Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel start codon mutation of the MERTK gene in a patient with retinitis pigmentosa

Purpose Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of inherited retinal degenerations characterized by progressive loss of photoreceptor cells and RPE functions. More than 70 causative genes are known to be responsible for RP. This study aimed to identify the causative gene in a patient from a consanguineous family with childhood-onset severe retinal dystrophy. Methods To identify the defective gene, whole exome sequencing was performed. Candidate causative variants were selected and validated using Sanger sequencing. Segregation analysis of the causative gene was performed in additional family members. To verify that the mutation has an effect on protein synthesis, an expression vector containing the first ten amino acids of the mutant protein fused with the DsRed2 fluorescent protein was constructed and transfected into HEK293T cells. Expression of the fusion protein in the transfected cells was measured using fluorescence microscopy. Results By filtering against public variant databases, a novel homozygous missense mutation (c.3G>A) localized in the start codon of the MERTK gene was detected as a potentially pathogenic mutation for autosomal recessive RP. The c.3G>A mutation cosegregated with the disease phenotype in the family. No expression of the first ten amino acids of the MerTK mutant fused with the DsRed2 fluorescent protein was detected in HEK293T cells, indicating that the mutation affects the translation initiation site of the gene that may lead to loss of function of the MerTK signaling pathway. Conclusions We report a novel missense mutation (c.3G>A, p.0? ) in the MERTK gene that causes severe vision impairment in a patient. Taken together with previous reports, our results expand the spectrum of MERTK mutations and extend our understanding of the role of the MerTK protein in the pathogenesis of retinitis pigmentosa.
Causes of Discordance between Allometries at and above Species Level: An Example with Aquatic Beetles

Covariation among organismal traits is nearly universal, occurring both within and among species (static and evolutionary allometry, respectively). If conserved developmental processes produce similarity in static and evolutionary allometry, then when species differ in development, it should be expressed in discordance between allometries. Here, we investigate whether rapidly evolving developmental processes result in discordant static and evolutionary allometries attributable to trade-offs in resource acquisition, allocation, or growth across 30 species of aquatic beetles. The highly divergent sperm phenotypes of these beetles might be an important contributor to allometric evolution of testis and accessory gland mass through altered requirements for the production of sperm and seminal fluids. We documented extensive discordance between static and evolutionary allometries, indicating that allometric relationships are flexibly modified over short time periods but subject to constraint over longer time spans. Among species, sperm phenotype did not influence relative investment in accessory glands but was weakly associated with investment in testes. Furthermore, except when sperm were long and simple, sperm phenotype was not associated with species-specific modification of the allometry of testis/accessory gland mass and body size. Our results demonstrate the utility of allometric discordance to infer species differences in the provisioning and growth of concurrently developing traits.
Lifting XML Schemas to Ontologies-The concept finder algorithm

In this paper we will present the Concept Finder algorithm. This algorithm is capable of creating mappings between the elements of a XML Schema and the concepts of an existing ontology. Furthermore we present results of a preliminary evaluation where real world schemas from the area of B2B communication were mapped to different ontologies using this algorithm.
Finding interesting associations without support pruning

Association rule mining has heretofore relied on the condition of high support to do its work efficiently. In particular, the well-known a-priori algorithm is only effective when the only rules of interest are relationships that occur very frequently. However, there are a number of applications, such as data mining, identification of similar Web documents, clustering and collaborative filtering, where the rules of interest have comparatively few instances in the data. In these cases, we must look for highly correlated items, or possibly even causal relationships between infrequent items. We develop a family of algorithms for solving this problem, employing a combination of random sampling and hashing techniques. We provide an analysis of the algorithms developed and conduct experiments on real and synthetic data to obtain a comparative performance analysis.
Effects of MDMA on Extracellular Dopamine and Serotonin Levels in Mice Lacking Dopamine and/or Serotonin Transporters

