Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonparametric analysis of casein complex genes' epistasis and their effects on phenotypic expression of milk yield and composition in Murciano-Granadina goats.

Improving knowledge on the causative polymorphisms or genes regulating the expression of milk quantitative and qualitative traits and their interconnections plays a major role in dairy goat breeding programs and genomic research. This information enables optimization of predictive and selective tools, to obtain better-performing animals to help satisfy market demands more efficiently. Goat milk casein proteins (αS1, αS2, β, and κ) are encoded by 4 loci (CSN1S1, CSN1S2, CSN2, and CSN3) clustered within 250 kb in chromosome 6. Among the statistical methods used to identify epistatic interactions in genome-wide qualitative association studies (GWAS), gene-based methods have recently grown in popularity due to their better statistical power and biological interpretability. However, most of these methods make strong assumptions about the magnitude of the relationships between SNP and phenotype, limiting statistical power. Thus, the aims of this study were to quantify the epistatic relationships among 48 SNP in the casein complex on the expression of milk yield and components (fat, protein, dry matter, lactose, and somatic cells) in Murciano-Granadina goats, to explain the qualitative nature of the SNP used to quantify the genotypes produced as a result. Categorical principal component analysis (CATPCA) was used to delimit and group the number of SNP studied depending on their implications in the explanation of milk yield and components variability. Afterward, nonlinear canonical correlation analysis was used to identify relationships among and within the SNP groups detected by CATPCA. Our results suggest that 79.65% of variability in the traits evaluated may be ascribed to the epistatic relationships across and within 7 SNP groups. Two partially overlapping groups of epistatically interrelated SNP were detected: one group of 21 SNP, explaining 57.56% of variability, and another group of 20 SNP, explaining 42.43% (multiple fit ≥ 0.1). Additionally, SNP18, 32, and 36 (CSN1S2, CSN1S1, and CSN2 loci, respectively) were the most significant SNP to explain intragroup epistatic variability (component loading > |0.5|). Conclusively, milk yield and quality may not only depend on the specific casein gene pool of individuals, but may also be relevantly conditioned by the relationships set across and within such genes. Hence, studying epistasis in isolation may be crucial to optimize selective practices for economically important dairy traits.
Isolation and identification of halophilicbacteria from Urmia Lake in Iran

Halophiles are in all three domains of life: Archaea, Bacteria and Eucarya. Halophilic microorganisms in addition to form major part of life biodiversity can have many biotechnological applications. The objective of this research is isolation and identification of halophilic bacteria from Urmia Lake in Iran and the study of its bacterial biodiversity. After sampling of brines from Urmia Lake from 10 stations and depth of approximately 30-50 cm, in April 2011 and transfer to the laboratory in the sterile conditions, samples were enriched and cultured on defined media, and incubated. After appearance of colonies, selected strains were studied based on morphology, physiology and biochemical characteristics. For phylogenetic identification, their genomic DNA were extracted and amplified by PCR technique. Therefore their sequences were determined by genetic experiment based on 16S rRNA gene sequence and their similarity were analysed in GenBank of EzTaxon database. Finally the phylogenetic tree was constructed. Studied strains belonged to three genera: Halomonas 50% (including H. andesensis LC6(T) [12.5%], H. gomseomensis M12(T) [12.5%], H. hydrothermalis Slthf2(T) [12.5%], H. boliviensis LC1(T) [6.25%] and H. janggokensis M24(T) [6.25%]), Salinivibrio 25% (including S.costicolasubsp. alcaliphilus DSM 16359(T) [18.75%] and S. sharmensis BAG(T) [6.25%]) and Idiomarina 25% (including I .loihiensis L2TR(T) [25%]).
Impact of Cognitive Frailty on Activities of Daily Living, Cognitive Function, and Conversion to Dementia Among Memory Clinic Patients with Mild Cognitive Impairment.

