Miracle-dz/UniFAR-FTUs huggingface dataset:
Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases

Molecular information theory was used to create sequence logos and promoter models for eight phages of the T7 group: T7, φA1122, T3, φYeO3-12, SP6, K1-5, gh-1 and K11. When these models were used to scan the corresponding genomes, a significant gap in the individual information distribution was observed between functional promoter sites and other sequences, suggesting that the models can be used to identify new T7-like promoters. When a combined 76-site model was used to scan the eight phages, 108 of the total 109 promoters were found, while none were found for other T7-like phages, φKMV, P60, VpV262, SIO1, PaP3, Xp10, P-SSP7 and Ppu40, indicating that these phages do not belong to the T7 group. We propose that the T7-like transcription system, which consists of a phage-specific RNA polymerase and a set of conserved T7-like promoters, is a hallmark feature of the T7 group and can be used to classify T7-like phages. Phylogenetic trees of the T7-like promoter models and their corresponding RNA polymerases are similar, suggesting that the eight phages of the T7 group can be classified into five subgroups. However the SP6-like polymerases have apparently diverged from other polymerases more than their promoters have diverged from other promoters.
Public attitudes toward life and death.

Opinion trends in this country indicate sharp divisions in public sentiment over a number of life-taking actions. While legal abortion and capital punishment clearly head a list, a number of other issues have gained national attention in recent years. The present paper explores the structure of belief systems giving rise to normative conflicts of this kind. Of particular interest is the notion of a "pro-life" or other generic life orientation (e.g., the alleged "right-to-die" orientation of those who favor "mercy killings" in the case of terminally ill patients) as a possible explanation for public attitudes toward specific issues such as suicide and euthanasia. The present analysis assesses the empirical claims associated with such a model. The results offer qualified support for the existence of generic value orientations as revealed by public attitudes toward legal abortion, suicide, euthanasia, and capital punishment.
Self-Consolidating Concrete in Fire

Many investigations on self-consolidating concrete (SCC) have been carried out in the last several years and the mechanical behavior of this type of concrete is well understood by now. The fire behavior of this specialized concrete, however, is not fully understood, and contradictory results on the fire behavior of SCC were presented in the literature. Therefore, different types of SCCs with compressive strengths between 25 and 65 MPa (3.6 and 9.4 ksi) were designed, and specimens with an edge length of 300 mm were subjected to fire according to ISO 834 at an age of 180 days. The compressive strength at 28 days, the weight loss due to drying, the spalling of the specimens, and the residual compressive strength of the concretes after fire testing were measured and related to the performance of a reference vibrated concrete.
An Open Trusted Computing Architecture — Secure Virtual Machines Enabling User-Defined Policy Enforcement

Virtualization of computers enables a wide variety of applications ranging from server consolidation to secure sandboxing of malicious content. Today, lack of security of virtual machines is a major obstacle for broad adoption of virtual machine technology. We address this obstacle by an open architecture that adds scalable trusted computing concepts to a virtual machine infrastructure. The platform has a layered system architecture, and from bottom to top consists of a Trusted Platform Module (TPM) specified by the Trusted Computing Group (TCG), a trusted virtualization layer with strong isolation properties (among virtual machines) and well-defined interfaces to the TPM, and security services (such as protected storage, security policy enforcement, and identity management). We describe the guiding principles and the overall architecture of the platform, and detail the advantages of such an architecture. The platform can be leveraged to significantly enhance the security and trust properties of the standard operating systems, middleware, and applications hosted atop the platform. We believe the platform has wide-ranging applicability particularly in the context of distributed scenarios with inherent, multilateral trust and security requirements. We give examples of such scenarios that would be enabled by the platform.
Antithrombotic Benefits and Hemorrhagic Risks of Direct Thrombin Antagonists

Both soluble and bound thrombin activate platelets at concentrations less than that required to convert fibrinogen to fibrin. Platelet cohesion is mediated through adhesive protein bridging between GPIIb/IIIa-receptors on adjacent activated platelets. Thrombin production on phosephatidylserine-rich activated platelet surfaces is amplified 300,000-fold via the tissue factor pathway. Fibrin consolidates the enlarging thrombolytic mass and binds with catalytically active thrombin. Aspirin inhibits the thromboxane A2 (TxA2) pathway of platelet recruitment by irreversibly inactivating cyclooxygenase. Triclopidine blocks all pathways of plateletrecruitment, perhaps by modifying membrane signal transduction. Antithrombins, such as hirudin, inhibit thrombin-induced platelet activation and fibrin generation. Inhibitors of GPnb/TOa-dependent platelet receptors prevent die recruitment of platelets into thrombus
TEMPERATURE DEPENDENCE OF PHASE TRANSFORMATION PRESSURE IN SILICON

In this experimental work the pressure induced phase transformation of silicon and Germanium has been studied. It was shown that at a particular value of applied pressure, (Pt), depending on the sample temperature, the electrical resistance of the specimen falls off to a metallic state. The main goal of this study was to find out how the phase transformation pressure, Pt, for a p-type silicon varies with the sample temperature. The results show that, the value of Pt decreases linearly as the temperature of the sample increases. Meanwhile, other related results including the rate of resistance change in accordance with applied pressure on the sample at different temperatures (~270-350K), both for the semiconductor and the metallic state of the specimen were determined. In another effort, the amount of Pt for an n-type germanium, but only at room temperature, was also determined.
Molecular line profiles as diagnostics of protostellar collapse: modelling the ‘blue asymmetry’ in inside-out infall

The evolution of star-forming core analogues undergoing inside-out collapse is studied with a multipoint chemodynamical model which self-consistently computes the abundance distribution of chemical species in the core. For several collapse periods the output chemistry of infalling tracer species such as HCO+, CS and N2H+ is then coupled to an accelerated Λ-iteration radiative transfer code, which predicts the emerging molecular line profiles using two different input gas/dust temperature distributions. We investigate the sensitivity of the predicted spectral line profiles and line asymmetry ratios to the core temperature distribution, the time-dependent model chemistry, as well as to ad hoc abundance distributions. The line asymmetry is found to be strongly dependent on the adopted chemical abundance distribution. In general, models with a warm central region show higher values of blue asymmetry in optically thick HCO+ and CS lines than models with a starless core temperature profile. We find that in the formal context of Shu-type inside-out infall, and in the absence of rotation or outflows, the relative blue asymmetry of certain HCO+ and CS transitions is a function of time and, subject to the foregoing caveats, can act as a collapse chronometer. The sensitivity of simulated HCO+ line profiles to linear radial variations, subsonic or supersonic, of the internal turbulence field is investigated in the separate case of static cores.
Imitation Learning in Relational Domains: A Functional-Gradient Boosting Approach

Imitation learning refers to the problem of learning how to behave by observing a teacher in action. We consider imitation learning in relational domains, in which there is a varying number of objects and relations among them. In prior work, simple relational policies are learned by viewing imitation learning as supervised learning of a function from states to actions. For propositional worlds, functional gradient methods have been proved to be beneficial. They are simpler to implement than most existing methods, more efficient, more naturally satisfy common constraints on the cost function, and better represent our prior beliefs about the form of the function. Building on recent generalizations of functional gradient boosting to relational representations, we implement a functional gradient boosting approach to imitation learning in relational domains. In particular, given a set of traces from the human teacher, our system learns a policy in the form of a set of relational regression trees that additively approximate the functional gradients. The use of multiple additive trees combined with relational representation allows for learning more expressive policies than what has been done before. We demonstrate the usefulness of our approach in several different domains.
LOCAL BOND OF DEFORMED BARS WITH DIFFERENT DIAMETERS IN CONFINED CONCRETE

