Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds. ” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep.
Patterns of Species Richness and Diversity of Insects Associated With Cucurbit Fruits in the Southern Part of Cameroon

Abstract Patterns of species diversity and community structure of insects associated with fruits of domesticated cucurbits were investigated from January 2009 to 2011 in three localities from two agroecological zones in the southern part of Cameroon. Rarefaction curves combined with nonparametric estimators of species richness were used to extrapolate species richness beyond our own data. Sampling efforts of over 92% were reached in each of the three study localities. Data collected revealed a total of 66 insect morphospecies belonging to 37 families and five orders, identified from a set of 57,510 insects. The orders Diptera (especially Tephritidae and Lonchaeidae) and Hymenoptera (mainly Braconidae and Eulophidae) were the most important, in terms of both abundance and species richness on the one hand, and effects on agronomic performance on the other. Values for both the species diversity (Shannon and Simpson) and the species richness indices (Margalef and Berger–Parker) calculated showed that the insect communities were species-rich but dominated, all to a similar extent, by five main species (including four fruit fly species and one parasitoid). Species abundance distributions in these communities ranged from the Zipf–Mandelbrot to Mandelbrot models. The communities are structured as tritrophic networks, including cucurbit fruits, fruit-feeding species (fruit flies) and carnivorous species (parasitoids). Within the guild of the parasitoids, about 30% of species, despite their low abundance, may potentially be of use in biological control of important pests. Our field data contribute in important ways to basic knowledge of biodiversity patterns in agrosystems and constitute baseline data for the planned implementation of biological control in Integrated Pest Management.
Role of eruption season in reconciling model and proxy responses to tropical volcanism

Significance The starting month of many historical tropical volcanic eruptions is unknown and often assumed constant in long model simulations. Here we use model simulations to show that the season of eruptions strongly affects both atmospheric circulation and the El Niño/Southern Oscillation within the eruption year and that this could explain some of the mismatches between model simulations and paleoclimate reconstructions. The response 1 year later depends much less on eruption season, and proxy reconstructions are also more consistent. Our results imply that models may actually be correctly representing eruption-year tropical climate responses and that the season of eruptions should be considered when evaluating the mechanisms for volcanic effects on climate. The response of the El Niño/Southern Oscillation (ENSO) to tropical volcanic eruptions has important worldwide implications, but remains poorly constrained. Paleoclimate records suggest an “El Niño-like” warming 1 year following major eruptions [Adams JB, Mann ME, Ammann CM (2003) Nature 426:274–278] and “La Niña-like” cooling within the eruption year [Li J, et al. (2013) Nat Clim Chang 3:822–826]. However, climate models currently cannot capture all these responses. Many eruption characteristics are poorly constrained, which may contribute to uncertainties in model solutions—for example, the season of eruption occurrence is often unknown and assigned arbitrarily. Here we isolate the effect of eruption season using experiments with the Community Earth System Model (CESM), varying the starting month of two large tropical eruptions. The eruption-year atmospheric circulation response is strongly seasonally dependent, with effects on European winter warming, the Intertropical Convergence Zone, and the southeast Asian monsoon. This creates substantial variations in eruption-year hydroclimate patterns, which do sometimes exhibit La Niña-like features as in the proxy record. However, eruption-year equatorial Pacific cooling is not driven by La Niña dynamics, but strictly by transient radiative cooling. In contrast, equatorial warming the following year occurs for all starting months and operates dynamically like El Niño. Proxy reconstructions confirm these results: eruption-year cooling is insignificant, whereas warming in the following year is more robust. This implies that accounting for the event season may be necessary to describe the initial response to volcanic eruptions and that climate models may be more accurately simulating volcanic influences than previously thought.
Fast life history traits promote invasion success in amphibians and reptiles

Abstract Competing theoretical models make different predictions on which life history strategies facilitate growth of small populations. While ‘fast’ strategies allow for rapid increase in population size and limit vulnerability to stochastic events, ‘slow’ strategies and bet‐hedging may reduce variance in vital rates in response to stochasticity. We test these predictions using biological invasions since founder alien populations start small, compiling the largest dataset yet of global herpetological introductions and life history traits. Using state‐of‐the‐art phylogenetic comparative methods, we show that successful invaders have fast traits, such as large and frequent clutches, at both establishment and spread stages. These results, together with recent findings in mammals and plants, support ‘fast advantage’ models and the importance of high potential population growth rate. Conversely, successful alien birds are bet‐hedgers. We propose that transient population dynamics and differences in longevity and behavioural flexibility can help reconcile apparently contrasting results across terrestrial vertebrate classes.
Single and modeled multifrequency electrical impedance myography parameters and their relationship to force production in the ALS SOD1G93A mouse

