Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional and physical interaction between the yeast splicing factors Slu7 and Prp18.

We show that the requirement for Prp18 during the second step of actin pre-mRNA splicing in vitro is dictated by the distance between the branch point and the 3'splice site. Prp18 is dispensable for splicing of precursor RNAs in which the interval between the branch point and 3'splice site is <12 nt. This resembles the requirement for another second step factor, Slu7. Excess Slu7 protein can bypass the need for Prp18 in vitro , suggesting that Slu7 and Prp18 function in a concerted manner. Physical interaction between Slu7 and Prp18 was demonstrated by using the two-hybrid assay. Deletion mutants of SLU7 were tested for their ability to support growth of a slu7 null strain. Removal of 199 amino acids from the N-terminus of the 382 amino acid Slu7 protein did not affect cell viability at 25 degrees C. A more extensive N-terminal deletion of 221 amino acids was lethal, as was a C-terminal deletion of 47 amino acids. Deleted versions of Slu7 were also tested for interaction with Prp18 in the two-hybrid system. We define a segment of Slu7 from residue 200 to 224 that is necessary for interaction with Prp18.
Activation specificity of arsonate-reactive T cell clones. Structural requirements for hapten recognition and comparison with monoclonal antibodies

We describe clones of hapten-specific inducer T cells from (BALB/c X A/J)F1 mice that respond to the p-azobenzenearsonate hapten conjugated to carrier proteins or directly conjugated to antigen-presenting cells. Some of the clones are also activated by haptens structurally related to arsonate. All activating analogues are recognized by each clone in association with the same major histocompatibility complex (MHC) protein as is arsonate. Weakly activating and nonactivating analogues are immunogenic in D2.GD amd (BALB/c X A/J)F1 mice, since they can effectively activate primed lymph node cells or long-term hapten- reactive cell lines. Hence the specificities of these clones may reflect their intrinsic recognition of arsonate and its analogues, rather than more efficient presentation of certain analogues than of others by antigen-presenting cells, or differential recognition of associated MHC epitopes by the clones. We compare the activation specificities of the clones with the binding specificities of monoclonal antibodies to arsonate, and discuss structural features of the analogues that may be important for activation and binding. Our results suggest that a site (or subsite) on arsonate-reactive T cell clones may interact directly with hapten, and may be experimentally separable from the site (or subsite) for MHC determinants.
The Effect of Hydrothermal Treatment on Olivine Nano-Silica

This paper provides an overview of the effects of ripening the olivine nano-silica to form particles with a lower specific surface area for optimal use in high performance concrete. The nano-silica was ripened using a hydrothermal treatment in a mixed batch reactor at 90 °C, pH ranging from 8 to 11.3 and a silica weight percentage of three and six percent. The specific surface area of the olivine nano-silica can be reduced by 62 percent by Ostwald ripening in 22 hours. This reduction corresponds to a 80 percent drop of the micropore surface area and a 57 percent drop of the external surface area. The different hydrothermal conditions did not affect the final specific surface area at the equilibrium. However, the use of a high energy mixer reduced the specific surface area by 52 percent in only five minutes. Despite the reduction in specific surface area, the aggregates of the original olivine nano-silica are not dissolved during the ripening process.
Multi-class assembly parts recognition using composite feature and random forest for robot programming by demonstration

In robot programming by demonstration (PBD) for assembly tasks, one of the important purposes is to identify multi-class objects during demonstration. In this paper, we propose a composite feature representation method using color histogram, LBP, aspect ratio, circularity and Zernike moment, which is invariant to image translation, rotation and scale. Then Random Forest algorithm is employed to be trained as the classifier, by which the weight parameters of the composite feature are obtained simultaneously. Experimental results on 20 different kinds of objects demonstrate that our approach achieves high recognition accuracy with 99.33%. According to comparisons with other composite features and classification algorithms, the effectiveness with fewer collected samples and the efficiency using less model training time of our approach are verified. Our approach has been successfully applied in two PBD tasks - flashlight assembly and building blocks assembly.
Nondestructive Measurement of Tomato Seedlings during Their Growth Based on Machine Vision

