Miracle-dz/UniFAR-FTUs huggingface dataset:
Text Mining Biomedical Literature for Genomic Knowledge Discovery

The last decade has been marked by unprecedented growth in both the production of biomedical data and the amount of published literature discussing it. Almost every known or postulated piece of information pertaining to genes, proteins, and their role in biological processes is reported somewhere in the vast amount of published biomedical literature. We believe the ability to rapidly survey and analyze this literature and extract pertinent information constitutes a necessary step toward both the design and the interpretation of any large-scale experiment. Moreover, automated literature mining offers a yet untapped opportunity to integrate many fragments of information gathered by researchers from multiple fields of expertise into a complete picture exposing the interrelated roles of various genes, proteins, and chemical reactions in cells and organisms. In this thesis, we show that functional keywords in biomedical literature, particularly Medline, represent very valuable information and can be used to discover “new” genomic knowledge. To validate our claim we present an investigation into text mining biomedical literature to assist microarray data analysis, yeast gene function classification, and biomedical literature categorization. We conduct following studies: (1) We test sets of genes to discover common functional keywords among them and use these keywords to cluster them into groups; (2) We show that it is possible to link genes to diseases by an expert human interpretation of the functional keywords for the genes—none of these diseases are as yet mentioned in public databases; (3) By clustering genes based on commonality of functional keywords it is possible to group genes into meaningful clusters that reveal more information about their functions, link to diseases and roles in metabolism pathways; (4) Using extracted functional keywords, we are able to demonstrate that for yeast genes, we can make a better functional grouping of genes in comparison to available public microarray and phylogenetic databases; (5) We show an application of our approach to literature classification. Using functional keywords as features, we are able to extract epidemiological abstracts automatically from Medline with higher sensitivity and accuracy than a human expert.
Molecular Cloning and Characterization of a Novel Retinoic Acid-inducible Gene That Encodes a Putative G Protein-coupled Receptor*

The effects of retinoids such as all-trans-retinoic acid (ATRA) on cell growth, differentiation, and apoptosis are thought to be mediated by nuclear retinoid receptors, which are involved in ligand-dependent transcriptional activation of target genes. Using differential display, we identified the cDNA of a novel gene, designated retinoic acid-inducible gene 1 (RAIG1), which was induced by ATRA in the squamous carcinoma cell line UMSCC-22B. Two RAIG1 transcripts of 2.4 and 6.8 kilobase pairs, respectively, have the same ORF that encodes a 357-amino acid polypeptide. RAIG1 mRNA is expressed at high level in fetal and adult lung tissues. Induction of RAIG1 expression by ATRA is rapid (within 2 h) and dose-dependent in the range between 1 nm to 1 μm. The constitutive RAIG1 mRNA levels, which were low in three of five head and neck and four of six lung cancer cell lines, increased after ATRA treatment in most cell lines. The deduced RAIG1 protein sequence contains seven transmembrane domains, characteristic of G protein-coupled receptors. A fusion protein of RAIG1 and the green fluorescent protein was localized in the cell surface membrane and perinuclear vesicles in transiently transfected cells. RAIG1 was mapped to chromosome 12p12.3-p13. Our results provide novel evidence for a possible interaction between retinoid and G protein signaling pathways.
Extending Kimmo's Two-Level Model of Morphology

This paper describes the problems faced while using Kimmo's two-level model to describe certain Indian languages such as Tamil and Hindi. The two-level model is shown to be descriptively inadequate to address these problems. A simple extension to the basic two-level model is introduced which allows conflicting phonological rules to coexist. The computational complexity of the extension is the same as Kimmo's two-level model.
Criteria for the Transition to Adulthood, Developmental Features of Emerging Adulthood, and Views of the Future Among Greek Studying Youth