ABSTRACT Objective: The relationship between muscle force production in ALS SOD1G93A mice and single and modeled multifrequency electrical impedance myography (EIM) parameters is unknown. We evaluated the relationship between multifrequency EIM data and paw grip and in situ force measurements, as well to standard measures including body weight and compound motor action potential (CMAP) amplitude. Methods: Twenty-nine SOD1 G93A mice aged 13–18 weeks (approximately 4–5 per week) and a group of similarly aged wild-type mice (N = 7) were studied with single and multifrequency EIM, CMAP, front and hind-limb paw grip measures, and in situ force measurements of the gastrocnemius. Results: Significant differences among WT, presymptomatic, and symptomatic ALS animals were identified for all standard measures and single 50 kHz frequency EIM parameters. Of the modeled multifrequency measures, the center frequency, fc , an index of cell size, showed the strongest relationship to force output. The two other multifrequency parameters corresponding to cell size distribution and cell density showed consistent although mostly non-significant differences. Conclusion: Reductions in force are reflected in single 50 kHz impedance values and in the fc. These data support the construct validity of EIM as an assessment tool of muscle dysfunction in diseases associated with motor neuron loss.
Strawberry Flavor: Diverse Chemical Compositions, a Seasonal Influence, and Effects on Sensory Perception

Fresh strawberries (Fragaria x ananassa) are valued for their characteristic red color, juicy texture, distinct aroma, and sweet fruity flavor. In this study, genetic and environmentally induced variation is exploited to capture biochemically diverse strawberry fruit for metabolite profiling and consumer rating. Analyses identify fruit attributes influencing hedonics and sensory perception of strawberry fruit using a psychophysics approach. Sweetness intensity, flavor intensity, and texture liking are dependent on sugar concentrations, specific volatile compounds, and fruit firmness, respectively. Overall liking is most greatly influenced by sweetness and strawberry flavor intensity, which are undermined by environmental pressures that reduce sucrose and total volatile content. The volatile profiles among commercial strawberry varieties are complex and distinct, but a list of perceptually impactful compounds from the larger mixture is better defined. Particular esters, terpenes, and furans have the most significant fits to strawberry flavor intensity. In total, thirty-one volatile compounds are found to be significantly correlated to strawberry flavor intensity, only one of them negatively. Further analysis identifies individual volatile compounds that have an enhancing effect on perceived sweetness intensity of fruit independent of sugar content. These findings allow for consumer influence in the breeding of more desirable fruits and vegetables. Also, this approach garners insights into fruit metabolomics, flavor chemistry, and a paradigm for enhancing liking of natural or processed products.
Direct Shear Box And Ring Shear Test Comparison: Why Internal Angle Of Friction Vary

The direct shear box and the ring shear test as conventionally used for measuring the strength parameters of soil for use in classical stability analyses have the major disadvantage that the stress conditions in the specimen during the test are not known. The ring shear test was specially instrumented with ‘artificial shear plane’ to investigate the shear deformations and stresses acting on the sample. The ‘artificial shear planes’ were made from plane papers with ink-marks and introduced into the specimen. New data is presented from internal measurements in terms of photographs just before failure in the ring shear. An interpretation is given for the internal angle of friction and its relationship with the strain propagation in both the methods, and a comparison made. Results are presented from both the direct shear box and the ring shear test, and these are compared. Both the tests yield varying internal angle of friction when carried out on the same specimen and conditions. Results reveal that the internal angle of friction obtained from a direct shear test is lower than that obtained from the ring shear test. It is established that the ring shear test has an inherent tendency to squeeze out material from the cell due to high stress accumulations at the outer edges. The inner edge is always understressed. The direct shear box has both of its sides equally stressed and this sharing of strains and stresses enable it to register lower bound values than those from the ring shear box. The structures which appear in the direct shear box sample before and after failure indicate that the central portion of the specimen is in simple shear. A close examination of the failure mechanism in the direct shear box shows that kinking is the dominant mode of deformation, which is different from that in the ring shear. In the ring shear, the sample is very small, and there is non-equal distribution of stresses. When this non-equal distribution of stresses is accompanied by a tendency to squeeze out of material, kinking does not dominate.
Contrasting Physiological Responses of Two Populations of the Razor Clam Tagelus dombeii with Different Histories of Exposure to Paralytic Shellfish Poisoning (PSP)

