Miracle-dz/UniFAR-FTUs huggingface dataset:
FunTree: advances in a resource for exploring and contextualising protein function evolution

FunTree is a resource that brings together protein sequence, structure and functional information, including overall chemical reaction and mechanistic data, for structurally defined domain superfamilies. Developed in tandem with the CATH database, the original FunTree contained just 276 superfamilies focused on enzymes. Here, we present an update of FunTree that has expanded to include 2340 superfamilies including both enzymes and proteins with non-enzymatic functions annotated by Gene Ontology (GO) terms. This allows the investigation of how novel functions have evolved within a structurally defined superfamily and provides a means to analyse trends across many superfamilies. This is done not only within the context of a protein's sequence and structure but also the relationships of their functions. New measures of functional similarity have been integrated, including for enzymes comparisons of overall reactions based on overall bond changes, reaction centres (the local environment atoms involved in the reaction) and the sub-structure similarities of the metabolites involved in the reaction and for non-enzymes semantic similarities based on the GO. To identify and highlight changes in function through evolution, ancestral character estimations are made and presented. All this is accessible through a new re-designed web interface that can be found at http://www.funtree. info.
MULTI-TEMPORAL ANALYSIS IN THE NIGER INLAND DELTA USING ERS 1/2 AND ASAR DATA

Due to annual flooding the Niger Inland Delta plays an important role in the Sahel. The flooding influences deciding the land covers inside and in the immediate vicinity of the delta. Using remote sensing technology is an effective way to observe and verify changes in landscape. With its weather and daylight independence Synthetic Aperture Radar (SAR) data emphasize as particularly suitable for large-scaled monitoring. The system parameters of the ERS AMI sensor are quite similar to the available images from the ASAR sensor placed on the environmental satellite ENVISAT. Via four ERS and two ASAR images three change detection methods were performed to analyze which regions are affected byflooding. These areas are the foundation of living (fishery, live stock) for the people in the Inland Delta.
Space object classification using model driven and data driven methods

In recent years there has been an increase in the number of inactive and debris Space Objects (SOs). This work examines both data driven and model driven SO classification. The model driven approach investigated for this work is based on the Multiple Model Adaptive Estimation approach to extract SO characteristics from observations while estimating the probability the observations belonging to a given class of objects. The data driven methods are based on Principle Component Analysis and Convolutional Neural Network Classification approaches. The performance of these strategies for SO classification is demonstrated via simulated scenarios.
The SUMO E3-ligase PIAS1 couples reactive oxygen species-dependent JNK activation to oxidative cell death

Human endometrial stromal cells (HESCs) exposed to reactive oxygen species (ROS) mount a hypersumoylation response in a c‐Jun N‐terminal kinase (JNK)‐dependent manner. The mechanism that couples JNK signaling to the small ubiquitin‐related modifier (SUMO) pathway and its functional consequences are not understood. We show that ROS‐dependent JNK activation converges on the SUMO pathway via PIAS1 (protein inhibitor of activated STAT1). Unexpectedly, PIAS1 knockdown not only prevented ROS‐dependent hypersumoylation but also enhanced JNK signaling in HESCs. Conversely, PIAS overexpression increased sumoylation of various substrates, including c‐Jun, yet inhibited basal and ROS‐dependent JNK activity independently of its SUMO ligase function. Expression profiling demonstrated that PIAS1 knockdown enhances and profoundly modifies the transcriptional response to oxidative stress signals. Using a cutoff of 2‐fold change or more, a total of 250 ROS‐sensitive genes were identified, 97 of which were not dependent on PIAS1. PIAS1 knockdown abolished the regulation of 43 genes but also sensitized 110 other genes to ROS. Importantly, PIAS1 silencing was obligatory for the induction of several cellular defense genes in response to oxidative stress. In agreement, PIAS1 knockdown attenuated ROS‐dependent caspase‐3/7 activation and subsequent apoptosis. Thus, PIAS1 determines the level of JNK activity in HESCs, couples ROS signaling to the SUMO pathway, and promotes oxidative cell death. —Leitao, B. B. , Jones, M. C. , Brosens, J. J. The SUMO E3‐ligase PIAS1 couples reactive oxygen species‐dependent JNK activation to oxidative cell death. FASEB J. 25, 3416–3425 (2011). www.fasebj. org
Predictors of pain severity 3 months after serious injury.

