Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk of self-harm and suicide in people with specific psychiatric and physical disorders: comparisons between disorders using English national record linkage

Background Psychiatric illnesses are known risk factors for self-harm but associations between self-harm and physical illnesses are less well established. We aimed to stratify selected chronic physical and psychiatric illnesses according to their relative risk of self-harm. Design Retrospective cohort studies using a linked dataset of Hospital Episode Statistics (HES) for 1999–2011. Participants Individuals with selected psychiatric or physical conditions were compared with a reference cohort constructed from patients admitted for a variety of other conditions and procedures. Setting All admissions and day cases in National Health Service (NHS) hospitals in England. Main outcome measures Hospital episodes of self-harm. Rate ratios (RRs) were derived by comparing admission for self-harm between cohorts. Results The psychiatric illnesses studied (depression, bipolar disorder, alcohol abuse, anxiety disorders, eating disorders, schizophrenia and substance abuse) all had very high RRs (> 5) for self-harm. Of the physical illnesses studied, an increased risk of self-harm was associated with epilepsy (RR = 2.9, 95% confidence interval [CI] 2.8–2.9), asthma (1.8, 1.8–1.9), migraine (1.8, 1.7–1.8), psoriasis (1.6, 1.5–1.7), diabetes mellitus (1.6, 1.5–1.6), eczema (1.4, 1.3–1.5) and inflammatory polyarthropathies (1.4, 1.3–1.4). RRs were significantly low for cancers (0.95, 0.93–0.97), congenital heart disease (0.9, 0.8–0.9), ulcerative colitis (0.8, 0.7–0.8), sickle cell anaemia (0.7, 0.6–0.8) and Down's syndrome (0.1, 0.1–0.2). Conclusions Psychiatric illnesses carry a greatly increased risk of self-harm as well as of suicide. Many chronic physical illnesses are also associated with an increased risk of both self-harm and suicide. Identifying those at risk will allow provision of appropriate monitoring and support.
Galactomannan and Polymerase Chain Reaction-Based Screening for Invasive Aspergillosis Among High-Risk Hematology Patients: A Diagnostic Meta-analysis.

BACKGROUND Screening of high-risk patients for invasive aspergillosis (IA) has the potential to decrease the use of empiric antifungal agents. However, the performance of different screening methods has not been studied. METHODS We performed a meta-analysis of published studies to assess the diagnostic performance of galactomannan (GM) and polymerase chain reaction (PCR) as weekly screening tests in high-risk populations. The sensitivity and specificity of 6 approaches combining GM and PCR were estimated using the bivariate model. RESULTS Thirteen studies with 1670 patients met our inclusion criteria. Single positive test results had modest sensitivity and specificity for screening (respectively, 92% and 90% for GM; 84% and 76% for PCR). The screening approach with the highest sensitivity was the one that used at least 1 GM- or PCR-positive result to define a positive episode, achieving a sensitivity of 99%, significantly higher than any single test (P = .0018 compared with GM and P < .0001 compared with PCR). Meanwhile, when both GM and PCR were positive for the same patient, the specificity increased to 98%, which was not significantly different compared to the specificity of at least 2 positive GM (95%, P = .56 for the comparison) or PCR results (93%, P = .07 for the comparison). CONCLUSIONS When screening high-risk patients for IA with GM and PCR tests, the absence of any positive test can obviate the need for antifungal agents with a negative predictive value of 100%, whereas the presence of at least 2 positive results is highly suggestive of an active infection with a positive predictive value of 88%.
Computing for construals in distributed participatory design : principles and tools

