Miracle-dz/UniFAR-FTUs huggingface dataset:
An Event-Driven Approach for Querying Graph-Structured Data Using Natural Language

An ideal way for people to query graph-based knowledge, including triplestores in the semantic web, would be for them to ask questions in a natural language (NL). However, existing NL query interfaces to graph-based data have limited expressive power and cannot accommodate arbitrarilynested quantification (i.e. phrases such as “a gangster who joined every gang”) together with multiple complex prepositional phrases, such as “in a city located in Illinois in 1918 using a set of keys that was stolen from a gangster”. It would appear that the commonly-used “entity-based” triplestores, together with what has become the de-facto approach of converting NL queries to SPARQL queries before being evaluated, hinders the development of expressive NL query processors. The reason is that entity-based triples are not conducive to the development of semantic theories of complex prepositional phrases, and the development of such theories is made considerably more complex when translation to SPARQL has to be taken into account. An alternative approach, which uses “event-based” triplestores, treats (bracketed) English queries as expressions of the lambda calculus which can be evaluated directly with respect to the triplestore. This approach facilitates the development of a formal denotational semantics of English queries which easily accommodates complex prepositional phrases. The approach described here could be used to develop a denotational semantics for a highly-expressive NL query language, and then that semantics could be used to guide the design of an NL query to SPARQL translator, thereby taking advantage of SPARQL optimizations.
Gene-Methylguanine-DNA Methyltransferase 6 O Silencing of the Flanking Region Denote ′ Methylation Hot Spots in the 5 Updated Version

The mechanism whereby the DNA repair protein O@-methylguaalne DNA methyltransferase (MGMT) is silenced in repair-deficient (Mer) human tumor cells is unknown. The role of methylation of the 5' CpG island in MGMT gene suppression is controversial. Although we previ ously showed by restriction enzyme analysis that CpG methylatlon in this region was associated with gene suppression, methylation at such sites was generally Incomplete, suggesting heterogeneity. To clarify this issue, we have unequivocally defined the methylation status of every CpG by genomic sequencing ofindividual cloned copies of bisulfite-modified DNA. The region from â€”249to +259 at the transcription start site was virtually methylation free in HT29 cells (Mer@),whereas in BE or HeLa S3 cells (Mer), this region was substantially metbylated in every DNA copy, with â€œhot spotsâ€•from â€”249to â€”103and from +107 to +196. Up-regulation of MGMT In HeLa S3 cells Induced by 5-azacytidine was accompanied by progressive demethylation and the appearance of totally unmethylated copies of DNA. We conclude that, in Mer cells, the MGMT promoter contains specific CpG methylation hot spots that are tightly linked to and are potential markers of gene silencing.
ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

ATTED-II (http://atted.jp) is a database of coexpressed genes that was originally developed to identify functionally related genes in Arabidopsis and rice. Herein, we describe an updated version of ATTED-II, which expands this resource to include additional agriculturally important plants. To improve the quality of the coexpression data for Arabidopsis and rice, we included more gene expression data from microarray and RNA sequencing studies. The RNA sequencing-based coexpression data now cover 94% of the Arabidopsis protein-encoding genes, representing a substantial increase from previously available microarray-based coexpression data (76% coverage). We also generated coexpression data for four dicots (soybean, poplar, grape and alfalfa) and one monocot (maize). As both the quantity and quality of expression data for the non-model species are generally poorer than for the model species, we verified coexpression data associated with these new species using multiple methods. First, the overall performance of the coexpression data was evaluated using gene ontology annotations and the coincidence of a genomic feature. Secondly, the reliability of each guide gene was determined by comparing coexpressed gene lists between platforms. With the expanded and newly evaluated coexpression data, ATTED-II represents an important resource for identifying functionally related genes in agriculturally important plants.
Mitochondrial Transmembrane Potential Changes Support the Concept of Mitochondrial Heterogeneity During Apoptosis

Dissipation of mitochondrial membrane potential (Δψm) and release of cytochrome c from mitochondria appear to be key events during apoptosis. The precise relationship (cause or consequence) between both is currently unclear. We previously showed in a model of serum-free cultured granulosa explants that cytochrome c is retained in a subset of respiring mitochondria until late in the apoptotic process. In this study we further investigated the issue of heterogeneity by using the Δψm-sensitive probe CM-H2TMRos in combination with a DNA fluorochrome. Changes of Δψm were assessed qualitatively by epifluorescence microscopy and were quantified using digital imaging microscopy. This approach yielded the following results: (a) CM-H2TMRos staining is a reliable and specific procedure to detect Δψm changes in granulosa cells explants; (b) dissipation of transmembrane potential is an early event during apoptosis preceding nuclear changes but is confined to a subpopulation of mitochondria within an individual cell; (c) in frankly apoptotic cells a few polarized mitochondria can be detected. These findings support the hypothesis that ATP needed for completion of the apoptotic cascade can be generated during apoptosis in a subset of respiring mitochondria and is not necessarily derived from anaerobic glycolysis.
Non-Invasive Stimulation-Based Tactile Sensation for Upper-Extremity Prosthesis: A Review

An ideal hand prosthesis should provide satisfying functionality based on reliable decoding of the user’s intentions and deliver tactile feedback in a natural manner. The absence of tactile feedback impedes the functionality and efficiency of dexterous hand prostheses, which leads to a high rejection rate from prostheses users. Thus, it is expected that integration of tactile feedback with hand prostheses will improve the manipulation performance and enhance perceptual embodiment for users. This paper reviews the state-of-the-art of non-invasive stimulation-based tactile sensation for upper-extremity prostheses, from the physiology of the human skin, to tactile sensing techniques, non-invasive tactile stimulation, and an emphasis on electrotactile feedback. The paper concludes with a detailed discussion of recent applications, challenging issues, and future developments.
Vaccination of Chickens with SPI1-lon and SPI1-lon-fliC Mutant of Salmonella enterica Serovar Enteritidis

The prevalence of Salmonella enterica serovar Enteritidis is gradually decreasing in poultry flocks in the EU, which may result in the demand for a vaccine that allows for the differentiation of vaccinated flocks from those infected by wild-type S. Enteritidis. In this study, we therefore constructed a (Salmonella Pathogenicity Island 1) SPI1-lon mutant with or without fliC encoding for S. Enteritidis flagellin. The combination of SPI1-lon mutations resulted in attenuated but immunogenic mutant suitable for oral vaccination of poultry. In addition, the vaccination of chickens with the SPI1-lon-fliC mutant enabled the serological differentiation of vaccinated and infected chickens. The absence of fliC therefore did not affect the immunogenicity of the vaccine strain and allowed for serological differentiation of the vaccinated chickens. The SPI1-lon-fliC mutant is therefore a suitable marker vaccine strain for oral vaccination of poultry.
The DMD Locus Harbours Multiple Long Non-Coding RNAs Which Orchestrate and Control Transcription of Muscle Dystrophin mRNA Isoforms

The 2.2 Mb long dystrophin (DMD) gene, the largest gene in the human genome, corresponds to roughly 0.1% of the entire human DNA sequence. Mutations in this gene cause Duchenne muscular dystrophy and other milder X-linked, recessive dystrophinopathies. Using a custom-made tiling array, specifically designed for the DMD locus, we identified a variety of novel long non-coding RNAs (lncRNAs), both sense and antisense oriented, whose expression profiles mirror that of DMD gene. Importantly, these transcripts are intronic in origin and specifically localized to the nucleus and are transcribed contextually with dystrophin isoforms or primed by MyoD-induced myogenic differentiation. Furthermore, their forced ectopic expression in both human muscle and neuronal cells causes a specific and negative regulation of endogenous dystrophin full length isoforms and significantly down-regulate the activity of a luciferase reporter construct carrying the minimal promoter regions of the muscle dystrophin isoform. Consistent with this apparently repressive role, we found that, in muscle samples of dystrophinopathic female carriers, lncRNAs expression levels inversely correlate with those of muscle full length DMD isoforms. Overall these findings unveil an unprecedented complexity of the transcriptional pattern of the DMD locus and reveal that DMD lncRNAs may contribute to the orchestration and homeostasis of the muscle dystrophin expression pattern by either selective targeting and down-modulating the dystrophin promoter transcriptional activity.
Removal of Duodenum Elicits GLP-1 Secretion

