Miracle-dz/UniFAR-FTUs huggingface dataset:
Pharmacophore Identification, in Silico Screening, and Virtual Library Design for Inhibitors of the Human Factor Xa

Factor Xa inhibitors are innovative anticoagulant agents that provide a better safety/efficacy profile compared to other anticoagulative drugs. A chemical feature-based modeling approach was applied to identify crucial pharmacophore patterns from 3D crystal structures of inhibitors bound to human factor Xa (Pdb entries 1fjs, 1kns, 1eqz) using the software LIGANDSCOUT and CATALYST. The complex structures were selected regarding the criteria of high inhibitory potency (i.e. all ligands show K(i) values against factor Xa in the subnanomolar range) and good resolution (i.e. at least 2.2 A) in order to generate selective and high quality pharmacophore models. The resulting chemical-feature based hypotheses were used for virtual screening of commercial molecular databases such as the WDI database. Furthermore, a ligand-based molecular modeling approach was performed to obtain common-feature hypotheses that represent the relevant chemical interactions between 10 bioactive factor Xa inhibitors and the protein, respectively. In a next step a virtual combinatorial library was designed in order to generate new compounds with similar chemical and spatial properties as known inhibitors. The software tool ILIB DIVERSE was used for this procedure in order to provide new scaffolds of this group of anticoagulants. Finally we present the combination of these two techniques, hence virtual screening was performed with selective pharmacophore models in a focused virtual combinatorial database. De novo derived molecular scaffolds that were able to adequately satisfy the pharmacophore criteria are revealed and are promising templates for candidates for further development.
A mixed Time-/condition-Based Precognitive Maintenance Framework for Zero-breakdown Industrial Systems

Forecasting of process outages for reducing downtime and machine scrap parts have been actively pursued in the manufacturing industries to ensure that maintenance is carried out only when required. In this paper, we propose a precognitive maintenance framework based on mixed timeand condition-based models to predict both wear and degradation stage of realistic engineering systems. The decision-making framework performs stage classification using support vector machines and wear estimation using time-based autoregressive moving average with exogenous inputs models. Our proposed framework is supported by mathematical rigour, and its effectiveness is evaluated with experimental results on a high-speed industrial computer numerical control milling machine for tool wear stage identification and wear estimation.
Normothermic and subnormothermic ex-vivo liver perfusion in liver transplantation

Purpose of reviewIn the current era of extreme organ shortage, warm (subnormothermic and normothermic) ex-vivo liver perfusion has emerged as a novel strategy to recover marginal organs and increase the organ pool. Over the last decade, significant progress in the field has taken this technology from bench to bedside. This review will cover the most relevant contributions to the field in 2015. Recent findingsSeveral groups made significant advances in warm ex-vivo liver perfusion for optimizing preservation of liver grafts. With transition to clinical use underway, significant interest has focused on exploring the safety and feasibility of the technique. Other areas of exploration included novel perfusates and rewarming strategies. This review will also summarize the most recent advances in the clinical setting. SummaryWarm ex-vivo liver perfusion has established itself as a novel approach for the preservation of liver grafts for transplantation. Although the optimal perfusion conditions and techniques have not been established, the safety of this technique has been demonstrated in preclinical and clinical studies. Thus far, most investigation has focused on the rescue of marginal grafts. However, further development in the field has the potential to yield novel graft interventions and modification.
Neurotensin Changes Propulsive Activity into a Segmental Motor Pattern in the Rat Colon

