TerraSAR-X is capable of providing useful data for this purpose.
Performance Evaluation of MANET Routing Protocols: Simulations and Experiments

A Mobile Ad hoc Network (MANET) is a collection of wireless mobile terminals that are able to dynamically form a temporary network without any aid from fixed infrastructure or centralized administration. In this paper, we present the implementation and analysis of our implemented MANET testbed and simulation system considering Ad-hoc On demand Distance Vector (AODV) and Optimized Link State Routing (OLSR) protocols for wireless multi-hop networking. We investigate the effect of mobility and topology changing in MANET. We evaluate and compare the performance by simulation (using ns-2 simulator) and experiments in a real environment. In this work, we consider two models: stationary and mobile. We assess the performance of our testbed and simulation in terms of throughput, number of received packets and hop distance. From the results, we found that the AODV protocol has a good performance when the relay node is moving. Also, the AODV protocol provides a flexible and effective routing for indoor environments.
Schizophrenic outpatient perceptions of psychiatric treatment and psychotic symptomatology: An investigation using structural equation modeling

Abstract Schizophrenic patient perceptions of treatment have clinical value and deserve detailed psychiatric investigation. The present study sought a model indicating statistically estimated cause–effect relationships of perceptions and psychotic symptomatology of outpatients with schizophrenia by applying a method of structural equation modeling. The perceptions included in this model were patient satisfaction with treatment, perceptions of their treating psychiatrists, and patient‐role perception. Scores of Positive and Negative Syndrome Scale and poor insight measures were added to the model as possible influential factors. The constructed model revealed that the poor insight exerted a major influence on the patient‐role perception that had small effects on the reliable therapist perception and the satisfaction. It was also shown that satisfaction was chiefly determined by the reliable therapist perception that was formed in the treatment relationship, rather independently of the other construct. These findings were valuable in terms of their implications for understanding the makeup of the perceptions and the strategy for interventions to improve them.
Wavelet Domain Local Binary Pattern Features For Writer Identification

The representation of writing styles is a crucial step of writer identification schemes. However, the large intra-writer variance makes it a challenging task. Thus, a good feature of writing style plays a key role in writer identification. In this paper, we present a simple and effective feature for off-line, text-independent writer identification, namely wavelet domain local binary patterns (WD-LBP). Based on WD-LBP, a writer identification algorithm is developed. WD-LBP is able to capture the essence of characteristics of writer while ignoring the variations intrinsic to every single writer. Unlike other texture framework method, we do not assign any statistical distribution assumption to the proposed method. This prevent us from making any, possibly erroneous, assumptions about the handwritten image feature distributions. The experimental results show that the proposed writer identification method achieves high accuracy of identification and outperforms recent writer identification method such as wavelet-GGD model and Gabor filtering method.
ServicesCross-lingual Information Transformation and Summarisation for Portable End-devices with : the MEMPHIS Toolboxproject

The MEMPHIS project (http://www.istmemphis.org) aims at developing a platform for cross-lingual premium content services, targeting mainly portable thin clients, like mobile phones, PDAs, etc. The core of the system is a cross-lingual transformation layer integrating cross-lingual information extraction and summarization of source documents, translation to the customers' target languages as well as multilingual generation of documents according to the restrictions and requirements of the various target devices for distribution. This paper will present an overview of MEMPHIS focusing on its NL technologies.
Psychoanalytic culture : psychoanalytic discourse in western society

Introduction Psychoanalysis and Discourse PART ONE: OBJECT RELATIONS THEORIES: SELF AND SOCIETY Groups, Identity and Forms of Knowledge Religious Belief, Charity and Crooked Cures War Breaking Out, in Inner and Outer Space PART TWO: CRITICAL THEORIES: INDIVIDUALITY AND CULTURE Individuality, Enlightenment and the Psy-Complex Authoritarianism, Ideology and Masculinity Culture and Nature after Enlightenment PART THREE: POST-THEORIES: SUBJECTIVITY AND THE SOCIAL Symbolic Orders, Subjects and Cyberspace Mirroring, Imagining and Escaping the Local Economy Real Things, Recovery and Therapy
Differential Recruitment of Pre-mRNA Splicing Factors to Alternatively Spliced Transcripts In Vivo

Alternative splicing in mammalian cells has been suggested to be largely controlled by combinatorial binding of basal splicing factors to pre-mRNA templates. This model predicts that distinct sets of pre-mRNA splicing factors are associated with alternatively spliced transcripts. However, no experimental evidence for differential recruitment of splicing factors to transcripts with distinct splicing fates is available. Here we have used quantitative single-cell imaging to test this key prediction in vivo. We show that distinct combinations of splicing factors are recruited to sites of alternatively spliced transcripts in intact cells. While a subset of serine/arginine protein splicing factors, including SF2/ASF, SC35, and SRp20, is efficiently recruited to the tau gene when exon 10 is included, these factors are less frequently associated with tau transcription sites when exon 10 is excluded. In contrast, the frequency of recruitment of several other splicing factors is independent of splicing outcome. Mutation analysis of SF2/ASF shows that both protein–protein as well as protein–RNA interactions are required for differential recruitment. The differential behavior of the various splicing factors provides the basis for combinatorial occupancy at pre-mRNAs. These observations represent the first in vivo evidence for differential association of pre-mRNA splicing factors with alternatively spliced transcripts. They confirm a key prediction of a stochastic model of alternative splicing, in which distinct combinatorial sets of generic pre-mRNA splicing factors contribute to splicing outcome.
Atherosclerosis Is Attenuated by Limiting Superoxide Generation in Both Macrophages and Vessel Wall Cells

Objective—We previously showed that NAD(P)H oxidase deficiency significantly reduces atherosclerosis in apoE−/− mice. The present study was designed to determine the relative contribution of monocyte/macrophage versus vascular wall cell NAD(P)H oxidase to atherogenesis in this model. Methods and Results—Cell-specific NAD(P)H oxidase inhibition was achieved via allogenic, sex-mismatched bone marrow transplantation. Aortic atherosclerosis and superoxide production in apoE−/− mice (Control) with functional NAD(P)H oxidase in both monocytes/macrophages and vascular wall cells was compared with that in apoE−/− mice with nonfunctional monocyte/macrophage NAD(P)H oxidase (BMO) or nonfunctional vessel wall NAD(P)H oxidase (VWO). A significant decrease in superoxide production and atherosclerotic lesions was observed in BMO and VWO mice compared with control mice. Interestingly, BMO mice had significantly lower plasma oxidized LDL levels compared with control and VWO mice, whereas aortic sections of VWO mice showed decreased expression of cellular adhesion molecules compared with control and BMO mice. NAD(P)H oxidase deficiency also attenuated neointimal hyperplasia and mitogenic protein activation in apoE−/− mice after arterial injury. Conclusions—We conclude that (1) both monocyte/macrophages and vessel wall cells play critical roles in atherogenesis; (2) decrease in atherosclerosis results from attenuated superoxide generation in monocyte/macrophages or vessel wall cells; and (3) superoxide generation may impact atherosclerosis, in part, by activating smooth muscle cell mitogenic signaling pathways.
Cardiac coherence and posttraumatic stress disorder in combat veterans.

BACKGROUND The need for treatment of posttraumatic stress disorder (PTSD) among combat veterans returning from Afghanistan and Iraq is a growing concern. PTSD has been associated with reduced cardiac coherence (an indicator of heart rate variability [HRV]) and deficits in early stage information processing (attention and immediate memory) in different studies. However, the co-occurrence of reduced coherence and cognition in combat veterans with PTSD has not been studied before. PRIMARY STUDY OBJECTIVE A pilot study was undertaken to assess the covariance of coherence and information processing in combat veterans. An additional study goal was assessment of effects of HRV biofeedback (HRVB) on coherence and information processing in these veterans. METHODS/DESIGN A two-group (combat veterans with and without PTSD), pre-post study of coherence and information processing was employed with baseline psychometric covariates. SETTING The study was conducted at a VA Medical Center outpatient mental health clinic. PARTICIPANTS Five combat veterans from Iraq or Afghanistan with PTSD and five active-duty soldiers with comparable combat exposure who were without PTSD. INTERVENTION Participants met with an HRVB professional once weekly for 4 weeks and received visual feedback in HRV patterns while receiving training in resonance frequency breathing and positive emotion induction. PRIMARY OUTCOME MEASURES Cardiac coherence, word list learning, commissions (false alarms) in go-no go reaction time, digits backward. RESULTS Cardiac coherence was achieved in all participants, and the increase in coherence ratio was significant post-HRVB training. Significant improvements in the information processing indicators were achieved. Degree of increase in coherence was the likely mediator of cognitive improvement. CONCLUSION Cardiac coherence is an index of strength of control of parasympathetic cardiac deceleration in an individual that has cardinal importance for the individual's attention and affect regulation.
Semantic Business Process Management: An Empirical Case Study

Semantic technologies promise fully leveraging the content of enterprise and business process models by applying reasoning techniques to query the process space or using ontological mappings for bridging the business-IT divide. Such an approach is known as semantic business process management. We conducted an empirical case study to explore semantic business process management. The case study was replicated 13 times with 17 participants from 8 different industrial and scientific organisations following a strict case study methodology to ensure validity and reliability of the results. The results show that participants embrace the possibilities of semantic technologies, but there are still open problems. In this paper, we present the case study design and discuss the results achieved.
Chapter 14 Dynamics of Human Gait Transitions

What is responsible for the organization of complex actions? In this chapter, we address this question by focusing on the transition from walking to running in humans. First, we consider the concept of a motor program as a source of the organization seen in human gait. We then present evidence consistent with a dynamic theory of the shift between gaits. Results from our studies indicate that preferred gaits are attractors that exhibit stable phase relationships between the leg segments, whereas gait transitions are bifurcations characterized by a loss of stability. We conclude that complex behaviors such as locomotion likely emerge from the dynamics of the motor system and task constraints, and that they are not imposed on the system by a motor program. Complex actions require a large number of degrees of freedom to be coordinated in a precise manner (Bernstein, 1967). For instance, during bipedal locomotion the legs move 180 0 out-of-phase with each other, and the segments within each leg exhibit specific phase relationships (Diedrich and Warren, 1995b). What is responsible for these complex sequences of limb movements? In this paper, we approach this question by considering the walk-run transition in humans. First, we consider motor programs as a possible source of the organization seen in human gait. We then discuss a dynamic theory of human gait and present supporting evidence from several recent experiments. We conclude that actions such as gait likely emerge from the dynamics of the action system and task constraints. It is often assumed that the organization and timing of movements is due to the prior organization of some entity in the motor system. An example from psychology is the motor program, typically defined as a hierarchical memory structure that specifies many aspects of a movement, beginning with the order, phasing, and relative force of its components, and ending