OBJECTIVE Injury is a common initiating event for persistent pain. The presentation of injured patients to hospital represents an opportunity to identify patients at high risk of persistent pain and triage them to early intervention. Although a range of physical, psychological, and social risk factors have been implicated in the transition from acute to persistent pain, these factors have not been tested concurrently in a prospective study. This study aimed to determine the degree to which pain severity at 3 months can be predicted at the time of injury and which independent factors predicted pain severity. DESIGN A large prospective cohort study was conducted recruiting patients from two trauma hospitals during their acute admission. Patients were assessed with a comprehensive battery of known and possible risk factors for persistent pain. Patients were assessed for pain severity on a visual analog scale over the past 24 hours at 3 months. RESULTS Two hundred ninety patients were recruited, and 242 were followed up at 3 months. Older age, female gender, past alcohol dependence, lower physical role function, pain severity, amount of morphine equivalents administered on the day of assessment, and pain control attitudes predicted pain severity at 3 months. The variance attributed to these factors was 22%. CONCLUSIONS Injured patients with a number of these factors may warrant increased monitoring and early triage to specialist pain services.
Analysis of Non-Persistent CSMA Protocols with Exponential Backoff Scheduling

This paper studies the performance of Non-persistent CSMA/CA protocols with Exponential Backoff scheduling algorithms. A multi-queue single-server system is proposed to model multiple access networks. The input buffer of each access node is modeled as a Geo/G/1 queue, and the service time distribution of head-of-line packets is derived from the Markov chain of underlying scheduling algorithm. The main results include the complete analysis of the throughput and delay distribution, from which we derived the characteristic equation of network throughput and obtained stable regions with respect to the throughput and bounded mean delay of the Exponential Backoff scheme. We show that the stable throughput region of Exponential Backoff can be obtained even for an infinite population. Since the variance of service time of Exponential Backoff can be unbounded due to the capture effect; thus, its bounded delay region is only a sub-set of its stable throughput region, and the maximum achievable throughput of the network within this region is slightly smaller than the absolute maximum throughput. Analytical results presented in this paper are all verified by simulation.
Oxygen cost of treadmill running in 24-month-old Fischer-344 rats.

The oxygen cost of treadmill running is well documented in young adult rats. However, to our knowledge there are no detailed reports concerning the oxygen cost of treadmill running in senescent rats. Young adult (4 months; N = 8) and senescent (24 months; N = 8) female Fischer-344 rats were tested for O2 cost of treadmill running. One-half of the animals tested in each age group had completed 10 wk of endurance training. Oxygen cost of treadmill running, using a flow-through system, was measured on a per minute basis from 7-10 min of each work bout and averaged. Separate work bouts were performed at 0%, 5%, and 10% grade at 15, 20, 25, and 30 m.min-1. Oxygen cost of treadmill running for trained rats for all speeds and grades were not significantly different (P = 0.77) from untrained animals; thus, data were pooled for oxygen cost of running. Results revealed significantly lower (P < 0.05) VO2 (expressed as ml.kg-1.min-1) for senescent rats vs young adult rats rest and at all comparable treadmill grades and speeds except for 5% grade, 25 m.min-1 and 10% grade, 20 m.min-1. In addition, resting VO2 was significantly lower (P < 0.05) in old rats when compared with young rats. Thus, we conclude that the oxygen cost of treadmill running is lower for 24-month-old rats than in 4-month-old rats except at higher work levels.
Long‐term memory underlying hippocampus‐dependent social recognition in mice