This study investigated emerging adulthood and transition to adulthood in Greece, a highly underresearched issue in this country. Participants were 784 university students aged 17.5-27.5 years. Criteria for the transition to adulthood, developmental features of emerging adulthood, perceived adult status, views of the future (optimism), and sociodemographic variables were assessed. The results support the existence of emerging adulthood as a distinct life period in Greece. More than two thirds of the sample were self-perceived emerging adults. Most prevalent criteria were Norm compliance and Family capacities. Developmental features of emerging adulthood ranked high, especially Identity exploration, Experimentation/possibilities, and Feeling “in-between”. Statistically significant variations emerged as a function of gender, age, living arrangement, job experience, and perceived adult status. Views of the future were cautiously optimistic. Similarities with existing data and differences related to the specific characteristics of the Southern European context are discussed.
Acute contact toxicity of selected conventional and novel insecticides to Trichogramma japonicum Ashmead (Hymenoptera: Trichogrammatidae)

Eighteen insecticides belonging to conventional and novel chemical classes were evaluated for their toxic effects on the hymenopteran egg parasitoid Trichogramma japonicum Ashmead following the protocols recommended by International Organization for Biological Control (IOBC) in the Toxicology laboratory at College of Horticulture, Kerala Agricultural University during 2012-13. Commonly used conventional insecticides comprising six organophoshates (acephate 75 SP, chlorpyriphos 20 EC, dichlorvos 76 EC, dimethoate 30 EC, malathion 50 EC and quinalphos 25 EC); one carbamate (carbaryl 5 DP); one synthetic pyrethroid (fenvalerate 20 EC) and ten novel insecticides viz; acetamiprid 20 SP, emmamectin benzoate 5 SG, fipronil 80 WG, imidachloprid 200 SL, indoxacarb 14.5 SC, buprofezin 25 SC, chlorantraniliprole 18.5 SC, flubendiamide 480 SC, spinosad 2.5 SC and thiamethoxam 25 WDG at field recommended concentrations were tested for their acute contact toxicity against T. japonicum by adopting residual film bioassay method. The toxicity of insecticides was manifested as lethal effect on the adult parasitoids. Among the eighteen insecticides tested, acephate caused the highest mortality of 88.75 % and chlorantraniliprole caused the lowest mortality (21.25 %) to the adults of T. japonicum. Novel insecticides viz., emmemectin benzoate, fipronil, imidachloprid, indoxacarb, buprofezin and chlorantraniliprole were rated as ‘harmless’ as per IOBC safety classification whereas spinosad, thiamethoxam and flubendiamide were found ‘slightly harmful’ to T. japonicum. Conventional organophosphates viz., acephate, chlorpyriphos and dichlorvos were ‘moderately harmful’. Dimethoate, malathion, quinalphos carbaryl, fenvalerate and acetamiprid caused a mortality of 30 – 79 % leading them to be rated as ‘slightly harmful’ to adults of T. japonicum.
Caracterización molecular de cepas de Mycobacterium tuberculosis drogorresistentes en el estado de Veracruz

La tuberculosis (TB) es una enfermedad que ha afectado a la humanidad desde hace mucho tiempo y continua siendo un problema de salud publica; actualmente la resistencia a farmacos, es uno de los factores que han agravado su situacion. Veracruz es uno de los estados con mas casos de tuberculosis farmacorresistente a nivel nacional; sin embargo, no hay estudios que describan las caracteristicas genetico - mole culares y epidemiologicas de las cepas causantes de dicha enfermedad en la region. Por lo tanto el objetivo de este trabajo fue r ealizar una caracterizacion genetica de las cepas de Mycobacterium drogorresistentes presentes en el estado de Veracruz. Para l o cual se secuenciaron fragmentos de los genes: rrS, katG, inhA, rpoB, embB y pncA, implicados en la resistencia a farmacos de primera linea. Las mutaciones encontradas, se relacionaron con variables epidemiologicas de los portadores, con la finalidad de identificar factores de riesgo asociaciones y/o agrupamientos.
An information technology framework for strengthening telehealthcare service delivery.