This study describes the physiological performance of two populations of the razor clam Tagelus dombeii from two geographic areas with different histories of exposure to paralytic shellfish poisoning (PSP) linked to the toxic dinoflagellate Alexandrium catenella. Clams from Melinka-Aysén, which are frequently exposed to PSP, were not affected by the presence of toxins in the diet. However, clams from Corral-Valdivia, which have never been exposed to PSP, exhibited significantly reduced filtration activity and absorption, affecting the energy allocated to scope for growth (SFG). Ammonia excretion and oxygen uptake were not affected significantly by the presence of A. catenella in the diet. Measurements of energy acquisition and expenditure were performed during a 12-day intoxication period. According to three-way repeated measure ANOVAs, the origin of the clams had a highly significant effect on all physiological variables, and the interaction between diet and origin was significant for the clearance and absorption rates and for the scope for growth. The scope for growth index showed similar positive values for both the toxic and non-toxic individuals from the Melinka-Aysén population. However, it was significantly reduced in individuals from Corral-Valdivia when exposed to the diet containing A. catenella. The absence of differences between the physiological response of the toxic and non-toxic clams from Melinka-Aysén may be related to the frequent presence of A. catenella in the environment, indicating that this bivalve does not suffer negative consequences from PSP. By contrast, A. catenella has a negative effect on the physiological performance, primarily on the energy gained from the environment, on T. dombeii from Corral-Valdivia. This study supports the hypothesis that the history of PSP exposure plays an important role in the physiological performance and fitness of filter feeding bivalves.
Susceptibility of the Lesser Mealworm, Alphitobius diaperinus (Coleoptera: Tenebrionidae), From Broiler Farms of Southern Brazil to Insecticides

Abstract The lesser mealworm, Alphitobius diaperinus (Panzer, 1797) (Coleoptera: Tenebrionidae), is considered the primary insect pest in broiler farms in Brazil. In this study, we characterized the susceptibility of A. diaperinus populations from broiler farms of southern Brazil to cypermethrin and chlorpyrifos. Larvae and adults of A. diaperinus were exposed to these technical insecticides diluted in acetone in residual bioassays. A geographic variation in the susceptibility of larvae and adults of A. diaperinus to both insecticides was detected. The larval LC50 for cypermethrin ranged from 0.43 to 7.33 µg a.i./cm2. Two populations from Santa Catarina state presented higher resistance ratios of 13.6- and 17-fold. When adults were exposed to cypermethrin, the LC50 ranged from 0.46 to 4.93 µg a.i./cm2, with population SC-3 from Santa Catarina having lower susceptibility (resistance ratio of 10.7-fold). When exposed to chlorpyrifos, A. diaperinus larvae present LC50 values ranging from 0.21 to 4.30 µg a.i./cm2. Larvae from Paraná and Santa Catarina (SC-1 population) presented the highest resistance ratios, ranging from 10- to 20-fold. In adults, the LC50 of chlorpyrifos ranged from 0.17 to 5.30 µg a.i./cm2, showing a maximum resistance ratio of 31-fold in a population from Paraná state. Based on LC99 values, candidate diagnostic concentrations of 15 and 12 µg a.i./cm2 of cypermethrin and chlorpyrifos, respectively, were also estimated for the resistance monitoring of A. diaperinus in Brazil. The implications of these results in Insect Resistance Management are discussed.
Evaluation of a High Throughput Starch Analysis Optimised for Wood

Starch is the most important long-term reserve in trees, and the analysis of starch is therefore useful source of physiological information. Currently published protocols for wood starch analysis impose several limitations, such as long procedures and a neutralization step. The high-throughput standard protocols for starch analysis in food and feed represent a valuable alternative. However, they have not been optimised or tested with woody samples. These have particular chemical and structural characteristics, including the presence of interfering secondary metabolites, low reactivity of starch, and low starch content. In this study, a standard method for starch analysis used for food and feed (AOAC standard method 996.11) was optimised to improve precision and accuracy for the analysis of starch in wood. Key modifications were introduced in the digestion conditions and in the glucose assay. The optimised protocol was then evaluated through 430 starch analyses of standards at known starch content, matrix polysaccharides, and wood collected from three organs (roots, twigs, mature wood) of four species (coniferous and flowering plants). The optimised protocol proved to be remarkably precise and accurate (3%), suitable for a high throughput routine analysis (35 samples a day) of specimens with a starch content between 40 mg and 21 µg. Samples may include lignified organs of coniferous and flowering plants and non-lignified organs, such as leaves, fruits and rhizomes.
Prenatal Alcohol Exposure and Fetal Programming: Effects on Neuroendocrine and Immune Function