3,4-Methylendioxymethamphetamine (MDMA) has both stimulatory and hallucinogenic properties which make its psychoactive effects unique and different from those of typical psychostimulant and hallucinogenic agents. The present study investigated the effects of MDMA on extracellular dopamine (DAex) and serotonin (5-HTex) levels in the striatum and prefrontal cortex (PFC) using in vivo microdialysis techniques in mice lacking DA transporters (DAT) and/or 5-HT transporters (SERT). subcutaneous injection of MDMA (3, 10 mg/kg) significantly increased striatal DAex in wild-type mice, SERT knockout mice, and DAT knockout mice, but not in DAT/SERT double-knockout mice. The MDMA-induced increase in striatal DAex in SERT knockout mice was significantly less than in wildtype mice. In the PFC, MDMA dose-dependently increased DAex levels in wildtype, DAT knockout, SERT knockout and DAT/SERT double-knockout mice to a similar extent. In contrast, MDMA markedly increased 5-HTex in wildtype and DAT knockout mice and slightly increased 5-HTex in SERT-KO and DAT/SERT double-knockout mice. The results confirm that MDMA acts at both DAT and SERT and increases DAex and 5-HTex.
A parallel cross-modal search engine over large-scale multimedia collections with interactive relevance feedback

Indexing web-scale multimedia is only possible by distributing storage and computing efforts. Existing large-scale content-based indexing services mostly do not offer interactive relevance feedback. Here, we propose a running demonstrator of our Cross-Modal Search Engine (CMSE) implementing a query-by-example search strategy with relevance feedback and distributed over a cluster of 20 Dual core machines using MPI. We present the performance gain in terms of interactivity (search time) using a part of the Image-Net collection containing more than one million images as base example.
Automatic summarization of music videos

In this article, we propose a novel approach for automatic music video summarization. The proposed summarization scheme is different from the current methods used for video summarization. The music video is separated into the music track and video track. For the music track, a music summary is created by analyzing the music content using music features, an adaptive clustering algorithm, and music domain knowledge. Then, shots in the video track are detected and clustered. Finally, the music video summary is created by aligning the music summary and clustered video shots. Subjective studies by experienced users have been conducted to evaluate the quality of music summaries and effectiveness of the proposed summarization approach. Experiments are performed on different genres of music videos and comparisons are made with the summaries generated based on music track, video track, and manually. The evaluation results indicate that summaries generated using the proposed method are effective in helping realize users' expectations.
Immunochemical Visualization and Quantitation of Cyclic AMP in Single Cells*

Adenosine 3′:5′-cyclic monophosphate (cAMP) is a key second messenger in signaling pathways governing many cellular processes. To define the subcellular localization and relative abundance of cAMP, we developed a novel immunochemical approach based on acrolein fixation to visualize cAMP within cells. We describe here the fixation and immobilization of cAMP within cells and the production of specific, high titer polyclonal antibodies that recognize cAMP. Relative levels of cAMP immunofluorescence were quantitated in glial cells (oligodendrocytes, astrocytes, Schwann cells, and glioma cells) that were either untreated or treated with activators of endogenous adenylyl cyclase to raise cAMP levels. In treated cells, cAMP immunofluorescence is strongly localized in the perinuclear cytoplasm.
A Comprehensive Real-Time Indoor Air-Quality Level Indicator

The growing concern about Indoor Air-Quality has accelerated the development of small, low-cost air-quality monitoring systems. These systems are capable of monitoring various indoor air pollutants in real time, notifying users about the current air-quality status and gathering the information to the central server. However, most Internet of Things (IoT)-based air-quality monitoring systems numerically present the sensed value per pollutant, making it difficult for general users to identify how polluted the air is. Therefore, in this paper, we first introduce a tiny air-quality monitoring system that we developed and, based on the system, we also test the applicability of the comprehensive Air-Quality Index (AQI), which is widely used all over the world, in terms of its capacity for a comprehensive indoor air-quality indication. We also develop design considerations for an IoT-based air-quality monitoring system and propose a real-time comprehensive indoor air-quality level indication method, which effectively copes with dynamic changes and is efficient in terms of processing and memory overhead.
Upregulation of RANTES Gene Expression in Neuroglia by Japanese Encephalitis Virus Infection