OBJECTIVE To evaluate the effect of removal of the duodenum on the complex interplay between incretins, insulin, and glucagon in nondiabetic subjects. RESEARCH DESIGN AND METHODS For evaluation of hormonal secretion and insulin sensitivity, 10 overweight patients without type 2 diabetes (age 61 ± 19.3 years and BMI 27.9 ± 5.3 kg/m2) underwent a mixed-meal test and a hyperinsulinemic-euglycemic clamp before and after pylorus-preserving pancreatoduodenectomy for ampulloma. RESULTS All patients experienced a reduction in insulin (P = 0.002), C-peptide (P = 0.0002), and gastric inhibitory peptide (GIP) secretion (P = 0.0004), while both fasting and postprandial glucose levels increased (P = 0.0001); GLP-1 and glucagon responses to the mixed meal increased significantly after surgery (P = 0.02 and 0.031). While changes in GIP levels did not correlate with insulin, glucagon, and glucose levels, the increase in GLP-1 secretion was inversely related to the postsurgery decrease in insulin secretion (R2 = 0.56; P = 0.012) but not to the increased glucagon secretion, which correlated inversely with the reduction of insulin (R2 = 0.46; P = 0.03) and C-peptide (R2 = 0.37; P = 0.04). Given that the remaining pancreas presumably has preserved intraislet anatomy, insulin secretory capacity, and α- and β-cell interplay, our data suggest that the increased glucagon secretion is related to decreased systemic insulin. CONCLUSIONS Pylorus-preserving pancreatoduodenectomy was associated with a decrease in GIP and a remarkable increase in GLP-1 levels, which was not translated into increased insulin secretion. Rather, the hypoinsulinemia may have caused an increase in glucagon secretion.
Exponential Separation of Quantum and Classical One-Way Communication Complexity for a Boolean Function

We give an exponential separation between one-way quantum and classical communication complexity for a Boolean function. Earlier such a separation was known only for a relation. A very similar result was obtained earlier but independently by Kerenidis and Raz [KR06]. Our version of the result gives an example in the bounded storage model of cryptography, where the key is secure if the adversary has a certain amount of classical storage, but is completely insecure if he has a similar amount of quantum storage.
Peripheral astigmatism in emmetropic eyes

The long‐term aim of the work introduced here is to investigate the influence of off‐axis aberrations on human vision, especially for subjects with a large central scotoma. The latter use their peripheral vision in spite of its poor off‐axis optical quality, and a correction of the off‐axis aberrations might be of great assistance. The eccentric fixation angles used by these subjects can be up to 20–30°. In this initial study we have measured oblique astigmatism, the major off‐axis aberration, in 20 emmetropic eyes in 10° steps out to 60° nasally and temporally using a ‘double pass’ setup. The results show very large individual differences and the oblique astigmatism also varies from nasal to temporal side. In an off‐axis measurement angle of 30° the astigmatism varied between subjects from 1 to 7‐D, with a mean astigmatism of about 4‐D on the nasal side and about 1.5‐D lower on the temporal side. At 60° temporally, the mean astigmatism was 7‐D. At 60° nasally, all subjects had astigmatism larger than 8‐D and the mean astigmatism was 11‐D. The results indicate that any attempt to correct the off axis astigmatism in an eye with central scotoma cannot be based on central refraction; instead, individual measurements are necessary.
Learning-based vessel segmentaion in mamographic images

—In this paper we propose using a learning-based method for vessel segmentation in mammographic images. To capture the large variation in vessel patterns not only across subjects, but also within a subject, we create a feature pool containing local, Gabor and Haar features extracted from mammographic images generating a feature space of very high dimension. We also employ a huge number of training samples, which essentially contains the pixels in the training images. To deal with the very high dimensional feature space and the huge number of training samples, we apply a forest with boosting trees for vessel segmentation. Speciﬁcally, we use the standard AdaBoost algorithm for each tree in the forest. The randomness is encoded, when training each AdaBoost tree, using randomly sampled training set (pixels) and randomly selected features from the whole feature pool. The proposed method is tested using a real dataset with 20 anonymous mammographic images. The effectiveness of the proposed features and classiﬁers is demonstrated in the experiments where we compare different approaches and feature combinations. In the paper, we also present full analysis of different types of features.
Cytoskeletal Interactions at the Nuclear Envelope Mediated by Nesprins