BACKGROUND Very few studies have investigated the impact of cognitive frailty in clinical settings, especially in memory clinic populations. OBJECTIVE To examine the impact of cognitive frailty on activities of daily living (ADL), cognitive function, and conversion to dementia among memory clinic patients with mild cognitive impairment (MCI). METHODS The subjects of this retrospective study were 248 MCI patients (mean age, 76.3±5.4 years; females, 60.9%). All subjects completed a comprehensive geriatric assessment at baseline and at least one assessment during 3-year follow-up. Frailty was defined by generating a frailty index (FI), and MCI patients with frailty (FI≥0.25) were considered to represent cognitive frailty. As primary outcomes, the Barthel Index, Mini-Mental State Examination, and incident dementia were evaluated during follow-up. At baseline, patients were assessed for apolipoprotein E (APOE) phenotype. A linear mixed model, as well as a Cox proportional hazards regression model with adjustment for confounding variables, was performed. RESULTS Of these patients, 75 (30.2%) were classified as cognitive frail. APOEɛ4 carriers accounted for 26.7% of those with cognitive frailty and 44.5% of those without (p = 0.008). Cognitive frail patients showed a faster ADL decline (estimate, -1.04; standard error, 0.38; p = 0.007) than patients without cognitive frailty. Cognitive frailty was not associated with cognitive decline and incident dementia. CONCLUSION Our findings demonstrated cognitive frailty increases the risk of dependence but not cognitive outcomes. Cognitive frailty may have heterogeneous conditions, including APOEɛ4-related pathologies, which may affect the cognitive trajectories of patients with MCI.
PPARγ Recruitment to Active ERK during Memory Consolidation Is Required for Alzheimer's Disease-Related Cognitive Enhancement

Cognitive impairment is a quintessential feature of Alzheimer's disease (AD) and AD mouse models. The peroxisome proliferator-activated receptor-γ (PPARγ) agonist rosiglitazone improves hippocampus-dependent cognitive deficits in some AD patients and ameliorates deficits in the Tg2576 mouse model for AD amyloidosis. Tg2576 cognitive enhancement occurs through the induction of a gene and protein expression profile reflecting convergence of the PPARγ signaling axis and the extracellular signal-regulated protein kinase (ERK) cascade, a critical mediator of memory consolidation. We therefore tested whether PPARγ and ERK associated in protein complexes that subserve cognitive enhancement through PPARγ agonism. Coimmunoprecipitation of hippocampal extracts revealed that PPARγ and activated, phosphorylated ERK (pERK) associated in Tg2576 in vivo, and that PPARγ agonism facilitated recruitment of PPARγ to pERK during memory consolidation. Furthermore, the amount of PPARγ recruited to pERK correlated with the cognitive reserve in humans with AD and in Tg2576. Our findings implicate a previously unidentified PPARγ–pERK complex that provides a molecular mechanism for the convergence of these pathways during cognitive enhancement, thereby offering new targets for therapeutic development in AD.
RETRACTED: Impact of Information Bandwidth of In-Vehicle Technologies on Young Drivers’ Attention Maintenance Performance: A Driving Simulator Study

This proceedings paper was inadvertently published after the authors notified the journal of their desire to withdraw the paper from the conference. The paper was not actually presented at the conference. This retraction is being issued at the authors’ request. The Journal, Human Factors, and SAGE apologize to the authors and readers for the inadvertent publication.
The origins of directional persistence in amoeboid motility

Directional persistence is crucial for graduate school as well as for life on Earth. Persistently directed motion enables neutrophils to target wound sites, growing axons to find their targets, migrating cells to create a correctly developed embryo, and Dictyostelium discoideum amoebas to hunt their bacterial prey. While chemical signals guide the cells in these examples, an underlying persistence in eukaryotic motility greatly enhances navigation toward a target. For amoeboid cells, this basal persistence results from a tendency of cells to zig-zag. Whence this zig-zag bias, and thereby whence directional persistence, is the question addressed by this thesis. First, a new automated and unbiased pseudopod detection algorithm is presented. This algorithm is used to experimentally test a new model of pseudopod zig-zagging, in which pseudopods are excitable bursts of protrusive activity. The key assumption is that pseudopods produce a memory of their own activity, which serves to make the cortex locally more excitable in the future. This is a top-down, network level model that makes minimal assumptions and maintains an appropriate level of abstraction, while retaining biological interpretations and predictive power. The model’s predictive power is evidenced by four novel results that are tested and supported by new experimental data. Previous evidence suggested that pseudopod memory might be found in the specific delocalization of myosin II at growing pseudopods, though this evidence has been either low resolution or disconnected from local pseudopod dynamics. The possibility of memory via myosin delocalization is tested by relating pseudopod production to cortical protein localization. This approach reveals that myosin II iii delocalizes in growing pseudopods, myosin remains lower for a time after pseudopods stop, cortical regions with lower myosin are more excitable, and pseudopodial myosin delocalization is due neither to dilution from membrane extension nor to targeted disassembly through MHCK A. Rather, it appears that myosin is locally excluded by the dense actin meshwork created by a growing pseudopod. This suggests a model that intimately links the memory of a pseudopod to its very existence.
FOOD STORAGE BY A WANDERING GROUND SPIDER (ARANEAE, AMMOXENIDAE, AMMOXENUS)

Abstract Members of genus Ammoxenus are known predators of harvester termites (Hodotermes mossambicus). An A. amphalodes female was observed catching and paralyzing a termite in the field. The paralyzed termite was deposited in a silk sac with other paralyzed termites. This confirms that Ammoxenus spp. use different methods of catching and utilizing prey. Termites are either killed and fed upon or paralyzed and stored for feeding at a later time.
Challenges and Perspectives in the Management of Late-Stage Parkinson’s Disease

Parkinson’s disease (PD) is a common neurodegenerative disorder, with a continuously increasing prevalence. With improved clinical and therapeutic management of PD, more patients reach later stages of the disease, meaning they may face new clinical problems that were not commonly approached. This gave way to the description of a new PD stage, late-stage PD (LSPD), which is clinically discernible from the advanced-stage one. Therefore, LSPD patients have new and different needs, regarding pharmacological and non pharmacological interventions, including palliative care and multidisciplinary teams. LSPD patients constitute an‘orphan population’, who traditionally was excluded from previous studies, due to its high disability. With this manuscript, we intend to review specific management challenges of LSPD patients, covering this new concept and its clinical features, how to assess these patients, therapeutic recommendations, as well as discussing ongoing research and future perspectives.
Pmr1, a Gene for Resistance to Powdery Mildew in Sweet Cherry

Most sweet cherry (Prunus avium L.) cultivars grown commercially in the United States are susceptible to powdery mildew, caused by the fungus Podosphaera clandestina (Wall.:Fr.) Lev. Recently, hybrid populations segregating for resistance to powdery mildew were developed by crossing a mildew-resistant sweet cherry selection, PMR-1, with the susceptible cultivars Bing, Rainier, and Van. Although segregation within these populations indicated a single gene was responsible for the powdery mildew resistance conferred by PMR-1, the gene action could not be determined. Therefore, a reciprocal cross between 'Bing' and 'Van' was made to determine the allelic state of the susceptible parents used previously. All progeny (n = 286) from this cross were susceptible to powdery mildew. This information, combined with results from previous segregation data, indicate the powdery mildew resistance gene is inherited in a dominant manner and is present in PMR-1 in the heterozygous allelic state. We have named this gene Pmr1. Furthermore, in combination with known pedigree information, we have been able to predict the susceptibil- ity of more than 60 additional commercial and recently released sweet cherry cultivars.
SALINITY REACTIONS OF SOME FRESH- AND BRACKISH-WATER CRUSTACEANS

1. The salinity reactions of Asellus aquaticus from fresh and Baltic brackish water (6‰), of Idotea baltica and of Gammarus spp. from brackish water were studied with the apparatus of Hodgson (1951). Both natural brackish-water and pure NaCl solutions were used.2. None of the experimental animals had, for brackish water, reaction thresholds low enough to allow behavioral selection of salinities to occur in natural conditions.3. The reaction threshold for NaCl solutions was higher in brackish-water than in fresh-water specimens of Asellus. Asellus always preferred the more dilute concentration. Idotea baltica and Gammarus preferred brackish water to fresh water. Gammarus preferred even 6‰ NaCl to fresh water.4. In Asellus, the chemoreceptors mediating the response to salinity variations seem, for the most part, to be situated on the antennae and/or antennulae. In Gammarus, the salinity receptors are situated on the antennae and antennulae.
Caracterización de la diversidad genética en el pez Brycon henni (Characiformes: Characidae) en Colombia central por medio de marcadores RAPD