The ability to learn and remember individuals is critical for the stability of social groups. Social recognition reflects the ability of mice to identify and remember conspecifics. Social recognition is assessed as a decrease in spontaneous investigation behaviors observed in a mouse reexposed to a familiar conspecific. Our results demonstrate that group‐housed mice show social memory for a familiar juvenile when tested immediately, 30 min, 24 h, 3 days, and 7 days after a single 2‐min‐long interaction. Interestingly, chronic social isolation disrupts long‐term, but not 30‐min, social memory. Even a 24‐h period of isolation disrupts long‐term social memory, a result that may explain why previous investigators only observed short‐term social memory in individually housed rodents. Although it has no obvious configural, relational, or spatial characteristics, here we show that social memory shares characteristics of other hippocampus‐dependent memories. Ibotenic acid lesions of the hippocampus disrupt social recognition at 30 min, but not immediately after training. Furthermore, long‐term, but not short‐term social memory is dependent on protein synthesis and cyclic AMP responsive element binding protein (CREB) function. These results outline behavioral, systems, and molecular determinants of social recognition in mice, and they suggest that it is a powerful paradigm to investigate hippocampal learning and memory. Hippocampus 2000;10:47–56. © 2000 Wiley‐Liss, Inc.
Individual Differences and State-Dependent Responses in Transcranial Direct Current Stimulation

Transcranial direct current stimulation (tDCS) has been extensively used to examine whether neural activities can be selectively increased or decreased with manipulations of current polarity. Recently, the field has reevaluated the traditional anodal-increase and cathodal-decrease assumption due to the growing number of mixed findings that report the effects of the opposite directions. Therefore, the directionality of tDCS polarities and how it affects each individual still remain unclear. In this study, we used a visual working memory (VWM) paradigm and systematically manipulated tDCS polarities, types of different independent baseline measures, and task difficulty to investigate how these factors interact to determine the outcome effect of tDCS. We observed that only low-performers, as defined by their no-tDCS corsi block tapping (CBT) performance, persistently showed a decrement in VWM performance after anodal stimulation, whereas no tDCS effect was found when participants were divided by their performance in digit span. In addition, only the optimal level of task difficulty revealed any significant tDCS effect. All these findings were consistent across different blocks, suggesting that the tDCS effect was stable across a short period of time. Lastly, there was a high degree of intra-individual consistency in one’s responsiveness to tDCS, namely that participants who showed positive or negative effect to anodal stimulation are also more likely to show the same direction of effects for cathodal stimulation. Together, these findings imply that tDCS effect is interactive and state dependent: task difficulty and consistent individual differences modulate one’s responsiveness to tDCS, while researchers’ choices of independent behavioral baseline measures can also critically affect how the effect of tDCS is evaluated. These factors together are likely the key contributors to the wide range of “noises” in tDCS effects between individuals, between stimulation protocols, and between different studies in the literature. Future studies using tDCS, and possibly tACS, should take such state-dependent condition in tDCS responsiveness into account.
Prospect of Bioflavonoid Fisetin as a Quadruplex DNA Ligand: A Biophysical Approach

Quadruplex (G4) forming sequences in telomeric DNA and c-myc promoter regions of human DNA are associated with tumorogenesis. Ligands that can facilitate or stabilize the formation and increase the stabilization of G4 can prevent tumor cell proliferation and have been regarded as potential anti-cancer drugs. In the present study, steady state and time-resolved fluorescence measurements provide important structural and dynamical insights into the free and bound states of the therapeutically potent plant flavonoid fisetin (3,3′,4′,7-tetrahydroxyflavone) in a G4 DNA matrix. The excited state intra-molecular proton transfer (ESPT) of fisetin plays an important role in observing and understanding the binding of fisetin with the G4 DNA. Differential absorption spectra, thermal melting, and circular dichroism spectroscopic studies provide evidences for the formation of G4 DNA and size exclusion chromatography (SEC) proves the binding and 1∶1 stoichiometry of fisetin in the DNA matrix. Comparative analysis of binding in the presence of EtBr proves that fisetin favors binding at the face of the G-quartet, mostly along the diagonal loop. Time resolved fluorescence anisotropy decay analysis indicates the increase in the restrictions in motion from the free to bound fisetin. We have also investigated the fingerprints of the binding of fisetin in the antiparallel quadruplex using Raman spectroscopy. Preliminary results indicate fisetin to be a prospective candidate as a G4 ligand.
Malignancy-Associated Dyslipidemia

