Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection of near‐native poses in CAPRI rounds 13‐19

In CAPRI rounds 13–19, we submitted models that are of acceptable or higher quality for 6 of the total of 13 targets. This success builds on our record in previous CAPRI rounds. The docking problem can be divided into two steps. In the first, translational/rotational and conformational space is searched to generate a pool of docked poses; the success of this search step is measured by whether near‐native poses are included in the pool. In the second step, the pool is selected for near‐native poses. In our previous assessment of CAPRI results, we suggested that the search problem is largely solved; a remaining problem is to select near‐native poses. Our work in these new rounds of CAPRI was guided by this assessment. To solve the selection problem, we used an assortment of criteria on the interfaces of candidate poses. In one extreme, represented by T29, with very little known interface information, our criterion for top models was based on interface prediction. Poses in which the predicted interface residues occurred in interfaces were selected. Our model 1 for T29 was of medium quality. In the other extreme, represented by T40, with reliably known interface information, our selection was solely based on such information. Nine of the ten models submitted for T40 were of high (3 models), medium (4 models), and acceptable (2 models) quality. Our strategy of mixing predicted and known interface information appears to be widely applicable for the selection of near‐native poses. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Effect of subthalamic nucleus interconnectivity at deep brain stimulation onset and offset: A simulation study

Deep brain stimulation (DBS) has been demonstrated to effectively improve the motor symptoms of Parkinson's disease. However, the underlying mechanisms are not known. It has been reported that a period of time is required before the full effect on motor symptoms is realized after DBS is initiated and that suppression of symptoms persists after DBS ends under parkinsonian conditions. A computational model is presented to investigate the hypothesis that interconnectivity and transmission delays within the subthalamic nucleus (STN) neurons may induce a gradual decay and recovery of pathological oscillations at DBS onset and offset under simulated parkinsonian conditions. Interconnectivity strength between the STN neurons and the number of STN neurons directly stimulated by DBS are both varied to examine the gradual decay and recovery of oscillatory STN activity. Weaker interconnectivity and lower numbers of STN neurons directly receiving DBS input were found to result in longer decay and recovery times at the onset and offset of DBS, respectively.
Fractional Fourier Texture Masks: Guiding Near‐Regular Texture Synthesis

Recently, the special kind of near-regular texture has drawn signiﬁcant attention from researchers in the ﬁeld of texture synthesis. Near-regular textures contain global regular structures that pose signiﬁcant problems to the popular sample-based approaches, and irregular stochastic structures that can not be reproduced by simple tiling. Existing work tries to overcome this problem by user assisted modeling of the regular structures and then relies on regular tiling. In this paper we use the concept of fractional Fourier analysis to perform a fully automatic separation of the global regular structure from the irregular structure. The actual synthesis is performed by generating a fractional Fourier texture mask from the extracted global regular structure which is used to guide the synthesis of irregular texture details. Our new method allows for automatic and efﬁcient synthesis of a wide range of near-regular textures preserving their regular structures and faithfully reproducing their stochastic elements. Categories and Subject Descriptors (according to ACM CCS) : I.3. 7 [Computer Graphics]: Three-Dimensional Graphics and Realism – Color, shading, shadowing, and texture, I.4. 7 [Image Processing and Computer Vison]: Feature Measurement – Texture
Virtual Intervention to Support Self-Management of Antiretroviral Therapy Among People Living With HIV