As one of the most important technologies for plant growth modelling, the research of nondestructive measurement based on machine vision is of great significance in hastening development of digital agriculture. In this paper, we have given the example applied to nondestructive measurement of tomato seedlings during their growth in greenhouse. The leaf areas of tomato seedlings are obtained nondestructively by the nondestructive detection image capturing and image processing algorithm proposed. By analyzing the results between the machine vision based measurements and manual measurements, the best correlation coefficient of leaf areas is 0.9822, which shows that the algorithm can be used in nondestructive measurement of the tomato seedlings.
Design and implementation of a Security Manager for WirelessHART networks

WirelessHART is the first open standard for Wireless Sensor Networks designed specifically for industrial process automation and control systems. WirelessHART is a secure protocol; however, it relies on a Security Manager for the management of the security keys and the authentication of new devices. The WirelessHART standard does not provide the specification and design of the Security Manager. Also, the security specifications in the standard are not well organized and are dispersed throughout the standard which makes an implementation of the standard more difficult. In this paper we provide the detailed specification and design as well as an implementation of the Security Manager for the WirelessHART standard. We evaluate our Security Manager against different cryptographic algorithms and measure the latency between the Network Manager and the Security Manager. Our evaluation shows that the proposed Security Manager meets the WirelessHART requirements. Our analysis shows that the provided Security Manager is capable of securing both the wireless and wired part of the WirelessHART network.
A Bioinspired Soft Actuated Material

A class of soft actuated materials that can achieve lifelike motion is presented. By embedding pneumatic actuators in a soft material inspired by a biological muscle fibril architecture, and developing a simple finite element simulation of the same, tunable biomimetic motion can be achieved with fully soft structures, exemplified here by an active left ventricle simulator.
Integral quadratic constraint approach vs. multiplier approach

Integral quadratic constraints (IQC) arise in many optimal and/or robust control problems. The IQC approach can be viewed as a generalization of the classical multiplier approach in the absolute stability theory. In this paper, we study the relationship between the two approaches for robust stability analysis. The key result shows that for many applications, the existence of an IQC is equivalent to the existence of a multiplier. Because the multiplier approach is typically simpler and more intuitive, this result suggests that the multiplier approach may be more useful than the IQC approach in many applications.
Defect Generation during Plastic Deformation of Si-Rich Cz-Grown SiGe Crystals

The IR absorption spectra and kinetics of the oxygen solid solution decay were studied in the Si1¡xGex crystals (0 · x · 0:055) plastically deformed at 680±C up to the 2{5% residual strain. It is found that the defects of non-dislocation nature, the dislocation trails, are formed during the plastic deformation of all studied SiGe crystals. The ¯ne structure of the IR absorption spectra around the 1000 cm¡1 wave number is found to be nearly identical in the pure Si (no Ge) samples and Si1¡xGex crystals with x · 0:02. At higher x the ¯ne structure was not detected due to the alloy-related broadening. In all studied crystals, the decay of the supersaturated oxygen solid solution at 650±C is determined by oxygen agglomeration at the dislocation trails as shown by the comparison with the samples annealed at 1150±C.
Oriented 2D Covalent Organic Framework Thin Films on Single-Layer Graphene

Microporous covalent organic frameworks, which usually form as insoluble powders, grow as crystalline films on graphene. Covalent organic frameworks (COFs), in which molecular building blocks form robust microporous networks, are usually synthesized as insoluble and unprocessable powders. We have grown two-dimensional (2D) COF films on single-layer graphene (SLG) under operationally simple solvothermal conditions. The layered films stack normal to the SLG surface and show improved crystallinity compared with COF powders. We used SLG surfaces supported on copper, silicon carbide, and transparent fused silica (SiO2) substrates, enabling optical spectroscopy of COFs in transmission mode. Three chemically distinct COF films grown on SLG exhibit similar vertical alignment and long-range order, and two of these are of interest for organic electronic devices for which thin-film formation is a prerequisite for characterizing their optoelectronic properties.
DNS over Datagram Transport Layer Security (DTLS)