Distributed participatory design aspires to standards of inclusivity and humanity in introducing technology to the workplace that are hard to attain. The demands it makes upon the development and use of computing technology are particularly topical, as the potential for automation and distribution through embedded and mobile devices continues to develop. Standard views of computation propose ways in which to interpret all products of computing as programs, but give limited conceptual support for understanding computer-based design artifacts whose role in communication and elaboration eludes capture in a functional specification. Empirical Modelling is a body of principles and tools that can be applied to the development of a variety of computer-based artifacts relating to analysis, design and use that are most appropriately interpreted as construals rather than programs. This paper, a revised and extended version of Beynon and Chan (2006), illustrates some of the ways in which Empirical Modelling principles can be used in developing construals that can assist distributed participatory design. The theme adopted for illustrative purposes is that of understanding the quintessentially British game of cricket, renowned for the complexity and subtlety of its rules and its rich concepts and vocabulary.
The 2006 slow slip event and nonvolcanic tremor in the Mexican subduction zone

The last decade featured an explosive sequence of discoveries of slow slip events (SSE) and nonvolcanic tremor (NVT) in different subduction zones and continental faults. Many observations show that SSE is usually associated with an increased NVT activity but it is not clear yet if those events are the result of the same process or are independent expressions of a common underlying seismotectonic source. A large SSE in Central Mexico occurred in 2006 during the Meso‐American Subduction Experiment (MASE) which provided continuous observations of the NVT for the years 2005–2007. GPS and abundant seismic data show that although the NVT energy increased notably during the 2006 SSE, the two phenomena were separated spatially and not completely synchronized in time. Significant NVT episodes occur during the period between SSEs, suggesting again that large slow slip events and NVT observed in the Mexican subduction zone are of different origins. The results presented here contribute to uncovering the nature of these two separate phenomena that have been indistinguishable in some other regions.
Structural Model of the Rev Regulatory Protein from Equine Infectious Anemia Virus

Rev is an essential regulatory protein in the equine infectious anemia virus (EIAV) and other lentiviruses, including HIV-1. It binds incompletely spliced viral mRNAs and shuttles them from the nucleus to the cytoplasm, a critical prerequisite for the production of viral structural proteins and genomic RNA. Despite its important role in production of infectious virus, the development of antiviral therapies directed against Rev has been hampered by the lack of an experimentally-determined structure of the full length protein. We have used a combined computational and biochemical approach to generate and evaluate a structural model of the Rev protein. The modeled EIAV Rev (ERev) structure includes a total of 6 helices, four of which form an anti-parallel four-helix bundle. The first helix contains the leucine-rich nuclear export signal (NES). An arginine-rich RNA binding motif, RRDRW, is located in a solvent-exposed loop region. An ERLE motif required for Rev activity is predicted to be buried in the core of modeled structure where it plays an essential role in stabilization of the Rev fold. This structural model is supported by existing genetic and functional data as well as by targeted mutagenesis of residues predicted to be essential for overall structural integrity. Our predicted structure should increase understanding of structure-function relationships in Rev and may provide a basis for the design of new therapies for lentiviral diseases.
Photomodulation of strigolactone biosynthesis and accumulation during sunflower seedling growth

Present investigations report the presence of strigolactones (SLs) and photomodulation of their biosynthesis in sunflower seedlings (roots, cotyledons and first pair of leaves) during early phase of seedling development. Qualitative analyses and characterization by HPLC, ESI-MS and FT-IR revealed the presence of more than one type of SLs. Orobanchyl acetate was detected both in roots and leaves. Five-deoxystrigol, sorgolactone and orobanchol were exclusively detected in seedling roots. Sorgomol was detectable only in leaves. HPLC eluted fraction from seedling roots and leaves co-chromatographing with GR24 (a synthetic SL) could also bring about germination in Orobanche cernua (a weed) seeds, which are established to exhibit SL – mediated germination, thereby indicating the SL identity of the eluates using this bioassay. SLs accumulation was always more in the roots of light-grown seedlings, it being maximum at 4 d stage. Although significant activity of carotenoid cleavage dioxygenase (CCD, the enzyme critical for SL biosynthesis) was detected in 2 d old seedling roots, SLs remained undetectable in cotyledons at all stages of development and also in the roots of 2 d old light and dark-grown seedlings. Roots of light-grown seedlings showed maximum CCD activity during early (2 d) stage of development, thereby confirming photomodulation of enzyme activity. These observations indicate the migration of a probable light-sensitized signaling molecule (yet to be identified) or a SL precursor from light exposed aerial parts to the seedling roots maintained in dark. Thus, a photomodulation and migration of SL precursor/s is evident from the present work.
Cell-dependent requirement of human immunodeficiency virus type 1 Vif protein for maturation of virus particles

A highly sensitive single-round infection assay using a bacterial chloramphenicol acetyltransferase was developed to analyze an early stage of human immunodeficiency virus type 1 replication. By a combination of transfection and single-round infection assay, a virus with a vif mutation, depending on host cells from which the virus was derived, was demonstrated to be defective at the early phase of infection cycle. Analysis of viral proteins synthesized in cells indicated that incorporation of the Env surface protein into virions of the vif mutant, again in a cell-dependent way, was greatly restricted. Taken together, it is concluded that the Vif protein acts through modulation of the Env protein in the virions, directly or indirectly, to enhance viral infectivity in a certain cell type.
ROS-mediated EB1 phosphorylation through Akt/GSK3β pathway: implication in cancer cell response to microtubule-targeting agents

Microtubule-targeting agents (MTAs) are largely administered in adults and children cancers. Better deciphering their mechanism of action is of prime importance to develop more convenient therapy strategies. Here, we addressed the question of how reactive oxygen species (ROS) generation by mitochondria can be necessary for MTA efficacy. We showed for the first time that EB1 associates with microtubules in a phosphorylation-dependent manner, under control of ROS. By using phospho-defective mutants, we further characterized the Serine 155 residue as critical for EB1 accumulation at microtubule plus-ends, and both cancer cell migration and proliferation. Phosphorylation of EB1 on the Threonine 166 residue triggered opposite effects, and was identified as a requisite molecular switch in MTA activities. We then showed that GSK3β activation was responsible for MTA-triggered EB1 phosphorylation, resulting from ROS-mediated inhibition of upstream Akt. We thus disclosed here a novel pathway by which generation of mitochondrial ROS modulates microtubule dynamics through phosphorylation of EB1, improving our fundamental knowledge about this oncogenic protein, and pointing out the need to re-examine the current dogma of microtubule targeting by MTAs. The present work also provides a strong mechanistic rational to the promising therapeutic strategies that currently combine MTAs with anti-Akt targeted therapies.
Association of Combined Maternal-Fetal TNF-α Gene G308A Genotypes with Preterm Delivery: A Gene-Gene Interaction Study

Preterm delivery (PTD) is a complicated perinatal adverse event. We were interested in association of G308A polymorphism in tumor necrosis factor-α (TNF-α) gene with PTD; so we conducted a genetic epidemiology study in Anqing City, Anhui Province, China. Case families and control families were all collected between July 1999 and June 2002. To control potential population stratification as we could, all eligible subjects were ethnic Han Chinese. 250 case families and 247 control families were included in data analysis. A hybrid design which combines case-parent triads and control parents was employed, to test maternal-fetal genotype (MFG) incompatibility. The method is based on a log-linear modeling approach. In summary, we found that when the mother's or child's genotype was G/A, there was a reduced risk of PTD; however when the mother's or child's genotype was genotype A/A, there was a relatively higher risk of PTD. Combined maternal-fetal genotype GA/GA showed the most reduced risk of PTD. Comparison of the LRTs showed that the model with maternal-fetal genotype effects fits significantly better than the model with only maternal and fetal genotype main effects (log-likelihood = −719.4, P = .023, significant at 0.05 level). That means that the combined maternal-fetal genotype incompatibility was significantly associated with PTD. The model with maternal-fetal genotype effects can be considered a gene-gene interaction model. We claim that both maternal effects and fetal effects should be considered together while investigating genetic factors of certain perinatal diseases.
Low power and high performance clock delayed domino logic using saturated keeper

In this work, domino logic with a saturated keeper technique is proposed. The circuit, which is used to implement the technique, is as simple as the utilized NOT gate in standard domino. By using the simple structure, we can obtain better performance, noise immunity, and lower power consumption. The simulation results for a 70 nm CMOS technology show an improvement between 7% and 62.5% in delay and 9% and 14% in power consumption, over its previous suggestions
Canine model of ischemic stroke with permanent middle cerebral artery occlusion: clinical and histopathological findings

The aim of the present study was to assess the clinical and histopathological findings in a canine model of ischemic stroke. Cerebral ischemic stroke was induced by middle cerebral artery occlusion in four healthy beagle dogs using silicone plugs. They showed neurological signs of forebrain dysfunction such as reduced responsiveness, head turning, circling, postural reaction deficits, perceptual deficits, and hemianopsia. These signs gradually regressed within 4 weeks without therapy. On magnetic resonance imaging, T2 hyperintensity and T1 hypointensity were found in the cerebral cortex and basal ganglia. These lesions were well-defined and sharply demarcated from adjacent brain parenchyma with a homogenous appearance. No abnormalities of the cerebrospinal fluid were observed. At necropsy, atrophic and necrotic lesions were observed in the cerebral cortex. The cerebral cortex, basal ganglia, and thalamus were partially unstained with triphenyl-tetrazolium chloride. Histopathologically, typical features of infarction were identified in cortical and thalamic lesions. This study demonstrates that our canine model resembles the conditions of real stroke patients.
Staphylococcus aureus and Micrococcus luteus peptidoglycan transglycosylases that are not penicillin-binding proteins

Major peptidoglycan transglycosylase activities, which synthesize uncross-linked peptidoglycan from lipid-linked precursors, were solubilized from the membranes of Staphylococcus aureus and Micrococcus luteus and were partially purified. The transglycosylase activities were separated from penicillin-binding proteins by solubilization and by purification steps. Therefore, we concluded that these activities were not activities of the penicillin-binding proteins, which are the presumptive peptidoglycan transpeptidases in these gram-positive cocci. Unlike Escherichia coli, in which the network structure of peptidoglycan is synthesized by multiple two-headed penicillin-binding proteins with both transpeptidase and transglycosylase activities, these gram-positive cocci have cell wall peptidoglycan which seems to be synthesized by penicillin-binding protein transpeptidases and a separate transglycosylase.
Development of hybrid hydraulic–electric power units for field and service robots

Energetic autonomy of a hydraulic-based mobile robot requires a power source capable of both hydraulic and electrical power generation. The hydraulic power is used for locomotion, and the electric power is used for the control computer, sensors and other peripherals. In addition, the power source must be lightweight and quiet. This study presents several designs of internal combustion engine-based power units. Each power unit is evaluated with a Ragone plot which shows its performance over a wide range of operation times. Several hydraulic–electric power units (HEPUs) were built and successfully demonstrated on the Berkeley lower extremity exoskeleton (BLEEX). The best-performing design of the HEPUs, based upon the Ragone plot analysis, is described in detail. This HEPU produces constant pressure hydraulic power and constant voltage electric power. The pressure and voltage are controlled on board the power unit by a computer. A novel characteristic of this power unit is its cooling system in which hydraulic fluid is used to cool the engine cylinders. The prototype power unit weighs 27 kg and produces 2.3 kW (3.0 hp) hydraulic power at 6.9 MPa (1000 p.s.i.) and 220 W of electric power at 15 V DC.
Reducing Costs in Cloud Application Execution Using Redundancy-Based Scheduling

Public providers around the world offer computing, storage, and communication services as virtual machines in a pay-per-use model. From the user perspective, it is important to choose providers and charging models to run distributed applications with quality of service at lower costs. In this work, we introduce an innovative strategy to decrease the cost of VM requests scheduling on different public cloud providers. The mechanism is based on redundancy with a mixed utilization of reserved and spot virtual machine (VM) instances, and it allows the balancing between cost and availability. We implemented a QoS-aware architecture that allows the scheduling of applications considering different VM charging models. Then, we propose an integer linear program (ILP) and a heuristic algorithm to compute the QoS-aware scheduling. Experimental results show that the proposed approach computes schedules with smaller costs than alternative approaches.
Exploiting Intel TSX for fault-tolerant execution in safety-critical systems

Safety-critical systems demand increasing computational power, which requests high-performance embedded systems. While commercial-of-the-shelf (COTS) processors offer high computational performance for a low price, they do not provide hardware support for fault-tolerant execution. However, pure software-based fault-tolerance methods entail high design complexity and runtime overhead. In this paper, we present an efficient software/hardware-based redundant execution scheme for a COTS ×86 processor, which exploits the Transactional Synchronization Extensions (TSX) introduced with the Intel Haswell microarchitecture. Our approach extends a static binary instrumentation tool to insert fault-tolerant transactions and fault-detection instructions at function granularity. TSX hardware support is used for error containment and recovery. The average runtime overhead for selected SPEC2006 benchmarks was only 49% compared to a non-fault-tolerant execution.
Screening of stress enhancer based on analysis of gene expression profiles: Enhancement of hyperthermia‐induced tumor necrosis by an MMP‐3 inhibitor

To improve the therapeutic benefit of hyperthermia, we examined changes of global gene expression after heat shock using DNA microarrays consisting of 12 814 clones. HeLa cells were treated for 1 h at 44°C and RNA was extracted from the cells 0, 3, 6, and 12 h after heat shock. The 664 genes that were up or down‐regulated after heat shock were classified into 7 clusters using fuzzy adaptive resonance theory (fuzzy ART). There were 41 genes in two clusters that were induced in the early phase after heat shock. In addition to shock response genes, such as hsp70 and hsp40, the stress response genes c‐jun, c‐fos and egr‐1 were expressed in the early phase after heat shock. We also found that expression of matrix metalloproteinase 3 (MMP‐3) was enhanced during the early response. We therefore investigated the role of MMP‐3 in the heat shock response by examining HeLa cell survival after heat treatment in the presence and absence of an MMP‐3 inhibitor, N‐isobutyl‐N‐(4‐methoxyphenyl‐sulfonyl)glycylhydroxamic acid (NNGH) or N‐hydroxy‐2(R)‐[[4‐methoxysulfonyl] (3‐picolyl)amino]‐3‐methylbutaneamide hydro‐chloride (MMI270). The number of surviving cells 3 days after heat treatment significantly decreased, reaching 3.5% for NNGH and 0.2% for MMI270. These results indicate that the MMP‐3 inhibitors enhanced heat shock‐induced cell death and behaved as stress enhancers in cancer cells. This valuable conclusion was reached as a direct result of the gene expression profiling that was performed in these studies.
Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana[OPEN]

Genes that have been duplicated through whole-genome duplication events show mutual expression patterns in tip-growth tissues and aerial tissues of Arabidopsis thaliana and likely coordinated functional divergence in growth and defense. Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub- or neofunctionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana. We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues. We provide evidence that this pattern of gene expression divergence seems to involve genes with a role in cell polarity and that likely function in the maintenance of cell wall integrity. Following WGD, many of these duplicated genes evolved separate functions through subfunctionalization in growth/development and stress response. Uncoupling these processes through genome duplications likely provided important adaptations with respect to growth and morphogenesis and defense against biotic and abiotic stress.
Query Suggestion by Query Search: A New Approach to User Support in Web Search

This paper introduces and analyzes a new approach to query suggestion. After the user issues a query q_0, for every document retrieved in a certain rank range [Theta_1,Theta_2], a query search procedure constructs queries that rank the document high enough for the user to see it. From this set of queries the suggestions to be presented to the user are then selected so as to give the best possible access to the documents that were ranked in [Theta_1,Theta_2] for the user's initial query q_0. This approach turns out to be successful under certain assumptions, which are discussed in this paper.