ABSTRACT Infection with Japanese encephalitis virus (JEV) causes cerebral inflammation and stimulates inflammatory cytokine expression. Glial cells orchestrate immunocyte recruitment to focal sites of viral infection within the central nervous system (CNS) and synchronize immune cell functions through a regulated network of cytokines and chemokines. Since immune cell infiltration is prominent, we investigated the production of a responding chemoattractant, RANTES (regulated upon activation, normal T-cell expressed and secreted), in response to JEV infection of glial cells. Infection with JEV was found to elicit the production of RANTES from primary neurons/glia, mixed glia, microglia, and astrocytes but not from neuron cultures. The production of RANTES did not seem to be directly responsible for JEV-induced neuronal death but instead contributed to the recruitment of immune cells. RANTES expression required viral replication and the activation of extracellular signal-regulated kinase (ERK) as well as transcription factors, including nuclear factor kappa B (NF-κB) and nuclear factor IL-6 (NF-IL-6). The induction of RANTES expression by JEV infection in glial cells needed the coordinate activation of NF-κB and NF-IL-6. Using enzymatic inhibitors, we demonstrated a strong correlation between the ERK signaling pathway and RANTES expression. However, JEV replication was not dependent on the activation of ERK, NF-κB, and NF-IL-6. Altogether, these results demonstrated that infection of glial cells by JEV provided the early ERK-, NF-κB-, and NF-IL-6-mediated signals that directly activated RANTES expression, which might be involved in the initiation and amplification of inflammatory responses in the CNS.
Chapel , Fortress and X10 : novel languages for HPC

Chapel, Fortress and X10 are novel languages focussed on the HPC community. They have been developed with the aim to facilitate the programming of large next- generation parallel systems and increase both the productivity of the programs' developers and the scalability of the developed codes. This report introduces these languages by offering on overview of the design and specification of each language. The report will focus on each language's way of handling task and data parallelism. At the time of writing, all three languages are still in early development stages and any available compilers are experimental. For this reason (in part also for licensing reasons), the report does not touch on language or code performance. This is a Technical Report from the HPCx Consortium c HPCx UoE Ltd 2007
Sonodynamic Therapy Decreased Neointimal Hyperplasia After Stenting in the Rabbit Iliac Artery

Background—In-stent restenosis remains a pivotal problem after coronary and peripheral stenting. Sonodynamic therapy inhibits tumor growth by means of cytotoxicity after the activation of sonochemical sensitizers by ultrasound. PAD-S31 is known to be a water-soluble, chlorin-derivative sonochemical sensitizer. We assessed the efficacy of sonodynamic therapy using this sensitizer on neointimal hyperplasia in a rabbit stent model. Methods and Results—Stents were implanted in the iliac arteries of 16 rabbits. A total of 32 stented arteries were randomized to sonodynamic therapy, control, ultrasound exposure, and PAD-S31 groups. One hour after the intravenous administration of PAD-S31 (25 mg/kg body weight), ultrasound energy (1 MHz, 0.3 W/cm2) was delivered transdermally to the sonodynamic therapy group. At 28 days, all stent sites were analyzed morphometrically. The size of the intimal cross-sectional area was smaller in the sonodynamic therapy group than in the control, ultrasound, and PAD-S31 groups (0.31±0.07 versus 1.38±0.47, 1.66±0.71, and 1.61±0.42 mm2, respectively;P <0.05). The ratio of the intimal and medial cross-sectional area was smaller in the sonodynamic therapy group than in the control, ultrasound, and PAD-S31 groups (0.71±0.22 versus 2.53±1.39, 2.48±0.60, and 3.45±1.42 mm2;P <0.05). Conclusions—Sonodynamic therapy with PAD-S31 is considered to be a feasible treatment modality for noninvasively inhibiting neointimal hyperplasia in a rabbit iliac stent model.
Divergence of above- and belowground C and N pool within predominant plant species along two precipitation gradients in North China

