Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.

Brief summaries describing the function of each gene's product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene's product, which we edited for consistency to produce a 'gene snapshot'. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature. Database URL: https://flybase.org/

Acid-sensing ion channels 1a (ASIC1a) inhibit neuromuscular transmission in female mice

Acid-sensing ion channels (ASIC) open in response to extracellular acidosis. ASIC1a, a particular subtype of these channels, has been described to have a postsynaptic distribution in the brain, being involved not only in ischemia and epilepsy, but also in fear and psychiatric pathologies. High-frequency stimulation of skeletal motor nerve terminals (MNTs) can induce presynaptic pH changes in combination with an acidification of the synaptic cleft, known to contribute to muscle fatigue. Here, we studied the role of ASIC1a channels on neuromuscular transmission. We combined a behavioral wire hanging test with electrophysiology, pharmacological, and immunofluorescence techniques to compare wild-type and ASIC1a lacking mice (ASIC1a −/− knockout). Our results showed that 1) ASIC1a −/− female mice were weaker than wild type, presenting shorter times during the wire hanging test; 2) spontaneous neurotransmitter release was reduced by ASIC1a activation, suggesting a presynaptic location of these channels at individual MNTs; 3) ASIC1a-mediated effects were emulated by extracellular local application of acid saline solutions (pH = 6.0; HEPES/MES-based solution); and 4) immunofluorescence techniques revealed the presence of ASIC1a antigens on MNTs. These results suggest that ASIC1a channels might be involved in controlling neuromuscular transmission, muscle contraction and fatigue in female mice.Fil: Urbano Suarez, Francisco Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Lino, Noelia Gisele. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: González Inchauspe, Carlota María Fabiola. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Gonzalez, Laura Elisabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Colettis, Natalia Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Vattino, Lucas Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Wunsch, Amanda M.. University of Iowa; Estados UnidosFil: Wemmie, John A.. University of Iowa; Estados UnidosFil: Uchitel, Osvaldo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentin

Pedunculopontine nucleus gamma band activity-preconscious awareness, waking, and REM sleep

The pedunculopontine nucleus (PPN) is a major component of the reticular activating system (RAS) that regulates waking and REM sleep, states of high-frequency EEG activity. Recently,we described the presence of high threshold, voltage-dependent N- and P/Q-type calcium channels in RAS nuclei that subserve gamma band oscillations in the mesopontine PPN, intralaminar parafascicular nucleus (Pf), and pontine subcoeruleus nucleus dorsalis (SubCD). Cortical gamma band activity participates in sensory perception, problem solving, and memory. Rather than participating in the temporal binding of sensory events as in the cortex, gamma band activity in the RAS may participate in the processes of preconscious awareness, and provide the essential stream of information for the formulation of many of our actions.That is, the RAS may play an early permissive role in volition. Our latest results suggest that (1) the manifestation of gamma band activity during waking may employ a separate intracellular pathway compared to that during REM sleep, (2) neuronal calcium sensor (NCS-1) protein, which is over expressed in schizophrenia and bipolar disorder, modulates gamma band oscillations in the PPN in a concentration-dependent manner, (3) leptin, which undergoes resistance in obesity resulting in sleep dysregulation, decreases sodium currents in PPN neurons, accounting for its normal attenuation of waking, and (4) following our discovery of electrical coupling in the RAS, we Hypothesize that there are cell clusters within the PPN that may act in concert. These results provide novel information on the mechanisms controlling high-frequency activity related to waking and REM sleep by elements of the RAS.Fil: Urbano Suarez, Francisco Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas (i); ArgentinaFil: Donofrio, Stasia M.. University Of Arkansas For Medical Sciences; Estados UnidosFil: Luster, Brennon R.. University Of Arkansas For Medical Sciences; Estados UnidosFil: Beck, Paige B.. University Of Arkansas For Medical Sciences; Estados UnidosFil: Hyde, James Robert. University Of Arkansas For Medical Sciences; Estados UnidosFil: Bisagno, Veronica. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas (i); Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Garcia Rill, Edgar. University Of Arkansas For Medical Sciences; Estados Unido

Photo-Fenton process at natural conditions of pH, iron, ions, and humic acids for degradation of diuron and amoxicillin

