NCBI GEO: archive for high-throughput functional genomic data

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as ‘Minimum Information About a Microarray Experiment’ (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/

Efecto de la oferta de pasto kikuyo y ensilaje de avena sobre la producción y calidad composicional de la leche bovina

The effects of the offer of kikuyu grass and oats silage on production and compositional quality of milk was evaluated using 18 Holstein cows in early and mid lactation, between 2 and 4 births, with a live weight (LW) of 585 kg and a milk production of 22.0 L/d. The experiment was carried out at Marengo Agricultural Center of the National University of Colombia. Three offers of silage (dry matter, DM); 0%, 0.7% y 1.4% of LW) were evaluated complemented with kikuyu grass in grazing to reach a total offer of 4%. The animals were supplemented daily with a balanced supplement. Kikuyu grass intake was estimated using chromium (external marker) and acid detergent indigestible fiber (internal marker). Kikuyu intake decreased (p < 0.001) to increase the proportion of silage in early and mid lactation cows. The milk production was affected by interaction kikuyu-silage offer, lactating stage and time of sampling (p < 0.01). Protein (0.2 units) (p < 0.05) and casein (0.35 units) concentration (p < 0.05) increased in early lactation cows offered oat silage at a level of 0.7% LW milk, while an offer of 1.4% LW decreased protein concentration (0.15 units) and slightly increased casein concentration (0.05 units) (p < 0.05). Milk fat tended to increase as oat silage was offered in the diet (p < 0.1).  Se evaluó la oferta de pasto kikuyo y ensilaje de avena sobre la producción y calidad composicional de la leche; utilizando 18 vacas Holstein entre 2 y 4 partos en primer y segundo tercio de lactancia con un peso vivo (PV) de 585 kg y una producción de leche de 22,0 L/d. El experimento se realizó en el Centro Agropecuario Marengo de la Universidad Nacional de Colombia. Se evaluaron tres ofertas de ensilaje (materia seca; MS); 0%, 0,7% y 1,4% del PV, complementados con kikuyo en pastoreo hasta alcanzar una oferta total del 4%. Los animales se suplementaron diariamente con un alimento balanceado. Se estimó el consumo de kikuyo utilizando óxido de cromo (marcador externo) y la fibra en detergente ácido indigerible (marcador interno). El consumo de kikuyo disminuyó (p < 0,001) al aumentar la oferta de ensilaje para vacas de primero y segundo tercio. La producción de leche estuvo afectada por la interacción de la oferta kikuyo-ensilaje, tercios de lactancia y días de medición (p < 0,01). Al ofrecer ensilaje de avena (0,7% PV) se incrementó la concentración de proteína (0,2 unidades) (p < 0,05) y caseína en leche (0,35 unidades) (p < 0,05), mientras una oferta de ensilaje de 1,4% PV disminuyó la concentración de proteína (0,15 unidades) e incrementó levemente la concentración de caseína (0,05 unidades) respecto al kikuyo solo en vacas de primer tercio de lactancia (p < 0,05). Ofertas de ensilaje de avena tienden (p < 0,1) a aumentar la concentración de grasa en leche.   

GEOTHERMOBAROMETRY OF GRANULITES OF THE JUIZ DE FORA COMPLEX AND THE ANDRELÂNDIA GROUP IN THE REGION OF ABRE CAMPO AND MANHUAÇU, MINAS GERAIS, BRAZIL

