Miracle-dz/UniFAR-FTUs huggingface dataset:
Variety of Antiprion Compounds Discovered through an In Silico Screen Based on Cellular-Form Prion Protein Structure: Correlation between Antiprion Activity and Binding Affinity

ABSTRACT Transmissible spongiform encephalopathies are associated with the conformational conversion of the prion protein from the cellular form (PrPC) to the scrapie form. This process could be disrupted by stabilizing the PrPC conformation, using a specific ligand identified as a chemical chaperone. To discover such compounds, we employed an in silico screen that was based on the nuclear magnetic resonance structure of PrPC. In combination, we performed ex vivo screening using the Fukuoka-1 strain-infected neuronal mouse cell line at a compound concentration of 10 μM and surface plasmon resonance. Initially, we selected 590 compounds according to the calculated docked energy and finally discovered 24 efficient antiprion compounds, whose chemical structures are quite diverse. Surface plasmon resonance studies showed that the binding affinities of compounds for PrPC roughly correlated with the compounds' antiprion activities, indicating that the identification of chemical chaperones that bind to the PrPC structure and stabilize it is one efficient strategy for antiprion drug discovery. However, some compounds possessed antiprion activities with low affinities for PrPC, indicating a mechanism involving additional modulation factors. We classified the compounds roughly into five categories: (i) binding and effective, (ii) low binding and effective, (iii) binding and not effective, (iv) low binding and not effective, and (v) acceleration. In conclusion, we found a spectrum of compounds, many of which are able to modulate the pathogenic conversion reaction. The appropriate categorization of these diverse compounds would facilitate antiprion drug discovery and help to elucidate the pathogenic conversion mechanism.
WIP: more than a WASp‐interacting protein

WIP plays an important role in the remodeling of the actin cytoskeleton, which controls cellular activation, proliferation, and function. WIP regulates actin polymerization by linking the actin machinery to signaling cascades. WIP binding to WASp and to its homolog, N‐WASp, which are central activators of the actin‐nucleating complex Arp2/3, regulates their cellular distribution, function, and stability. By binding to WASp, WIP protects it from degradation and thus, is crucial for WASp retention. Indeed, most mutations that result in WAS, an X‐linked immunodeficiency caused by defective/absent WASp activity, are located in the WIP‐binding region of WASp. In addition, by binding directly to actin, WIP promotes the formation and stabilization of actin filaments. WASp‐independent activities of WIP constitute a new research frontier and are discussed extensively in this article. Here, we review the current information on WIP in human and mouse systems, focusing on its associated proteins, its molecular‐regulatory mechanisms, and its role as a key regulator of actin‐based processes in the immune system.
Indoor Pedestrian Trajectory Detection with LSTM Network

This paper proposes a novel technique to detect the main moving trajectory of indoor pedestrians. Based on Long Short- Term Memory(LSTM) Network, this deep learning network is capable of learning the trajectory of human beings using indoor Wi-Fi positioning data. The data is collected by Wi-Fi detectors densely installed in a public building in the urban area, which can ensure the detection of any portable devices as long as the Wi-Fi module is turned on. Then the model works in the form of sequence modeling to learn the trajectory of the main stream extracted from massive pedestrian positioning data. In compare with methods like Recurrent Neural Network (RNN) and Gated Recurrent Unit(GRU), there is an obvious performance improvement of this method.
A multiplex culture system for the long‐term growth of fission yeast cells