OBJECTIVE Telehealthcare has been used to provide healthcare service, and information technology infrastructure appears to be essential while providing telehealthcare service. Insufficiencies have been identified, such as lack of integration, need of accommodation of diverse biometric sensors, and accessing diverse networks as different houses have varying facilities, which challenge the promotion of telehealthcare. This study designs an information technology framework to strengthen telehealthcare delivery. MATERIALS AND METHODS The proposed framework consists of a system architecture design and a network transmission design. The aim of the framework is to integrate data from existing information systems, to adopt medical informatics standards, to integrate diverse biometric sensors, and to provide different data transmission networks to support a patient's house network despite the facilities. The proposed framework has been evaluated with a case study of two telehealthcare programs, with and without the adoption of the framework. RESULTS The proposed framework facilitates the functionality of the program and enables steady patient enrollments. The overall patient participations are increased, and the patient outcomes appear positive. The attitudes toward the service and self-improvement also are positive. CONCLUSIONS The findings of this study add up to the construction of a telehealthcare system. Implementing the proposed framework further assists the functionality of the service and enhances the availability of the service and patient acceptances.
Design of a two degree-of-freedom ankle-foot orthosis for robotic rehabilitation

An ankle-foot orthosis (AFO) is commonly used to help subjects with weakness of ankle dorsiflexor muscles due to peripheral or central nervous system disorders. Both these disorders are due to the weakness of the tibialis anterior muscle which results in lack of dorsiflexion assist moment. The deformity and muscle weakness of one joint in the lower extremity influences the stability of the adjacent joints, thereby requiring compensatory adaptations. We present an innovative ankle-foot orthosis (AFO) that was designed to allow two degree-of-freedom motion while serving to maintain proper foot position for subjects. The prototype AFO would introduce greater functionality over currently marketed devices by means of its inversion-eversion degree-of-freedom in addition to flexion/extension. The flexion/extension is controlled with the help of an actuator and inversion/eversion with a spring and a damper.
Feature detection and matching on atmospheric nuclear detonation video

Automated feature matching of nuclear detonations (NUDETs) enables three-dimensional point cloud reconstruction, and establishment a volume-based model to reduce uncertainty in estimating the yield of NUDETs solely from video. Establishing a volume-based model requires feature correspondences between wide viewpoints of 58°–110° that are larger than scale-invariant feature transform-based techniques can reliably match. The presented technique detects relative bright features in the NUDET known as ‘hotspots,’ and matches them across wide viewpoints using a spherical based object model. Results show that hotspots can be detected with a 71.95% hit rate and 86.03% precision. Hotspots are matched to films from different viewpoints with 76.6% correctness and a standard deviation of 16.4%. Hotspot descriptors are also matched in time sequence with 99.6% correctness and a standard deviation of 1.07%. The results demonstrate that a spherical model can serve as a viable descriptor model for matching across wide viewpoints when the object is known to be spherical. It also demonstrates an automated feature detection and matching combination that enables features to be matched from unsynchronised video across wide viewpoints of 58°–110° on spherical objects where state-of-the-art techniques are insufficient.
Does regular online testing enhance student learning in the numerical sciences? Robust evidence from a large data set

While a number of studies have been conducted on the impact of online assessment and teaching methods on student learning, the field does not seem settled around the promised benefits of such approaches. It is argued that the reason for this state of affairs is that few studies have been able to control for a number of confounding factors in student performance. We report on the introduction of a regular (every 3 weeks) low-mark online assessment tool in a large, first-year business mathematics course at the University of New South Wales, a major Australian university. Using a retrospective regression methodology together with a very large and rich data set, we test the proposition that exposure to the online assessment instrument enhances student learning. Significantly, we are able to control for prior student aptitude, in-course mastery, gender and even effort via a voluntary class attendance proxy. Furthermore, the study incorporates two large, and statistically diverse cohorts as well as manipulations in the model tested to robustly examine the outcomes. Our central result is that higher exposure to the online instrument robustly leads to higher student learning, all else being equal. Various implications for online assessment design, implementation and targeting are also discussed. [ABSTRACT FROM AUTHOR]
Learning and recalling of phase pattern in coupled BVP oscillators

We study a learning and recalling model of phase patterns in a coupled oscillators system. The model used is BVP oscillators coupled from the excitatory unit to both the excitatory and the inhibitory unit. Both coupling strengths are modulated based on the general Hebbian learning rule that depends on the activity of the oscillators. We introduce a parameter, /spl alpha/, which adjusts the ratio of each loading. Applying the phase dynamics theory, which was proposed by Kuramoto, to the present model we determine the adjustable parameter /spl alpha/ in order to bring the stable phase point in the phase equation to the teacher phase relation under a first-order approximation. We numerically ascertain that the recalling phase patterns agree well with the teacher phase pattern all over the range at a certain value of /spl alpha/. Our results show that the exact recalling of the various teacher phase pattern can be achieved by the present model with the Hebbian rule, independent of the number of oscillators.
Simultaneous measurement of cytosolic free Ca2+ in macula densa cells and in cortical thick ascending limb cells using fluorescence digital imaging microscopy.