Background/Aims Neurotensin is a gut-brain peptide with both inhibitory and excitatory actions on the colonic musculature; our objective was to understand the implications of this for motor patterns occurring in the intact colon of the rat. Methods The effects of neurotensin with concentrations ranging from 0.1–100 nM were studied in the intact rat colon in vitro, by investigating spatio-temporal maps created from video recordings of colonic motility before and after neurotensin. Results Low concentration of neurotensin (0.1–1 nM) inhibited propagating long distance contractions and rhythmic propagating motor complexes; in its place a slow propagating rhythmic segmental motor pattern developed. The neurotensin receptor 1 antagonist SR-48692 prevented the development of the segmental motor pattern. Higher concentrations of neurotensin (10 nM and 100 nM) were capable of restoring long distance contraction activity and inhibiting the segmental activity. The slow propagating segmental contraction showed a rhythmic contraction—relaxation cycle at the slow wave frequency originating from the interstitial cells of Cajal associated with the myenteric plexus pacemaker. High concentrations given without prior additions of low concentrations did not evoke the segmental motor pattern. These actions occurred when neurotensin was given in the bath solution or intraluminally. The segmental motor pattern evoked by neurotensin was inhibited by the neural conduction blocker lidocaine. Conclusions Neurotensin (0.1–1 nM) inhibits the dominant propulsive motor patterns of the colon and a distinct motor pattern of rhythmic slow propagating segmental contractions develops. This motor pattern has the hallmarks of haustral boundary contractions.
A Model of Website Usage Visualization Estimated on Clickstream Data with Apache Flume Using Improved Markov Chain Approximation

Visualization of the website clickstream data has been a pivotal process as it aids in defining the user preferences. It includes the processes of gathering, investigating and reporting about the web pages that are being viewed by the users. Clickstream visualization is primarily employed by organizations which focuses on gaining the user preferences and improve their products or services towards achieving maximum satisfaction of users. Most existing visualization tools come up short in helping the organizations achieve this goal. Markov chain model is the commonly utilized method for developing data visualization tools. However the issues such as occlusion and inability to provide clear data visualization display makes the tools volatile. This paper aims at developing a visualization tool named as WebClickviz by resolving the above mentioned issues by improving the Markov chain modelling. A heuristic method of Kolmogorov– Smirnov distance and maximum likelihood estimator is introduced for improving the clear display of visualization. These concepts are employed between the underlying distribution states to minimize the Markov distribution. The proposed model named as WebClickviz is performed in Hadoop Apache Flume which is a highly advanced tool. Through the experiments conducted on evaluation dataset, it can be shown that the proposed model outperforms the existing models with higher visualization accuracy.
Evolution of Information Techonology in Healthcare

The healthcare sector is growing rapidly and taking up a significant portion of the GDP in developed countries. The healthcare industry faces significant challenges such as ballooning costs, shortage of qualified personnel, rapidly aging population, and increase of chronic and epidemic diseases. Information technology (IT) has been suggested as a mitigator for some of these challenges. Particularly, IT can enable automation, management, and integration of clinical and business operations for greater efficiency and effectiveness. Studying the evolution of IT in healthcare is essential to be able to understand the past trends, address the current situation, move to the nest stage, and make use of IT to advance the future. However, although there is considerable literature on IT evolution, we observe a lack of studies specific to the evolution of healthcare IT. With the unique challenges of this sector, we attempt to address this gap in this paper. This study will start with a literature review on IT evolution and then develop a model for the evolution of healthcare IT based on the Nolan stage model and its subsequent refinements. The model will be developed with an initial focus on healthcare IT in Singapore. The reason for choosing Singapore is because of its advanced IT and medical infrastructure, yet the spending on healthcare is relatively low compared to other developed countries. In future, our model will be extended to other developed countries in the AsiaPacific region e.g., Australia and New Zealand, as well as the UK and US.
Hyperphosphorylation of Nucleoplasmin Facilitates Xenopus Sperm Decondensation at Fertilization (*)

Previous studies showed that the nuclear phosphoprotein nucleoplasmin performs the first stage of chromatin decondensation of Xenopus sperm at fertilization. It binds and removes sperm basic proteins replacing them with histones. We now show that this activity depends upon the massive hyperphosphorylation of nucleoplasmin that occurs when oocytes mature into eggs. Egg extracts or purified hyperphosphorylated egg nucleoplasmin decondense sperm chromatin and remove sperm basic proteins much faster than oocyte extracts or hypophosphorylated oocyte nucleoplasmin. Furthermore, dephosphorylation of egg nucleoplasmin slows sperm decondensation and prevents basic protein removal from sperm chromatin. We conclude that hyperphosphorylation of nucleoplasmin is used to modulate the rapid changes in chromatin structure that accompany early development in Xenopus.
Reconstruction of sparse signals from l1 dimensionality-reduced Cauchy random-projections