Maintenance of long‐term cultures of yeast cells is central to a broad range of investigations, from metabolic studies to laboratory evolution assays. However, repeated dilutions of batch cultures lead to variations in medium composition, with implications for cell physiology. In Saccharomyces cerevisiae, powerful miniaturized chemostat setups, or ministat arrays, have been shown to allow for constant dilution of multiple independent cultures. Here we set out to adapt these arrays for continuous culture of a morphologically and physiologically distinct yeast, the fission yeast Schizosaccharomyces pombe, with the goal of maintaining constant population density over time. First, we demonstrated that the original ministats are incompatible with growing fission yeast for more than a few generations, prompting us to modify different aspects of the system design. Next, we identified critical parameters for sustaining unbiased vegetative growth in these conditions. This requires deletion of the gsf2 flocculin‐encoding gene, along with addition of galactose to the medium and lowering of the culture temperature. Importantly, we improved the flexibility of the ministats by developing a piezo‐pump module for the independent regulation of the dilution rate of each culture. This made it possible to easily grow strains that have different generation times in the same assay. Our system therefore allows for maintaining multiple fission yeast cultures in exponential growth, adapting the dilution of each culture over time to keep constant population density for hundreds of generations. These multiplex culture systems open the door to a new range of long‐term experiments using this model organism. © 2017 The Authors. Yeast published by John Wiley & Sons, Ltd.
Kinetics of the Distribution and Excretion of Lead in the Rat

The kinetics of the distribution and excretion of lead (210Pb) were studied in rats for 14 days after single intravenous injections of 100 μg. of lead per rat. The results show that in the blood the lead is bound mainly to the cells, and that the ratio of lead in the cells and plasma is constant throughout the whole period. 210Pb is rapidly distributed in the tissues, the highest concentrations being in the kidneys, liver, and bones. The kinetics of the disappearance of 210Pb from the organs and tissues follow the pattern of first order reactions. The disappearance curves in the blood, plasma, haematic cells, and some other tissues can be expressed as sums of exponential functions. In contrast, the removal of metal from the bone tissue occurs at a constant and extremely slow rate. The metal is excreted by the faeces and urine. The rates reach their maxima within 24 hours and decrease asymptotically afterwards. More 210Pb was excreted in the faeces (35·7%) than in the urine (15·9%) during the 14 days of observation.
Genetic flexibility of regulatory networks

Gene regulatory networks are based on simple building blocks such as promoters, transcription factors (TFs) and their binding sites on DNA. But how diverse are the functions that can be obtained by different arrangements of promoters and TF binding sites? In this work we constructed synthetic regulatory regions using promoter elements and binding sites of two noninteracting TFs, each sensing a single environmental input signal. We show that simply by combining these three kinds of elements, we can obtain 11 of the 16 Boolean logic gates that integrate two environmental signals in vivo. Further, we demonstrate how combination of logic gates can result in new logic functions. Our results suggest that simple elements of transcription regulation form a highly flexible toolbox that can generate diverse functions under natural selection.
Design of low power 4-bit flash ADC based on standard cells

In this paper, a standard cell low power 4-bit flash analog-to-digital converter (ADC) is proposed. The converter utilizes comparators created using only logic gates for converting analog input signals to digital values. This novel flash architecture consists of several CMOS gates with inputs connected to a common input node or to one of the supply lines. Depending on the relationship between the input signal and a given gate's threshold voltage, the output will either be `0' or `1'. The comparator is followed by an encoder to convert the thermometer code to binary code. Low power consumption is achieved by switching off the unused parallel voltage comparators. The proposed ADC was implemented at the transistor level in a 180nm CMOS technology with a 1.8 V supply voltage and was simulated using Cadence Spectre simulator. Simulation results show that for the same speed, this ADC provides about 70% power reduction compared to a previously proposed design.
Effets de la couleur des sites web marchands sur la mémorisation et sur l'intention d'achat de l'internaute