Granulitos máficos e félsicos ortoderivados do Complexo Juiz de Fora e granulitos aluminosos paraderivados do Grupo Andrelândia são encontrados na região de Abre Campo e Manhuaçu, estado de Minas Gerais. As rochas orto- e paraderivadas estão tectonicamente intecaladas como resultado da edificação do Orógeno Araçuaí de idade Neoproterozóica. Os granulitos máficos são formados pela associação mineral plagioclásio + ortopiroxênio + clinopiroxênio ± hornblenda. Os granulitos félsicos são compostos por plagioclásio + quartzo + biotita ± feldspato potássico ± ortopiroxênio ± granada. A associação mineral dos granulitos aluminosos é dada por plagioclásio + quartzo + granada + biotita ± feldspato potássico ± sillimanita. Os cálculos utilizando a geotermobarometria convencional e o programa THERMOCALC resultaram em temperaturas entre 748°C e 870°C e pressões entre 5,7 kbar e 7,5 kbar para o metamorfismo de fácies granulito que gerou essas rochas durante o desenvolvimento do Orógeno Araçuaí. A ocorrência local de foliação milonítica e de porfiroclastos fortemente deformados é provavelmente associada ao estágio de exumação ao longo de zonas de cisalhamento Neoproterozóicas, como as de Manhuaçu e de Abre Campo, durante o colapso gravitacional do Orógeno Araçuaí

Gravitational waves: search results, data analysis and parameter estimation

The Amaldi 10 Parallel Session C2 on gravitational wave (GW) search results, data analysis and parameter estimation included three lively sessions of lectures by 13 presenters, and 34 posters. The talks and posters covered a huge range of material, including results and analysis techniques for ground-based GW detectors, targeting anticipated signals from different astrophysical sources: compact binary inspiral, merger and ringdown; GW bursts from intermediate mass binary black hole mergers, cosmic string cusps, core-collapse supernovae, and other unmodeled sources; continuous waves from spinning neutron stars; and a stochastic GW background. There was considerable emphasis on Bayesian techniques for estimating the parameters of coalescing compact binary systems from the gravitational waveforms extracted from the data from the advanced detector network. This included methods to distinguish deviations of the signals from what is expected in the context of General Relativity

Geotermobarometria de granulitos do complexo Juiz de Fora e do grupo Andrel?ndia na regi?o de Abre Campo e Manhua?u, Minas Gerais, Brasil.

Granulitos m?ficos e f?lsicos ortoderivados do Complexo Juiz de Fora e granulitos aluminosos paraderivados do Grupo Andrel?ndia ocorrem na regi?o de Abre Campo e Manhua?u, estado de Minas Gerais. As rochas orto- e paraderivadas est?o tectonicamente intercaladas como resultado da edifica??o do Or?geno Ara?ua? de idade neoproterozoica. Os granulitos m?ficos s?o formados pela associa??o mineral plagiocl?sio + ortopirox?nio + clinopirox?nio ? hornblenda. Os granulitos f?lsicos s?o compostos por plagiocl?sio + quartzo ? feldspato pot?ssico ? ortopirox?nio ? granada. A associa??o mineral dos granulitos aluminosos ? dada por plagiocl?sio + quartzo + granada + biotita ? feldspato pot?ssico ? sillimanita. Os c?lculos utilizando a geotermobarometria convencional e o programa THERMOCALC resultaram em temperaturas entre 748 ?C e 870 ?C e press?es entre 5,7 kbar e 7,5 kbar para o metamorfismo de f?cies granulito que gerou essas rochas durante o desenvolvimento do Or?geno Ara?ua?. A ocorr?ncia local de folia??o milon?tica e de porfiroclastos intensamente deformados ? associada a reativa??o das zonas cisalhamento Manhua?u e Abre Campo durante o escape lateral da por??o sul do or?geno. Esse est?gio ? caracterizado pelo desenvolvimento de grandes zonas de cisalhamento transcorrentes dextrais. A exuma??o dos granulitos do Complexo Juiz de Fora e do Grupo Andrel?ndia est? relacionada ao colapso gravitacional do Or?geno Ara?ua?.Mafic and felsic ortho-derived granulites of the Juiz de Fora Complex and para-derived aluminous granulites of the Andrel?ndia Group occur in the Abre Campo and Manhua?u regions, state of Minas Gerais. The ortho- and para-derived rocks are tectonic intercalated as result of the edification of the neoproterozoic Ara?ua? Orogen. The mafic granulites are formed by the mineral assemblage of plagioclase + orthopyroxene + clinopyroxene ? hornblende. The felsic granulites are composed of plagioclase + quartz + potassium feldspar ? orthopyroxene ? garnet. The mineral assemblage of the aluminous granulites is plagioclase + quartz + garnet + biotite ? potassium feldspar ? sillimanite. Calculations using conventional geothermobarometry and the THERMOCALC software resulted in temperatures between 748 ?C and 870 ?C and pressures between 5.7 kbar and 7.5 kbar for the granulite facies metamorphism related to the development of the Ara?ua? Orogen. The local presence of a mylonitic foliation as well as of intensily deformed porphyroclasts is associated to the reactivation of shear zones as those of Manhua?u and Abre Campo during southward escape of orogen. This stage is characterized for development of large dextral shear zones. The exhumation of granulites of Juiz de Fora Complex and Andrelandia Group are related to the gravitational collapse of the Ara?ua? Orogen

