Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving protein–protein interactions prediction accuracy using protein evolutionary information and relevance vector machine model

Predicting protein–protein interactions (PPIs) is a challenging task and essential to construct the protein interaction networks, which is important for facilitating our understanding of the mechanisms of biological systems. Although a number of high‐throughput technologies have been proposed to predict PPIs, there are unavoidable shortcomings, including high cost, time intensity, and inherently high false positive rates. For these reasons, many computational methods have been proposed for predicting PPIs. However, the problem is still far from being solved. In this article, we propose a novel computational method called RVM‐BiGP that combines the relevance vector machine (RVM) model and Bi‐gram Probabilities (BiGP) for PPIs detection from protein sequences. The major improvement includes (1) Protein sequences are represented using the Bi‐gram probabilities (BiGP) feature representation on a Position Specific Scoring Matrix (PSSM), in which the protein evolutionary information is contained; (2) For reducing the influence of noise, the Principal Component Analysis (PCA) method is used to reduce the dimension of BiGP vector; (3) The powerful and robust Relevance Vector Machine (RVM) algorithm is used for classification. Five‐fold cross‐validation experiments executed on yeast and Helicobacter pylori datasets, which achieved very high accuracies of 94.57 and 90.57%, respectively. Experimental results are significantly better than previous methods. To further evaluate the proposed method, we compare it with the state‐of‐the‐art support vector machine (SVM) classifier on the yeast dataset. The experimental results demonstrate that our RVM‐BiGP method is significantly better than the SVM‐based method. In addition, we achieved 97.15% accuracy on imbalance yeast dataset, which is higher than that of balance yeast dataset. The promising experimental results show the efficiency and robust of the proposed method, which can be an automatic decision support tool for future proteomics research. For facilitating extensive studies for future proteomics research, we developed a freely available web server called RVM‐BiGP‐PPIs in Hypertext Preprocessor (PHP) for predicting PPIs. The web server including source code and the datasets are available at http://219.219. 62.123:8888/BiGP/.
On the Sensitivity of Transmit Wiener Filtering for Broadcast Channels with Respect to Channel Estimation Errors

We consider the behavior of the transmit Wiener filter for broadcast channels with non-cooperating users under channel uncertainties. We derive a second-order approximation to the excess mean-square error (EMSE) induced by using a channel estimate as if it were the true channel. In the high SNR cases, we develop a simple approximation to the EMSE. It turns out that the EMSE is proportional to the minimum mean square error with the proportionality factor determined by the total transmit power and the length of the training block.
Explaining Employee Job Performance: The Role of Online and Offline Workplace Communication Networks

By distinguishing between employees' online and offline workplace communication networks, this paper incorporates technology into social network theory to understand employees' job performance. Specifically, we conceptualize network ties as direct and indirect ties in both online and offline workplace communication networks, thus resulting in four distinct types of ties. We theorize that employees' ties in online and offline workplace communication networks are complementary resources that interact to influence their job performance. We found support for our model in a field study among 104 employees in a large telecommunication company. The paper concludes with theoretical and practical implications.
CLINICAL PERSPECTIVE What Is New?

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
Synesthesia: an introduction

Synesthesia is a rare experience where one property of a stimulus evokes a second experience not associated with the first. For example, in lexical-gustatory synesthesia words evoke the experience of tastes (Ward and Simner, 2003). There are at least 60 known variants of synesthesia (Day, 2013), including reports of synesthetic experiences of color (Baron-Cohen et al., 1987), taste (Ward and Simner, 2003), touch (Ward et al., 2008), and sound (Saenz and Koch, 2008). The lower bound prevalence of the condition is considered to be approximately 4% (Simner et al., 2006). While synesthetic experiences have been documented since the 1800s (Jewanski et al., 2009), it is only in the last few decades that the authenticity of synesthetic experiences and mechanisms that contribute to them has been explored in depth (Ward, 2013). This resurgence in research has led to developments in our understanding of mechanisms that contribute to the synesthetic experience and the use of synesthesia as a unique experimental preparation to inform us about typical models of cognition and perception (e.g., Cohen Kadosh and Henik, 2007; Simner, 2007; Bargary and Mitchell, 2008; Rouw et al., 2011). This has also resulted in many open questions and debates, several of which are touched upon in this research topic. Specifically, this research topic is focused around the following themes: What constitutes synesthesia and how does it relate to typical cross-modal interactions? What mechanisms contribute to synesthetic experiences? Are there broader cognitive and perceptual traits associated with synesthesia, and what mechanisms mediate their relationship? In total, there are 20 articles, each addressing at least one of these themes.
Vesicular Systems (Niosomes and Liposomes) for Delivery of Sodium Stibogluconate in Experimental Murine Visceral Leishmaniasis