Nesprin-1 is a giant tail-anchored nuclear envelope protein composed of an N-terminal F-actin binding domain, a long linker region formed by multiple spectrin repeats and a C-terminal transmembrane domain. Based on this structure, it connects the nucleus to the actin cytoskeleton. Earlier reports had shown that Nesprin-1 binds to nuclear envelope proteins emerin and lamin through C-terminal spectrin repeats. These repeats can also self-associate. We focus on the N-terminal Nesprin-1 sequences and show that they interact with Nesprin-3, a further member of the Nesprin family, which connects the nucleus to the intermediate filament network. We show that upon ectopic expression of Nesprin-3 in COS7 cells, which are nearly devoid of Nesprin-3 in vitro, vimentin filaments are recruited to the nucleus and provide evidence for an F-actin interaction of Nesprin-3 in vitro. We propose that Nesprins through interactions amongst themselves and amongst the various Nesprins form a network around the nucleus and connect the nucleus to several cytoskeletal networks of the cell.
Effects of short glass fibers on the mechanical properties of glass fiber fabric/PVC composites

Fiber-reinforced composites using glass fiber and polyvinylchloride (PVC) have been used widely as architectural materials, electrical applications, automotive sector, and packing materials because of their reasonable price, chemical resistance, and dimensional stability. On the other hand, most of the composites are short fiber-reinforced PVC composites. In particular, in the case of fabric reinforced composites, undulated regions exist where there is only resin due to the characteristics of the weave construction, which causes a decrease in strength. In this paper, PVC was reinforced with chopped glass fibers with different lengths and contents to produce glass fiber fabric/PVC composites. The physical properties of the composites, such as thickness, density, volume fraction (Vf), and void content (Vc) were identified. The mechanical properties, including tensile strength, flexural strength, and interlaminar shear strength (ILSS) were also identified. A cross section of the composites was observed by scanning electron microscopy. Compared to the fabric reinforced composite without chopped glass fiber, the tensile strength was increased by 3.90% (from 316.15 MPa to 328.48 MPa at 5 wt.% chopped fibers with 3 mm length), flexural strength was increased by 7.15% (from 87.07 MPa to 93.30 MPa at 10 wt.% chopped fibers with 2 mm length), and ILSS was increased by 8.71% (from 7.34 MPa to 7.98 MPa at 10 wt.% chopped fibers with 1 mm length). Therefore, the critical fiber aspect ratio of chopped fiber works differently on each of the three mechanical properties.
Advancing the Understanding of Water Distribution System Corrosion: Effects of Chlorine and Aluminum on Copper Pitting, Temperature Gradients on Copper Corrosion, and Silica on Iron Release

When severe copper pitting problems impacted customers at a large utility, studies were begun to attempt to diagnose the problem and identify potential solutions. A series of tests were conducted to characterize the nature of pitting. Desktop comparisons of pinhole leak frequency and treatment practices at nearly utilities were also documented to identify treatment factors that might be influencing the initiation and propagation of leaks. Factors identified included the presence of relatively high levels of free chlorine and aluminum in the distribution system. Experiments were conducted to examine the effect of these constituents on copper pitting under stagnant and flow conditions. That led to discovery of a synergistic redox reaction between chlorine, aluminum solids, and copper metal as evidenced by increased chlorine decay rates, non-uniform corrosion, and rising corrosion potentials. Temperature changes had been suspected to increase copper pitting frequency and copper release to drinking water. Experiments examined the effect of temperature gradients on copper pipe corrosion during stagnant conditions. The pipe orientation in relation to the temperature gradient determined whether convective mixing would occur, which influenced temperature gradients within the pipe. This work is the first to demonstrate that temperature gradients lead to thermogalvanic currents, influences copper leaching and scale type. Iron release from corroding water mains is another concern of many water utilities, but little is known about chemistry factors that influence the problem. In laboratory experiments, higher levels of silica caused more iron release to the water and decreased the size of suspended iron particles. Silica levels also changed during the experiment: it decreased through incorporation into a dense scale, and increased by release from cast iron during corrosion. Silica slightly decreased iron corrosion rates near the end of this 6-month test.
Preparation of -Cyclodextrin modified Polystyrene Nanofiber and Its Application in the Extraction of Rhodamine B

