Miracle-dz/UniFAR-FTUs huggingface dataset:
A fast and automated solution for accurately resolving protein domain architectures

MOTIVATION Accurate prediction of the domain content and arrangement in multi-domain proteins (which make up >65% of the large-scale protein databases) provides a valuable tool for function prediction, comparative genomics and studies of molecular evolution. However, scanning a multi-domain protein against a database of domain sequence profiles can often produce conflicting and overlapping matches. We have developed a novel method that employs heaviest weighted clique-finding (HCF), which we show significantly outperforms standard published approaches based on successively assigning the best non-overlapping match (Best Match Cascade, BMC). RESULTS We created benchmark data set of structural domain assignments in the CATH database and a corresponding set of Hidden Markov Model-based domain predictions. Using these, we demonstrate that by considering all possible combinations of matches using the HCF approach, we achieve much higher prediction accuracy than the standard BMC method. We also show that it is essential to allow overlapping domain matches to a query in order to identify correct domain assignments. Furthermore, we introduce a straightforward and effective protocol for resolving any overlapping assignments, and producing a single set of non-overlapping predicted domains. AVAILABILITY AND IMPLEMENTATION The new approach will be used to determine MDAs for UniProt and Ensembl, and made available via the Gene3D website: http://gene3d.biochem.ucl.ac.uk/Gene3D/. The software has been implemented in C++ and compiled for Linux: source code and binaries can be found at: ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/DomainFinder3/ CONTACT yeats@biochem.ucl.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Molecular Detection of Mixed Infections of Mycobacterium tuberculosis Strains in Sputum Samples from Patients in Karonga District, Malawi

ABSTRACT The occurrence of mixed infections of Mycobacterium tuberculosis is no longer disputed. However, their frequency, and the impact they may have on our understanding of tuberculosis (TB) pathogenesis and epidemiology, remains undetermined. Most previous studies of frequency applied genotyping techniques to cultured M. tuberculosis isolates and found mixed infections to be rare. PCR-based techniques may be more sensitive for detecting multiple M. tuberculosis strains and can be applied to sputum. To date, one study in South Africa has used a PCR approach and suggested that mixed infection could be common. We investigated mixed infections in northern Malawi using two lineage-specific PCR assays targeting the Latin American-Mediterranean (LAM) and Beijing lineages. Compared with spoligotyping, the specificity and sensitivity of both assays was 100%. From 160 culture-positive sputa, mixed LAM and non-LAM strains were detected in 4 sputa belonging to 2 (2.8%) patients. Both patients were HIV positive, with no history of TB. Cultured isolates from both patients showed only LAM by PCR and spoligotyping. In a set of 377 cultured isolates, 4 were mixed LAM and non-LAM. Only one showed evidence of more than one M. tuberculosis strain using IS6110-based restriction fragment length polymorphism (IS6110-RFLP) and spoligotyping analyses. Corresponding sputa for the 4 isolates were unavailable. Mixed Beijing and non-Beijing strains were not detected in this study. Mixed infections appear to be rare in our setting and are unlikely to affect findings based on DNA fingerprinting data. Molecular methods, which avoid the selective nature of culture and target distinct strains, are well suited to detection of mixed infections.
Critical Care Management of the Patient with Traumatic Brain Injury

Abstract The critical care management of patients with traumatic brain injury is complex. The primary goal is to minimize the effects of secondary injury that would otherwise serve to further worsen neurologic function. This requires an understanding of the abnormal brain physiology that is found in these patients. In this article the authors discuss this physiology and describe suggested treatment strategies for these patients based on evidence-based guidelines.
A novel system for stereotactic surgery: Preliminary evaluation of targeting accuracy

A new stereotactic system for deep brain stimulation has been previously proposed and its method for creating the stereotactic frame has been validated. In this study, the system was evaluated for its targeting accuracy based on a plastic skull model. A micro stereotactic frame is created based on the CT volume image acquired from the skull model. During the experiment, the frame is attached to skull-implanted screws that extend through the skull. The frame provides guidance for parallel cannulas as they are advanced through a burr hole to the target. During the experiment, a micro camera was placed in the skull model to record the whole procedure of the needle touching the target. The results showed that our stereotactic frame could fulfill the requirements of the DBS surgery.
Research Paper: Adoption of Order Entry with Decision Support for Chronic Care by Physician Organizations

OBJECTIVE This study sought to explore physician organizations' adoption of chronic care guidelines in order entry systems and to investigate the organizational and market-related factors associated with this adoption. DESIGN A quantitative nationwide survey of all primary care medical groups in the United States with 20 or more physicians; data were collected on 1,104 physician organizations, representing a 70% response rate. MEASUREMENTS Measurements were the presence of an asthma, diabetes, or congestive heart failure guideline in a physician organization's order entry system; size; age of the organization; number of clinic locations; type of ownership; health maintenance organization market penetration; urban/rural location; and presence of external incentives to improve quality of care. RESULTS Only 27% of organizations reported access to order entry with decision support for chronic disease care. External incentives for quality is the only factor significantly associated with adoption of these tools. Organizations experiencing greater external incentives for quality are more likely to adopt order entry with decision support. CONCLUSION Because external incentives are strong drivers of adoption, policies requiring reporting of chronic care measurements and rewarding improvement as well as financial incentives for use of specific information technology tools are likely to accelerate adoption of order entry with decision support.
Autoantibodies to neuronal surface antigens in thyroid antibody-positive and -negative limbic encephalitis.

BACKGROUND Thyroid antibodies (Thy-Abs) are frequently detected in various autoimmune disorders in coexistence with other systemic autoantibodies. In association with an encephalopathy, they are often taken as evidence of Hashimoto's encephalitis (HE). However, the presence of Thy-Abs in a cohort of limbic encephalitis (LE) patients and their association with anti-neuronal autoimmunity has not been explored. PATIENTS AND METHODS We investigated thyroid and anti-neuronal antibodies in the sera of 24 LE patients without identified tumors by cell-based assay and radioimmunoassay and evaluated their clinical features. RESULTS There was a female predominance in Thy-Ab-positive LE patients. Five of the eight Thy-Ab-positive patients and six of the 16 Thy-Ab-negative patients had antibodies to voltage-gated potassium channel (VGKC), N-methyl-D-aspartate receptor (NMDAR) or undefined surface antigens on cultured hippocampal neurons. There were trends towards fewer VGKC antibodies (1/8 vs. 5/16, P = 0.159) and more NMDAR antibodies (2/8 vs. 1/16, P = 0.095) among the Thy-Ab-positive LE patients; antibodies to undefined surface antigens were only identified in Thy-Ab-positive patients (2/8 vs. 0/16, P = 0.018). There were no distinguishing clinical features between Thy-Ab-positive patients with and without neuronal antibodies. However, patients with anti-neuronal antibodies showed a better treatment response. CONCLUSION Thy-Abs can be found in a high proportion of patients with non-paraneoplastic LE, often in association with antibodies to specific or as yet undefined neuronal surface antigens. These results suggest that acute idiopathic encephalitis patients with Thy-Abs should be closely monitored for ion-channel antibodies and it should not be assumed that they have HE.
Adaptive Markov Models for Information-Theoretic Empirical-Bayesian MRI Denoising

This paper presents a novel framework for denoising magnetic resonance images. The framework relies on adaptive Markov-random-field (MRF) image models that we infer nonparametrically from the corrupted input data itself. The proposed denoising method produces an optimal reconstruction based on principles in empirical-Bayesian estimation and information theory. Given the corrupted input data and the knowledge of the Rician noise model, the Bayesian-denoising method bootstraps itself by estimating the uncorrupted-signal Markov statistics, by optimizing an informationtheoretic metric using the expectation-maximization (EM) algorithm. It then employs the inferred uncorrupted-signal Markov statistics as an adaptive prior in a Bayesian-denoising process at each pixel. Furthermore, it proposes a novel Bayesian-inference algorithm on MRFs incorporating entropy reduction, namely iterated conditional entropy reduction (ICER). The results demonstrate that the method denoises conservatively while ensuring the preservation of most of the important features in brain-MR images. Qualitative and quantitative comparisons with the state of the art clearly depict the advantages of the proposed method.
Colorblind and Multicultural Ideologies Are Associated With Faculty Adoption of Inclusive Teaching Practices

Professional workshops aimed at increasing student diversity typically urge college-level science, technology, engineering, and math (STEM) educators to implement inclusive teaching practices. A model of the process by which educators adopt such practices, and the relationship between adoption and 2 ideologies of diversity is tested here. One ideology, colorblindness, downplays differences based on gender or color. The other, multiculturalism, embraces differences. Pathway modeling revealed reliable, discrete steps in the process of adoption. Independently, greater endorsement of colorblindness predicted adoption of fewer inclusive teaching practices, and multiculturalism predicted adoption of more practices. These findings inform national-level intervention efforts about the process by which educators adopt inclusive teaching practices, and suggest that interventions might consider educators’ personal beliefs and approaches to diversity.
‘To be a woman is to make a plan’: a qualitative study exploring mothers’ experiences of the Child Support Grant in supporting children’s diets and nutrition in South Africa

Food security and good nutrition are key determinants of child well-being. There is strong evidence that cash transfers such as South Africa’s Child Support Grant (CSG) have the potential to help address some of the underlying drivers of food insecurity and malnutrition by providing income to caregivers in poor households, but it is unclear how precisely they work to affect child well-being and nutrition. We present results from a qualitative study conducted to explore the role of the CSG in food security and child well-being in poor households in an urban and a rural setting in South Africa. Setting Mt Frere, Eastern Cape (rural area); Langa, Western Cape (urban township). Participants CSG recipient caregivers and community members in the two sites . We conducted a total of 40 in-depth interviews with mothers or primary caregivers in receipt of the CSG for children under the age of 5 years. In addition, five focus group discussions with approximately eight members per group were conducted. Data were analysed using manifest and latent thematic content analysis methods. Results The CSG is too small on its own to improve child nutrition and well-being. Providing for children’s diets and nutrition competes with other priorities that are equally important for child well-being and nutrition. Conclusions In addition to raising the value of the CSG so that it is linked to the cost of a nutritious basket of food, more emphasis should be placed on parallel structural solutions that are vital for good child nutrition outcomes and well-being, such as access to free quality early child development services that provide adequate nutritious meals, access to adequate basic services and the promotion of appropriate feeding, hygiene and care practices.
Efficient Indices Using Graph Partitioning in RDF Triple Stores

With the advance of the Semantic Web, varying RDF data were increasingly generated, published, queried, and reused via the Web. For example, the DBpedia, a community effort to extract structured data from Wikipedia articles, broke 100 million RDF triples in its latest release. Initiated by Tim Berners-Lee,likewise, the Linking Open Data (LOD) project has published and interlinked many open licence datasets which consisted of over 2 billion RDF triples so far. In this context, fast query response over such large scaled data would be one of the challenges to existing RDF data stores. In this paper, we propose a novel triple indexing scheme to help RDF query engine fast locate the instances within a small scope. By considering the RDF data as a graph, we would partition the graph into multiple subgraph pieces and store them individually, over which a signature tree would be built up to index the URIs. When a query arrives, the signature tree index is used to fast locate the partitions that might include the matches of the query by its constant URIs. Our experiments indicate that the indexing scheme dramatically reduces the query processing time in most cases because many partitions would be early filtered out and the expensive exact matching is only performed over a quite small scope against the original dataset.
A novel immune function biomarker identifies patients at risk of clinical events early following liver transplantation

Balancing immunosuppression after liver transplant is difficult, with clinical events common. We investigate whether a novel immune biomarker based on a laboratory platform with widespread availability that measures interferon γ (IFNγ) after stimulation with a lyophilized ball containing an adaptive and innate immune stimulant can predict events following transplantation. A total of 75 adult transplant recipients were prospectively monitored in a blinded, observational study; 55/75 (73.3%) patients experienced a total of 89 clinical events. Most events occurred within the first month. Low week 1 results were significantly associated with risk of early infection (area under the receiver operating characteristic curve [AUROC], 0.74; P = 0.008). IFNγ ≤ 1.30 IU/mL (likelihood ratio positive, 1.93; sensitivity, 71.4%; specificity, 63.0%) was associated with the highest risk for infection with minimal rejection risk. Nearly half the cohort (27/60, 45.0%) expressed IFNγ ≤ 1.30 IU/mL. Moreover, an elevated week 1 result was significantly associated with the risk of rejection within the first month after transplant (AUROC, 0.77; P = 0.002), but no episodes of infection. On multivariate logistic regression, IFNγ ≥ 4.49 IU/mL (odds ratio, 4.75) may be an independent predictor of rejection (P = 0.05). In conclusion, low IFNγ suggesting oversuppression is associated with infections, whereas high IFNγ indicating undersuppression is associated with rejection. This assay offers the potential to allow individualization and optimization of immunosuppression that could fundamentally alter the way patients are managed following transplantation. Liver Transplantation 23 487–497 2017 AASLD.
Hybrid algorithm for hand gesture recognition

Using gesture for interaction is a notion of natural human computer interaction. The use of gesture requires a correct identification of the intended pose by the system. Already numerous algorithms are working on it but not paying much attention on the complexity. Hence in this paper, a hybrid algorithm is being introduced to reduce the complexity of process also to make it insensitive with respect to the position of camera by making use of Gabor filter to get the structure of the hand followed by the Mel scaling in order to reduce the dimensions along with feature extraction using triangular filters. For the classification purpose Support vector machine has been used as a classifier.
Desferrioxamine biosynthesis: diverse hydroxamate assembly by substrate-tolerant acyl transferase DesC

Hydroxamate groups play key roles in the biological function of diverse natural products. Important examples include trichostatin A, which inhibits histone deacetylases via coordination of the active site zinc(II) ion with a hydroxamate group, and the desferrioxamines, which use three hydroxamate groups to chelate ferric iron. Desferrioxamine biosynthesis in Streptomyces species involves the DesD-catalysed condensation of various N-acylated derivatives of N-hydroxycadaverine with two molecules of N-succinyl-N-hydroxycadaverine to form a range of linear and macrocyclic tris-hydroxamates. However, the mechanism for assembly of the various N-acyl-N-hydroxycadaverine substrates of DesD from N-hydroxycadaverine has until now been unclear. Here we show that the desC gene of Streptomyces coelicolor encodes the acyl transferase responsible for this process. DesC catalyses the N-acylation of N-hydroxycadaverine with acetyl, succinyl and myristoyl-CoA, accounting for the diverse array of desferrioxamines produced by S. coelicolor. The X-ray crystal structure of DesE, the ferrioxamine lipoprotein receptor, in complex with ferrioxamine B (which is derived from two units of N-succinyl-N-hydroxycadaverine and one of N-acetyl-N-hydroxycadaverine) was also determined. This showed that the acetyl group of ferrioxamine B is solvent exposed, suggesting that the corresponding acyl group in longer chain congeners can protrude from the binding pocket, providing insights into their likely function. This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology'. This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology’.
An author-centred scientometric analysis of Daniel Gile's œuvre

The article begins with a quantitative scientometric study of Daniel Gile’s published writings. The study focuses on the diachronic development of Gile’s writings and several other aspects of his scientific oeuvre such as types of publications; languages of publication; media of publication; topics; and co-authorships. The co-authorship data are then displayed by means of a coauthorship network and discussed within the framework of network analysis. In addition, a brief keyword analysis of the titles of the publications provides a first glimpse into the range of topics which are tackled in Daniel Gile’s publications. The paper then goes on to deepen the insights gleaned from the scientometric study in an analysis of citations of Gile’s writings by other authors. The citation analysis represents a first attempt to investigate Gile’s “impact” on the scientific community, even though it is inherent to the nature of citation analysis that the data obtained by such an approach can never be complete. We think that all three approaches can provide interesting insights into Gile’s oeuvre. Owing to his pioneering publications on scientometrics and citation analysis, Daniel Gile strikes us as a perfect “candidate” for such an author-centred scientometric approach.
The roles of ethylene and transcription factors in the regulation of onset of leaf senescence

Leaf senescence is the last stage of leaf development and is accompanied by cell death. In contrast to senescence in individual organisms that leads to death, leaf senescence is associated with dynamic processes that include the translocation of nutrients from old leaves to newly developing or storage tissues within the same plant. The onset of leaf senescence is largely regulated by age and internal and external stimuli, which include the plant hormone ethylene. Earlier studies have documented the important role of ethylene in the regulation of leaf senescence. The production of ethylene coincides with the onset of leaf senescence, whereas the application of ethylene to plants induces precocious leaf senescence. Recently, many studies have described the components of ethylene signaling and biosynthetic pathways that are involved in modulating the onset of leaf senescence. Particularly, transcription factors (TFs) integrate ethylene signals with those from environmental and developmental factors to accelerate or delay leaf senescence. This review aims to discuss the regulatory cascade involving ethylene and TFs in the regulation of onset of leaf senescence.
Spectrum Occupancy Estimation in Wireless Channels with Asymmetric Transmitter Powers

In proposed cognitive radio schemes, channel occupancy is often offered as the metric to determine if a channel is free to open a new communication channel. Channel occupancy is the time average of detected transmissions above a certain power level. In many systems the transmission power between the uplink side and down-link side are asymmetric. If a single power threshold is used, then a system may underestimate channel occupancy on the low power down-link side. This results in an increased probability of interference in an existing channel if a listen-before-talking scheme is used. To avoid this hidden terminal problem, cognitive radios need to better understand the receiver properties of existing wireless channels.
The effect of communication pattern on opportunistic mobile networks

Social-based forwarding algorithms provide a new perspective on the study of routing in opportunistic mobile networks, and all of these schemes assume a uniform pattern for message generating rule. However, this is unconvincing due to the heterogeneity of contact rates in human communication patterns. In this paper we propose three social-based communication pattern models and utilize them to evaluate the network performance of different social-based routing protocols based on several human mobility traces. We find that communication patterns could significantly affect the network performance and the influence degree largely depends on the social metrics which these communication patterns are based on. We contend that considering communication pattern is quite important for designing a practical routing algorithm in opportunistic mobile networks.
Interactive pose calibration of a set of cameras for video surveillance

There has been an increase of video surveillance systems in operation in public areas. The classical systems simply send the images to monitors. Nevertheless, there is a demand on giving more intelligence on these systems and asking them to automatically track objects or recognise people. One of the basic low-level tasks that these systems have to face with is the accurate deduction of the cameras' poses. We present a method that deducts these poses in an interactive way when the automatic method fails or generates a large error. The user is asked for mapping some points between the images from these cameras when the alignment between them fails in a completely automatic way. Experimental validation has demonstrated that with really few interactions, the reduction of the pose error is considerable.