Dimensionality reduction via linear random projections are used in numerous applications including data streaming, information retrieval, data mining, and compressive sensing (CS). While CS has traditionally relied on normal random projections, corresponding to l 2 distance preservation, a large body of work has emerged for applications where l 1 approximate distances may be preferred. Dimensionality reduction in l 1 use Cauchy random projections that multiply the original data matrix B ∈ 葷D×n with a Cauchy random matrix R ∈ 葷n×k (k « min(n,D)), resulting in a projected matrix C ∈ 葷D×k. This paper focuses on developing signal reconstruction algorithms from Cauchy random projections, where the large suite of reconstruction algorithms developed in compressive sensing perform poorly due to the lack of finite second-order statistics in the projections. In particular, a set of regularized coordinate-descent Myriad regression based reconstruction algorithms are developed using, both l 0 and Lorentzian norms as sparsity inducing terms. The l 0 -regularized algorithm shows superior performance to other standard approaches. Simulations illustrate and compare accuracy of reconstruction.
A continuous positive airway pressure trial as a novel approach to the diagnosis of the obstructive sleep apnea syndrome.

OBJECTIVES Treatment of obstructive sleep apnea syndrome (OSA) is often delayed because polysomnography, the recommended standard diagnostic test, is not readily available. We evaluated whether the diagnosis of sleep apnea could be inferred from the response to a treatment trial with nasal continuous positive airway pressure (CPAP). DESIGN Study on diagnostic accuracy. SETTING Sleep-disorders clinic of a university hospital. PATIENTS Seventy-six sleepy snorers consecutively referred for sleep apnea evaluation. INTERVENTIONS CPAP treatment trial over 2 weeks as an initial diagnostic test in comparison with polysomnography, and treatment success over > or = 4 months. MEASUREMENTS AND RESULTS The main outcome was diagnostic accuracy of the CPAP trial. The trial result was positive if the patient had used CPAP for > 2 h per night and wished to continue therapy. This suggested sleep apnea. The trial was evaluated in terms of predicting an obstructive apnea/hypopnea index (AHI) > 10/h during polysomnography performed for validation, and in terms of identifying sleep apnea patients treated successfully over > or = 4 months. Forty-four of 76 patients (58%) had sleep apnea as confirmed by an AHI > 10/h. The CPAP trial predicted sleep apnea with a sensitivity of 80%, a specificity of 97%, and positive and negative predictive values of 97% and 78%, respectively. In 35 of 76 sleep apnea patients (46%) with positive CPAP trial results, polysomnography could have been avoided. These patients were prescribed long-term CPAP therapy. After 4 months, 33 of 35 patients (94%) still used CPAP, and their symptoms remained improved. These patients were identified by the CPAP trial with positive and negative predictive values of 92% and 100%, respectively. CONCLUSIONS In a selected population, a CPAP trial may help to diagnose OSA, to identify patients who benefit from CPAP, and to reduce the need for polysomnography.
Improvement of Conversion Efficiency of Inverted Organic Photovoltaic With PEDOT: PSS:WOx  by Thermal Annealing

We report the effects of postannealing on the photovoltaic performance of ITO/LZO/P3HT:ICBA/PEDOT:PSS: WOx/Al. The electrical characteristics of the PEDOT:PSS:WOx film can be controlled through an annealing treatment, which exhibits a short-circuit current density of 9.37 mA/cm2, an open-circuit voltage of 0.86V, and a power conversion efficiency of 5.54% under AM1.5 illumination (100 mW/cm2). By annealing the device at 150°C, a favorable phase separation in the PEDOT:PSS:WOx is obtained, and the PCE increases by 23.27% compared with that of the nonannealed device. The Voc increases with the annealing temperature, and it is worth noting that the PEDOT:PSS device only experienced a 2.40% decrease in PCE after 150°C annealing treatment.
A SPICE Model of the $\textrm{Ta}_{2}\textrm{O}_{5}/\textrm{TaO}_\textrm{x}$ Bi-Layered RRAM