L’objectif de cette recherche est d’etudier les effets de la couleur des sites web marchands en tant que variable atmospherique de l’interface, sur la memorisation et l’intention d’achat. En nous appuyant sur une revue de litterature ainsi que sur des investigations issues d’une analyse qualitative exploratoire, nous introduisons les bases theoriques et methodologiques repondant a cette problematique. Un modele conceptuel est developpe sur la base du modele S. O. R. Il montre l’effet de la couleur du site marchand et ses composantes Teinte, Luminosite et Saturation sur les reponses comportementales de l’internaute (memorisation et intention d’achat). Ces reponses sont vehiculees par les etats internes de l’organisme que sont les emotions et l’humeur. Les relations du modele sont moderees par certaines variables. La collecte des donnees a ete effectuee lors d’une experimentation en laboratoire afin de respecter la mesure de l’apparence coloree des sites web marchands. Les participants (non daltoniens) ont visite une des 8 versions d’un site de vente de CD de musique concu pour la recherche. L’analyse des donnees a l’aide d’ANOVA, de regressions et d’analyses issues de modeles lineaires generalises, montre un impact significatif des effets de la couleur sur la memorisation, vehicule par l’affect et modere par l’implication. L’interaction de la teinte et de la luminosite, lors de l’utilisation de couleurs chromatiques des couleurs dominante (fond) et dynamique (texte), favorise la memorisation et l’intention d’achat quand le contraste repose sur une situation de luminosite faible. L’etat affectif (emotions et humeur) montre qu’une humeur negative entraine une meilleure memorisation mais une intention d’achat decroissante, de meme que la stimulation agit positivement sur l’intention d’achat. Les implications manageriales, methodologiques et theoriques, ainsi que les voies futures de recherches ont ete mises en perspective.
Dynamic linear controller design for a class of high-order nonlinear systems via state-feedback

The objective of this paper is to address the linear state-feedback control problem for a family of high-order uncertain nonlinear systems. Based on the adding a power integrator technique, the authors recursively construct a linear controller with dynamic gains, which can be used to deal with the uncertain nonlinear terms and simplify the controller structure. Moreover, it is proved that the proposed control law can globally regulate system states to the origin and guarantee the boundedness of all the signals of the closed-loop system as well. Finally, a simulation example is presented with some comparison with the existing result so as to demonstrate the effectiveness of the proposed design scheme.
The role of active muscle vasodilatation in the alerting stage of the defence reaction

Muscle vasodilatation, produced by cholinergic nerve fibres of the sympathetic system, appears to be an integral feature of the defence reaction which an animal displays as a reflex response to any sudden stimulus (Abrahams, Hilton & Zbroiyna, 1960b). This vasodilatation is itself only one component of a complex pattern of cardiovascular change in which a greatly increased cardiac output is directed chiefly through the skeletal musculature. As previously emphasized, the defence reaction is a graded response whose behavioural expression is manifested initially as alerting. With sufficiently intense stimulation it will culminate in flight or attack, and the complex cardiovascular reaction seems best regarded as a preparatory adjustment of the animal for the muscular exertion inseparable from these activities (Abrahams et al. 1960b; Abrahams, Hilton & Malcolm, 1962). Studies of the changes of muscle blood flow in the conscious cat have reinforced this view (Abrahams, Hilton & Zbroiyna, 1960a). The experimental results which are described here show that atropinesensitive muscle vasodilatation occurs when the earliest behavioural signs of alerting are seen, whether such alerting has been produced by direct electrical stimulation of the appropriate brain-stem regions, or by a sudden environmental stimulus such as a flash of light or the sound of a buzzer. Further, the vasodilatation is readily obtained as a conditioned-reflex response. In all these experiments use has been made of temperature changes of the whole-limb venous effluent as an index of muscle blood flow in the conscious animal (Abrahams, 1959). The results of experiments on anaesthetized cats which demonstrate the validity of this technique are included in this paper.
Adversarial Memory Networks for Action Prediction

Action prediction aims to infer the forthcoming human action with partially-observed videos, which is a challenging task due to the limited information underlying early observations. Existing methods mainly adopt a reconstruction strategy to handle this task, expecting to learn a single mapping function from partial observations to full videos to facilitate the prediction process. In this study, we propose adversarial memory networks (AMemNet) to generate the"full video"feature conditioning on a partial video query from two new aspects. Firstly, a key-value structured memory generator is designed to memorize different partial videos as key memories and dynamically write full videos in value memories with gating mechanism and querying attention. Secondly, we develop a class-aware discriminator to guide the memory generator to deliver not only realistic but also discriminative full video features upon adversarial training. The final prediction result of AMemNet is given by late fusion over RGB and optical flow streams. Extensive experimental results on two benchmark video datasets, UCF-101 and HMDB51, are provided to demonstrate the effectiveness of the proposed AMemNet model over state-of-the-art methods.
CmeABC Multidrug Efflux Pump Contributes to Antibiotic Resistance and Promotes Campylobacter jejuni Survival and Multiplication in Acanthamoeba polyphaga