An unique pretreatment and detection of rhodamine B in chilli sanples was described. The pretreatment method was based on-Cyclodextrin modified polystyrene (PS) nanofiber. The modified nanofiber obtained was studied by scanning electron microscopy and fourier transform infrared spectroscopy, respectively. The modified PS nanofiber extraction efficiency was higher than unmodified PS nanofiber.
A 1 mW low phase-noise relaxation oscillator

We present a new RC relaxation oscillator with pulse self biasing, to reduce power consumption, and with harmonic filtering and resistor feedback, to reduce phase-noise. A circuit prototype in the hundreds of MHz range, designed in a 130 nm CMOS technology has a very low phase-noise, −132.6 dBc/Hz @ 10 MHz offset, and the power consumption is only 1 mW, which leads to a figure of merit (FOM) of −159.1 dBc/Hz.
The mortality rate from anorexia nervosa.

OBJECTIVE We determined the standardized mortality ratio (SMR) in our anorexia nervosa (AN) patient population. METHOD We used a cross-sectional design to study an inception cohort (1981-2000) drawn from the provincial tertiary care eating disorders program at St. Paul's Hospital (British Columbia, Canada). All patients who completed their initial assessment for an eating disorder were included in the study. Vital status, date and cause of death from British Columbia Vital Statistics Agency, date of assessment, date of birth, and diagnosis at the time of assessment were collected for each patient. RESULTS Of 954 patients, 326 diagnosed with AN completed an assessment over the 20 years. The SMR was 10.5 (95% confidence interval [CI] = 5.5-15.5) for AN. DISCUSSION Some studies in the literature report that AN has the highest mortality rate of any psychiatric disorder in young females. However, others dispute this fact and report an SMR lower than the normal population mortality (SMR = 0.71). Contrary to some reports in the literature, our study confirms a high mortality rate within the AN population.
Verification of timed chi models using uppaal

Due to increasing system complexity and growing competition and costs, powerful techniques are needed to design and analyze manufacturing systems. One of the most popular techniques to do performance analysis is simulation. However, simulation-based analysis cannot guarantee the correctness of a system. Our research focuses on examining other methods to make performance analysis and functional analysis, and combining the two. One of the approaches is to translate a simulation model that is used for performance analysis to a model written in an input language of an existing verification tool. The process algebraic language χ is intended for modeling, simulation, verification and real-time control and has been used extensively to simulate large manufacturing systems. UPPAAL is an integrated tool environment for modeling, validation and verification of real-time systems and has been applied successfully in case studies ranging from communication protocols to multimedia applications. In this paper, we represent a translation scheme that is used to translate simulation models written inχ language toUPPAAL timed automata and show a small example of the translation. Future work includes defining an equivalence relation between χ andUPPAAL transition systems, implementing the translator as a part of the χ toolset, and applying it for verification of models of manufacturing systems.
Improving photoanodes to obtain highly efficient dye-sensitized solar cells: a brief review

Dye-sensitized solar cells (DSSCs) feature low cost, stability, and environment friendliness and are thus a promising substitute for traditional silicon solar cells. DSSCs have received intensive research attention and have been rapidly developing in the last two decades. The efficiency of DSSCs should be increased to promote their commercialization and large-scale application. This brief review summarizes the major progress in advanced nano/micromaterials to improve photoanodes and enhance the conversion efficiencies of DSSCs. Commonly used methods to improve photoanodes include semiconductor film nanoarchitecture, light-scattering material application, compositing, doping, interfacial engineering, and TiCl4 post-treatment. This review provides insights into DSSC improvement and development of other photovoltaics, such as perovskite solar cells and photoelectrochemical cells.