Miracle-dz/UniFAR-FTUs huggingface dataset:
Semantics question analysis model for question answering system

Question Answering (QA) system takes Natural Language (NL) questions and output the exact answer extracted from Knowledge Base (KB). Handling NL question requires semantic analysis and interpretation to obtain the potential relevant answers from the KB. Providing users with the most relevant answers to their questions is an issue. Many answers returned are not relevant to the questions. The purpose of this paper is to present a semantic question analysis model for question answering system that correctly interpret the user’s question in order to yield correct answers. The Semantic Question Analysis Model exploits the approach of User Modelling and Relevance Feedback. To measure the ability of Semantic Question Analysis Model in analysing and translating user NL question, the model is implemented in an ontology-based question answering system (known as QAUF). Comparison of the results is done to determine the success of the proposed model with the existing QA systems, AquaLog and FREyA. The Semantic Question Analysis Model in QAUF shows a relatively increased in the QAUF F-measure. The finding of this study demonstrates that QAUF has a good precision percentage in returning relevant answers for each NL question.
Photoreceptor cells dissociated from the compound lateral eye of the horseshoe crab, Limulus polyphemus, I: Structure and ultrastructure

Abstract Isolated photoreceptors are desirable for whole-cell and patch-clamp studies of functional properties of visual processes that cannot be clearly analyzed when the photoreceptors are coupled. The retina of the compound lateral eye of the horseshoe crab, Limulus polyphemus, was dissociated into individual retinular cells using an enzyme pretreatment consisting of collagenase, papain, and trypsin, and a two-stage mechanical dissociation. These photoreceptors are functionally viable in an organ culture medium for up to 1 week and possess naked arhabdomeral and rhabdomeral segment membranes which are easily accessible for whole-cell recordings. A dissection technique was also developed whereby the retinal epidermis and neural plexus, as well as the second-order eccentric cells, could be separated from the ommatidia of the compound lateral eye in one simple step, providing viable isolated ommatidia attached to the cornea. The enzyme pretreatment used for dissociating the retina was then used to remove the individual ommatidia from the corneal cones. Hoffman modulation contrast microscopy was used to develop a reliable method for sorting and collecting viable isolated retinular cells for morphological and electrophysiological studies. Morphological analysis using light microscopy and scanning and transmission electron microscopy revealed that isolated retinular cells are morphologically nearly identical to retinular cells in situ. Isolated retinular cells possess a normal rhabdomere with no apparent loss of microvillar membrane as a result of the isolation process. Ommatidia can presently be isolated with up to six retinular cells possessing essentially normal structure and ultrastructure including thick rays of rhabdom. Isolated ommatidia possess naked A-segment membranes which are also well suited for whole-cell recording techniques.
Getting What You Ask For: On the Selectivity of Depression Rating Scales

A large number of rating scales has been developed to assess depression severity and change during antidepressant therapy. When reviewing the literature, the choice of the rating scales used in a particular study often seems arbitrary. The most frequently used observer rating scales, the Hamilton Depression Rating Scale (HDRS) and the Montgomery-Åsberg Depression Rating Scale (MADRS), and the most frequently used self-rating scale (the Beck Depression Inventory, or BDI) were developed more than 20 years ago. Their historical background is too often forgotten and they are reflections of their origin: the HDRS and the MADRS reflect antidepressant activity while the BDI reflects psychotherapy. Moreover, the HDRS is at risk of putting ‘all depressions in one basket’, while the MADRS is at risk of putting ‘all antidepressants in one basket’. Therefore, the question whether a particular antidepressant could be more effective in a particular subtype of depression cannot be answered. Observer rating scales are more frequently used than self-rating scales, and when scales are used that do exist in an observer rating and a self-rating version, interesting differences are found. The present paper does not suggest that one scale is better than another, but suggests that a better knowledge of their differential background can help the researcher choose the correct scale for his purposes.
Potential to Improve Outcomes: Causes of 30-Day Readmission After Cardioverter Defibrillator Implantation

Under newly restructured Centers for Medicare and Medicaid Services guidelines, hospitals are at risk for reduction in reimbursement for patients with heart failure (HF) who are readmitted within 30 days after discharge. Patients with HF who are admitted for an implantable cardioverter defibrillator (ICD) are routinely admitted with a primary diagnosis of HF. To reduce the occurrence of readmission, this article identifies the causes of 30-day readmission and recommends that patient follow-up after ICD placement should include assessment and management of HF symptoms.
Assembly and function of type III secretory systems.

Type III secretion systems allow Yersinia spp. , Salmonella spp. , Shigella spp. , Bordetella spp. , and Pseudomonas aeruginosa and enteropathogenic Escherichia coli adhering at the surface of a eukaryotic cell to inject bacterial proteins across the two bacterial membranes and the eukaryotic cell membrane to destroy or subvert the target cell. These systems consist of a secretion apparatus, made of approximately 25 proteins, and an array of proteins released by this apparatus. Some of these released proteins are "effectors," which are delivered into the cytosol of the target cell, whereas the others are "translocators," which help the effectors to cross the membrane of the eukaryotic cell. Most of the effectors act on the cytoskeleton or on intracellular-signaling cascades. A protein injected by the enteropathogenic E. coli serves as a membrane receptor for the docking of the bacterium itself at the surface of the cell. Type III secretion systems also occur in plant pathogens where they are involved both in causing disease in susceptible hosts and in eliciting the so-called hypersensitive response in resistant or nonhost plants. They consist of 15-20 Hrp proteins building a secretion apparatus and two groups of effectors: harpins and avirulence proteins. Harpins are presumably secreted in the extracellular compartment, whereas avirulence proteins are thought to be targeted into plant cells. Although a coherent picture is clearly emerging, basic questions remain to be answered. In particular, little is known about how the type III apparatus fits together to deliver proteins in animal cells. It is even more mysterious for plant cells where a thick wall has to be crossed. In spite of these haunting questions, type III secretion appears as a fascinating trans-kingdom communication device.
Geometric distribution of chordae tendineae: an important anatomic feature in mitral valve function.

BACKGROUND AND AIM OF THE STUDY This study examined the geometric distribution of chordae tendineae and their importance in compensating for papillary muscle (PM) displacement. METHODS Anatomic, chordal mechanics and hemodynamic measurements were performed with porcine mitral valves. For hemodynamic measurements, physiological pulsatile flow conditions were maintained, and PM positions varied. Leaflet coaptation was documented by 2-D echocardiography, and regurgitation measured directly. RESULTS Anatomic measurements showed the sum of marginal leaflet and marginal chordal lengths to exceed basal chordal length (1.8+/-0.4 versus 2.8+/-0.7 cm for anterior leaflets; 1.6+/-0.3 versus 2.5+/-0.6 cm for posterior leaflets). Triangular structures existed between basal chordae and marginal chordae with the marginal leaflet as the third side. Basal chordae resisted apical PM displacement in static experiments, while marginal chordae governed leaflet closure in hemodynamic experiments. Under pulsatile flow conditions, apical PM displacement decreased leaflet coaptation length and increased regurgitation (9.4+/-2.1 versus 4.0+/-1.6 ml). When marginal chordae were fused to the basal chordae, eliminating the role of the marginal chordae, severe regurgitation resulted (28.5+/-5.0 ml with apical PM displacement). CONCLUSION Based on triangular structures involving the basal and marginal chordae, a compensatory mechanism was described which explains how the severity of mitral regurgitation can vary following PM displacement. Basal chordae provide a constant connection between the annulus and papillary muscles, while marginal chordae maintain marginal leaflet flexibility, governing proper valve closure. This study relates chordal distribution to normal valve function, and provides a better understanding of breakdown in valve function under pathophysiological conditions.
Altered expression of BRCA1, BRCA2, and a newly identified BRCA2 exon 12 deletion variant in malignant human ovarian, prostate, and breast cancer cell lines