Abstract— Suppression of Leishmania donovani liver amastigotes by sodium stibogluconate has been determined in a murine model of experimental visceral leishmaniasis. Niosomal and liposomal drug formulations were equiactive and both increased drug efficacy by an order of magnitude compared with that of free drug. Niosomes containing 30 mol % cholesterol were prepared from three different non‐ionic surfactants and no significant difference in activity was detected among the different drug‐loaded niosomes. Both negatively charged and neutral vesicles were found to be equally effective. However, vesicle cholesterol content had a slight influence on the antiparasitic activity of the drug‐loaded niosomes. Empty vesicles produced a dose‐dependent parasite suppression for all vesicles studied. Studies of antimony distribution in the mouse using neutron activation analysis showed high liver levels after i.v. administration of the carrier forms of the drug.
Automatic dysfluency detection in dysarthric speech using deep belief networks

Dysarthria is a speech disorder caused by difficulties in controlling muscles, such as the tongue and lips, that are needed to produce speech. These differences in motor skills cause speech to be slurred, mumbled, and spoken relatively slowly, and can also increase the likelihood of dysfluency. This includes nonspeech sounds, and ‘stuttering’, defined here as a disruption in the fluency of speech manifested by prolongations, stop-gaps, and repetitions. This paper investigates different types of input features used by deep neural networks (DNNs) to automatically detect repetition stuttering and non-speech dysfluencies within dysarthric speech. The experiments test the effects of dimensionality within Mel-frequency cepstral coefficients (MFCCs) and linear predictive cepstral coefficients (LPCCs), and explore the detection capabilities in dyarthric versus non-dysarthric speech. The results obtained using MFCC and LPCC features produced similar recognition accuracies; repetition stuttering in dysarthric speech was identified correctly at approximately 86% and 84% for non-dysarthric speech. Non-speech sounds were recognized with approximately 75% accuracy in dysarthric speakers.
Holocene relative sea-level records from coral microatolls in Western Borneo, South China Sea

The spatial variability of Holocene relative sea level (RSL) in the South China Sea is unknown, with data restricted to Thailand, the Malay Peninsula, and a few other isolated sites. In this study, we present new continuous RSL records for Borneo using surveyed and U–Th dated coral microatolls from four sites in western Sarawak. The record spans 450 years of RSL from 7450 to 7000 yr BP. Our data suggest that RSL was higher than present and rapid RSL rise had ceased by 7450 yr BP. We compare these RSL reconstructions with a regional model of glacial-isostatic adjustment (GIA). The RSL reconstructions from three sites off the coast of Sarawak show a spatial gradient opposite to that predicted by the GIA model. This disagreement can best be explained by tectonic deformation since 7000 yr BP, which was previously unrecognized. We propose vertical land motion of 0.7–1.45 m due to slip on the Serabang fault, which runs between our four sites. This slip may have occurred in response to the loading of the Sunda Shelf by rising sea level.
Naming the Pain in Requirements Engineering: Comparing Practices in Brazil and Germany

As part of the Naming the Pain in Requirements Engineering (NaPiRE) initiative, researchers compared problems that companies in Brazil and Germany encountered during requirements engineering (RE). The key takeaway was that in RE, human interaction is necessary for eliciting and specifying high-quality requirements, regardless of country, project type, or company size.
Electrical Neuroimaging of Voluntary Audiospatial Attention: Evidence for a Supramodal Attention Control Network

Previous attempts to investigate the supramodal nature of attentional control have focused primarily on identifying neuroanatomical overlap in the frontoparietal systems activated during voluntary shifts of spatial attention in different sensory modalities. However, the activation of the same neural structures is insufficient evidence for a supramodal system, as the same brain regions could interact with one another in very different ways during shifts of attention in different modalities. Thus, to explore the similarity of the functional networks, it is necessary to identify the neural structures involved and to examine the timing and sequence of activities within the network. To this end, we used an electrical neuroimaging technique to localize the neural sources of electroencephalographic signals recorded from human subjects during audiospatial shifts of attention and to examine the timing and sequence of activities within several regions of interest. We then compared the results to an analogous study of visuospatial attention shifts. Similar frontal and parietal regions were activated during visual and auditory shifts of attention, and the timing of activities within these regions was nearly identical. Following this modality-independent sequence of attention-control activity, activity in the relevant sensory cortex was enhanced in anticipation of the response-relevant target. These results are consistent with the hypothesis that a single supramodal network of frontal and parietal regions mediates voluntary shifts of spatial attention and controls the flow of sensory information in modality-specific sensory pathways.
THE NATURE OF FIBRILLARY CONTRACTION OF THE HEART. ‐ ITS RELATION TO TISSUE MASS AND FORM 1