Etude visant a mesurer simultanement le taux de Ca 2+ libre cytosolique dans les cellules de la macula densa et dans les cellules de la branche ascendante corticale epaisse de lapin. Utilisation de la technique de fluorescence digitale a image microscopique
Genome‐specific introgression between wheat and its wild relative Aegilops triuncialis

Introgression of sequences from crop species in wild relatives is of fundamental and practical concern. Here, we address gene flow between cultivated wheat and its widespread polyploid relative, Aegilops triuncialis, using 12 EST‐SSR markers mapped on wheat chromosomes. The presence of wheat diagnostic alleles in natural populations of the barbed goatgrass growing in proximity to cultivated fields highlights that substantial gene flow occurred when both species coexisted. Furthermore, loci from the A subgenome of wheat were significantly less introgressed than sequences from other subgenomes, indicating differential introgression into Ae. triuncialis. Gene flow between such species sharing nonhomeologous chromosomes addresses the evolutionary outcomes of hybridization and may be important for efficient gene containment.
Immunochemical detection of peptides and proteins on press‐blots after direct tissue gel isoelectric focusing

A sensitive method is described for the detection of tissue peptides and proteins. They are separated by tissue isoelectric focusing using thin large‐pore polyacrylamide gels, containing detergent and dimethylformamide, and are fixed with either glutaraldehyde or formaldehyde in gelatin‐coated nitrocellulose membranes using press‐blotting. The fixed peptide and protein antigens are visualized by immunoperoxidase staining. The spectrum of fixed tissue constituents may also be used to test antiserum reactivity and specificity in immunocytochemical staining procedures. Isoelectric focusing of 2 μL homogenates of the neurointermediate lobe of the pituitary allowed the immunodetection of peptides and proteins of various sizes and the determination of isoelectric points. However, direct application onto gels of small pieces of frozen tissue sections, sliced in a cryostat, appeared to be more efficient. By direct tissue isoelectric focusing of brain tissue, peptides were effectively eluted and separated from sections up to 100 μm thickness. This allowed the detection of small peptides with a detection limit of approximately 10 pg/section.
Reduction of glyoxylate by human serum.

Glyoxylate is enzymically reduced by human serum. Optimal concentrations of hydrogen ion, substrate, and coenzyme for this reduction by sera from healthy persons and from patients with disease of the heart or liver have been determined at 37°C. At this temperature, the reaction proceeds faster than with pyruvate or 2-oxobutyrate but more slowly than with hydroxypyruvate. Lactate dehydrogenase appears to be the enzyme involved.
Integrative classification of morphology and molecular genetics in central nervous system malformations

We propose a scheme to classify central nervous system (CNS) malformations that integrates morphology and genetics by using patterns of genetic expression as its basis. The precise genetic mutations are not necessary to know in all cases. The premises of this classification are (1) genetic expression in the neural tube follows gradients in the axes that are established at the time of gastrulation: vertical (dorsoventral and ventrodorsal); rostrocaudal; mediolateral. (2) Overexpression in one of these gradients generally results in duplication or hyperplasia of structures, or ectopic segmental (i.e., neuromeric) expression. (3) Underexpression in a gradient generally results in hypoplasia, noncleavage in the midline of paired structures or segmental deletion of neuromeres. These gradients may also affect the formation and migration of neural crest tissue, affecting non‐neural structures such as the face in the case of the mesencephalic neural crest, or induction of paraxial mesodermal in the posterior fossa. Additional criteria of the new classification allow for other genetic influences on developmental processes, such as cellular lineage, exemplified by tuberous sclerosis, and hemimegalencephaly. It is essential that the CNS be considered as a whole and classification not be regionalized, as to the cerebral cortex, because the limit of the rostrocaudal gradient may account for variability in clinical manifestations. © 2004 Wiley‐Liss, Inc.
ARTERIAL HYPERTENSION SALT , THE KIDNEYS , AND ARTERIAL HYPERTENSION