Background Living with human immunodeficiency virus (HIV) necessitates long-term health care follow-up, particularly with respect to antiretroviral therapy (ART) management. Taking advantage of the enormous possibilities afforded by information and communication technologies (ICT), we developed a virtual nursing intervention (VIH-TAVIE) intended to empower HIV patients to manage their ART and their symptoms optimally. ICT interventions hold great promise across the entire continuum of HIV patient care but further research is needed to properly evaluate their effectiveness. Objective The objective of the study was to compare the effectiveness of two types of follow-up—traditional and virtual—in terms of promoting ART adherence among HIV patients. Methods A quasi-experimental study was conducted. Participants were 179 HIV patients on ART for at least 6 months, of which 99 were recruited at a site offering virtual follow-up and 80 at another site offering only traditional follow-up. The primary outcome was medication adherence and the secondary outcomes were the following cognitive and affective variables: self-efficacy, attitude toward medication intake, symptom-related discomfort, stress, and social support. These were evaluated by self-administered questionnaire at baseline (T0), and 3 (T3) and 6 months (T6) later. Results On average, participants had been living with HIV for 14 years and had been on ART for 11 years. The groups were highly heterogeneous, differing on a number of sociodemographic dimensions: education, income, marital status, employment status, and living arrangements. Adherence at baseline was high, reaching 80% (59/74) in the traditional follow-up group and 84% (81/97) in the virtual follow-up group. A generalized estimating equations (GEE) analysis was run, controlling for sociodemographic characteristics at baseline. A time effect was detected indicating that both groups improved in adherence over time but did not differ in this regard. Improvement at 6 months was significantly greater than at 3 months in both groups. Analysis of variance revealed no significant group-by-time interaction effect on any of the secondary outcomes. A time effect was observed for the two kinds of follow-ups; both groups improved on symptom-related discomfort and social support. Conclusions Results showed that both interventions improved adherence to ART. Thus, the two kinds of follow-up can be used to promote treatment adherence among HIV patients on ART.
Neurophysiological evidence for the in fl uence of past experience on fi gure – ground perception

A fundamental aspect of perceptual organization entails segregating visual input into shaped figures presented against shapeless backgrounds; an outcome termed “figure–ground perception” or “shape assignment. ” The present study examined how early in processing past experience exerts an influence on shape assignment. Event-related potential (ERP) measures of brain activity were recorded while observers viewed silhouettes of novel objects that differed in whether or not a familiar shape was suggested on the outsideVthe groundsideVof their bounding edges (experimental versus control silhouettes, respectively). Observers perceived both types of silhouettes as novel shapes and were unaware of the familiar shape suggested on the groundside of experimental silhouettes. Nevertheless, we expected that the familiar shape would be implicitly identified early in processing and would compete for figural status with the novel shape on the inside. Early (106–156 ms) ERPs were larger for experimental silhouettes than for control silhouettes lacking familiarity cues. The early ERP difference occurred during a time interval within which edge-segmentation-dependent response differences have been observed in previous neurophysiological investigations of figure–ground perception. These results provide the first neurophysiological evidence for an influence of past experience during the earliest stages of shape assignment.
A New Data Selection Principle for Semi-Supervised Incremental Learning

Current semi-supervised incremental learning approaches select unlabeled examples with predicted high confidence for model re-training. We show that for many applications this data selection strategy is not correct. This is because the confidence score is primarily a metric to measure the classification correctness on a particular example, rather than one to measure the example's contribution to the training of an improved model, especially in the case that the information used in the confidence annotator is correlated with that generated by the classifier. To address this problem, we propose a performance-driven principle for unlabeled data selection in which only the unlabeled examples that help to improve classification accuracy are selected for semi-supervised learning. Encouraging results are presented for a variety of public benchmark datasets
Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21

Cell surface Fc receptors activate inflammation and are tightly controlled to prevent autoimmunity. Antibodies also simulate potent immune signalling from inside the cell via the cytosolic antibody receptor TRIM21, but how this is regulated is unknown. Here we show that TRIM21 signalling is constitutively repressed by its B-Box domain and activated by phosphorylation. The B-Box occupies an E2 binding site on the catalytic RING domain by mimicking E2-E3 interactions, inhibiting TRIM21 ubiquitination and preventing immune activation. TRIM21 is derepressed by IKKβ and TBK1 phosphorylation of an LxxIS motif in the RING domain, at the interface with the B-Box. Incorporation of phosphoserine or a phosphomimetic within this motif relieves B-Box inhibition, promoting E2 binding, RING catalysis, NF-κB activation and cytokine transcription upon infection with DNA or RNA viruses. These data explain how intracellular antibody signalling is regulated and reveal that the B-Box is a critical regulator of RING E3 ligase activity.
The children and sunscreen study: a crossover trial investigating children's sunscreen application thickness and the influence of age and dispenser type.

OBJECTIVES To measure the thickness at which primary schoolchildren apply sunscreen on school day mornings and to compare it with the thickness (2.00 mg/cm(2)) at which sunscreen is tested during product development, as well as to investigate how application thickness was influenced by age of the child (school grades 1-7) and by dispenser type (500-mL pump, 125-mL squeeze bottle, or 50-mL roll-on). DESIGN A crossover quasiexperimental study design comparing 3 sunscreen dispenser types. SETTING Children aged 5 to 12 years from public primary schools (grades 1-7) in Queensland, Australia. PARTICIPANTS Children (n=87) and their parents randomly recruited from the enrollment lists of 7 primary schools. Each child provided up to 3 observations (n=258). INTERVENTION Children applied sunscreen during 3 consecutive school weeks (Monday through Friday) for the first application of the day using a different dispenser each week. MAIN OUTCOME MEASURE Thickness of sunscreen application (in milligrams per square centimeter). The dispensers were weighed before and after use to calculate the weight of sunscreen applied. This was divided by the coverage area of application (in square centimeters), which was calculated by multiplying the children's body surface area by the percentage of the body covered with sunscreen. RESULTS Children applied their sunscreen at a median thickness of 0.48 mg/cm(2). Children applied significantly more sunscreen when using the pump (0.75 mg/cm(2)) and the squeeze bottle (0.57 mg/cm(2)) compared with the roll-on (0.22 mg/cm(2)) (P<.001 for both). CONCLUSIONS Regardless of age, primary schoolchildren apply sunscreen at substantially less than 1.00 mg/cm(2), similar to what has been observed among adults. Some sunscreen dispensers seem to facilitate thicker application than others.
Repeatability of extra‐pair mating in tree swallows

Models of sexual selection assume that female mating preferences are heritable and, thus, repeatable for individual females across multiple mating episodes. Previous studies of the repeatability of female preference have examined individuals in captivity and focused presumably on social mate choice. However, extra‐pair mating is widespread and can also influence sexual selection. We examined the repeatability of extra‐pair mating in a wild population of tree swallows (Tachycineta bicolor) by experimentally inducing females to lay two clutches in rapid succession within the same season. We found that the proportion of extra‐pair young and the number of extra‐pair sires were highly repeatable for individual females. However, the repeatability of specific extra‐pair sires was low. We suggest that this unusual pattern of mating may be due to females maximizing the heterozygosity of their offspring.
Interaction of Fluorescent 2-(1-Methoxynaphthalen-4-Yl)-1-(4-Methoxyphenyl)-4, 5-Diphenyl-1H-Imidazole with Pristine Zno, Cu-Doped Zno and Ag-Doped Zno Nanoparticles

A sensitive 2-(1-methoxynaphthalen-4-yl)-1-(4-methoxyphenyl)-4, 5-diphenyl-1H-imidazole (MNMPI) fluorescent sensor for nanoparticulates like ZnO, Cu-doped ZnO and Ag-doped ZnO has been designed and synthesized. Facile preparation of ZnO, Cu-doped ZnO and Ag-doped ZnO nanoparticles by sol-gel method using PVP K-30 as templating agents is reported and characterised by powder X-ray diffraction (XRD), scanning electron microscopy (SEM), UVVisible spectroscopy and photoluminescence spectroscopy (PL). The synthesized sensor release is enhanced by nanocrystalline pristine ZnO but is suppressed by Cu-doped ZnO and Ag-doped ZnO nanoparticles. The suppression of fluorescence is additional by copper than by silver doping. The LUMO and HOMO energy gap of MNMPI associated with Cu-doped ZnO are lowers compared to those of pristine ZnO and thus red shift compared to that with pristine ZnO. The average crystallite sizes of ZnO, Cu-doped ZnO and Ag-doped ZnO have been deduced as 32 nm, 36 nm and 26 nm and calculated surface area for ZnO, Cu-doped ZnO and Ag-doped ZnO are 30.04 m2/g, 40.66 m2/g and 29.37 m2/g respectively. The observed enhanced absorbance with the distributed semiconductor nanoparticle is due to adsorption of MNMPI on semiconductor surface. This is because of the efficient transfer of electron from the excited state of the MNMPI to the conduction band of the semiconductor nanoparticle.
Konrad-zuse-zentrum F ¨ Ur Informationstechnik Berlin Multiple Semi-flexible 3d Superposition of Drug-sized Molecules Multiple Semi-flexible 3d Superposition of Drug-sized Molecules

In this paper we describe a new algorithm for multiple semi-flexible superpositioning of drug-sized molecules. The algorithm identifies structural similarities of two or more molecules. When comparing a set of molecules on the basis of their three-dimensional structures, one is faced with two main problems. (1) Molecular structures are not fixed but flexible , i.e., a molecule adopts different forms. To address this problem, we consider a set of conformers per molecule. As conformers we use representatives of conformational ensembles, generated by the program ZIBMol. (2) The degree of similarity may vary considerably among the molecules. This problem is addressed by searching for similar substructures present in arbitrary subsets of the given set of molecules. The algorithm requires to preselect a reference molecule. All molecules are compared to this reference molecule. For this pairwise comparison we use a two-step approach. Clique detection on the correspondence graph of the molecular structures is used to generate start transformations, which are then iteratively improved to compute large common substructures. The results of the pairwise comparisons are efficiently merged using binary matching trees. All common substructures that were found, whether they are common to all or only a few molecules, are ranked according to different criteria, such as number of molecules containing the substructure, size of sub-structure, and geometric fit. For evaluating the geometric fit, we extend a known scoring function by introducing weights which allow to favor potential pharmacophore points. Despite considering the full atomic information for identifying multiple structural similarities, our algorithm is quite fast. Thus it is well suited as an interactive tool for the exploration of structural similarities of drug-sized molecules.
Bags versus flasks: a comparison of cell culture systems for the production of dendritic cell–based immunotherapies

In recent years, cell‐based therapies targeting the immune system have emerged as promising strategies for cancer treatment. This review summarizes manufacturing challenges related to production of antigen presenting cells as a patient‐tailored cancer therapy. Understanding cell‐material interactions is essential because in vitro cell culture manipulations to obtain mature antigen‐producing cells can significantly alter their in vivo performance. Traditional antigen‐producing cell culture protocols often rely on cell adhesion to surface‐treated hydrophilic polystyrene flasks. More recent commercial and investigational cancer immunotherapy products were manufactured using suspension cell culture in closed hydrophobic fluoropolymer bags. The shift to closed cell culture systems can decrease risks of contamination by individual operators, as well as facilitate scale‐up and automation. Selecting closed cell culture bags over traditional open culture systems entails different handling procedures and processing controls, which can affect product quality. Changes in culture vessels also entail changes in vessel materials and geometry, which may alter the cell microenvironment and resulting cell fate decisions. Strategically designed culture systems will pave the way for the generation of more sophisticated and highly potent cell‐based cancer vaccines. As an increasing number of cell‐based therapies enter the clinic, the selection of appropriate cell culture vessels and materials becomes a critical consideration that can impact the therapeutic efficacy of the product, and hence clinical outcomes and patient quality of life.
The Importance of Music in Preschool Teacher Education

At a few universities in Sweden students can chose a preschool teacher education programme with a music profile. At one of these universities, a study was undertaken that aimed to explore student teachers ́ understanding of self as musician, their future professional role as a preschool teacher and how the education equips for that. Sixteen students participated in focus group interviews, and thirty students answered a questionnaire. The study shows that almost three-quarters of the students did not choose the music profile for the sake of the specific profile in music. Instead, it happened that this was the programme they managed to get into or they found the location of the education suitable. How, then, to develop the design of a music profile that prepares preschool teacher students to become skilled leaders and a source of inspiration for music in preschools?
Incidence of Cancer in ANCA-Associated Vasculitis: A Meta-Analysis of Observational Studies

