Miracle-dz/UniFAR-FTUs huggingface dataset:
Seeing sunlit owls in a new light: orienting Snowy Owls may not be displaying

Snowy Owls Bubo scandiacus often face the sun when sitting on the ground or when perched. Such sun-orienting has been suggested to represent a visual display to conspecifics but other explanations have not been thoroughly examined. We observed the orientation of wintering Snowy Owls to both the sun and the wind, and their perching behaviour during two winters in central Saskatchewan, Canada. We proposed three new explanations for sun orientation in addition to the display hypothesis: thermoregulation, hunting and defense against predators. On sunny days, 44% of 710 owls faced the sun; this was non-random because few did so on overcast days. Sun as opposed to wind orienting was strongly associated with weather conditions. Logistic regressions indicated that at temperatures below -13 °C and at wind speeds greater than about 18 km/ hr, owls tended to orient to the wind rather than the sun. The likelihood of wind-orienting increased if the owl perched above the ground whereas the likelihood of sun-orientating increased slightly when the owl was sitting on the ground. There was no difference between the sexes in orienting behaviour. Snowy Owls seemed to prioritize wind-orienting for thermoregulation but the results are also consistent with the idea that sun-orientation can reduce heat loss. Facing into the sun did not support the hunting explanation because the birds would have been blinded and not able to see prey but was consistent with the protection explanation if it helps to increase vigilance against enemies. Although we cannot completely rule out the display explanation, the spatial context of sunning owls and a lack of a sex effect makes it unlikely that this is the main function. Instead, owls seem to trade off wind versus sun orienting according to the prevailing weather conditions and do so mainly to thermoregulate and perhaps to maintain vigilance. This article is protected by copyright. All rights reserved.
The foraging ecology of two Namib Desert harvester ant species

Forager abundance, activity, dispersion and diet of Messor denticomis and Tetramorium rufescens was studied on a monthly basis for 17 months. There were large fluctuations in forager abundance with both species exhibiting similar patterns; the first peak in abundance occurring five months after a peak in food availability and the second peak in abundance coinciding with a second, smaller pulse of food. Food supplementation experiments demonstrated that availability of food partially regulated the absolute numbers of ants foraging. Both species shared similar activity patterns with the majority of activity occurring at night. Foragers were randomly dispersed within the 16 ha study plot. Most of the food collected by both species was Enneapogon brachystachyus seeds. These seeds were collected during the first half of the study when seeds were apparently superabundant. With declining seed availability both species took more non-seed plant matter and arthropods. In both species, diet range fluctuated widely, .
The Chemical Composition of Cuticular Lipids from Dragonflies (Odonata)

The cuticular lipids of 4 species (Aeschna grandis, A. mixta, Sympetrum sanguineum, S. danae) of the insect order Odonata (dragonflies) have been analysed. Alkanes, triglycerides, and free fatty acids predominate and minor amounts of monoester waxes have been detected. Among the hydrocarbons unbranched odd-numbered (56 - 66%) predominate, followed by monometnyl-alkanes with the branch in the middle of molecule (11 - 19%), 3-methylalkanes (7 - 15%), and 2-methyl-alkanes (1 - 13%). Moreover, alkanes (1 - 12%) were detected. The composition of triglycerides and free fatty acids were very similar with 14 : 0, 16 : 0, 18 : 0, 16 : 1. 18 : 1 and 18 : 2 being main constituents. Ester waxes were composed of unbranched and predominantly even-numbered fatty acids and alcohols with chain lengths C14- C30. The results are discussed from a chemotaxonomic viewpoint. Similarities of the integumental lipjids from Odonata and Plecoptera were found.
Thymic output and CD4 T-cell reconstitution in HIV-infected children on early and interrupted antiretroviral treatment: evidence from the CHER trial

OBJECTIVES: Early treatment of HIV-infected children and adults is important for optimal immune reconstitution. Infants’ immune systems are more plastic and dynamic than older children’s or adults’, and deserve particular attention. This study aimed to understand the response of the HIV-infected infant immune system to early antiretroviral therapy (ART) and planned ART interruption and re-start. DESIGN: We used linear and nonlinear regression and mixed-effects models to describe children’s CD4 trajectories and to identify predictors of CD4 count during early and interrupted ART. METHODS: Data from HIV-infected children enrolled CHER trial, starting ART aged between 6 and 12 weeks, was used to explore the effect of ART on immune reconstitution. RESULTS: Early treatment arrested the decline in CD4 count but did not fully restore it to the levels observed in HIV-uninfected children. Treatment interruption at 40 or 96 weeks resulted in a rapid decline in CD4 T-cells, which on retreatment returned to levels observed before interruption. Naive CD4 T-cell count was an important determinant of overall CD4 levels. A strong correlation was observed between thymic output and the stable CD4 count both before and after treatment interruption. CONCLUSIONS: Early identification and treatment of HIV-infected infants is important to stabilize CD4 counts at the highest levels possible. Once stabilized, children’s CD4 counts appear resilient, with good potential for recovery following treatment interruption. The naive T-cell pool and thymic production of naive cells are key determinants of children’s CD4 levels.
Inhibition of Lipid Oxidation with Phosphates in Muscle Foods

Lipid oxidation degrades the quality and decreases the shelf-stability of muscle foods. The depletion of phosphates prior to cooking may be a major factor in this undesirable reaction. Thus, the effects on lipid oxidation with the use of an encapsulate to protect the phosphates during raw storage was investigated. Unencapsulated and encapsulated sodium tripolyphosphate (STP) and sodium acid pyrophosphate (SAPP), at a level of 0.5%, were compared to control samples in cooked, ground beef patties at 0 and 6 days. The unencapsulated and encapsulated treated samples were different (P<0.05) from the controls with an 81.1% to 89.7% improvement in the reduction of lipid oxidation. However, encapsulated phosphates did not decrease the level of oxidation beyond the unencapsulated treatment. This observation was attributable to the lack of a storage time prior to evaluating rancidity. Therefore, with an increase of precooked storage time, the 0.10% active encapsulated STP was essentially as effective as 0.20% unencapsulated STP for both 3 and 11 days. Unencapsulated STP (0.3% or 0.5%), encapsulated STP (0.3% or 0.5% active), a blend of unencapsulated (0.3%) and encapsulated (0.2% active) STP, and a control treatment was incorporated in ground turkey breast and stored at 3 °C for 0, 5, and 10
Low-dosage antibiotic intake can disturb gut microbiota in mice

ABSTRACT The proportion of different microbial populations in gut microbiota (GM) is an important factor that in recent years has been linked to obesity and numerous metabolic diseases. Antibiotics are one of the factors that can dramatically alter GM at therapeutic dosages, but their effects at subtherapeutic doses have been less investigated. Here, a mouse model using a total of 60 C57BL/6J mice was used to compare the evolution of total microbiota, four phyla and two genera considered as probiotics in control mice, and mice exposed to 50 µg/kg of ampicillin, 100 µg/kg of tetracycline or 100 µg/kg of sulphadiazine. The results obtained found that the presence of antibiotics in foods, even at trace concentrations, can disturb mouse GM, causing in all antibiotics significant increases of Proteobacteria (about 2 log CFU/g) or decreases of Bifidobacterium and Lactobacillus (about 1 log CFU/g) for the cases of ampicillin and sulphadiazine.
Multi-objective optimized breeding strategies

Multi-objective optimization is an emerging field in mathematical optimization which involves optimization a set of objective functions simultaneously. The purpose of most plant and animal breeding programs is to make decisions that will lead to sustainable genetic gains in more than one traits while controlling the amount of co-ancestry in the breeding population. The decisions at each cycle in a breeding program involve multiple, usually competing, objectives; these complex decisions can be supported by the insights that are gained by using the multi-objective optimization principles in breeding. The discussion here includes the definition of several multi-objective optimized breeding approaches and the comparison of these approaches with the standard multi-trait breeding schemes such as tandem selection, culling and index selection. We have illustrated the newly proposed methods with two empirical data sets and with simulations.
Environmental change impacts on the shell characteristics of rhynchonelliform brachiopods

Since the Industrial Revolution, anthropogenically-increased CO 2 has altered oceanic surface seawaters through warming and acidification. Previous ocean acidification research has mainly focussed on short-term laboratory manipulations of conditions. Incorporating different approaches investigating both the impacts of past and future environmental change provides a more complete understanding of organisms’ responses. Rhynchonelliform brachiopods inhabit all of the world’s oceans, have been important marine taxa for 550 million years and are potentially one of the most vulnerable phyla to ocean acidification because >90% of their dry mass resides in their skeleton. Little is known, however, about the effects of lowered pH and warming on these taxa. A polar (Liothyrella uva) and a temperate (Calloria inconspicua) brachiopod were cultured under predicted end-century environmental conditions in separate CO 2 perturbation experiments for 7 months and 3 months, respectively. Multiple shell characteristics were analysed to determine the effects of future ocean acidification and warming on shell production and maintenance. Impacts of past environmental change were also evaluated on shell characteristics of C. inconspicua using museum specimens collected from the same sampling site in New Zealand every decade since 1900 to the present day. In the experiments on live specimens, lowered pH did not affect shell growth rates, ability to repair shells, punctal densities, calcite fibre size or elemental composition in either species. Shell dissolution with decreasing pH will impose a threat to both species, with more extensive dissolution occurring in L. uva because of the lower temperatures in its habitat. This was correlated with a decrease in the thickness of the primary layer that was counteracted by an increase in secondary layer thickness and total shell thickness in L. uva. The less extensive dissolution in C. inconspicua was reflected in the unaffected inner shell layers thicknesses and total shell thickness with decreasing pH. Shell growth rate was only affected by temperature in L. uva, with a 2°C rise increasing growth. Similarly, calcification index, total shell thickness, primary and secondary layer thickness, punctal density and elemental composition of C. inconspicua have not changed over the last century. Shell density in C. inconspicua, however, increased from 1900 to 2014 as this species appeared to lay down more shell by constructing thinner punctae. The majority of shell characteristics have remained unchanged over the last 110 years and are likely to continue to be unaffected by environmental change over the next 84 years. This indicates that shell production and maintenance are robust in a polar and a temperate brachiopod to recent past and predicted end-century acidified and warming conditions. Long-term laboratory experiments and historical specimens in this study have produced insights into how these species can acclimate and their possible ability to adapt to future change.
Características de la estructura molecular de las proteínas E del virus del Zika y E1 del virus de la rubéola y posibles implicaciones en el neurotropismo y en las alteraciones del sistema nervioso

Introducción. El virus del Zika (ZIKV) es un flavivirus con envoltura, transmitido a los seres humanos principalmente por el vector Aedes aegypti. La infección por ZIKV se ha asociado con un gran neurotropismo y con efectos neuropáticos, como el síndrome de Guillain-Barré en el adulto y la microcefalia fetal y posnatal, así como con un síndrome de infección congénita similar al producido por el virus de la rubéola (RV). Objetivo. Comparar las estructuras moleculares de la proteína de envoltura E del virus del Zika (E-ZIKV) y de la E1 del virus de la rubéola (E1-RV), y plantear posibles implicaciones en el neurotropismo y en las alteraciones del sistema nervioso asociadas con el ZIKV.Materiales y métodos. La secuencia de aminoácidos de la proteína E-ZIKV (PDB: 5iZ7) se alineó con la de la glucopreteína E1 del virus de la rubéola (PDB: 4ADG). Los elementos de la estructura secundaria se determinaron usando los programas Vector NTI Advance®, DSSP y POSA, así como herramientas de gestión de datos (AlignX®). Uno de los criterios principales de comparación y alineación fue la asignación de residuos estructuralmente equivalentes, con más de 70 % de identidad.Resultados. La organización estructural de la proteína E-ZIKV (PDB: 5iZ7) fue similar a la de E1-RV (PDB: 4ADG) (70 a 80 % de identidad), y se observó una correspondencia con la estructura definida para las glucoproteínas de fusión de membrana de clase II de los virus con envoltura. E-ZIKV y E1-RV exhibieron elementos estructurales de fusión muy conservados en la región distal del dominio II, asociados con la unión a los receptores celulares de entrada del virus de la rubéola (glucoproteína de mielina del oligodendrocito, Myelin Oligodendrocyte Glycoprotein, MOG), y con los receptores celulares Axl del ZIKV y de otros flavivirus. Conclusión. La comparación de las proteínas E-ZIKV y E1-RV es un paso necesario hacia la definición de otros factores moleculares determinantes del neurotropismo y la patogenia del ZIKV, el cual puede contribuir a generar estrategias de diagnóstico, prevención y tratamiento de las complicaciones neurológicas inducidas por el ZIKV.
Egg quality characteristics as influenced by different body sizes in four close-bred flocks of Japanese quails (Coturnix coturnix japonica).

The present study was conducted to investigate some egg quality traits in four close-bred flocks of adult Japanese quails responded by different body sizes maintained at Avian Research and Training Centre, University of Veterinary and Animal Sciences, Lahore. A total of 432 adult (12 weeks-old) quails, comprising 108 males and 324 females were randomly divided into 108 experimental units, comprising one male and three females each. These experimental units were randomly assigned to 12 treatment groups having 4 close-bred flocks x 3 female body weights (heavy 300-350g, medium 250-300g and small 200-250g) with randomized complete block design in factorial arrangements having 9 replicates in each treatment. Egg weight (g), shell weight (g), shell thickness (mm), haugh unit, yolk index and blood and meat spots were studied. The significant (p<0.05) differences were noted in mean egg weight, shell weight, shell thickness and yolk index, whereas, haugh unit value was not significantly different in all the close-bred flocks of Japanese quails. With respect to body size categories, differences for egg weight, shell weight, shell thickness, yolk index and haugh unit value were significant (p<0.05). The interaction between flocks and body size was significant (p<0.05) in respect of all the above egg quality traits. The egg weight was higher in imported flock than local-1 and local-2 flocks and egg shell weight was higher in imported flock than in other local flocks. However, egg shell thickness and haugh unit were found to be higher in local-2 than local-1, 3 and imported flocks. The heavy weight quails had maximum egg weight, egg shell weight, shell thickness and yolk index followed by those in the medium and small size groups. Blood and meat spots were not observed during the course of this study.
Meta-análisis de la historia del estudio de las tortugas continentales de Colombia

The citations contained in a recent literature review on the freshwater turtle and tortoise species of Colombia were analyzed. Publishing rates on these species have been increasing exponentially since the 1950s, although many of the publications would not be detected using internet-based literature searches. The most common topics of publications were systematics and phylogeography, nesting ecology, and management. In the 1970s and 1980s, the rate of publishing on the ecology and genetics of Colombian populations lagged behind the rate of publishing on these topics for populations of Colombian freshwater turtle and tortoise species located in other countries, but currently the production of the two regions is comparable. Also, in other countries there were trends towards publishing more over time in English and in journals with higher impact factors, but these trends were not significant for publications on Colombian populations. In Colombia, a disproportionate number of studies have been published on large-bodied species that face conservation problems. We argue that future studies of already well-studied Colombian species should focus on evaluating the effectiveness of management programs, and priority also should be given to increasing our knowledge of the many poorly-studied species in the country, especially those currently classified by the IUCN as data deficient (DD).
Functionalized gold nanostars for label-free detection of PKA phosphorylation using surface-enhanced Raman spectroscopy

Protein phosphorylation controls fundamental biological processes. Dysregulation of protein kinase is associated with a series of human diseases including cancer. Protein kinase A (PKA) activity has been reported to serve as a potential prognostic marker for cancer. To this end, we developed a non-radioactive, rapid, cheap and robust scheme based on surface-enhanced Raman spectroscopy (SERS) for label-free detection of PKA phosphorylation using gold nanostars (AuNS) functionalized with BSA-kemptide. While bovine serum albumin (BSA) proteins stabilized the AuNS, kemptide, which is a high affinity substrate peptide specific for PKA, were phosphorylated in vitro to generate Raman signals that were identified by performing principal component analysis (PCA) on the acquired SERS spectra.
Investigating the role of Epstein-Barr virus lytic key regulator protein Zta in transcriptional regulation

Epstein-Barr virus (EBV) is a human herpes virus that, upon primary infection, establishes life-long persistence in B cells (latency). One viral protein, the immediate early lytic protein Zta (also known as BZLF1, ZEBRA, EB1, and Z) plays a significant role in disturbing this latency and inducing a viral productive (lytic) cycle. Expression of Zta, a basic leucine zipper transcription factor, induces a cascade of viral lytic cycle gene expression. The activation of many lytic genes requires the direct binding of Zta to its response elements (ZREs) within proximal promoters of these genes. Much research in recent years has focused on investigating Zta reactivation of latency and its role in lytic viral DNA replication. This has revealed a wealth of knowledge about Zta as a multifunctional transcription factor. However, a complete understanding of Zta transcriptional activation is still missing. Here, utilising ChIP-qPCR, we showed conserved binding patterns for Zta across several EBV lytic gene promoters in two different EBV systems including a non-B cell EBV-infected cell line. Also, using luciferase reporter assays, we show the first functional evidence for a possible role of Zta in controlling transcription regulation at distal regulatory elements (enhancers). Importantly, we identified BNLF2a, an essential viral immune evasion gene, as a direct target for Zta. We identified five ZREs and mapped functional ones within the BNLF2a promoter using mutational analysis and luciferase reporter assays. We also expressed and purified a recombinant GFP-bZIP Zta protein to address Zta binding to BNLF2a ZREs in vitro. Interestingly, using in silico approach, we also identified a conserved sequence in the ZRE flanking region of all five ZREs within BNLF2a promoter and uncovered a role for a possible repressor at ZRE2 flanking region. Our work not only adds to our understanding of Zta transcription regulation but characterises for the first time the regulation of a novel Zta target that has a role in evading the host immune system during EBV pre-latency and lytic cycle.
Computational Methods for Sequencing and Analysis of Heterogeneous RNA Populations

Next-generation sequencing (NGS) and mass spectrometry technologies bring unprecedented throughput, scalability and speed, facilitating the studies of biological systems. These technologies allow to sequence and analyze heterogeneous RNA populations rather than single sequences. In particular, they provide the opportunity to implement massive viral surveillance and transcriptome quantification. However, in order to fully exploit the capabilities of NGS technology we need to develop computational methods able to analyze billions of reads for assembly and characterization of sampled RNA populations. In this work we present novel computational methods for costand time-effective analysis of sequencing data from viral and RNA samples. In particular, we describe: i) computational methods for transcriptome reconstruction and quantification; ii) method for mass spectrometry data analysis; iii) combinatorial pooling method; iv) computational methods for analysis of intra-host viral populations. INDEX WORDS: Next-Generation Sequencing, RNA-sequencing, Transcriptome quantification and reconstruction, Mass spectrometry, Combinatorial pooling, Genetic relatedness, Molecular surveillance, Viral transmission networks COMPUTATIONAL METHODS FOR SEQUENCING AND ANALYSIS OF HETEROGENEOUS RNA POPULATIONS