Germline mutations of BRCA1 and BRCA2 predispose to hereditary breast, ovarian, and possibly prostate cancer, yet structural mutations in these genes are infrequent in sporadic cancer cases. To better define the involvement of these genes in sporadic cancers, we characterized expression levels of BRCA1 and BRCA2 transcripts in cancer cell lines derived from neoplasms of the ovary, prostate, and breast and compared them with those expressed in primary cultures of normal epithelial cells established from these organs. We observed upregulation of BRCA1 and/or BRCA2 expression in six of seven ovarian cancer cell lines (OVCA420, OVCA429, OVCA432, ALST, DOV13, and SKOV3) when compared with levels found in normal ovary surface epithelial cells. Furthermore, five cancerous or immortalized prostatic epithelial cell lines (BPH‐1, TSU‐Pr1, LNCaP, PC‐3, and DU145) also expressed higher levels of BRCA1 and/or BRCA2 mRNA than did primary cultures of normal prostatic epithelial cells. In contrast, only the estrogen receptor–positive MCF‐7 cell line overexpressed these messages, whereas the estrogen receptor–negative breast cancer cell lines Hs578T, MDA‐MB‐231, and MDA‐MB‐468 showed no change in expression levels when compared with normal breast epithelial cells. In addition, expanding on our recent identification of a novel BRCA2 transcript variant carrying an in‐frame exon 12 deletion (BRCA2Δ12), we report increased expression of this variant in several ovarian, prostate, and mammary cancer cell lines (OVCA420, OVCA433, ALST, DOV13, SKOV3, TSU‐Pr1, DU145, and MDA‐MB‐468). Most notably, high levels of BRCA2Δ12 mRNA were detected in an estrogen receptor–positive breast cancer cell line, MCF‐7, and in an androgen‐independent prostate cancer cell line, DU‐145. Interestingly, the wild‐type BRCA2 transcript was barely detectable in DU145, which could be used as a model system for future investigations on BRCA2Δ12 function. Taken together, our data suggest disruption of BRCA1 and/or BRCA2 gene expression in certain epithelial cancer cell lines of the ovary, prostate, and breast. Because wild‐type BRCA1 and BRCA2 gene products increase during cell‐cycle progression and are believed to exert growth‐inhibitory action, enhanced expression of these genes in cancer cells may represent a negative feedback mechanism for curbing proliferation in fast‐growing cells. At present, the functionality of BRCA2Δ12 remains elusive. Mol. Carcinog. 28:236–246, 2000. © 2000 Wiley‐Liss, Inc.
Identification and Characterization of a Novel Constitutional PIK3CA Mutation in a Child Lacking the Typical Segmental Overgrowth of “PIK3CA‐Related Overgrowth Spectrum”

Activating somatic PIK3CA mutations underlie a growing heterogeneous spectrum of segmental overgrowth disorders. We report the identification and evaluation of a novel de novo constitutional PIK3CA mutation (NM_006218.2:c.335T>A, p.Ile112Asn) in a child with congenital megalencephaly and macrosomia. Functional characterization of patient cells using a variety of endpoints demonstrates increased phosphatidylinositol‐3‐kinase (PI3K) activity. The mutation lies in a linker region adjacent to the p85 (PIK3R2) binding domain of the p110α (PIK3CA) catalytic subunit of PI3K. We show that altered stoichiometry within the p85–p110 complex likely underlies the hyperactive PI3K‐AKT‐mTOR signaling in this instance. Our findings expand upon the recently proposed “PIK3CA‐related overgrowth spectrum” associated with PIKC3A mutations and PI3K hyperactivation, adding constitutional PIK3CA mutations as an underlying cause of megalencephaly and macrosomia in newborns.
Imaging Vascular Pathology

Examining the mechanisms of renal microvascular alterations in disease and the ramifications they have for overall organ function has remained a challenge due to the complexity of the renal microvascular system and the inability to examine it with sufficient resolution in vivo. However, advances in intravital microscopy have provided opportunities to meet these challenges. In this review we will examine specific areas where intravital imaging has advanced our knowledge of renal disease processes and present areas where these techniques, especially intravital multiphoton microscopy, have even further potential to integrate our knowledge of renal vascular pathology.
Increased adherence to vaginal epithelial cells and phagocytic killing of gonococci and urogenital meningococci associated with heat modifiable proteins

Urogenital Neisseria meningitidis were characterized with regard to serogroup, colony morphology, the presence of heat modifiable proteins (HMP), attachment to human vaginal and buccal epithelial cells, and phagocytic killing by polymorphonuclear leukocytes. The findings were compared with those on gonococci, and with those on meningococci isolated from blood or cerebrospinal fluid, with regard to colony morphology, HMP and piliation. The opacity colony morphology characteristic could be used to predict the presence of HMP in gonococci but not in meningococci, and sodium dodecyl sulphate polyacrylamide gel electrophoresis had to be used to demonstrate this surface protein. The urogenital meningococci, serogroup Y, attached significantly more efficinetly to vaginal epithelial cells in the presence of HMP and behaved in this respect like those of gonococci. Gonococci and meningococci containing HMP were more sensitive to phagocytic killing than those without HMP. Meningococci from opaque and transparent colonies and isolated from patients with meningococcal disease had no demonstrable HMP. They showed low adherence to vaginal and buccal epithelial cells, with no difference between organisms from opaque or transparent colonies.
The thymic cortical epithelium determines the TCR repertoire of IL‐17‐producing γδT cells

The thymus provides a specialized microenvironment in which distinct subsets of thymic epithelial cells (TECs) support T‐cell development. Here, we describe the significance of cortical TECs (cTECs) in T‐cell development, using a newly established mouse model of cTEC deficiency. The deficiency of mature cTECs caused a massive loss of thymic cellularity and impaired the development of αβT cells and invariant natural killer T cells. Unexpectedly, the differentiation of certain γδT‐cell subpopulations—interleukin‐17‐producing Vγ4 and Vγ6 cells—was strongly dysregulated, resulting in the perturbation of γδT‐mediated inflammatory responses in peripheral tissues. These findings show that cTECs contribute to the shaping of the TCR repertoire, not only of “conventional” αβT cells but also of inflammatory “innate” γδT cells.
Mudanças Climáticas Globais e a Agricultura no Brasil

Neste artigo procurou-se descrever o contexto atual das interacoes entre as mudancas climaticas globais e a agricultura no Brasil. Sao discutidas contribuicoes da agricultura para o agravamento do efeito estufa e das mudancas climaticas e os impactos das mudancas climaticas sobre a agricultura brasileira, focando-se na definicao de cenarios agricolas futuros baseados em modelos matematicos que representem os processos envolvidos nos sistemas produtivos. Tambem sao apresentadas diversas faces do problema e formas de aborda-las em uma rede de pesquisa multidisciplinar. Por fim, exemplifica-se com a proposta de abordagem institucional da Embrapa, que visa analisar os sistemas agro/florestais e propor medidas de mitigacao e adaptacao, embasadas numa analise de risco e sustentabilidade ambiental, social e economica e buscando colaborar para a definicao de politicas publicas que busquem meios de financiar e implantar de fato tais medidas. Embora nao seja uma revisao da literatura cientifica, procura trazer os pontos mais relevantes das discussoes cientificas sobre o tema das relacoes entre a agricultura e as mudancas climaticas.
Promotion and Attenuation of FGF Signaling Through the Ras-MAPK Pathway

The fibroblast growth factors (FGFs) represent a large family of ligands that activate signal transduction pathways leading to diverse biological responses, including many involved in various processes during development. Here, we discuss the discovery of a subset of conserved FGF target genes that encode feedback regulators of FGF signaling itself. Members of the Sprouty, Sef, and mitogen-activated protein kinase phosphatase families are negative modulators of FGF signaling, whereas positive factors that promote FGF signaling include the ETS transcription factors ERM and PEA3 and the transmembrane protein XFLRT3. These molecules affect the FGF signaling cascade at different levels to regulate the final output of the pathway. This multilayered regulation suggests that precise adjustment of FGF signaling is critical in development.
Treatment of HIV Infection with a Raltegravir-Based Regimen Increases LDL Levels, but Improves HDL Cholesterol Efflux Capacity

Background Persons infected with HIV often have altered lipid profiles that may be affected by antiretroviral therapies (ART). Traditional lipid measurements may be insufficient to assess cardiovascular disease (CVD) risk in this population. Methods We report results from 39 ART-naive participants in a substudy of A5248, a single-arm study of raltegravir, emtricitabine/tenofovir administration. Samples were collected at baseline, 12, 24 and 48 weeks after ART initiation. We performed advanced lipid phenotyping using nuclear magnetic resonance spectroscopy (Liposcience, Raleigh, NC, USA) for lipid particle size and number, and examined high-density lipoprotein (HDL) function measuring reverse cholesterol transport using J774 macrophages. Results We report significant increases in total cholesterol (13 mg/dl; P<0.001) and low-density lipoprotein (LDL; 8 mg/dl; P=0.03), with no change in triglycerides and without an increase in LDL particle number (P>0.1 all time points). HDL levels were increased over baseline levels at all time points (P<0.003), but reached a peak at week 12 and subsequently declined. HDL particle numbers also increased from baseline (P<0.002) and HDL function improved at week 48 (7% increase in efflux capacity; P<0.001). Oxidized LDL (oxLDL) levels decreased by week 12, but rose subsequently, and were not different from baseline at later time points. Conclusions HDL increases were associated with increases in beneficial HDL particles and HDL cholesterol efflux capacity, which may reduce future CVD events. Persistent inflammation in these HIV+ participants, may be a cause or consequence of oxLDL levels, and may contribute to declining levels of HDL over time. Clinicaltrials.gov NCT00660972.
Jump Test Performance and Sarcopenia Status in Men and Women, 55 to 75 Years of Age

Background and Purpose:Jumping mechanography uses maximal countermovement jumps to test obtain such as jump power (JPow). Recently, it has been shown to be a safe method for assessing muscle function in older adults; however, little is known about the relationships between JPow, muscle strength, and sarcopenia status. The purpose of this study was to examine jump performance, muscle strength, and sarcopenia status in older adults. Methods:This was a cross-sectional study that included men (n = 27) and women (n = 33) (55–75 years) recruited from the general community. Participants completed health status and physical activity questionnaires. Body composition, including appendicular skeletal muscle mass (ASM), bone free lean body mass, and relative skeletal muscle mass index, were assessed by total body dual-energy x-ray absorptiometry scans. The criteria for sarcopenia were relative skeletal muscle mass index values less than 7.26 kg/m2 for men and less than 5.45 kg/m2 for women. Three vertical jumps on a jump mat were performed to assess JPow, jump velocity (JVel), and jump height (JHt). Muscle strength was measured by 1RM testing for leg press (LP) and right and left hip abduction isotonic resistance exercises. Results:Sarcopenia was found in 20% (12/60) of the participants. Jump power was significantly lower (P = .001) in the sarcopenia group than in the normal group, 651.1 (41.7) W versus 851.0 (27.4) W, respectively. Jump power and JHt were significantly (P < .01) positively correlated (r = 0.54−0.77) with ASM and bone free lean body mass. Significant (P < .01) positive correlations (r = 0.43−0.70) were also reported between jump test variables (JPow, JVel, JHt) and muscle strength (LP, right and left hip abduction). Discussion:The jump test protocol was conducted safely with no injuries or balance issues. Our finding of lower JPow in sarcopenic individuals adds new information to the existing literature on age-related declines in muscle power. Conclusion:Community-dwelling individuals classified as sarcopenic had significantly lower JPow but not muscle strength compared with their counterparts with normal amounts of muscle mass. Jump test variables were positively correlated with lean tissue and lower body muscle strength. Based on our findings, JPow may be useful for sarcopenia screening in the middle-aged and older adults; however, more research is needed to determine the utility of this method in clinical populations.
Image De-noising Using Multilevel Filtering Approach

Visual information transmitted in the form of digital images is becoming a major method of communication in the modern age, but the image obtained after transmission is often corrupted with noise. The received image needs processing before it can be used in applications. Image denoising involves the manipulation of the image data to produce a visually high quality image. Salt & pepper (Impulse) noise and the additive white Gaussian noise and blurredness are the types of noise that occur during transmission and capturing. To remove these types of noise we have many filters like mean filter, median filter, inverse filter, wiener filter. No single one filter can remove both types of noise. A new approach for de-noising based on multilevel filter is proposed in this paper. The numerical computation has been done using MATLAB 7.8. 0. Keywords: Peak Signal to noise ratio, Image denoising, Image restoration, Filter.
Distributed image retrieval with color and keypoint features

Big data term refers to different variations of large datasets to complex to be processed by traditional computing methods. The paper presents a system for retrieving images in relational databases in a distributed environment. Content of the query image and images in the database is compared using global color information and local image keypoints. Image keypoints are indexed by fuzzy sets directly in a relational database. To distribute the process to several machines we use the Apache Hadoop software framework with HDFS.