DNS queries and responses are visible to network elements on the path between the DNS client and its server. These queries and responses can contain privacy-sensitive information, which is valuable to protect. This document proposes the use of Datagram Transport Layer Security (DTLS) for DNS, to protect against passive listeners and certain active attacks. As latency is critical for DNS, this proposal also discusses mechanisms to reduce DTLS round trips and reduce the DTLS handshake size. The proposed mechanism runs over port 853.
Protein subcellular location pattern classification in cellular images using latent discriminative models

Motivation: Knowledge of the subcellular location of a protein is crucial for understanding its functions. The subcellular pattern of a protein is typically represented as the set of cellular components in which it is located, and an important task is to determine this set from microscope images. In this article, we address this classification problem using confocal immunofluorescence images from the Human Protein Atlas (HPA) project. The HPA contains images of cells stained for many proteins; each is also stained for three reference components, but there are many other components that are invisible. Given one such cell, the task is to classify the pattern type of the stained protein. We first randomly select local image regions within the cells, and then extract various carefully designed features from these regions. This region-based approach enables us to explicitly study the relationship between proteins and different cell components, as well as the interactions between these components. To achieve these two goals, we propose two discriminative models that extend logistic regression with structured latent variables. The first model allows the same protein pattern class to be expressed differently according to the underlying components in different regions. The second model further captures the spatial dependencies between the components within the same cell so that we can better infer these components. To learn these models, we propose a fast approximate algorithm for inference, and then use gradient-based methods to maximize the data likelihood. Results: In the experiments, we show that the proposed models help improve the classification accuracies on synthetic data and real cellular images. The best overall accuracy we report in this article for classifying 942 proteins into 13 classes of patterns is about 84.6%, which to our knowledge is the best so far. In addition, the dependencies learned are consistent with prior knowledge of cell organization. Availability: http://murphylab.web. cmu.edu/software/. Contact: Jeff.Schneider@cs.cmu.edu, murphy@cmu.edu
Microbial Biomass and Enzyme Activities in Chromium and Lead-Contaminated Sediments

The relationship between microbial biomass and enzyme activities under heavy metal pollution had attracted much attention in ecology. The experimental sediment samples were supplemented with Pb and Cr and incubated at room temperature for a month. Microbial properties such as microbial biomass, urease, catalase and cellulase activities, together with several chemical properties such as pH, total organic carbon , oxidation-reduction potential, total nitrogen and phosphorus were measured to evaluate changes in sediment qualities. Our results demonstrate that heavy metals would inhibit sediment microbe biomass and enzyme activities. Such decreases in sediments microbial biomass and enzyme activities by Pb and Cr contamination may help to evaluate heavy metals contaminated soil ecologies.
Addressing social determinants of health inequities: learning from doing.

In its 1988 landmark report and again in 2003 in an updated report,1,2 the Institute of Medicine defined public health as "what we as a society do to collectively assure the conditions in which people can be healthy. " The literature describing the relationship between conditions needed for health and health outcomes is as old as the public health endeavor itself and continues to grow, now almost exponentially. That certain conditions commonly referred to as social determinants—including access to affordable healthy food, potable water, safe housing, and supportive social networks—are linked to health outcomes is something on which most of us .
Epitaxial III-V nanowires on silicon

We present results of ideal epitaxial nucleation and growth of III−V semiconductor nanowires on silicon substrates. This addresses the long-time challenge of integrating high performance III−V semiconductors with mainstream Si technology. Efficient room-temperature generation of light on silicon is demonstrated by the incorporation of double heterostructure segments in such nanowires. We expect that advanced heterostructure devices, such as resonant tunneling diodes, superlattice device structures, and heterostructure photonic devices for on-chip communication, could now become available as complementary device technologies for integration with silicon.
22R-Hydroxycholesterol and 9-cis-Retinoic Acid Induce ATP-binding Cassette Transporter A1 Expression and Cholesterol Efflux in Brain Cells and Decrease Amyloid β Secretion*