The kidneys play a major role in the regulation of the salt balance and thereby, regulate blood pressure. Salt sensitivity is acquired or genetically-induced and is noted in about 50% of patients with essential hypertension. This property leads to a high cardiovascular risk. In this situation, the benefi t of salt restriction is signifi cant, and this dietary change should be associated with a high potassium intake. In patients treated by antihypertensive drugs, salt restriction improves the blood pressure control, which can permit a reduction of the number of drugs required to achieve a normal blood pressure. The recommended maximal salt intake should not exceed 6 grams/day (NaCl). Because most dietary salt comes from processed foods, the help of the food industry is crucial for a long-term compliance with a reduced salt intake, which could yield an additional important benefi t in the reduction of cardiovascular risk. INTRODUCTION Salt (sodium chloride, NaCl) is essential for life. Many mechanisms work in concert in the body to tightly regulate the body’s sodium content and concentrations. These are essential for the maintenance of circulatory volume and cell membrane potential. Sodium chloride is a primary determinant of extracellular fl uid volume and thereby has an important role in blood pressure (BP) regulation. Kidney function determines the blood and plasma volume, and these affect the heart function, such as stroke volume. This, and the peripheral arterial resistance, determine the blood pressure. Dynamic regulation of renal sodium excretion is needed to respond to variations in dietary sodium intake. Of the physiological mechanisms invoked to maintain sodium balance, pressure-natriuresis is pre-eminent. Although essential hypertension (HTN) is a complex disease with polygenic and environmental contributions, a large body of evidence exists for the notion that increased salt intake contributes to the development of essential HTN (1). SODIUM AND HYPERTENSION The understanding of the role of sodium in human HTN can be divided into four parts, which are chronologically overlapping: dietary and drug manipulations, experimental HTN, epidemiological studies, and suggested pathophysiological mechanisms (Table 1). The fi rst part began with Ambard and Beaujard in 1904 (2) who reported that chloride deprivation may be associated with a decline in the blood pressure (BP) of hypertensive patients. As reported in the 1940s, the rice-fruit diet of Kempner (3) was successful in reversing malignant HTN in 2/3 of the patients studied.
Divergent Distribution of HIV-1 Drug-Resistant Variants on and off Antiretroviral Therapy

Objective To investigate the distribution of drug-resistant HIV-1 variants in plasma RNA and peripheral blood monuclear cell (PBMC) DNA at treatment failure while on therapy and after stopping therapy. Design Fifty-eight patients failing their first highly active antiretroviral treatment while on therapy and 50 patients after a median of 18.6 weeks after treatment interruption following multiple treatment failures were analysed. Methods Paired plasma HIV-1 RNA and PBMC HIV-1 DNA were used for genotypic antiretroviral resistance testing. Drug resistance was computed by using the Stanford on-line genotype interpretation system. Results The extent of drug resistance was larger in plasma RNA than in PBMC DNA in the on-therapy group (P=0.004) and in PBMC DNA than in plasma RNA in the off-therapy group (P=0.04). Interpretation of genotype based on PBMC DNA and plasma RNA in the on-therapy and in the off-therapy group would have missed detection of resistance to one or more drugs in 21 and 22% of the patients, respectively, compared to interpretation based on the other blood compartment. In a subset of 27 patients for whom a sample before stopping therapy was available, there was a significant decrease in the number of RNA (mean 8.1 to 5.3, P=0.004), but not DNA (mean 6.8 to 5.7, P=0.143), resistance mutations following treatment interruption. Conclusion While plasma RNA is the material of choice for early detection of drug resistance while on therapy, analysis of PBMC DNA may additionally support and possibly improve sensitivity of resistance testing in the absence of therapy.