ABSTRACT Campylobacter jejuni is a foodborne pathogen that is recognized as the leading cause of human bacterial gastroenteritis. The widespread use of antibiotics in medicine and in animal husbandry has led to an increased incidence of antibiotic resistance in Campylobacter. In addition to a role in multidrug resistance (MDR), the Campylobacter CmeABC resistance-nodulation-division (RND)-type efflux pump may be involved in virulence. As a vehicle for pathogenic microorganisms, the protozoan Acanthamoeba is a good model for investigations of bacterial survival in the environment and the molecular mechanisms of pathogenicity. The interaction between C. jejuni 81-176 and Acanthamoeba polyphaga was investigated in this study by using a modified gentamicin protection assay. In addition, a possible role for the CmeABC MDR pump in this interaction was explored. Here we report that this MDR pump is beneficial for the intracellular survival and multiplication of C. jejuni in A. polyphaga but is dispensable for biofilm formation and motility. IMPORTANCE The endosymbiotic relationship between amoebae and microbial pathogens may contribute to persistence and spreading of the latter in the environment, which has significant implications for human health. In this study, we found that Campylobacter jejuni was able to survive and to multiply inside Acanthamoeba polyphaga; since these microorganisms can coexist in the same environment (e.g., on poultry farms), the latter may increase the risk of infection with Campylobacter. Our data suggest that, in addition to its role in antibiotic resistance, the CmeABC MDR efflux pump plays a role in bacterial survival within amoebae. Furthermore, we demonstrated synergistic effects of the CmeABC MDR efflux pump and TetO on bacterial resistance to tetracycline. Due to its role in both the antibiotic resistance and the virulence of C. jejuni, the CmeABC MDR efflux pump could be considered a good target for the development of antibacterial drugs against this pathogen.
Synopsis of Commelina L. (Commelinaceae) in the state of Rio de Janeiro, reveals a new white-flowered species endemic to Brazil

Abstract A synopsis for the genus Commelina in the state of Rio de Janeiro, Brazil, is presented here, including a new species, ten new synonyms, five designated lectotypes, two designated epitypes and an excluded name. Commelina huntii, a new species, is remarkable due to the combination of rusty to rusty-brown hairs at the margin of its leaf-sheaths, connate spathes, white flowers with auriculate medial petal, ovaries with sparse black papillae and dehiscent fruits. Additionally, we provide an identification key, illustrations, and conservation status for the species of Commelina recorded in the state of Rio de Janeiro.
Exercise Enhances Survival Rate in Mice Infected with Salmonella typhimurium

Abstract Mice voluntarily trained on exercise wheels for 16-18 days and were then infected with an approximate LD50 dose of Salmonella typhimurium. These trained mice exhibited a small, but statistically significant (P = 0.037) increase in survival rate (34/77) compared to sedentary control mice (23/79) after 7 days.
On the Nature of Valence Charge and Spin Excitations via Multi-Orbital Hubbard Models for Infinite-Layer Nickelates

Building upon the recent progress on the intriguing underlying physics for the newly discovered infinite-layer nickelates, in this article we review an examination of valence charge and spin excitations via multi-orbital Hubbard models as way to determine the fundamental building blocks for Hamiltonians that can describe the low energy properties of infinite-layer nickelates. We summarize key results from density-functional approaches, and apply them to the study of x-ray absorption to determine the valence ground states of infinite-layer nickelates in their parent form, and show that a fundamental d 9 configuration as in the cuprates is incompatible with a self-doped ground state having holes in both d x 2 − y 2 and a rare-earth-derived axial orbital. When doped, we determine that the rare-earth-derived orbitals empty and additional holes form low spin (S = 0) d 8 Ni states, which can be well-described as a doped single-band Hubbard model. Using exact diagonalization for a 2-orbital model involving Ni and rare-earth orbitals, we find clear magnons at 1/2 filling that persist when doped, albeit with larger damping, and with a dependence on the precise orbital energy separation between the Ni- and rare-earth-derived orbitals. Taken together, a full two-band model for infinite-layer nickelates can well describe the valence charge and spin excitations observed experimentally.
A critical analysis of candidacy for penile revascularization.