The ATP-binding cassette transporter A1 (ABCA1) is a major regulator of peripheral cholesterol efflux and plasma high density lipoprotein metabolism. In adult rat brain we found high expression of ABCA1 in neurons in the hypothalamus, thalamus, amygdala, cholinergic basal forebrain, and hippocampus. Large neurons of the cholinergic nucleus basalis together with CA1 and CA3 pyramidal neurons were among the most abundantly immunolabeled neurons. Glia cells were largely negative. Because cholesterol homeostasis may have an essential role in central nervous system function and neurodegeneration, we examined ABCA1 expression and function in different brain cell types using cultures of primary neurons, astrocytes, and microglia isolated from embryonic rat brain. The basal ABCA1 mRNA and protein levels detected in these cell types were increased markedly after exposure to oxysterols and 9-cis-retinoic acid, which are ligands for the nuclear hormone liver X receptors and retinoic X receptors, respectively. Functionally, the increased ABCA1 expression caused by these ligands was followed by elevated apoA-I- and apoE-specific cholesterol efflux in neurons and glia. In non-neuronal and neuronal cells overexpressing a human Swedish variant of amyloid precursor protein, 22R-hydroxycholesterol and 9-cis-retinoic acid induced ABCA1 expression and increased apoA-I-mediated cholesterol efflux consequently decreasing cellular cholesterol content. More importantly, we demonstrated that these ligands alone or in combination with apoA-I caused a substantial reduction in the stability of amyloid precursor protein C-terminal fragments and decreased amyloid β production. These effects of 22R-hydroxycholesterol may provide a novel strategy to decrease amyloid β secretion and consequently reduce the amyloid burden in the brain.
Preparation and Characterization of Sodium Alginate–Based Hydrogels and Their In Vitro Release Studies

In the present work, polymer hydrogels have been used as the drug carrier for delivery systems of anticancer drugs. This investigation involves the formation of alginate hydrogels by a combination of three different monomers. The sodium alginate (SA) hydrogels were developed by free-radical polymerization of selective water-soluble monomers such as acrylamide (Am), methacrylamide (MAm), N-isopropylacrylamide (NIPAAm), and water-soluble polysaccharide (SA). The structural and morphological characterizations of the developed hydrogels were obtained from FTIR spectroscopy, differential scanning calorimetry, and scanning electron microscopy studies. Then, the hydrogels developed were encapsulated with a model cancer drug 5-fluorouracil (5-FU) and hydrogels containing 5-FU drug were evaluated for in vitro release studies. The released profiles of the drug showed that between 95% and 34% the loaded drug was released in the first half-an-hour at a buffer solution of 7.4 and the rest of the drug was released slowly. The results suggest that poly(N-isopropylacrylamide-sodium alginate) P(NIPAAm-SA) hydrogels show better properties than such as P(Am-SA) and P(MAm-SA). The drug release kinetic parameters suggested that the Am and MAm hydrogel networks are anomalous in nature, and the diffusion type of NIPAAM systems shows a slightly Fickian phenomenon. P(Am-SA), P(MAm-SA), and P(NIPAAm-SA) hydrogel formulations showed up to 97.13%, 95.53%, and 98. 36% cumulative release in 24 h, respectively. © 2013 Wiley Periodicals, Inc. Adv Polym Technol 2013, 32, 21340; View this article online at wileyonlinelibrary.com. DOI 10.1002/adv.21340
Cryogenic Collection of Complete Subsurface Samples for Molecular Biological Analysis

Abstract : The objective of this project has been to demonstrate the efficacy of cryogenic core technology as an integrated approach to sample collection and handling for use as a tool for monitoring subsurface remediation. This has included the development of a in situ cryogenic coring system, the evaluation of molecular biological tools (MBTs) analysis in conjunction with that system and the demonstration that the cryogenic sampling protocols are robust and ready for application by the remediation user community. In addition, cryogenic sample handling has allowed development of a new approach to directly determine local degradation activity using the ratio of labile mRNA to stable DNA for target genes.
Recent Developments in the Chemistry of Sandalwood Odorants