Cholesterol and triglycerides, important lipid constituents of cell, are essential to carry out several vital physiological functions. Lipids might be associated with cancers because they play a key role in the maintenance of cell integrity. The pathway for cholesterol synthesis may also produce various tumorigenic compounds and cholesterol serves as a precursor for the synthesis of many sex hormones linked to increased risk of various cancers. In some malignant diseases, blood cholesterol undergoes early and significant changes. The mechanism for the link between cancer and cholesterol remains controversial. The dates from studies are confusing because both hypolipidemia and hypercholesterolemia might be connected with malignancy. Not only cancers but also antineoplastic therapies have an influence on lipid profile. There are also dates suggesting that antihyperlipemic drugs might nfluenced malignancy.
FabH Mutations Confer Resistance to FabF-Directed Antibiotics in Staphylococcus aureus

ABSTRACT Delineating the mechanisms for genetically acquired antibiotic resistance is a robust approach to target validation and anticipates the evolution of clinical drug resistance. This study defines a spectrum of mutations in fabH that render Staphylococcus aureus resistant to multiple natural products known to inhibit the elongation condensing enzyme (FabF) of bacterial type II fatty acid synthesis. Twenty independently isolated clones resistant to platensimycin, platencin, or thiolactomycin were isolated. All mutants selected against one antibiotic were cross-resistant to the other two antibiotics. Mutations were not detected in fabF, but the resistant strains harbored missense mutations in fabH. The altered amino acids clustered in and around the FabH active-site tunnel. The mutant FabH proteins were catalytically compromised based on the low activities of the purified enzymes, a fatty acid-dependent growth phenotype, and elevated expression of the fabHF operon in the mutant strains. Independent manipulation of fabF and fabH expression levels showed that the FabH/FabF activity ratio was a major determinant of antibiotic sensitivity. Missense mutations that reduce FabH activity are sufficient to confer resistance to multiple antibiotics that bind to the FabF acyl-enzyme intermediate in S. aureus.
Finite time tracking of unilaterally constrained planar systems with pre-specified settling time: Second order sliding mode synthesis and chattering-free digital implementation

In this paper, tuning rules are established when a second order sliding mode controller is utilized to achieve finite time tracking for a class of unilaterally constrained planar systems in the presence of external disturbances in continuous and discrete-event phases. Rigid body inelastic impacts are incorporated at the unstable equilibrium. A numerical chattering-free digital implementation is also presented. This implementation, while being based on strong theoretical foundations, appears to bring the present advances in the area closer to industrial application.
PCA-Based 3D Face Photography

This paper presents a 3D face photography system based on a small set of training facial range images. The training set is composed by 2D texture and 3D range images (i.e. geometry) of a single subject with different facial expressions. The basic idea behind the method is to create texture and geometry spaces based on the training set and transformations to go from one space to the other. The main goal of the proposed approach is to obtain a geometry representation of a given face provided as a texture image, which undergoes a series of transformations through the texture and geometry spaces. Facial feature points are obtained by an active shape model (ASM) extracted from the 2D gray-level images. PCA then is used to represent the face dataset, thus defining an orthonormal basis of texture and range data. An input face is given by a gray-level face image to which the ASM is matched. The extracted ASM is fed to the PCA basis representation and a 3D version of the 2D input image is built. The experimental results on static images and video sequences using seven samples as training dataset show rapid reconstructed 3D faces which maintain spatial coherence similar to the human perception, thus corroborating the efficiency of our approach.
Direct Phosphorylation and Activation of a Nim1-related Kinase Gin4 by Elm1 in Budding Yeast*