Characterization of the genetic diversity of the fish Brycon henni (Characiformes: Characidae) in central Colombia with RAPD markers. Knowledge on the genetic diversity of wild fish species is essential for conservation and appropriate management of individuals in repopulation programs. In Colombia, Brycon henni has been reported in the Magdalena and Cauca river basins, but the population and range have diminished as a consequence of anthropic activities. In this study, the Random Amplified Polymorphic DNA (RAPD) was used to estimate the actual genetic structure in this species. For the purpose, six sample sites located in the department of Antioquia (Central Chain Mountains of Colombia) were used. Thirty five primers (87.5 %), out of forty used, yielded 1 466 reliable and consistent fragments; 417 were considered as unique fragments able to discriminate among the Magdalena (Humarada-1 and Humarada-2) and Cauca (Piedras, La Clara y Guaracu) river basins samples, suggesting that each is a discrete unit. This diversity suggests that anthropic effects of over fishing, dam building, deforestation and water pollution, have contributed to the isolation of these fish groups on the high mountains. Brycon moorei and Colossoma macropomum, as an interspecific control groups, were placed out of the B. henni general group, confirming their taxonomic classification through morphologic data. The RAPD technique was useful to know the genetic diversity and to discriminate among B. henni populations from different geographic origins, as a basis for an appropriate plan of repopulation, conservation and wildlife management. Rev. Biol. Trop. 55 (3-4): 1025-1035. Epub 2007 December, 28.
GEOPHAGY IN THE AFRICAN ELEPHANT IN RELATION TO AVAILABILITY OF DIETARY SODIUM

Abstract We studied the use of mineral licks by African elephants (Loxodonta africana) during the dry season in a Kalahari-sand habitat in Hwange National Park, Zimbabwe, to investigate the role of geophagy as a mechanism for supplementing low Na+ levels in browse and natural water supplies. Plant, water, and soil macrominerals were measured to evaluate mineral availability for elephants during the dry season. Elephant behavior was monitored at licks to investigate the intensity of geophagy (measured by number of mouthfuls of soil consumed) in relation to fecal-Na+ loss. Female elephants, which probably had greater requirements than did males because of pregnancy and lactation, consumed more mouthfuls of soil and spent a greater part of their activity budget feeding on soil than did males, suggesting that geophagy may be driven by a nutritional requirement. We found the following consistent with the Na+-supplementation hypothesis: 1) unlike other minerals, Na+ in woody plants and natural water supplies may be inadequate to meet the minimum requirements of elephants during the dry season; 2) soils consumed by elephants differed from other soils primarily in their high Na+ content; 3) intensity of geophagy was negatively correlated with fecal Na+; and 4) elephants in non–Kalahari-sand habitats do not appear to create or use licks, probably because they are able to meet their Na+ requirements from ubiquitous Na+-rich water supplies, which do not occur naturally in Kalahari-sand habitats.
Improvement of Antioxidant Activity and Related Compounds in Fenugreek Sprouts through Nitric Oxide Priming

Nitric oxide (NO) is an important signalling molecule in plants. In the present work, the effect of some nitric oxide donors namely, sodium nitroprusside (SNP), sodium nitrite (NN) and potassium ferricyanide (FCN) on the antioxidant activity of Trigonella foenum- graecum L. was studied during germination. The treated seeds were germinated in dark for 72 h and the antioxidant activity were determined at interval of 24 h up to 3 days. The in vitro antioxidant activity was determined spectrophotometrically by the following methods, DPPH, ABTS, nitric oxide, anti-lipid peroxidation, beta-carotene bleaching, ferric reducing power and metal chelating as well as phytochemicals such as phenol, flavonol and carotene content were also evaluated. The results demonstrated that the seeds treated with nitric oxide donors showed gradual increase in their antioxidant potential from 24 h to 48 h and then declined at 72 h stages. Overall, the seeds treated with sodium nitroprusside and potassium ferricyanide showed higher antioxidant potential particularly at concentration 80 mM and 40 mM respectively, when compared with control. Our data supported the hypothesis that NO is a signalling molecule that plays an important role as an antioxidant component in plants.
Xylella Fastidiosa: Xylem-Limited Bacterial Pathogen of Plants

Strains of Xylella fastidiosa have been associated with diseases that cause tremendous losses in many economically important plants, including grapevine, alfalfa, peach, plum, almond, elm, sycamore, oak, maple, and possibly citrus (24, 28, 32, 35, 42, 43, 49, 57, 70, 72, 73, 78). This Gram-negative, xylem-limited bacterium (XLB) was first discovered associ­ ated with Pierce's disease (PD) of grapevine in 1973 (28, 42) and was first grown in axenic culture in 1978 (12). While there has been considerable progress in the study of this bacterium over the past 15 years, our knowledge of X. fastidiosa is still very limited. Much of the research to date has been of the descriptive type, involving symptom description and fulfillment of Koch's postulates. However, a few excellent fundamental studies have been done with X. faslidiosa and the diseases that it causes. Since it was the first to be cultured, more research has been done with the PD of grapevine strain of X. fastidiosa than with other strains. Pierce's disease may also be the most economically significant, especially in the southeastern USA where it is endemic and is the principal factor preventing the development of a grape industry based on the high-quality Vilis vinifera and V. labrusca grapes (33). Phony peach disease in the southeastern USA and plum leaf scald in Japanese plum on the delta of the Parana River, Argentina, are also responsible for severe losses (46, 49). X.fastidiosa causes serious leaf scorch and tree decline diseases in many different urban trees (32, 50, 51). X. fastidiosa may also be involved in some of the current forest decline problems that are of unkown etiology. These diseases in urban shade
DNA microsatellite in fruit crops: Isolation, length polymorphism, inheritance, somatic stability and cross-species conservation

We have isolated and sequenced microsatellites in several fruit crop species, such as grape (Vitis vinifera L.), kiwifruit (Actinidia, chinensis Planch), olive (Olea europea L.), and peach (Prunus persica (L.) Batsch), using microsatellite repeat-enriched genomic libraries. The efficiency of the enrichment procedure was variable (about 50 % of positive plaques in kiwifruit and peach, lower values in grape and olive). The re-amplification from the source genomic DNA was obtained in most cases. The polymorphism was high in all species assayed (5 to 15 alleles/locus in grape, 9 to 17 alleles/locus in kiwifruit, 2 to 8 alleles/locus in peach, data for olive are still being scrutinised). The Mendelian segregation was demonstrated for 8/10 SSR analysed in grape, 99/233 SSR analysed in kiwifruit, and 17/26 SSR analysed in peach. All microsatellites segregated as a single locus in peach, whereas in kiwifruit, grape, and olive several primer pairs amplified two loci each, in agreement with the suspected polyploid origin of the last species. The somatic stability was assayed in peach and olive, using three long-living accessions of cv. 'Redhaven' of different origin and 2-4 centuries-old plants of olive for each of the eight cultivars assayed. No pattern variation of the 26 microsatellites analysed was found in peach, whereas in olive rare intra-variety polymorphisms were observed in several of the 35 microsatellites analysed up to now. The assays on cross-species transportability were carried out in species representative of each genus (14 species of Vitis, 8 species of Actinidia, and 7 species of Prunus) and gave positive amplifications in high percentages (91 % of microsatellites amplified in all Vitis species, 52 % in all Prunus species, and 75 % in all Actinidia species). In some cases, successful amplifications were obtained also in related genera such as Parthenocissus, a genus close to Vitis, and Malus, which together with the genus Prunus belong to the Rosaceae family.
The new world screwworm: prospective distribution and role of weather in eradication

The new world screwworm [Cochliomyia hominivorax (Coquerel)] was eradicated in North America, Libya and other locations using the sterile insect technique (SIT). To examine the role of weather in its eradication, a physiologically‐based demographic model was developed and used to characterize its range of year‐round persistence. Published data on developmental times, fecundity and mortality rates on temperature were used to parameterize the model. The lower and upper thermal thresholds for development are 14.5 and 43.5 °C, and the optimal temperature for survival is 27.2 °C. An index of favourability based on annual rainfall was used as an approximate estimate of the limiting effects of moisture in arid areas. The open source geographical information system software grass was used to map the simulation results, as well as county level myiasis incidence data for Texas for the 1962–1983 SIT eradication programme. Winter temperature and rainfall are shown to have a strong influence on screwworm outbreaks and in facilitating eradication in North America and Libya. Prospective analysis for the Mediterranean Basin suggests that eastern areas are most favourable for screwworm establishment (e.g. the Nile River area of Egypt). The SIT eradication programme and its possible extension into South America are discussed. Expected +2 °C climate warming is predicted to increase the potential year‐round range of screwworm in the southeast U.S.A.