Abstract. The coupling of carbon cycle and nitrogen cycle drives the food web structure and biogeochemistry of an ecosystem. However, across precipitation gradients, there may be a shift in C pool and N pool from above- to belowground because of shifting plant stoichiometry and allocation. Based on previous evidence, biomass allocation to roots should increase with aridity, while leaf [N] should increase. If their effect sizes are equal, they should cancel each other out, and the above- and belowground proportions of the N would remain constant. Here, we present the first study to explicitly compare above- and belowground pool sizes of N and C within predominant plant species along precipitation gradients. Biomass and nutrient concentrations of leaves, stems and roots of three predominant species were measured along two major precipitation gradients in Inner Mongolia, China. Along the two gradients, the effect sizes of the biomass shifts were remarkably consistent among three predominant species. However, the size of the shift in aboveground [N] was not, leading to a species-specific pattern in above- and belowground pool size. In two species (Stipa grandis and Artemisia ordosica) the effect sizes of biomass allocation and [N] were equal and the proportion of N of above- and belowground did not change with aridity, but in S. bungeana the increase in leaf [N] with aridity was much weaker than the biomass shift, leading to a decrease in the proportion of N aboveground at dry sites. We have found examples of consistent N pool sizes above- and belowground and a shift to a greater proportion of belowground N in drier sites depending on the species. We suggest that precipitation gradients do potentially decouple the C and N pool, but the exact nature of the decoupling depends on the dominant species' capacity for intraspecific variation.
Dimensional Conceptualizations of Impulsivity

Impulsivity is a transdiagnostic dimension of crucial importance to understanding psychopathology, as it is highly relevant to a wide array of maladaptive life outcomes including substance use, criminality, and other risky behaviors. There exist a variety of operationalizations of impulsivity across the literature distinct nomological networks. In fact, research suggests that “impulsivity” is a multifaceted construct comprised of at least 4 distinct traits that have unique pathways to maladaptive behaviors. Those traits are positive and negative urgency, sensation seeking, premeditation, and perseverance. Thus, it is crucial that any diagnostic system, or model of maladaptive traits, capture the nuances among these impulsigenic traits. The present study investigated the conceptualization of impulsigenic traits within the Diagnostic and Statistical Manual of Mental Disorders (DSM–5; American Psychiatric Association, 2013). Alternative personality disorder model and an alternative trait model to determine how well they captured these variants. This study obtained questionnaire ratings and behavioral task data from 450 community-dwelling adults oversampled for a history of involvement in the legal and/or mental health systems. The results showed that although the DSM–5 trait model captures well a broad conceptualization of impulsivity, some lower-order facets lack specificity.
Automatic broadcast news speech summarization

As the numbers of speech and video documents available on the web and on handheld devices soar to new levels, it becomes increasingly important to enable users to find relevant, significant and interesting parts of the documents automatically. In this dissertation, we present a system for summarizing Broadcast News (BN), ConciseSpeech, that identifies important segments of speech using lexical, acoustic/prosodic, and structural information, and combines them, optimizing significance, length and redundancy of the summary. There are many obstacles particular to speech such as word errors, disfluencies and the lack of segmentation that make speech summarization challenging. We present methods to address these problems. We show the use of Automatic Speech Recognition (ASR) confidence scores to compensate for word errors; present a phrase-level machine translation approach using weighted finite state transducers for detecting disfluency; and present the possibility of using intonational phrase segments for summarization. We also describe structural properties of BN used in determining which segments should be selected for a summary, including speaker roles, soundbites and commercials. We present Information Extraction (IE) techniques based on statistical methods such as conditional random fields and decision trees to automatically identify such structural properties. ConciseSpeech was built for handling single spoken documents, but we have extended it to handle user queries that can summarize multiple documents. For the query-focused version of ConciseSpeech we also built a knowledge resource (NE-NET) that can find related named entities to significantly improve the document retrieval task of query-focused summarization. We show how all these techniques improve speech summarization when compared to traditional text-based methods applied to speech transcripts.
Research on Mechanism of Low Speed Pre-Ignition and Knock Process in Boosted Direct Injection Spark Ignition Gasoline Engines

The mechanism of low speed pre-ignition (LSPI) and knock process in boosted direct injection spark ignition (DISI) gasoline engines are researched in this study. A single cylinder boosted DISI engine test bench was set up and operated at LSPI caused by oil, whose results are used to verify the feasibility of the calculation models. The geometric model is therefore established and the numerical simulation working at different injection times when the engine speed at 1200rpm and 1600rpm are conducted with the AVL FIRE CFD software.
Model for left ventricular contractility related to time-varying elastance based on echocardiographic measurements

Obesity is associated with haemodynamic overload. In addition to the increased preload, left ventricular (LV) afterload is also elevated in obese individuals; an increased LV mass can alter LV filling indexes. End-systolic pressure-volume relation (ESPVR) is relatively load independent and sensitive to changes in LV contractility. In this paper, end-systole ventricular contractility Ees was determined using a previously validated noninvasive single-beat method, based on two-dimensional echocardiographic and brachial blood pressure measurements. At the same time, using the results of a computer model, the correlations between non-invasive determined end systolic LV elastances and end systolic LV elastances simulated values, body mass index (BMI) and left ventricular mass (LVM), were investigated.
Environmental Toxicology EFFECTS OF IN OVO EXPOSURE OF WHITE LEGHORN CHICKEN , COMMON PHEASANT , AND JAPANESE QUAIL TO 2 , 3 , 7 , 8-TETRACHLORODIBENZO-p-DIOXIN AND TWO CHLORINATED DIBENZOFURANS ON CYP 1 A INDUCTION

In birds, activation of the aryl hydrocarbon receptor (AhR) by some polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) results in induction of cytochrome P4501A (CYP1A) expression. This response has been useful for predicting relative sensitivity of birds to dioxin-like compounds. To further investigate species-sensitivity to dioxins and dioxin-like compounds induction of cytochrome P450 1A4 and 1A5 (CYP1A4 and CYP1A5) mRNA and ethoxyresorufin O-deethylase (EROD) activity were quantified in liver of posthatch white leghorn chicken, common pheasant, and Japanese quail exposed to 2,3,7,8tetrachlorodibenzo-p-dioxin (TCDD), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF), or 2,3,7,8-tetrachlorodibenzofuran (TCDF) via air cell injection. The rank-order of sensitivity of TCDDand TCDF-exposed birds, based on CYP1A, was chicken > pheasant > quail. Based on CYP1A5 mRNA expression and EROD induction, the order of sensitivity of PeCDF-exposed birds was identical to that for TCDD and TCDF. However, based onCYP1A4mRNA expression the rank-order was pheasant> chicken> quail. When comparing the potency of the three compounds in each species, based onCYP1A4mRNA expression, TCDDwas the most potent compound in chicken. However, PeCDF was equally potent to TCDD in quail and was more potent than TCDD in pheasant. These results suggest that quantitative real-time polymerase chain reaction (Q-PCR) analysis of CYP1A expression, particularly CYP1A4mRNA expression, may be a more sensitive biomarker of exposure than analysis of EROD induction, especially in less responsive avian species. Based on these findings future risk assessments should consider the sensitivity of the species inhabiting a site and the congeners of concern that are present. Environ. Toxicol. Chem. # 2010 SETAC Keywords—Dioxin Furan Cytochrome P4501A Avian Sensitivity