In budding yeast, Gin4, a Nim1-related kinase, plays an important role in proper organization of the septin ring at the mother-bud neck, a filamentous structure that is critical for diverse cellular processes including mitotic entry and cytokinesis. How Gin4 kinase activity is regulated is not known. Here we showed that a neck-associated Ser/Thr kinase Elm1, which is important for septin assembly, is critical for proper modification of Gin4 and its physiological substrate Shs1. In vitro studies with purified recombinant proteins demonstrated that Elm1 directly phosphorylates and activates Gin4, which in turn phosphorylates Shs1. Consistent with these observations, acute inhibition of Elm1 activity abolished mitotic Gin4 phosphorylation and Gin4-dependent Shs1 modification in vivo. In addition, a gin4 mutant lacking the Elm1-dependent phosphorylation sites exhibited an impaired localization to the bud-neck and, as a result, induced a significant growth defect with an elongated bud morphology. Thus, Elm1 regulates the septin assembly-dependent cellular events by directly phosphorylating and activating the Gin4-dependent pathway(s).
Triimidazolium tris(pyridine-2,6-dicarboxylato)dysprosate(III) trihydrate

The structure of the title compound, (C3N2H5)3[Dy(C7H3NO4)3]·3H2O, contains a mononuclear DyIII complex with the rare earth metal cation in a distorted tricapped trigonal–prismatic environment. The DyIII ion is in each case O,N,O′-chelated by three tridentate pyridine-2,6-dicarboxylate anions. Three protonated imidazole molecules act as counter-cations and three lattice water molecules are also present. Numerous N—H⋯O and O—H⋯O hydrogen bonding interactions, some of which are bifurcated, help to stabilize the packing of the structure.
Deception planning models for cyber security

Deception-based mechanisms are typically used to enhance overall security by causing misperception on adversaries who take actions in favor of defense. The process of creating deception is complex and demands careful planning to maximize the benefits while mitigating potential risks. Advances in creating deception planning processes for cyber security are generally based on military tactics, where deception has a long history. However, the complexity of computer systems demands deception planning processes that fit the needs of integrating deception into traditional software security mechanisms. This paper presents a survey of existing deception planning processes in military and digital realms. The goal of this review is to identify the scope of deception planning models, which tools have been used to plan deception, and how the planning is integrated into other activities in the software development phases. We identified 20 different features in the studies, which we used to compare them. The outcome of this survey can be used to facilitate the understanding of how deception planning has been conducted and supported while identifying potential gaps to be addressed in future research.
Dynamic resource allocation and power management in virtualized data centers

We investigate optimal resource allocation and power management in virtualized data centers with time-varying workloads and heterogeneous applications. Prior work in this area uses prediction based approaches for resource provisioning. In this work, we take an alternate approach that makes use of the queueing information available in the system to make online control decisions. Specifically, we use the recently developed technique of Lyapunov Optimization to design an online admission control, routing, and resource allocation algorithm for a virtualized data center. This algorithm maximizes a joint utility of the average application throughput and energy costs of the data center. Our approach is adaptive to unpredictable changes in the workload and does not require estimation and prediction of its statistics.
Scottish NHS offers cash to get smokers to quit

The NHS in Scotland is offering smokers £12.50 (€13; $18) a week to quit cigarettes, in a two year pilot scheme that will test if financial incentives help. The Quit4u project is being run in Dundee and targeted at people who live in the city’s deprived areas, where smoking rates are high and cessation levels low. The money will be credited to an electronic card that can be redeemed in supermarkets for fresh food and groceries. The incentive will be paid for …
Central Bank Independence and Conservatism Under Uncertainty: Substitutes or Complements?

The paper examines the optimal combination of central bank independence and conservatism in the presence of uncertain central bank preferences. We develop a model of endogenous monetary policy delegation in which government chooses the central bank's degree of inde-pendence and conservatism so as to minimise society's loss function. We find that the optimal combination between independence and conservatism is not necessarily characterised by substitutability. When uncertainty about the central bank's preferences is high, independence and conservatism can become complements. In this case, giving more independence to the central bank increases the need for conservatism.