Objective The purpose of this paper is to examine cancer incidence in patients with ANCA-associated vasculitis (AASV) derived from population-based cohort studies by means of meta-analysis. Methods Relevant electronic databases were searched for studies characterizing the associated risk of overall malignancy in patients with AASV. Standardized incidence rates (SIRs) with 95% confidence intervals (CIs) were used to evaluate the strength of association. We tested for publication bias and heterogeneity and stratified for site-specific cancers. Results Six studies (n = 2,578) were eventually identified, of which six provided the SIR for overall malignancy, five reported the SIR for non-melanoma skin cancer (NMSC), four for leukemia, five for bladder cancer, three for lymphoma, three for liver cancer, four for lung cancer, three for kidney cancer, four for prostate cancer, four for colon cancer and four for breast cancer. Overall, the pooled SIR of cancer in AASV patients was 1.74 (95%CI = 1.37–2.21), with moderate heterogeneity among these studies (I2 = 65.8%, P = 0.012). In sub-analyses for site-specific cancers, NMSC, leukemia and bladder cancer were more frequently observed in patients with AASV with SIR of 5.18 (95%CI = 3.47–7.73), 4.89 (95%CI = 2.93–8.16) and 3.84 (95%CI = 2.72–5.42) respectively. There was no significant increase in the risk of kidney cancer (SIR = 2.12, 95%CI = 0.66–6.85), prostate cancer (SIR = 1.45, 95%CI = 0.87–2.42), colon cancer (SIR = 1.26, 95%CI = 0.70–2.27), and breast cancer (SIR = 0.95, 95%CI = 0.50–1.79). Among these site-specific cancers, only NMSC showed moderate heterogeneity (I2 = 55.8%, P = 0.06). No publication bias was found by using the Begg’s test and Egger's test. Conclusions This meta-analysis shows that AASV patients treatment with cyclophosphamide (CYC) are at increased risk of late-occurring malignancies, particularly of the NMSC, leukemia and bladder cancer. However, there is no significant association between AASV and kidney cancer, prostate cancer, colon cancer and breast cancer. These findings emphasize monitoring and preventative management in AASV patients after cessation of CYC therapy is momentous.
On the design of a decision engine for connected vehicles with an application to congestion management

Vehicles are becoming connected entities. As a result, a likely scenario is that such entities might be literally bombarded with information from a multitude of devices. In this context, a key challenging requirement for both connected and autonomous vehicles is that they will need to become cognitive bodies, able to parse information and use only the pieces of information that are relevant to the vehicle in the context of a given journey. In order to address this fundamental requirement, a decision engine is presented in this paper. The engine makes it possible for the vehicle to understand which pieces of information are really relevant, and subsequently to process only those pieces of information. In order to illustrate the key features of our system, we show that it is possible to build upon the engine to develop a distributed traffic management system, and then we validate such a system via both conventional (numerical and SUMO-based) simulations and a Hardware-in-the-Loop (HIL) platform. Both the conventional simulations and the HIL validation showed that the engine can be effectively used to design a distributed traffic management system.
An image compositing solution at scale

The only proven method for performing distributed-memory parallel rendering at large scales, tens of thousands of nodes, is a class of algorithms called sort last. The fundamental operation of sort-last parallel rendering is an image composite, which combines a collection of images generated independently on each node into a single blended image. Over the years numerous image compositing algorithms have been proposed as well as several enhancements and rendering modes to these core algorithms. However, the testing of these image compositing algorithms has been with an arbitrary set of enhancements, if any are applied at all. In this paper we take a leading production-quality image compositing framework, IceT, and use it as a testing frame work for the leading image compositing algorithms of today. As we scale IceT to ever increasing job sizes, we consider the image compositing systems holistically, incorporate numerous optimizations, and discover several improvements to the process never considered before. We conclude by demonstrating our solution on 64K cores of the Intrepid Blue Gene/P at Argonne National Laboratories.