Miracle-dz/UniFAR-FTUs huggingface dataset:
The collection of multiple saliva samples from pigs and the effect on adrenocortical activity

Cook, N. J., Hayne, S. M. , Rioja-Lang, F. C. , Schaefer, A. L. and Gonyou, H. W. 2013. The collection of multiple saliva samples from pigs and the effect on adrenocortical activity. Can. J. Anim. Sci. 93: 329-333. The validity of collecting multiple saliva samples for the measurement of cortisol was tested in two sampling regimes in two weight classes of grower pigs (50 and 100 kg). The sampling regimes were a high-frequency, short-duration (HFSD) protocol involving collection of multiple samples within approximately 2 min of each other over a period 30 min. The second regime was a low-frequency, long-duration (LFLD) protocol in which samples were collected every 30 min for 3 h. Both sampling regimes were applied to individually housed pigs. The effect of repeated sampling of a focal pig on its cohorts in a group-housed pen was tested using the LFLD regime. There was no evidence of an effect of either of the sampling protocols on salivary cortisol concentrations in individually housed or group-housed pigs. There was some evidence that higher concentrations of salivary cortisol were associated with longer individual sampling durations in the HFSD regime for animals in the 50-kg weight class but not in the 100-kg weight class. The evidence from these experiments indicates that the collection of multiple saliva samples does not affect salivary cortisol concentrations in grower pigs, but that collection of individual samples in as short a time as possible would be prudent to avoid sampling effects in younger animals.
Antioxidant Protection of an Omega-3 Fatty Acid Fortified Dairy-Based Beverage

Skim, butter-derived aqueous phase, anhydrous milk fat, and fish oil were used to formulate ultra high temperature (UHT) processed extended shelf-life omega-3 fatty acid fortified dairy-based beverages with fat contents mimicking whole milk (3.25%). Oxidation of the lipids in the formulated beverages was investigated during storage for 35 days at 4°C using GC/MS analysis, conjugated diene analysis, and headspace solid phase micro-extraction GC/MS (SPME-GC/MS) analysis of headspace. Omega-3 fatty acid fortified dairy-based beverages were produced that mimicked the physical properties of 3.25% fat whole milk. Oxidation resulted in only small changes in omega-3 lipid content and sensory analysis by an untrained panel indicated that the overall aroma was no different than that of commercially available UHT processed milk. An omega-3 fatty acid fortified dairy-based beverage was produced that delivered 440mg of omega3 fatty acid per 8oz serving. When consumed daily, the beverage could provide the equivalent amount of omega-3 fatty acids recommended by the American Heart Association, and the equivalent amount of omega-3 fatty acids found in two fatty fish meals over the period of one week. Antioxidants were added to the lipid phase, immediately prior to processing, of additionally produced formulations to determine if a reduction in omega-3 lipid oxidation was observed. No overall reduction in oxidation was observed, as indicated by GC/MS and SPME-GC/MS analysis. Sensory analysis indicated that oxidative aromas increased during storage for the antioxidant and omega-3 fatty acid fortified dairy-based beverage. Ascorbyl palmitate was determined to have a pro-oxidative effect on the formulated omega-3 fortified dairy-based beverages. Antioxidants present in the commercial grade fish oil used for fortification were effective in controlling oxidation in the formulated omega-3 fatty acid fortified dairy-based beverages.
Blindness in Smoky Joe roosters results in advanced sexual maturation

Perttula, J. and Bédécarrats, G. Y. 2012. Blindness in Smoky Joe roosters results in advanced sexual maturation. Can. J. Anim. Sci. 92: 483-491. In chickens, an increase in photoperiod activates the hypothalamo-pituitary gonadal axis resulting in sexual maturation. Although it is well established that light can directly stimulate the hypothalamus, the relative contribution of the eye in the control of reproduction is still controversial. Using a genetically blind line of chickens (Smoky Joe), we investigated the relative importance of the retina of the eye in sexual maturation in roosters. Furthermore, to evaluate the effect of photostimulation, three generations of blind and sighted Smoky Joe roosters were utilize. Generation 1 (G1) was photostimulated at 17 wk of age, while generation 2 (G2) was left un-photostimulated and generation 3 (G3) was photostimulated at 12 wk of age. Blind roosters in G1 and G2 matured between 17 and 19 wk of age (testicular weight, comb length) independently of photostimulation whereas maturation of sighted animals was significantly delayed in G2. However, this advanced sexual maturation was no longer evident when birds were stimulated at 12 wk of age. Blind roosters in G2 showed advanced spermatogenesis when compared with sighted animals. No significant difference in plasma testosterone levels was observed for any of the three generations. In conclusion, although still photosensitive, blind rooster sexually matured spontaneously earlier than their sighted counterpart.
Produção de serapilheira em dois manguezais do estado do Paraná, Brasil

Serapilheira e a camada formada pela deposicao e pelo acumulo do material proveniente das especies vegetais e representa a maior contribuicao da entrada de nutrientes nos ecossistemas de manguezal. As variacoes encontradas na producao desse material sao resultantes da acao de diferentes fatores ambientais e intrinsecos das especies. Este estudo teve como objetivo estimar e comparar a producao da serapilheira de dois bosques de mangue no estado do Parana, com diferentes padroes estruturais. Foram instalados 15 coletores em cada area, e realizaram-se as coletas mensalmente. Em ambas as areas, a fracao folhas foi o principal componente da serapilheira, seguida por ramos, material reprodutivo e miscelânea. As especies apresentaram maior deposicao de folhas e material reprodutivo nos meses com maior temperatura e maior precipitacao. A salinidade parece ser o fator que mais influencia a producao total de serapilheira, resultando em uma baixa produtividade anual quando comparada com outras areas de latitudes semelhantes.
High night‐time humidity and dissolved organic carbon content support rapid decomposition of standing litter in a semi‐arid landscape

Summary Litter in arid and semi-arid ecosystems usually exhibits a prolonged standing dead phase after senescence; however, we know little about the ways in which abiotic and microbial processes affect standing litter decomposition. We conducted a 26-month in situ decomposition experiment in a steppe to investigate the potential mechanisms governing the decomposition of standing litter, and a 192-day laboratory incubation experiment to further explore the impacts of the standing dead stage on the subsequent litter decomposition and soil organic carbon (SOC) formation after the litter falls to the soil surface. Compared with soil surface litter, standing litter has higher dissolved organic carbon (DOC) content. Standing litter also experienced higher night-time relative humidity on its surface, which enhanced litter moisture content. The higher DOC concentration, combined with the greater night-time moisture content, stimulated more microbial activity in standing litter. The decomposition rate (k) of standing litter was 92% higher than that of soil surface litter. Moreover, the standing phase conditioned the litter, leading to more rapid decomposition after the litter fell to the soil surface, and increasing the efficiency with which the litter formed SOC. We conclude that the long-neglected standing phase greatly determines litter decomposition and soil carbon storage in semi-arid regions. Accounting for standing litter decomposition is critical for accurately simulating carbon turnover in arid and semi-arid ecosystems. A lay summary is available for this article.
Clinical significance of genomic alterations of the CDK4-pathway and sensitivity to the CDK4 inhibitor PD 0332991 in melanoma.

8520 Background: Activation of CDK4 by amplification, increased expression of Cyclin D1 (CCND1) or reduced expression of the CDK inhibitor p16 (CDKN2A) can contribute to transformation of melanocytes indicating that CDK4 can act as an oncogene in melanoma.To explore if CDK4 may be a viable target for the treatment of human melanoma we have analyzed the frequency and clinico-pathological associations of genomic alterations of the CDK4 pathway in primary human melanoma and examined the genomic predictors of sensitivity to the highly selective CDK4/6 inhibitor PD 0332991 (991) in a panel of melanoma cell lines. Methods: A series of 167 primary melanomas with clinical, molecular and pathological annotation, including median follow up of 6.6 years, were analyzed for copy number variation (CNV)- gain of CDK4 or CCND1 (average gene copy >2.4) or loss of CDKN2A (average gene copy <1.4), by fluorescence in situ hybridization. A panel of 39 cell lines were treated with 991 in vitro and GI50s calculated. The mean GI.
Identifying Patterns of Cancer Disease Mechanisms by Mining Alternative Representations of Genomic Alterations

Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying combinatorial patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and predicting outcome. However, identifying perturbed pathways is challenging, because different tumors can have the same perturbed pathways that are perturbed by different SGAs. We started off by designing a novel semantic representation that captures the functional similarity of distinct SGAs perturbing a common pathway in different tumors. This representation was used alongside the nested hierarchical Dirichlet process topic model in order to identify combinatorial patterns in altered signaling pathways. We found that the topic model was able to capture the functional relationships between topics. It was also able to identify cancer subtypes composed of tumors from different tissues of origin that exhibit different survival rates. These results led us to investigate the performance of the methodology on pan-cancer data, as well as in conjunction with cancer driver data. The results revealed that the framework was still able to identify clinically relevant features in pan-cancer. However, the addition of driver data decreased the noise in the data and improved the separation of tumors in the clustering results. This provided support for including the use of driver data in our methodology. In order to have gene representations independent of literature, we developed a biological representation that could identify functionally related genes. Its performance when used alongside topic modeling was tested. We found that the topic association patterns separated tumors by their tissue of origin. But, analyzing some of the cancer types on an individual basis still led to significant differences in survival. Our studies show the potential for using alternative representations in conjunction with topic modeling to investigate complex genomic diseases. With further research and refinement of this methodology, it has the potential to capture the relationship between pathways involved in cancer. This would contribute to a better understanding of cancer disease mechanisms and treatment.
Optimisation du diagnostic des thrombopénies constitutionnelles par l’utilisation des paramètres plaquettaires morphométriques

Les thrombopenies constitutionnelles (TC) sont des pathologies rares resultantes d’anomalies qualitatives et quantitatives des plaquettes. Diverses voies de signalisation, differents recepteurs ou etapes de la megacaryopoiese peuvent etre affectes et aboutir a ces pathologies. Aujourd’hui la grande heterogeneite de ces thrombopenies est representee par l’existence de 23 formes de TC portees sur 22 genes. Toutefois un certain nombre de patients reste encore actuellement sans diagnostic precis. Ce n’est que tres recemment qu’une publication de Noris et al. (2014) a etabli une classification des TC a partir de l’observation morphologique au microscope optique : les TC a plaquettes de petite taille, de taille normale, de taille augmentee et a plaquettes geantes. L’objectif principal de cette these est de reproduire cette classification, initialement realisee sur la basede mesures micrometriques des plaquettes, en utilisant les parametres automatises de l’hematimetre XN SYSMEX®. Pour ce faire, il a ete exploite principalement les donnees du canal dedie aux plaquettes, le PLT-F, marquant specifiquement par un fluorochrome les elements plaquettaires. Dans ce but, les differents parametres disponibles, leurs significations ainsi que leurs performances respectives seront detailles. Nous avons calcule pour chacun d’entre eux des seuils discriminants en fonction des differentes entites de TC. Puis par l’utilisation d’une combinaison de marqueurs, une classification des TC a ete obtenue avec des valeurs de sensibilite et specificite optimales. L’objectif secondaire de ce travail a ete d’etablir des algorithmes decisionnels afin d’aider au diagnostic de TC. Nous avons elabore des arbres a double lecture, selon que l’on se place dans un contexte de caracterisation d’une TC suspectee ou dans un contexte de validation biologique de routine d’une thrombopenie. Enfin un point a ete fait sur les possibilites et perspectives dedifferenciation des TC avec les PTI.
Involvement of the LFA-1 ligand JAM-A in inflammatory recruitment of mononuclear cells : identification of the JAM-A binding domain in LFA-1

s: Fraemohs, L. , Koenen, R.R. , Ostermann, G. , Zernecke, A. and Weber, C. (2005). The LFA-1 ligand JAM-A is involved in mononuclear cell recruitment on inflamed or atherosclerotic endothelium. Immunobiol 210, 411-412.
Molecular mediators and controlling mechanism of vascular calcification

Bone formation involves hydroxyapatite crystals, whose development begins in matrix vesicles that bud from osteoblasts. Vascular smooth muscle cells that have undergone osteoblast differentiation are also able to release similar vesicles with shared protein content. Such differentiation is restrained or inhibited under normal conditions, and there is a balance with osteoclast differentiation experienced by monocytes and macrophages within the vascular wall. Moreover, the reaction which allows crystal growth is thermodynamically unfavorable and is inhibited by pyrophosphate. In some situations, physiological balance is broken and vascular calcification (VC) is able to progress. VC has traditionally been considered to be a passive process that was associated with advanced age, atherosclerosis, uncommon genetic diseases, and some metabolic alterations such as diabetes mellitus and end-stage kidney failure. However, in the last years, VC has been proven to be an active and regulated process, similar to bone mineralization, in which different bone-related proteins are involved. VCs are actively regulated biological processes associated with crystallization of hydroxyapatite in the extracellular matrix and in cells of the media or intima of the arterial wall. Both patterns of VC often coincide and occur in patients with type II diabetes, chronic kidney disease, and other less frequent disorders; VCs are also typical in senile degeneration. Recent results question the classic classification of VC into intimal and medial calcification, at least in capacitance arteries. Pro- and anti-calcifying mechanisms play an active role in calcium deposit ion in vascular cells, making this area an active focus of research.
ETIOLOGY OF OROYA FEVER

With a view to determining the mode of infection in Carrion's disease, a study of the blood-sucking insects found in the districts of Peru where the disease prevails has been carried out, through the cooperation of The Rockefeller Institute and the Rockefeller Foundation. The material studied included ticks, mites, midges, lice, fleas, bedbugs, mosquitoes, buffalo gnats, horse-flies, "sheep ticks," 3 species of Streblidae, and 3 species of Phlebotomus, including Phlebotomus verrucarum Townsend and two new species which have been named Phlebotomus noguchii and Phlebotomus peruensis. The insects were collected without the use of chemicals, were prepared for transportation in such a manner as to prevent drying, and were shipped under conditions of refrigeration to New York, where they were inoculated into monkeys. The plan followed was to inject saline suspensions of the crushed insects intradermally into rhesus monkeys and to make cultures of the blood of the animals at intervals of 1 to 6 weeks after inoculation. The only class of insects in which the presence of Bartonella bacilliformis could be detected were phlebotomi. No cutaneous lesions were induced in monkeys injected with the crushed insects, but in the case of four different lots of phlebotomi the blood of the animals so injected yielded cultures of Bartonella bacilliformis which produced typical verrucous lesions on inoculation into other monkeys. The morphology and cultural characteristics of the Bartonella strains obtained from phlebotomi proved identical with those of strains isolated from human blood and skin lesions. Monkeys which had recovered from infection with the phlebotomus strains resisted inoculation with a human strain of Bartonella bacilliformis, and, conversely, monkeys which had passed through an infection induced by the human strain resisted inoculation with the strains obtained from phlebotomi. The experimental observations described in this paper lead us to conclude that certain phlebotomi act as insect vectors of Oroya fever and verruga peruana. The phlebotomi which have been shown quite certainly to carry the Bartonella bacilliformis are those of the species Phlebotomus noguchii. Phlebotomus verrucarum is also probably a vector, while Phlebotomus peruensis remains doubtful in this respect.
Nematicidal Activity of Streptomyces flavogriseus KRA15-528 to Meloidogyne incognita

Plant disease caused by root-knot nematode is a major problem in crop production. Using of chemical pesticides, one of the most efficient methods to control nematodes, have raised issues in toxicity to humans and animals and environmental pollution. In this study, to select actinomycete strains that have potential to serve as a microbial agent for control of nematodes, we investigated nematicidal activity of culture broth from 670 Streptomyces isolates. A culture filtrate of KRA15-528 isolate that was identified as S. flavogriseus on the basis of 16S rRNA sequence analysis, showed strong nematicidal activity against second stage of juveniles of Meloidogyne incognita and inhibited egg hatching; exposure to 10% of culture filtrate resulted in 71% juvenile mortality at 48 hours afters treatment and suppressed egg hatching by 54% at 9 days after treatment. When the KRA15-528 culture filtrate was partitioned with ethyl acetate and butanol, ethyl acetate layer exclusively showed strong activity; 91%, 53%, 30% of mortality at 1,000, 500, 250 μg/ml, respectively. Additionally, the culture filtrate suppressed gall formation on cucumber plant by M. incognita with no phytotoxicity. These results suggest that S. flavogriseus KRA15-528 has potential to serve as a microbial nematicide for the control of root-knot nematode disease.
Perkembangan Embrio dan Penentuan Jenis Kelamin DOC (Day-Old Chicken) Ayam Jawa Super

Super Javanese chicken is the result of a cross breeding between male domestic chicken and female layer chicken. There has not been much research aboutSuper Javanese chicken embryonic development. This study attempts to provide information about embryonic development and sexing on Super Javanese chicken. This study used Super Javanese chicken fertile eggs from Java Farm, Maguwoharjo, Depok, Sleman. These eggs were incubated at temperature of 37o-38oC. Samples were observed with Neutral Red and Hematoxilin Eosine (HE) staining. The measurement of the Super Javanese chicken embryo were about length of the third finger, beak, and the length of the embryo's body. This observation obtained embryonic development of the super Javanese chicken spesifically. This concluded that Super Javanese chicken as a first generation from cross breeding has slower growth in embryonic development
Concordance between antinuclear antibody determination by immunofluorescence and line immunoassay

Introduction: Indirect immunofluorescence (IFI) on Hep2 cells is the test used for screening autoantibodies in connective tissue diseases, while the profile of specific antibodies can be detected by immunometric methods such as solid support line immunoassay (LIA). Objectives: 1) To evaluate the performance
Genetic bases of immunity and disease resistance to White Band Disease in the Caribbean Staghorn coral Acropora cervicornis

III TABLE OF CONTENTS . V LIST OF FIGURES . VIII LIST OF TABLES . IX CHAPTER 1 Innate immunity, Acropora cervicornis, and White Band Disease. 1 Overview . 1 The innate immune system . 2 Immunity in corals . 4 Allorecognition in corals. 5 Acropora cervicornis . 6 White Band Disease . 9 References . 12 CHAPTER 2 RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with White Band Disease . 21 Abstract . 21. 2
Landscape disturbance models consistently explain variation in ecological integrity across large landscapes

The generally negative effect of anthropogenic disturbance on the quality of habitats for species viability makes it a common focus of conservation assessment and prioritization efforts. Although many available spatial models and metrics (e.g., distance to or density of disturbance) characterize impact patterns of anthropogenic disturbance on the landscape, a general evaluation of model performance against empirical measurements of ecological integrity is lacking. We tested both distance-based and disturbance-density models in relation to ecological indicators. The models included roads, residential and commercial development, agricultural land use, mining, energy development infrastructure, and transmission structures as disturbance sources. Model parameters were based on expert input and results from the published literature. The disturbance models were tested against two disparate and independent measures of habitat quality: a floristic quality index and measures of greater sage-grouse population integrity. Floristic quality scores were significantly lower in vegetation plots closer to disturbances in a general distance-based disturbance model across Colorado. Although the proportion of variation in floristic quality explained by anthropogenic disturbance was relatively low (8.5–11.8%), it appeared to represent a ubiquitous baseline negative effect of proximity to anthropogenic disturbance on the quality of vegetation communities. For both distance- and density-based greater sage-grouse models, modeled disturbance indices were significantly lower (10–12 times) near active than historic leks, and numbers of males counted at leks increased significantly (3.2–3.4 times) as modeled disturbance decreased. Our findings indicate that as a general class, geospatial models can depict effects of anthropogenic disturbance on both plant communities and individual animal species. Empirical validation of disturbance models focused on other species or regions is recommended to further evaluate the utility and reliability of these methods.