INTRODUCTION Penile revascularization (PR) is a potentially curative procedure for young men with isolated arteriogenic erectile dysfunction. Standard preoperative evaluation is erectile hemodynamics (HDX) using duplex Doppler penile ultrasound (DUS) and/or cavernosometry (DIC) and assessment of cavernosal arterial anatomy by selective internal pudendal arteriography (SIPA). AIM The aim of this study was to review our experience with men who sought a second opinion from us regarding their candidacy for PR. METHOD Study population consisted of men (i) who presented to us for a second opinion regarding PR; (ii) who had DUS/DIC and SIPA; and (iii) had been advised by outside surgeon to undergo PR. Review of the HDX study and SIPA was conducted. Discrepancies between these studies resulted in repeating the DIC in men with normal SIPA or repeating the SIPA in men with normal HDX studies. MAIN OUTCOME MEASURES Discrepancies between HDX and SIPA and the results of repeat HDX or SIPA were the main outcome measures. RESULT Forty-five patients participated in the study; mean age was 33 years with 4% ≥50 years old. Median vascular risk factor number was 1 (ranged 0-3). A credible trauma history was present in 11%. Thirty-three percent had prior DIC and 49% of patients had a significant discrepancy between HDX study and SIPA, including all patients seen by a community urologist. Thirty-eight percent had a discrepancy between side of abnormality on HDX and SIPA where both studies were abnormal (group A). Seven percent had abnormal HDX and normal SIPA (group B). Four percent had a normal HDX study with an abnormal SIPA (group C). Repeat DIC (n = 20) was conducted in groups A + B and was normal in 70% of cases. Repeat SIPA (n = 2) was conducted in group C and was normal in both patients. CONCLUSION Almost one half of patients had a significant discrepancy between HDX and SIPA. Of these, 73% had normal repeat studies, making them no longer candidates for penile revascularization.
COX: CUDA on X86 by Exposing Warp-Level Functions to CPUs

As CUDA programs become the de facto program among data parallel applications such as high-performance computing or machine learning applications, running CUDA on other platforms has been a compelling option. Although several efforts have attempted to support CUDA on other than NVIDIA GPU devices, due to extra steps in the translation, the support is always behind a few years from supporting CUDA's latest features. The examples are DPC, Hipfy, where CUDA source code have to be translated to their native supporting language and then they are supported. In particular, the new CUDA programming model exposes the warp concept in the programming language, which greatly changes the way the CUDA code should be mapped to CPU programs. In this paper, hierarchical collapsing that \emph{correctly} supports CUDA warp-level functions on CPUs is proposed. Based on hierarchical collapsing, a framework, COX, is developed that allows CUDA programs with the latest features to be executed efficiently on CPU platforms. COX consists of a compiler IR transformation (new LLVM pass) and a runtime system to execute the transformed programs on CPU devices. COX can support the most recent CUDA features, and the application coverage is much higher (90%) than for previous frameworks (68%) with comparable performance. We also show that the warp-level functions in CUDA can be efficiently executed by utilizing CPU SIMD (AVX) instructions.
Chemical-Induced Disease Detection Using Invariance-based Pattern Learning Model

In this work, we introduce a novel feature engineering approach named “algebraic invariance” to identify discriminative patterns for learning relation pair features for the chemical-disease relation (CDR) task of BioCreative V. Our method exploits the existing structural similarity of the key concepts of relation descriptions from the CDR corpus to generate robust linguistic patterns for SVM tree kernel-based learning. Preprocessing of the training data classifies the entity pairs as either related or unrelated to build instance types for both inter-sentential and intra-sentential scenarios. An invariant function is proposed to process and optimally cluster similar patterns for both positive and negative instances. The learning model for CDR pairs is based on the SVM tree kernel approach, which generates feature trees and vectors and is modeled on suitable invariance based patterns, bringing brevity, precision and context to the identifier features. Results demonstrate that our method outperformed other compared approaches, achieved a high recall rate of 85.08%, and averaged an F1-score of 54.34% without the use of any additional knowledge bases.