Slippage of the beam reinforcement crossing the interior joints in reinforced concrete frames can lead to large fixed-end rotations and overall beam deformations, causing major structural damage under severe seismic excitations. It is thus important to anchor adequately deformed bars inside the confined core of earthquake-resistant joints. The key factor governing the anchored-bar behavior in confined concrete is the local bond stress-slip relationship. This investigation addreses the effects of bar diameter on this relationship. Experimental data have been generated on the local bond behaviour for deformed bars of different diameters partially embedded in confined concrete. The results are used to assess the anchored bar-diameter effects of the ultimate local bond strenth and local bond stress-slip relationship in confined concrete. Based on the test data, an empirical local bond constitutive model has been generated that accounts for the bar diameter effects.
Cross-age effects on forensic face construction

The own-age bias (OAB) refers to recognition memory being more accurate for people of our own age than other age groups (e.g., Wright and Stroud, 2002). This paper investigated whether the OAB effect is present during construction of human faces (also known as facial composites, often for forensic/police use). In doing so, it adds to our understanding of factors influencing both facial memory across the life span as well as performance of facial composites. Participant-witnesses were grouped into younger (19–35 years) and older (51–80 years) adults, and constructed a single composite from memory of an own- or cross-age target face using the feature-based composite system PRO-fit. They also completed the shortened version of the glasgow face matching test (GFMT; Burton et al., 2010). A separate group of participants who were familiar with the relevant identities attempted to name the resulting composites. Correct naming of the composites revealed the presence of an OAB for older adults, who constructed more-identifiable composites of own-age than cross-age faces. For younger adults, age of target face did not influence correct naming and their composites were named at the same level as those constructed by older adults for younger targets. Also, there was no reliable correlation between face perception ability and composite quality. Overall, correct naming was fairly good across the experiment, and indicated benefit for older witnesses for older targets. Results are discussed in terms of contemporary theories of OAB, and implications of the work for forensic practice.
Weblogs as instruments for reflection on action in teacher education

This study examined the use of weblogs as a means to promote student teachers' reflective practice. The assumption was explored that weblogs are suitable tools to support and stimulate reflection on action in teacher training and consequently to enhance the students' ability to reflect. Three groups of student teachers used weblogs to reflect on teaching practice during an 8-week internship. Students were asked (a) to reflect on their own teaching experiences and (b) to provide peer feedback. Analyses of the student contributions show that weblogs are useful for reflection on critical incidents in the classroom and that they can stimulate interconnectivity in groups of students. However, weblogs do not incite deep reflection or spiral reflection, which can only be the result of explicit instruction. This exploratory study further shows that large-scale quantitative research is needed to support the premise that weblogs are suitable tools for reflection.
Total and Envelope Protein-Specific Antibody-Secreting Cell Response in Pediatric Dengue Is Highly Modulated by Age and Subsequent Infections

The response of antibody-secreting cells (ASC) induced by dengue has only recently started to be characterized. We propose that young age and previous infections could be simple factors that affect this response. Here, we evaluated the primary and secondary responses of circulating ASC in infants (6–12 months old) and children (1–14 years old) infected with dengue showing different degrees of clinical severity. The ASC response was delayed and of lower magnitude in infants, compared with older children. In primary infection (PI), the total and envelope (E) protein-specific IgM ASC were dominant in infants but not in children, and a negative correlation was found between age and the number of IgM ASC (rho = −0.59, P = 0.03). However, infants with plasma dengue-specific IgG detectable in the acute phase developed an intense ASC response largely dominated by IgG and comparable to that of children with secondary infection (SI). IgM and IgG produced by ASC circulating in PI or SI were highly cross-reactive among the four serotypes. Dengue infection caused the disturbance of B cell subsets, particularly a decrease in the relative frequency of naïve B cells. Higher frequencies of total and E protein-specific IgM ASC in the infants and IgG in the children were associated with clinically severe forms of infection. Therefore, the ASC response induced by dengue is highly influenced by the age at which infection occurs and previous immune status, and its magnitude is a relevant element in the clinical outcome. These results are important in the search for correlates of protection and for determining the ideal age for vaccinating against dengue.
Impaired Spatial Category Representations in Williams Syndrome; an Investigation of the Mechanistic Contributions of Non-verbal Cognition and Spatial Language Performance

The aims of this study were to: provide a precise characterisation of spatial category representations in Williams syndrome (WS); to determine the nature of the mechanistic contributions from spatial language performance and non-verbal cognition to spatial category representations in WS; and to explore the stability of spatial category representations in WS using error analysis. Spatial category representation was assessed across nine spatial categories (In, On, Under, In Front, Behind, Above, Below, Left, and Right) using an odd-one-out task. The performance of individuals with WS (N = 24; 12;00 years;months to 30;07 years;months) was compared to data from typically developing children aged four to 7 years (N = 75), published in Farran and Atkinson (2016). The WS group performed at the level of typical 4- and 5-year-olds. Despite this low level of ability, they demonstrated typical variation in their representation of easier to harder spatial categories, in line with the spatial category representation model (Farran and Atkinson, 2016). Error analysis of broad category understanding (i.e., category understanding which includes non-prototypical category members), however, showed that errors reflected fewer guess responses than expected by chance in the WS group only, which could suggest strategic responding in this group. Developmental trajectory analyses demonstrated a significant contributing influence of both non-verbal mental age and spatial language ability in the TD group. For the WS group, non-verbal mental age significantly contributed to spatial category representations, whilst the contributing influence of spatial language ability was marginally significant. With reference to level of ability, spatial category representations in the WS group were consistently lower than would be expected for non-verbal mental age, but on a par with their (low) spatial language mental age. Spatial category representations in WS are discussed with reference to their contribution to the hallmark deficit in spatial construction and drawing abilities in WS.
LSU Digital Commons LSU Digital Commons

Motivation: Many drugs interact with numerous proteins besides their intended therapeutic targets and a substantial portion of these interactions is yet to be elucidated. Protein–Drug Interaction Database (PDID) addresses incompleteness of these data by providing access to putative protein– drug interactions that cover the entire structural human proteome. Results: PDID covers 9652 structures from 3746 proteins and houses 16 800 putative interactions generated from close to 1.1 million accurate, all-atom structure-based predictions for several dozens of popular drugs. The predictions were generated with three modern methods: ILbind, SMAP and eFindSite. They are accompanied by propensity scores that quantify likelihood of interactions and coordinates of the putative location of the binding drugs in the corresponding protein structures. PDID complements the current databases that focus on the curated interactions and the BioDrugScreen database that relies on docking to ﬁnd putative interactions. Moreover, we also include experimentally curated interactions which are linked to their sources: DrugBank, BindingDB and Protein Data Bank. Our database can be used to facilitate studies related to polypharmacology of drugs including repurposing and explaining side effects of drugs.
d-myo-Inositol-3-Phosphate Affects Phosphatidylinositol-Mediated Endomembrane Function in Arabidopsis and Is Essential for Auxin-Regulated Embryogenesis[W][OA]

This work reveals the significant roles of myo-inositol in Arabidopsis embryogenesis. Experiments show that depletion of myo-inositol by knocking out multiple MIPS genes, which encode d-myo-inositol-3-phosphate synthase, could affect the membrane trafficking via the phosphatidylinositol metabolism by leading to altered auxin distribution in developing embryos. In animal cells, myo-inositol is an important regulatory molecule in several physiological and biochemical processes, including signal transduction and membrane biogenesis. However, the fundamental biological functions of myo-inositol are still far from clear in plants. Here, we report the genetic characterization of three Arabidopsis thaliana genes encoding d-myo-inositol-3-phosphate synthase (MIPS), which catalyzes the rate-limiting step in de novo synthesis of myo-inositol. Each of the three MIPS genes rescued the yeast ino1 mutant, which is defective in yeast MIPS gene INO1, and they had different dynamic expression patterns during Arabidopsis embryo development. Although single mips mutants showed no obvious phenotypes, the mips1 mips2 double mutant and the mips1 mips2 mips3 triple mutant were embryo lethal, whereas the mips1 mips3 and mips1 mips2+/− double mutants had abnormal embryos. The mips phenotypes resembled those of auxin mutants. Indeed, the double and triple mips mutants displayed abnormal expression patterns of DR5:green fluorescent protein, an auxin-responsive fusion protein, and they had altered PIN1 subcellular localization. Also, membrane trafficking was affected in mips1 mips3. Interestingly, overexpression of PHOSPHATIDYLINOSITOL SYNTHASE2, which converts myo-inositol to membrane phosphatidylinositol (PtdIns), largely rescued the cotyledon and endomembrane defects in mips1 mips3. We conclude that myo-inositol serves as the main substrate for synthesizing PtdIns and phosphatidylinositides, which are essential for endomembrane structure and trafficking and thus for auxin-regulated embryogenesis.
Integrating complete-system and user-level performance/power simulators: the SimWattch approach

Evaluating architectural impact of applications with a significant operating system interaction calls for integrating detailed microarchitectural user-level simulation with system-level simulation tools. This paper reports on our experience in integrating Simics - a system-simulation tool - with Wattch - a microarchitectural performance and power modeling user-level simulation tool built on top of SimpleScalar We first present the technical challenges we had to resolve in designing SimWattch - the integrated tool. We then use it to identify the type of errors a user-level simulator typically does when predicting performance and power consumption while omitting operating system activity. This case study is based on SPEC95, and SPEC JVM98 applications and TPC-B. We find that if operating system effects are omitted, performance is usually overestimated while energy used is underestimated. However a surprising result is that IPC, power and resource occupancy predictions from a user-level simulator often follow the trends of predictions from simulations factoring in operating system effects.
Video-assisted thoracoscopic correction and fusion of scoliosis.

OBJECTIVE To evaluate the operative technique and preliminary results of video-assisted thoracoscopic anterior correction and fusion of scoliosis. METHODS Eleven cases underwent thoracoscopic anterior correction and fusion of scoliosis from March 2003 to April 2005 in our hospital were reviewed. They were all females with an average age of 13.1 years old. Of which, 9 cases were idiopathic scoliosis, 1 case was congenital scoliosis, and 1 case was Marfan syndrome scoliosis. The coronal Cobb angle and apical vertebral translation before and after surgery as well as at final follow-up were measured. The operation time, blood loss during operation, and peri-operative complications were recorded. Results The mean operation time was 6.4 hours, mean instrumented vertebrae were 6.4 segments, and mean blood loss during operation was 364 mL. The coronal Cobb angles of the thoracic curve before and after surgery were 45.5 degrees and 15.4 degrees respectively, with an average correction rate of 65.4%. The lumbar curve was corrected from 28.4 degrees lation to 11.8 degrees, with an average simultaneous correction rate of 57.2%. All of the patients were followed up regularly with an average time of 21.4 months. At the final follow-up, the coronal Cobb angles of the thoracic and lumbar curves were 19.0 degrees and 20.1 degrees, with a 3.6 degrees and 8.3 degrees loss of correction, respectively. The apical vertebral translation was improved from 32.3 mm to 10.5 mm for the thoracic curve, and from 13.1 mm to 8.2 mm for the lumbar curve. There were 6 cases with peri-operative complications, including 1 case of thoracic effusion, 1 case of chylothorax, 1 case of locking plug loosing, 2 cases of aggravation of the unfused lumbar curve (1 case also with thoracolumbar kyphosis), and 1 case with a screw tip causing a contour deformity of the aorta. And 4 of them underwent revision surgery. CONCLUSIONS Video-assisted thoracoscopic anterior correction and fusion of scoliosis has good correction capability, less intraoperative bleeding, and favorable cosmetic effect for mild and moderate thoracic scoliosis, but with higher rates of correction loss of the lumbar curve and peri-operative complications. A surgeon should be cautious to perform this technique. ders