Miracle-dz/UniFAR-FTUs huggingface dataset:
LMM-22: An Enhanced Linear Mixed Model (LMM) Approach for Genome-Wide Association Studies (GWAS) for the Prediction of Diseases and Traits among Humans from Genomics Data

Increasingly, genomics is being used for the prediction of specific traits and diseases (phenotypes) among humans. Wider availability of genomics data through multiple research projects (such as International HapMap Project1 and 1000 Genomes2) has been a catalyst in that direction. With the recent advances in machine learning and big data analysis, data computation resources and data models needed for genomics data analysis are readily available. However, the prediction of traits and diseases has its own challenges in terms of computational requirements and computational analysis, statistical analysis (example: confounding variables), and limited quality of data collection. Linear Mixed Models (LMM, a type of linear regression) is a common approach for Genome-wide Association Studies (GWAS) for the prediction of common traits among humans using genomics. This paper researches the existing LMM-based approaches for Genome-wide Association Studies (GWAS), describes the experiment performed on FaST-LMM approach from Microsoft Research, and then proposes an enhanced approach (called LMM-22) on how to address computational and statistical issues. LMM-22 focuses on the parallelization of LMM computations and execution of LMM-22 on General Purpose Graphics Processing Units (GPU) as against CPUs to accelerate the LMM approach for GWAS studies.
Territorial occupancy and breeding performance in a migratory raptor do not follow ideal despotic distribution patterns

It has commonly been argued that many territorial species select their breeding sites following an ideal despotic distribution model, in which the most productive, high-quality territories are more frequently occupied. Theoretical and empirical studies have shown that this occupancy pattern may have population regulatory consequences, leading to density dependence in heterogeneous habitats. During a 9-year research project in a forested area of south-eastern Spain, we tested some of the predictions of the ideal despotic distribution model and the site-dependent population regulation theory in a migratory raptor species, the booted eagle Hieraaetus pennatus. Contrary to the predictions of the despotic model, our results showed that the temporal pattern of territorial occupation did not differ from randomness, and that the territory occupancy rate was not significantly related to the reproductive parameters considered. At population level, the breeding variables were density independent, suggesting the absence of site-dependent regulation. In addition, we were unable to find significant differences in the habitat characteristics between high-quality and low-quality territories, classified according to the criteria of both occupancy frequency and average productivity. Overall, our results suggest that booted eagles select their territories at random, probably due to the lack of strong environmental heterogeneity, and that occupancy rate is not a good measure of territory quality for the population studied.
Influence of parental age on reproductive performance of an aphidophagous ladybird, Propylea dissecta (Mulsant)

Abstract: In the present study the influence of maternal and paternal ages on reproductive performance of an aphidophagous ladybird, Propylea dissecta (Mulsant) were investigated. Maternal age strongly influenced fecundity and pre‐oviposition period while paternal age strongly influenced the egg viability. Maternal age also influenced percent egg viability, however, at lower levels of significance. The results revealed that the fecundity and percent egg viability increased up to the respective maternal and paternal ages of 30 days and thereafter declined, indicating the onset of senescence. The results of the present study can help in better mass multiplication of the ladybird concerned and in laying foundation for further age‐related studies.
Linking estuarine nematodes to their suspected food. A case study from the Westerschelde Estuary (south-west Netherlands)

The present study investigates correlations between abundances of nematodes (at the genus level) and benthic microalgae on an intertidal mudflat in the Westerschelde Estuary (south-west Netherlands), using both multi- and univariate methods. Two sample series, covering surface areas of 10 cm2 (meioscale) and 1.25 cm2 (microscale) per sample were analysed. Trophic type analysis indicated that an average of 31% of the nematode community were candidate grazers of microalgae. Multivariate data analysis indicated that only a limited part of the variation in the nematode data could be explained in relation to pigments. Total nematodes did not show any correlation with the pigment data. On the meioscale, the genera Tripyloides and Calyptronema correlated negatively with chlorophyll concentration (chl-a and chl-c, respectively), while Prochromadorella correlated positively with the ratio of fucoxanthin to chl-a, a ratio which at the present sampling site can be considered to be a measure of the proportion of diatoms in the total microalgal standing stock. On the microscale, up to ten genera, comprising 76% of total nematode numbers, were correlated with pigments. A majority (74%) correlated specifically with the ratio of fucoxanthin to chl-a, while much fewer nematodes showed a direct correlation to pigment concentrations. Whereas many of these correlations could be explained in terms of direct trophic links, several others probably represented indirect relationships, trophic or other. Food densities may be less important structuring factors of nematode communities on tidal flats than relative abundances of particular food sources. It is suggested that nematodes actively migrate towards ‘optimal’ food patches, and that this dynamic aspect of nematode–microalgae correlations is best revealed at a spatial-scale small enough to allow a rapid response of nematodes to changes in adjacent patches. Apparently, the microscale used in the present study is more adequate for the study of such intricate interactions than the meioscale.
How actors move from primary agency to institutional agency: A conceptual framework and empirical application

This article contributes to the understanding of actors and agency in the theorization of institutional work. We analyse institutional work as a specific kind of social action that involves exercising institutional agency (with an articulate awareness of institutions) as opposed to primary agency (taking institutions for granted). We propose a conceptual framework for combining a view of actors, who have agency and may engage in institutional work, with a view of actors as socially constructed, in line with critical-realist ontology. Applying this framework to the empirical case of the Spanish social movement 15M, we examine how actors moved from having primary agency to having institutional agency and how organization mattered for this process. We find that organizing by experienced organizers, the founding of new organizations and prefigurative organization were of crucial importance for the increase in institutional agency.
Pokémon GO y su relación con la actividad física, orientación espacial y socialización en usuarios mexicanos (Pokémon GO and its relationship with physical activity, spatial orientation and socialization in mexican users)

La practica regular de actividad fisica es un predictor de importantes beneficios a la salud. En ese sentido, Pokemon GO es un juego de realidad aumentada para telefonos moviles inteligentes en el que sus usuarios deben salir a caminar para dar cumplimiento a los objetivos del juego, lo que implica realizacion de actividad fisica. El objetivo de este estudio consistio en analizar la cantidad de tiempo de actividad fisica realizada, percepciones de mejora en habilidades de orientacion espacial, socializacion, conocimiento de nuevos sitios urbanos, asi como en el medio natural y accidentes relacionados a jugar Pokemon GO en usuarios mexicanos. Los resultados mostraron diferencias significativas entre los dias por semana y tiempo destinados a caminar antes y despues de comenzar a jugar Pokemon GO, asi como percepciones de mejora en habilidades de orientacion espacial, socializacion, asistencia a lugares de interes nuevos en la ciudad y en el medio natural, ademas de que los principales accidentes relacionados tienen que ver con elementos urbanos como postes, senales de transito o banquetas. En conclusion, a partir del uso de Pokemon GO, se ha identificado un incremento en la actividad fisica realizada, una percepcion de mejora en la habilidad de orientacion espacial, conocimiento de nuevas personas y visita de nuevos sitios de interes en la ciudad y en el medio natural, por lo que se puede revertir el tiempo de sedentarismo que podria ocasionar el uso del telefono movil, al jugar Pokemon GO. Abstract. The regular practice of physical activity is a predictor of important health benefits. In that sense, Pokemon GO is an augmented reality game for smartphones in which users must walk to meet the objectives of the game, which involves physical activity. The objective of this study was to analyze the amount of physical activity performed, perceptions of improvement in spatial orientation skills, socialization, knowledge of new urban sites, as well as natural environment and accidents related to playing Pokemon GO in Mexican users. The results showed significant differences between days per week and time per day spent walking before and after starting to play Pokemon GO, as well as perceptions of improved spatial orientation skills, socialization, assistance to new places of interest in the city and in the natural environment in addition to the fact that the main related accidents refer to urban elements such as poles, traffic signs, or sidewalks. In conclusion, an increase in physical activity performed has been identified from the use of Pokemon GO, as well as a perception of improvement in the ability of spatial orientation, knowledge of new people and visiting new places of interest in the city and the environment, so sedentary time, which is commonly encouraged by using of smartphone, could be reversed by playing Pokemon GO.
Electrically recorded probing behaviour of thrips species on optimal and suboptimal hosts

Although the biology of many thrips species is well-studied, there is a lack of knowledge on the physiology of feeding. In contrast to aphids (Homoptera) that mainly feed on phloem elements in which the sap is under pressure, thrips (Thysanoptera) have to actively imbibe the contents of separate cells or at best suck the sap of damaged tissues as it exudes from wounds (Lewis, 1973). Thrips feeding mechanisms are still incompletely understood and this hampers studies on the effect of host plant resistance factors on the behaviour of thrips species which cause considerable problems in horticulture and agriculture. Comparison of optimal and suboptimal plants could be facilitated if it were possible to elucidate how stylet penetration and feeding behaviour are arranged in time and how these activities are affected by host-plant factors.
The cold‐water coral community as hotspot of carbon cycling on continental margins: A food‐web analysis from Rockall Bank (northeast Atlantic)

We present a quantitative food‐web analysis of the cold‐water coral community, i.e., the assembly of living corals, dead coral branches and sediment beneath, associated with the reef‐building Lophelia pertusa on the giant carbonate mounds at ~800‐m depth at Rockall Bank. Carbon flows, 140 flows among 20 biotic and abiotic compartments, were reconstructed using linear inverse modeling by merging data on biomass, on‐board respiration, δ15N values, and literature constraints on assimilation and growth efficiencies. The carbon flux to the coral community was 75.1 mmol C m−2 d−1 and was partitioned among (phyto)detritus (81%) and zooplankton (19%). Carbon ingestion by the living coral was only 9% of the carbon ingestion by the whole community and was portioned among (phyto)detritus (72%) and zooplankton (28%). Carbon cycling in the community was dominated by suspension‐ and filter‐feeding macrofauna associated with dead coral branches. Sediment traps mounted on a bottom lander trapped 0.77 mmol C m−2 d−1 (annual average), which is almost two orders of magnitude lower than total carbon ingestion (75.1) and respiration (57.3 mmol C m−2 d−1) by the coral community. This discrepancy is explained in two ways: the coral community intercepts organic matter that would otherwise not settle on the seafloor, and through their action as ecosystem engineers, the increased turbulence generated by the coral framework and organic‐matter depletion in the boundary layer augment the influx to the coral community. A comparison of macrofaunal biomass and respiration data with soft sediments reveals that coral communities are hot spots of biomass and carbon cycling along continental margins.
Influence of Sex on Relationship Between Morphometric Trait Measurement and Carcass Traits in Broiler Chicken Raised in Humid Tropic

: This study was conducted to determine the influence of sex on relationship among carcass traits (carcass weight, breast, drumstick, thigh, wings) and morphometric traits (body weight, breast girth, keel length, shank length, thigh length, wing length and body length) in broiler chicken. And also to evaluate correlated relationship between the morphometric traits and carcass traits. The 60 broiler birds were divided into 2 treatment groups (male and female) each group was replicated thrice with 10 birds per replicate. The birds were rear in deep litter system till the attain 56 days of age, body weight and morphometric traits measurements were taken on the 56 day. The 18 birds (9 from each group) were randomly selected, slaughtered and the carcass traits measured and recorded. The data obtained from these studies were subjected to Pearson correlation analysis. The correlated relationship among most carcass traits and morphometric traits were significantly positive (p<0.001) with correlation coefficients ranging from 0.01-0.681 in Males (M) Females (F) and in combination of Males and Female (M+F). The correlation between morphometric traits and carcass traits showed that breast girth and live body weight were positively and significantly (p<0.001) correlated with all carcass traits in all the sex groups. The observed significant relationship among the morphometric traits
Adaptive significance of circadian rhythms of montium a subgroup of Drosophila: I – locomotor behaviour

The rest/activity rhythm is an innate ubiquitous and complex biological phenomenon. It is essential/crucial for an organism's survival such as feeding, mate choice, escape from the predator, etc. Studies have shown that locomotor behaviour is sensitive to environment. The present investigations were made to understand the effect of different light regimes on locomotor behaviour of the two co-existing species of montium, a subgroup of Drosophila. Locomotor activity rhythms were assayed using Drosophila Activity Monitor. The activity of two species was analyzed in light/dark (LD), continuous dark (DD) and continuous light (LL) for 15th and 30th generations and the amount of activity was measured. The results revealed that the mean activity recorded for D. gangotrii and D. jambulina was significant. Unlike that of Drosophila melanogaster, these species entrain to LD, arrhythmic in LL and free runs in DD. Activity was either unimodal or bimodal. There was tremendous reduction in the activity in 30th generation flies compared to the 15th generation ones. Interestingly, period (τ) in all the groups was approximately 24 h.
Rice transgenic resources with gain-of-function phenotypes

After the completion of its genomic sequencing, rice (Oryza sativa L.) has become firmly established as the premiere model plant among monocot crops. Various genetic resources have been developed for rice to accelerate the identification and characterization of rice genes with as-yet unknown functions. These resources include collections that carry natural variations and progeny derived from chemical and irradiation mutagenesis. Collections of rice strains with natural or artificial DNA insertions that create loss-of-function mutations have been of great importance for gene discovery and tagging. However, it is often difficult to observe mutant phenotypes for functionally duplicated genes and genes essential for plant growth and development. To overcome this disadvantage, gain-of-function strategies have been developed, including activation tagging and full-length cDNA overexpressing gene (FOX)-hunting systems. In this review, we summarize the current status and discuss the advantages and disadvantages of the gain-of-function approaches, and then, perspectives on accelerating discovery of rice genes.
Derivation of economic weights for carcass traits in Japanese Black cattle from field records.

Summary Economic weights for carcass traits of 5333 Japanese Black steers each month were derived from April 1988 to December 1990 by multiple regression analysis. The carcass traits considered were marbling score (BMS No.), rib-eye area, rib thickness and subcutaneous fat thickness. Two economic variables were adopted as aggregate genotype (i.e. breeding objectives): carcass unit price (yen/kg carcass) and carcass sale price (yen/head). The economic weight for marbling score increased from 1988 to 1990, indicating that the relative economic importance of marbling score increased during the 3 years in Japan. Correlations among two indices calculated from different economic weights (i.e. a maximum value versus a minimum value of each trait) were very high, whichever economic variable was adopted. The results indicated that the effect of variation in the economic weights on efficiency of selection might be quite small under field conditions. Furthermore, differences between the standard selection index with economic weights and a desired gains selection index were calculated using genetic parameters from the literature and the economic weights derived in this study. It is concluded that the use of the standard selection index with economic weights may be more practical for the improvement of carcass traits of the Japanese Black, because the economic weights can be derived from field data, breeding objectives of farmers may differ from those of breeders and there is little effect of variation of economic weights on selection efficiency in Japan. Zusammenfassung Ableitung wirtschaftlicher Gewichte fur Schlachtkorpermerkmale bei Japanischen Schwarzen Rindern aus Felddaten Die wirtschaftlicher Gewichte wurden an Schlachtkorpern von 5333 Ochsen der Japanischen Schwarzen Rasse abgeleitet, Multiple Regressionsanalyse wurde an dem zwischen April 1988 und Dezember 1990 angefallenem Material angewendet. Berucksichtigte Merkamele waren Marmorierungsstarke (BMS), Ruckenmuskelflache, Rippenmuskeldicke und subkutane Fettdicke. Zuchtziele, also aggregierter Genotyp, waren Preis pro Kg Schlachtkorper oder Schlachtkorperwert. Die wirtschafliche Bedeutung der Marmorierung nahm von 1988 bis 1990 zu. Korrelationen wurden zwischen Indices geschatzt, wo die Bedeutung eines Merkmals einmal maximal, das andere mal minimal war (hochster bzw. niedrigster Preis in den 33 Monaten der Untersuchungszeit). Die Korrelation waren eng, d.h. die im Laufe des Untersuchungszeitraumes auftretenden Preisschwankungen haben wenig Wirkung auf einen Index. Es wurde auch ein “erwunschter genetischer Fortschritt” Index unter Verwendung von Literaturwerten erstellt, dessen Korrelation mit den optimalen Indices deutlich niedriger war. Es wird daraus geschlossen, das ein Standard Selektionsindex mit realen wirtschaftlichen Gewichten vorzuziehen ist, da die wirtschaftlichen Gewichte von Bauern sich von denen der Zuchter unterscheiden durften und die Preisschwankungen relativ geringfugig sich auf Selektionseffizienz durch den Index auswirken.
Impacts of alien bees on native plant-pollinator relationships: A review with special emphasis on plant reproduction

Alien pollinators can disrupt mutualistic plant-animal interactions. Here we review studies on alien bee pollinators, demonstrating the ways in which invasive honeybees and bumblebees affect native plant seed production. Impacts of alien pollinators vary among pollination systems and among components of pollination success (visitation frequency, pollen transfer per visit, and pollen limitation). Reproduction of native bird-pollinated plants is little impacted by alien honeybees, because birds can pollinate even when honeybees visit target flowers. In bee-pollinated native plants, alien honeybee impacts on reproduction may be pervasive, but are not clearly defined in many cases; this lack of clarity arises because very few control sites without invasive bees are available, making comparative evaluation impossible. In bumblebee-pollinated plants, alien bumblebee effects are strong because native and invasive bee species are closely related congeners (of the genus Bombus) with similar pollinator mechanisms; alien bumblebees compete strongly with natives or replace them. In general, morphological, ecological, and behavioral similarities between native and alien pollinators are important for predicting their competitive interaction intensities and their effects on plant reproduction. The impacts of alien bees include (1) decreased pollen transfer per visit because of the loose morphological correspondence between flowers and alien bees, (2) increased competition for floral resources and exclusion of native pollinators because native and alien bees have similar ecological requirements, (3) changes in native pollinator visitation frequency and pollination efficiency caused by particular alien pollinator behavioral traits (such as stealing nectar or collecting previously-deposited pollen from stigmas). For a quantitative evaluation of invasion impacts, it is important to determine whether native plants suffer pollen limitation. To demonstrate pollen limitation, comparative studies with controls (that lack alien pollinators) are required. This approach is essential for discerning possible mechanisms responsible for observed patterns.
Screening of the interacting proteins with NifA in Azospirillum brasilense Sp7 by the yeast two-hybrid system

NifA in Azospirillum brasilense plays a key role in regulating the synthesis and activity of nitrogenase in response to ammonia and oxygen available. In this work we used the yeast two-hybrid system to identify the proteins that interact with NifA. The nifA gene was fused to the yeast two-hybrid vector pGBD-C2, and three A. brasilense Sp7 genomic libraries for use in yeast two-hybrid studies were constructed. Screening of the libraries identified four clones encoding proteins that interact with NifA. The confirmation of the interactions of each gene product of the four clones and NifA were carried out by exchanging the vectors for nifA and the four clones and by mutageneses of the four clones with shift reading frame experiments in yeast two-hybrid studies. DNA sequence analyses showed that two clones encode proteins containing PAS domains that play an important role in signal transduction. One clone has high similarity with the fhuE gene of Escherichia coli, whose gene product is involved in iron uptake and transportation, and the other clone encodes an unknown protein.