I T is a noteworthy fact that the hearts (ventricles) of large animals fibrillate with great ease and only rarely recover from the fibrillary state, while small hearts rarely fail to recover. It was noted by McWilliam 2 that “spontaneous recovery may take place readily in the hearts of the cat, rabbit, rat, mouse, hedgehog, and fowl. ” The ventricles of dogs do not usually recover spontaneously from fibrillation, although they do so in rare instances, as noted by Porter.3 The larger beef heart is one which enters into the fibrillary state with greatest ease and caprice. Erlanger 4 records this fact and states “that it is not often that fibrillation of the calves’ heart can be stopped, as in other hearts, by means of temporary perfusion with potassium chloride solution. ” In this connection we may also refer to the well-known fact that fibrillation of the thin walled auricles is usually of a transitory nature, while that of the thicker ventricles of the same heart is much more prone to persist. It would appear obvious, from a consideration of these facts, that the size of the tissue masses involved in the process may have an important bearing on the induction of and recovery from the fibrillary state, yet, so far as we have been able to ascertain, these phenomena have never been systematically investigated from this viewpoint,
Primary User Detection in Multi-Antenna Cognitive Radio

It is well known in the wireless telecommunications field that the most valuable resource available is the electromagnetic radio spectrum. Being a natural resource, it is obviously finite and has to be utilized in a rational fashion. Nevertheless the demand increase on wireless devices and services such as voice, short messages, Web, high-speed multimedia, as well as high quality of service (QoS) applications has led to a saturation of the currently available spectrum. On the other hand, it has be found that some of the major licensed bands like the ones used for television broadcasting are severely underutilized Federal Communications Commission (November) which at the end of the day results in a significant spectrum wastage. For this means, it is important to come upwith a new paradigm that allows us to take advantage of the unused spectrum. Cognitive radio has risen as a solution to overcome the spectrum underutilization problem Mitola & Maguire (1999),Haykin (2005). The main idea under cognitive radio systems is to allow unlicensed users or cognitive users (those who have not paid for utilizing the electromagnetic spectrum), under certain circumstances, to transmit within a licensed band. In order to perform this task, cognitive users need to continuously monitor the spectrum activities and find a suitable spectrum band that allows them to:
Design and Implementation of the Compound Noun Segmentation Algorithm Based on Statistical Information

This paper suggests a reverse segmentation algorithm using affix information and some preference pattern information of Korean compound nouns. The structure of Korean compound nouns is mostly derived from Chinese characters, and it includes some preference patterns utilized as a segmentation rule in this paper. To evaluate the accuracy of the proposed algorithm, an experiment was performed with 36,061 compound nouns. The experiment resulted in getting 99.3% of correct segmentation and showed excellent satisfactory results from the comparative experimentation with other algorithms. Especially, most of the four-syllable or five-syllable compound nouns were successfully segmented without fail.
A Statistical Approach Towards Robust Progress Estimation

The need for accurate SQL progress estimation in the context of decision support administration has led to a number of techniques proposed for this task. Unfortunately, no single one of these progress estimators behaves robustly across the variety of SQL queries encountered in practice, meaning that each technique performs poorly for a significant fraction of queries. This paper proposes a novel estimator selection framework that uses a statistical model to characterize the sets of conditions under which certain estimators outperform others, leading to a significant increase in estimation robustness. The generality of this framework also enables us to add a number of novel "special purpose" estimators which increase accuracy further. Most importantly, the resulting model generalizes well to queries very different from the ones used to train it. We validate our findings using a large number of industrial real-life and benchmark workloads.
Motor Areas of the Cerebral Cortex

The motor cortex includes several areas in the frontal agranular cortex. These areas receive inputs from sensory pathways, motor control structures, other cortical areas, and from “modulatory” pathways. Motor cortical outputs are widely distributed to many other parts of the nervous system and can thereby influence each of the major descending motor control pathways and spinal motor circuitry. The most intensively studied motor areas, the premotor area (PMA), supplementary motor area (SMA), and primary motor cortex (MI), appear to have different roles in movement. PMA is involved in coupling arbitrary cues to motor acts, whereas SMA appears to participate more in internal guidance or planning of movement. While MI has been implicated in control of muscle force or length, more recent data suggest that it encodes higher order parameters, such as move-ment direction. Two new views of motor cortex are presented. First, it is argued that MI contains functional subdivisions of the face, arm, and leg, and that each subdivision contains a highly overlapping, extensively interconnected and non-topographic internal organization. Second, motor representations can reorganize rapidly as a consequence of experience or peripheral lesions. These changes may arise through modifications in synaptic coupling among motor cortex neurons. These features of motor cortex suggest a role for motor cortex in learning and in performing voluntary movements.
A gene catalogue of the amphioxus nervous system

The elaboration of extremely complex nervous systems is a major success of evolution. However, at the dawn of the post-genomic era, few data have helped yet to unravel how a nervous system develops and evolves to complexity. On the evolutionary road to vertebrates, amphioxus occupies a key position to tackle this exciting issue. Its “simple” nervous system basically consists of a dorsal nerve cord and a diffuse net of peripheral neurons, which contrasts greatly with the complexity of vertebrate nervous systems. Notwithstanding, increasing data on gene expression has faced up this simplicity by revealing a mounting level of cryptic complexity, with unexpected levels of neuronal diversity, organisation and regionalisation of the central and peripheral nervous systems. Furthermore, recent gene expression data also point to the high neurogenic potential of the epidermis of amphioxus, suggestive of a skin-brain track for the evolution of the vertebrate nervous system. Here I attempt to catalogue and synthesise current gene expression data in the amphioxus nervous system. From this global point of view, I suggest scenarios for the evolutionary origin of complex features in the vertebrate nervous system, with special emphasis on the evolutionary origin of placodes and neural crest, and postulate a pre-patterned migratory pathway of cells, which, in the epidermis, may represent an intermediate state towards the deployment of one of the most striking innovative features of vertebrates: the neural crest and its derivatives.
Single-Channel Properties of Recombinant AMPA Receptors Depend on RNA Editing, Splice Variation, and Subunit Composition

Non-NMDA glutamate receptor subunits of the AMPA-preferring subfamily combine to form ion channels with heterogeneous functional properties. We have investigated the effects of RNA editing at the Q/R site, splice variation of the “flip/flop” cassette, and multimeric subunit assembly on the single-channel conductance and kinetic properties of the recombinant AMPA receptors formed from GluR2 and GluR4 expressed in HEK 293 cells. We found that AMPA receptor single-channel conductance was dependent on the Q/R site editing state of the subunits comprising the channel. Calcium-permeable (unedited) channels had resolvable single-channel events with main conductance states of 7–8 pS, whereas fully edited GluR2 channels had very low conductances of ∼300 fS (estimated from noise analysis). Additionally, the flip splice variant of GluR4 conferred agonist-dependent conductance properties reminiscent of those found for a subset of AMPA receptors in cultured cerebellar granule cells. These results provide a description of the single-channel properties of certain recombinant AMPA receptors and suggest that the single-channel conductance may be determined by the expression of edited GluR2 subunits in neurons.
A photostable near-infrared protein labeling dye for in vivo imaging.

The suitability of the near-infrared (NIR) region for in vivo imaging (e.g., deep tissue penetration, low auto-fluorescence background) has been extensively studied. [1–3] In vivo NIR imaging typically involves the administration of NIR probes, either in the form of fluorescent NIR small molecules with a specific localization/function in the body [4] or as proteins properly conjugated to NIR labeling tags. [5] NIR protein-labeling dyes must ideally retain highly fluorescent emission and good photostability profiles once conjugated to the protein of interest, and must maintain the specific recognition and functional abilities of the protein. The increasing importance of small-animal optical in vivo imaging has underscored the need for NIR protein-labeling compounds that fulfill such requirements. Herein, we report the synthesis and characterization of a tricarbocyanine-labeling compound (CyNE790). CyNE790 shows a strong NIR emission and excellent photostability before and after bioconjugation, and we confirmed its practical use as a NIR proteinlabeling dye for in vivo imaging studies. The tricarbocyanine scaffold (1) is a synthetically accessible structure with NIR emission, and it has shown improved fluorescent properties when compared to other heptamethine cyanines. [6, 7] We have previously reported the superior photostability of the amine-acetylated tricarbocyanine (CyNA) structure. The electron-withdrawing acetyl group incorporated into CyNA significantly increased the photostability properties of the amine tricarbocyanine core, and a combinatorial approach was used to identify CyNA-414 as a highly fluorescent and photostable NIR dye (Scheme 1). [8]
Generating Eecient Stack Code for Java

Optimizing Java byte code is complicated by the fact that it uses a stack-based execution model. Changing the intermediate representation from the stack-based to the register-based one brings the problem of Java byte code optimizations into well-studied domain of compiler optimizations for register-based codes. In this paper we describe the technique to convert a register-based code into the Java byte code. The code generation techniques developed for the stack-based computers are not directly applicable to this problem as the comparative cost of the local memory and stack manipulation instructions in JVM is quite diierent from that in the stack-based computers. Naive verbose translation of the register-based code into the Java byte code produces the code with many redundant store and load instructions. The tool that we have developed allows to remove 90-100 % of the stores to the local (i.e., non-global) variables. It produces the Java byte code that is slightly faster and shorter than the original byte code even when no optimizations except for register allocation are performed on the register-based code.