Effect of ferric ions at concentrations typically found in natural waters (0.05 to 1.06 mg L−1) and low H2O2 concentrations (between 0.5 and 17.9 mg L−1) on simulated sunlight-induced (300 W m−2) photo-Fenton degradation at initial neutral pH (7.0) of amoxicillin and diuron in Milli-Q water was studied using an rotatable central composite experimental design 22 with a central and two axial points. H2O2 concentration was the parameter playing the key role on the degradation of both pollutants. Despite that initial pH was 7.0 in Milli-Q water, this latter decreased rapidly in the first minutes, reaching values of 3.5 and 5.0 for diuron and amoxicillin respectively after 15 min of simulated sunlight irradiation. In contrast, in presence of bicarbonate/carbonate (HCO3 −/CO3 =), fluoride (F−), and humic acids (HAs) at concentrations found often in surface and well waters with ferric ion and H2O2 concentrations of 0.3 and 9.7 and 15.2 mg L−1 respectively, both pollutants exhibited a strong degradation keeping the circumneutral pH. Amoxicillin and diuron degradation byproducts found by HPLC/MS were compatible with HO• and/or CO3 –• radical attack. Several photo-induced processes such as photo-Fenton (by dissolved ferric-HA complexes), heterogeneous photocatalysis (by colloidal iron), UV-B H2O2 photolysis, irradiated-dissolved organic matter, and their reactions with pollutants would be the main oxidative route responsible of degradations. These findings demonstrated that it could be possible using iron concentrations often found in natural waters to oxidize via photo-Fenton processes among other events, organic pollutants at natural pH conditions.Fil: Buitrago, Jose L.. Universidad Tecnológica de Pereira; ColombiaFil: Sanabria, Janeth. Universidad del Valle; ColombiaFil: Gútierrez Zapata, Héctor M.. Universidad del Valle; ColombiaFil: Urbano Ceron, Frankly J.. Instituto Nacional de Medicina Legal y Ciencias Forenses; ColombiaFil: García Barco, Alejandra. Universidad Tecnológica de Pereira; ColombiaFil: Osorio Vargas, Paula Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Ciencias Aplicadas "Dr. Jorge J. Ronco". Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Ciencias Aplicadas; Argentina. Universidad Tecnológica de Pereira; Colombia. Universidad del Bio Bio; ChileFil: Rengifo Herrera, Julian Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Ciencias Aplicadas "Dr. Jorge J. Ronco". Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Ciencias Aplicadas; Argentin

Automated generation of gene summaries at the Alliance of Genome Resources

Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages

Desórdenes venosos pélvicos en la mujer debidos a varices pélvicas. Tratamiento mediante embolización. Breve revisión

El síndrome de congestión pélvica (SCP), actualmente englobado en los “desordenes venosos pélvicos en la mujer (DVPm) debidos a varices pélvicas”1 es una condición patológica que sufre un importante porcentaje de mujeres, y generalmente, se caracteriza por dolor abdominal que dura al menos 6 meses. Existen diferentes tipos de tratamientos, pero el más extendido es la embolización de las venas varicosas pélvicas. Presentamos una pequeña revisión del tema y aportamos nuestra experiencia de casi 20 años con más de 500 pacientes. La embolización de las varices pélvicas parece ser un tratamiento seguro y relativamente efectivo en la gran mayoría de las mujeres

Automated generation of gene summaries at the Alliance of Genome Resources.

Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages

The Effect of Goal Orientation to the Academic Performance in Mathematics of Grade 10 Students

Mathematics is a multifaceted activity; it has a lot of faces, even those one we can’t notice. Each facet is worth it to deal with so that every individual will be prepared for their future. It provides us with something to walk through difficulties. It is beneficial to set a goal for each individual, whether it is a short-term goal, long-term goal, or even the goal that falls in the middle. Setting a goal has been used extensively in a variety of ways, even on the outside of the school or in any settings. It could possibly bring you a positive achievement if follows correctly. The main purpose of this study was to determine if the goal orientation of the grade 10 students of one school in Region IV-A (CALABARZON) Rizal has a significant effect to their academic performance. As regards to the data of the significant effect of goal orientation to the academic performance of grade 10 students, the p-value of less than 0.001 revealed that the task goal orientation of the respondents has a significant effect to their academic performance in mathematics. The p-value of 0.007 implied that the ego goal orientation of the respondents has also had a significant effect on their academic performance in mathematics. Therefore, the researchers concluded that there is a significant effect of the respondents’ goal orientation, although the effect is very low and low, respectively. For the betterment, it is advised that researchers conducting a comparable study on goal orientation expand their scope to include student study habits, which may be influenced by a variety of circumstances

The Effect of Goal Orientation to the Academic Performance in Mathematics of Grade 10 Students

Mathematics is a multifaceted activity; it has a lot of faces, even those one we can’t notice. Each facet is worth it to deal with so that every individual will be prepared for their future. It provides us with something to walk through difficulties. It is beneficial to set a goal for each individual, whether it is a short-term goal, long-term goal, or even the goal that falls in the middle. Setting a goal has been used extensively in a variety of ways, even on the outside of the school or in any settings. It could possibly bring you a positive achievement if follows correctly. The main purpose of this study was to determine if the goal orientation of the grade 10 students of one school in Region IV-A (CALABARZON) Rizal has a significant effect to their academic performance. As regards to the data of the significant effect of goal orientation to the academic performance of grade 10 students, the p-value of less than 0.001 revealed that the task goal orientation of the respondents has a significant effect to their academic performance in mathematics. The p-value of 0.007 implied that the ego goal orientation of the respondents has also had a significant effect on their academic performance in mathematics. Therefore, the researchers concluded that there is a significant effect of the respondents’ goal orientation, although the effect is very low and low, respectively. For the betterment, it is advised that researchers conducting a comparable study on goal orientation expand their scope to include student study habits, which may be influenced by a variety of circumstances