Designing a SPICE model is a critical step toward understanding the behavior of the resistive random access memory (RRAM) devices when integrated in memory design for the future generation storage devices. In this paper, a SPICE model is developed for the Ta2O5/TaOx bi-layered RRAM. The proposed model emphasizes the impact of the change in the switching layer thickness on the device behavior at low resistance state (LRS), high resistance state (HRS), and the transitional period. The validity of the proposed model is verified through using three different sets of experimental data from Pt/Ta2O5/TaOx/Pt RRAM with switching layer thickness smaller than 5 nm. The SPICE model reproduced all the major features from the experimental results for the SET and RESET processes and also the asymmetric and the symmetric characteristics in HRS and LRS, respectively. The proposed SPICE model matches the measured experimental results with an average error of <; 11% and a maximum error of <; 70%. It also showed stable behavior for its HRS and LRS regions under different types of input signals. The model is parameterized in order to fit into Ta2O5/TaOx RRAM devices with switching layer thickness smaller than 5 nm, thus, facilitating the model usage. The model can be included in the SPICE-compatible circuit simulation and is suitable for the exploration of the Ta2O5/TaOx bi-layered RRAM device performance at circuit level.
Re-entrant Manufacturing Systems Scheduling Policies , Stability and Performance Analysis

Re-entrant manufacturing systems differ from traditional manufacturing systems in the sense that a job may visit a service station more than once, at various stages of the product development cycle. Several parts at different stages of processing may be in contention for service at the same machine, which gives rise to the need to solve scheduling problems. This document surveys some of the facets of such systems presented in the literature. A variety of scheduling policies for re-entrant lines is presented and their stability and performance discussed. Approximate Mean Value Analysis is carried out on a closed re-entrant line under two different scheduling schemes to compute the mean cycle time and mean throughput rate for different number of parts in the system. The results of this exercise are compared with the output of a linear program that provides an upper bound on the throughput rate. In the last section, the mean value analysis and dynamic programming techniques are compared in the context of re-entrant lines.
Selecting a healthy diet score: lessons from a study of diet and health in early old age (the Boyd Orr cohort)

Abstract Objectives To describe the selection and modification of an appropriate diet score to assess diet quality in early old age. Design and setting Cross-sectional analyses of the Boyd Orr cohort – a long-term follow-up of men and women whose families took part in a survey of diet and health in pre-war Britain. Dietary data were obtained from a 113-item food-frequency questionnaire. A nine-item Healthy Diet Indicator (HDI) developed by Huijbregts and colleagues was identified from the literature and modified because some dietary variables were unavailable and to accord more closely with recommendations of the UK Committee on Medical Aspects of Food Policy. Subjects In total, 1475 traced, surviving cohort members aged 60 years and over. Results Modification resulted in a 12-item Healthy Diet Score (HDS). We found that about half the variation in the HDS was explained by variation in the HDI (r = 0.71). There was, however, little misclassification of subjects (<10%) into extreme thirds of the distribution by the HDS compared with the HDI. Items of the score most strongly correlated with overall score were saturated fat (r = −0.57), red meat (r = −0.46), dietary fibre (r = 0.58), fruit and vegetables (r = 0.54) and percentage energy from carbohydrates (r = 0.51). Modifying existing items had greater impact on agreement between HDI and HDS than the addition of new items. Conclusions The selection and modification of diet scores is more complicated than often assumed. Furthermore, modest changes to an existing score can produce a score that is different from the original, and although it was not possible to test this issue, it may no longer predict subsequent health experience.
A feasibility study comparing checklists and global rating forms to assess resident performance in clinical skills