Alcohol abuse is known to result in clinical abnormalities of endocrine function and neuroendocrine regulation. However, most studies have been conducted on males. Only recently have studies begun to investigate the influence of alcohol on endocrine function in females and, more specifically, endocrine function during pregnancy. Alcohol-induced endocrine imbalances may contribute to the etiology of fetal alcohol syndrome. Alcohol crosses the placenta and can directly affect developing fetal cells and tissues. Alcohol-induced changes in maternal endocrine function can disrupt maternal-fetal hormonal interactions and affect the female’s ability to maintain a successful pregnancy, thus indirectly affecting the fetus. In this review, we focus on the adverse effects of prenatal alcohol exposure on neuroendocrine and immune function, with particular emphasis on the hypothalamic-pituitary-adrenal (HPA) axis and the concept of fetal programming. The HPA axis is highly susceptible to programming during fetal development. Early environmental experiences, including exposure to alcohol, can reprogram the HPA axis such that HPA tone is increased throughout life. We present data that demonstrate that maternal alcohol consumption increases HPA activity in both the maternal female and the offspring. Increased exposure to endogenous glucocorticoids throughout the lifespan can alter behavioral and physiologic responsiveness and increase vulnerability to illnesses or disorders later in life. Alterations in immune function may be one of the long-term consequences of fetal HPA programming. We discuss studies that demonstrate the adverse effects of alcohol on immune competence and the increased vulnerability of ethanol-exposed offspring to the immunosuppressive effects of stress. Fetal programming of HPA activity may underlie some of the long-term behavioral, cognitive, and immune deficits that are observed following prenatal alcohol exposure.
The Role of Water Channel Proteins in Facilitating Recovery of Leaf Hydraulic Conductance from Water Stress in Populus trichocarpa

Gas exchange is constrained by the whole-plant hydraulic conductance (K plant). Leaves account for an important fraction of K plant and may therefore represent a major determinant of plant productivity. Leaf hydraulic conductance (K leaf) decreases with increasing water stress, which is due to xylem embolism in leaf veins and/or the properties of the extra-xylary pathway. Water flow through living tissues is facilitated and regulated by water channel proteins called aquaporins (AQPs). Here we assessed changes in the hydraulic conductance of Populus trichocarpa leaves during a dehydration-rewatering episode. While leaves were highly sensitive to drought, K leaf recovered only 2 hours after plants were rewatered. Recovery of K leaf was absent when excised leaves were bench-dried and subsequently xylem-perfused with a solution containing AQP inhibitors. We examined the expression patterns of 12 highly expressed AQP genes during a dehydration-rehydration episode to identify isoforms that may be involved in leaf hydraulic adjustments. Among the AQPs tested, several genes encoding tonoplast intrinsic proteins (TIPs) showed large increases in expression in rehydrated leaves, suggesting that TIPs contribute to reversing drought-induced reductions in K leaf. TIPs were localized in xylem parenchyma, consistent with a role in facilitating water exchange between xylem vessels and adjacent living cells. Dye uptake experiments suggested that reversible embolism formation in minor leaf veins contributed to the observed changes in K leaf.
Age validation in the long life family study through a linkage to early-life census records.

OBJECTIVES Studies of health and longevity require accurate age reporting. Age misreporting among older adults in the United States is common. METHODS Participants in the Long Life Family Study (LLFS) were matched to early-life census records. Age recorded in the census was used to evaluate age reporting in the LLFS. The study population was 99% non-Hispanic white. RESULTS About 88% of the participants were matched to 1910, 1920, or 1930 U.S. censuses. Match success depended on the participant's education, place of birth, and the number of censuses available to be searched. Age at the time of the interview based on the reported date of birth and early-life census age were consistent for about 89% of the participants, and age consistency within 1 year was found for about 99% of the participants. DISCUSSION It is possible to match a high fraction of older study participants to their early-life census records when detailed information is available on participants' family of origin. Such record linkage can provide an important source of information for evaluating age reporting among the oldest old participants. Our results are consistent with recent studies suggesting that age reporting among older whites in the United States appears to be quite good.
Current trends in molecular diagnostics of chronic myeloid leukemia

Abstract Nearly 1.5 million people worldwide suffer from chronic myeloid leukemia (CML), characterized by the genetic translocation t(9;22)(q34;q11.2), involving the fusion of the Abelson oncogene (ABL1) with the breakpoint cluster region (BCR) gene. Early onset diagnosis coupled to current therapeutics allow for a treatment success rate of 90, which has focused research on the development of novel diagnostics approaches. In this review, we present a critical perspective on current strategies for CML diagnostics, comparing to gold standard methodologies and with an eye on the future trends on nanotheranostics.