Natural sandalwood oil, a unique and valuable ingredient in fine perfumery, has been the focus of scientific interest for many years. Due to its scarcity and its high price, the search for novel synthetic raw materials imitating the characteristic odor profile of sandalwood oil is as challenging as ever. In this context, the preparation of the novel sandalwood odorants 26, 33, and 39 will be discussed, including their sensory properties and structure–odor relationship.
Vitamin D Deficiency and Risk of Cardiovascular Disease

Background— Vitamin D receptors have a broad tissue distribution that includes vascular smooth muscle, endothelium, and cardiomyocytes. A growing body of evidence suggests that vitamin D deficiency may adversely affect the cardiovascular system, but data from longitudinal studies are lacking. Methods and Results— We studied 1739 Framingham Offspring Study participants (mean age 59 years; 55% women; all white) without prior cardiovascular disease. Vitamin D status was assessed by measuring 25-dihydroxyvitamin D (25-OH D) levels. Prespecified thresholds were used to characterize varying degrees of 25-OH D deficiency (<15 ng/mL, <10 ng/mL). Multivariable Cox regression models were adjusted for conventional risk factors. Overall, 28% of individuals had levels <15 ng/mL, and 9% had levels <10 ng/mL. During a mean follow-up of 5.4 years, 120 individuals developed a first cardiovascular event. Individuals with 25-OH D <15 ng/mL had a multivariable-adjusted hazard ratio of 1.62 (95% confidence interval 1.11 to 2.36, P=0.01) for incident cardiovascular events compared with those with 25-OH D ≥15 ng/mL. This effect was evident in participants with hypertension (hazard ratio 2.13, 95% confidence interval 1.30 to 3.48) but not in those without hypertension (hazard ratio 1.04, 95% confidence interval 0.55 to 1.96). There was a graded increase in cardiovascular risk across categories of 25-OH D, with multivariable-adjusted hazard ratios of 1.53 (95% confidence interval 1.00 to 2.36) for levels 10 to <15 ng/mL and 1.80 (95% confidence interval 1.05 to 3.08) for levels <10 ng/mL (P for linear trend=0.01). Further adjustment for C-reactive protein, physical activity, or vitamin use did not affect the findings. Conclusions— Vitamin D deficiency is associated with incident cardiovascular disease. Further clinical and experimental studies may be warranted to determine whether correction of vitamin D deficiency could contribute to the prevention of cardiovascular disease.
Datalog Rewriting Techniques for Non-Horn Ontologies

We study the closely related problems of rewriting disjunctive datalog programs and non-Horn DL ontologies into plain datalog programs that entail the same facts for every dataset. We first propose the class of markable disjunctive datalog programs, which is efficiently recognisable and admits polynomial rewritings into datalog. Markability naturally extends to SHI ontologies, and markable ontologies admit (possibly exponential) datalog rewritings. We then turn our attention to resolution-based rewriting techniques. We devise an enhanced resolution rewriting procedure for disjunctive datalog, and propose a second class of SHI ontologies that admits exponential datalog rewritings via resolution. Finally, we evaluate the feasibility of our techniques over a large corpus of ontologies, with encouraging results.
Genome-wide search for new genes controlling plasma lipid concentrations in mice and humans

Purpose of review Quantitative trait locus analysis has been used in both humans and mice for the purpose of finding new genes regulating plasma lipid levels. We review these methods and discuss new approaches that can help find quantitative trait locus genes. Recent findings Many quantitative trait loci have been found that regulate plasma levels for HDL cholesterol (37 in mice and 30 in humans), LDL cholesterol (25 in mice and 20 in humans) and triglycerides (19 in mice and 30 in humans). Most of the human quantitative trait loci have concordant mouse quantitative trait loci mapping to homologous regions (93% for HDL cholesterol, 100% for LDL cholesterol and 80% for triglycerides), suggesting that many genes identified in mice may also regulate the same traits in humans. New approaches based on recently developed genomic and bioinformatic technologies and resources should greatly facilitate finding these genes. Summary New genes regulating plasma lipid levels can be found in mice and then tested in humans. Some of these genes could be potential therapeutic targets for human atherosclerosis.