This study evaluated the feasibility of two different scoring forms for assessing the clinical performance of residents in anaesthesiology. One of the forms had a checklist format including task-specific items and the other was a global rating form with general dimensions of competence including ‘clinical skills’, ‘communication skills’ and ‘knowledge’. Thirty-two clinicians representing 25 (83%) of the 30 training hospitals in the country participated in the study. The clinicians were randomized into two groups, each of which used one of the scoring formats to assess a resident’s performance in four simulated clinical scenarios on videotape. Clinicians’ opinions about the appropriateness of the scoring forms were rated on a scale of 1–5. The checklist format was rated significantly higher compared with the global rating form (mean 4.6, sd 0.5 vs. mean 3.5, sd 1.4, p < 0.001). The inter-rater agreement regarding pass/fail decisions was poor irrespective of the scoring form used. This was explained by clinicians’ leniency as assessors rather than by lack of vigilance in the observations or disagreements on standards for good performance.
Induction into the Hall of Fame: tracing the lineage of Spemann's organizer

The grafting experiments of Spemann and Mangold have been a textbook classic for years, but as with many conclusions from experimental embryology, the idea that the dorsal lip of the blastopore `organized' the early patterning of the embryo has sometimes come under question. In their 1983 paper in JEEM, Smith and Slack extended these classical experiments in newts to the now-standard amphibian model Xenopus laevis. By using injected lineage tracers, they distinguished the fates of graft and host, and showed unambiguously that the organizer is responsible for neural induction and that it dorsalizes the mesoderm.
Automated robotic monitoring and inspection of steel structures and bridges

Summary This paper presents visual and 3D structure inspection for steel structures and bridges using a developed climbing robot. The robot can move freely on a steel surface, carry sensors, collect data and then send to the ground station in real-time for monitoring as well as further processing. Steel surface image stitching and 3D map building are conducted to provide a current condition of the structure. Also, a computer vision-based method is implemented to detect surface defects on stitched images. The effectiveness of the climbing robot's inspection is tested in multiple circumstances to ensure strong steel adhesion and successful data collection. The detection method was also successfully evaluated on various test images, where steel cracks could be automatically identified, without the requirement of some heuristic reasoning.
Carbon cycling in the deep eastern North Pacific benthic food web: Investigating the effect of organic carbon input

The deep ocean benthic environment plays a role in long‐term carbon sequestration. Understanding carbon cycling in the deep ocean floor is critical to evaluate the impact of changing climate on the oceanic systems. Linear inverse modeling was used to quantify carbon transfer between compartments in the benthic food web at a long time‐series study site in the abyssal northeastern Pacific (Station M). Linear inverse food web models were constructed for three separate years in the time‐series when particulate organic carbon (POC) flux was relatively high (1990: 0.63 mean mmol C m−2 d−1), intermediate (1995: 0.24) and low (1996: 0.12). Carbon cycling in all years was dominated by the flows involved in the microbial loop; dissolved organic carbon uptake by microbes (0.80–0.95 mean mmol C m−2 d−1), microbial respiration (0.52–0.61), microbial biomass dissolution (0.09–0.18) and the dissolution of refractory detritus (0.46–0.65). Moreover, the magnitude of carbon flows involved in the microbial loop changed in relation to POC input, with a decline in contribution during the high POC influxes, such as those recently experienced at Station M. Results indicate that during high POC episodic pulses the role of faunal mediated carbon cycling would increase. Semi‐labile detritus dominates benthic faunal diets and the role of labile detritus declined with increased total POC input. Linear inverse modeling represents an effective framework to analyze high‐resolution time‐series data and demonstrate the impact of climate change on the deep ocean carbon cycle in a coastal upwelling system.
Fractional quantum Hall effect in graphene

The electrons in most of the conductors can be described by non-relativistic quantum mechanics but the electrons in graphene behave as massless relativistic particles, called Dirac fermions, though their speed is given by the Fermi velocity. The relativistic nature of the energy dispersion relation of electrons in graphene modifies the inter electron interactions. This results in the observation of a number of peculiar properties e.g. anomalous quantum Hall effect. We study the fractional quantum Hall effect (FQHE) in graphene. The quantized Hall conductivity in graphene in FQHE is shown to be: ( ) 2 2 1 2 2 2 1 1 x y n e m n h + σ = ± + + , where n = 0, 1, 2, 3 … This fascinating result shows that the FQHE in graphene has a sequence of states which is different from the sequence found in the 2D electron gas.