Effect of the offer of kikuyu grass and oat silage on milk bovine production and quality composition

Se evaluó la oferta de pasto kikuyo y ensilaje de avena sobre la producción y calidad composicional de la leche, utilizando 18 vacas Holstein entre 2 y 4 partos en primer y segundo tercio de lactancia con un peso vivo (PV) de 585 kg y una producción de leche de 22,0 L/d. El experimento se realizó en el Centro Agropecuario Marengo de la Universidad Nacional de Colombia. Se evaluaron tres ofertas de ensilaje (materia seca, MS), 0%, 0,7% y 1,4% del PV, complementados con kikuyo en pastoreo hasta alcanzar una oferta total del 4%. Los animales se suplementaron diariamente con un alimento balanceado. Se estimó el consumo de kikuyo utilizando óxido de cromo (marcador externo) y la fibra en detergente ácido indigerible (marcador interno). El consumo de kikuyo disminuyó (p menor que 0,001) al aumentar la oferta de ensilaje para vacas de primero y segundo tercio. La producción de leche estuvo afectada por la interacción de la oferta kikuyo-ensilaje, tercios de lactancia y días de medición (p menor que 0,01). Al ofrecer ensilaje de avena (0,7% PV) se incrementó la concentración de proteína (0,2 unidades) (p menor que 0,05) y caseína en leche (0,35 unidades) (p menor que 0,05), mientras una oferta de ensilaje de 1,4% PV disminuyó la concentración de proteína (0,15 unidades) e incrementó levemente la concentración de caseína (0,05 unidades) respecto al kikuyo solo en vacas de primer tercio de lactancia (p menor que 0,05). Ofertas de ensilaje de avena tienden (p menor que 0,1) a aumentar la concentración de grasa en leche.;The effects of the offer of kikuyu grass and oats silage on production and compositional quality of milk was evaluated using 18 Holstein cows in early and mid lactation, between 2 and 4 births, with a live weight (LW) of 585 kg and a milk production of 22.0 L/d. The experiment was carried out at Marengo Agricultural Center of the National University of Colombia. Three offers of silage (dry matter, DM), 0%, 0.7% y 1.4% of LW) were evaluated complemented with kikuyu grass in grazing to reach a total offer of 4%. The animals were supplemented daily with a balanced supplement. Kikuyu grass intake was estimated using chromium (external marker) and acid detergent indigestible fiber (internal marker). Kikuyu intake decreased (p menor que 0.001) to increase the proportion of silage in early and mid lactation cows. The milk production was affected by interaction kikuyu-silage offer, lactating stage and time of sampling (p menor que 0.01). Protein (0.2 units) (p menor que 0.05) and casein (0.35 units) concentration (p menor que 0.05) increased in early lactation cows offered oat silage at a level of 0.7% LW milk, while an offer of 1.4% LW decreased protein concentration (0.15 units) and slightly increased casein concentration (0.05 units) (p menor que 0.05). Milk fat tended to increase as oat silage was offered in the diet (p menor que 0.1).Ganado de leche-Ganadería lech

NCBI GEO: archive for functional genomics data sets—10 years on

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/

Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera

Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection