Miracle-dz/UniFAR-FTUs huggingface dataset:
Connective tissue growth factor in tissue fibrosis

Systemic Sclerosis (SSc) is a connective tissue disease characterised by inflammation and autoimmunity, vasculopathy, and interstitial remodelling and fibrosis. This thesis focuses on CTGF (CCN2), a member of the CCN family of matricellular proteins, as elevated CTGF expression is a hallmark of chronic fibrotic diseases such as SSc. In addition to the association of CTGF expression and fibrosis in human disease, experimentally, fibroblast-specific overexpression of CTGF has been shown to induce a fibrotic phenotype, as demonstrated in the Col1a2-CTGF transgenic mice. Prominent features of fibrosis included a thickened dermis, as well as excess collagen deposition in the skin and lung. This CTGF overexpression also provoked changes in the alveolar epithelium. In the lung of Col1a2-CTGF mice, immunostaining revealed a marked increase in the number of cells co-expressing the epithelial marker, TTF-1 and mesenchymal cell markers α-SMA and Snai1, indicative of epithelial-to-mesenchymal transition (EMT)-like changes. This suggested a role for the paracrine effects of CTGF in promoting the phenotypic switching of alveolar epithelial cells. EMT is likely to contribute, at least in part, to the accumulation of interstitial fibroblasts during fibrosis. Complementary in vitro studies in alveolar epithelial cells (AECs) showed that CTGF knockdown using siRNA suppressed TGF-β-induced mesenchymal cell proteins while inducing redistribution of the epithelial cell marker E-cadherin. Immunostaining and Western blotting showed that recombinant CTGF induced EMT-like morphological changes and expression of α-SMA in AECs. Finally, we were interested in whether the reduction or absence of CTGF could abrogate fibrosis. Knockdown of CTGF suppressed the induction of fibrotic proteins in TGF-β-treated control fibroblasts and SSc lung fibroblasts. Deletion of the CTGF gene showed reduced bleomycin-induced pulmonary fibrosis in mice. Overall, these results support that CTGF plays a pivotal role in fibrosis and blocking CTGF activity may be useful as a specific target of attenuating fibrosis in SSc.
Feed Additives in Swine Diets

Feed additives are compounds used in swine diets with the purpose of enhancing performance and health. Many non-antibiotic feed additives have been proposed or evaluated for improving growth performance, regulating gut microbiota, supporting immunity, ameliorating environmental challenges, and enhancing reproductive performance. However, the main challenge with non-antibiotic feed additives is the fact that many have not generated consistent effects or have not been economically justified. A brief overview of non-antibiotic feed additives available for inclusion in swine diets, the proposed mode of action, and the summary of effects on performance are provided in this fact sheet.
Análisis del comportamiento de personas mediante mapas de calor

Data Analysis is a discipline that everyday gains importance. In many fields of our society exists a huge number of information to analice and the visualization techniques are not enough. Among the visualization techniques of today are the heat maps, which allow to represent the information in an easy and accesible way for everyone. There are companies which commercialize this kind of solutions, even if they have limited functionality and they are proprietary and closed systems. The solution proposed in this document is an image processing based system that generates heat maps to represent the movement of people and objects in any scene and technologically independent.
Cooperation Among Animals: An Evolutionary Perspective

Chapter 1 Historical perspectives on cooperative behavior Chapter 2 Theoretical perspectives on the evolution of cooperation Chapter 3 Cooperation in fishes Chapter 4 Cooperation in birds Chapter 5 Cooperation in mammals I: non-primates Chapter 6 Cooperation in mammals II: non-human primates Chapter 7 Cooperation in insects Chapter 8 To the future
Physiological Genomics of the Rat Renal Failure QTLs Rf-1 through Rf-5

Linkage analysis of a cross of FHH and renal-resistant ACI rats revealed five QTLs, named Rf-1 through Rf-5 influencing susceptibility to renal damage. This thesis describes the physiological genomics of the rat renal failure QTLs Rf-1 through Rf-5. Congenic rats were generated carrying one of the Rf-QTLs or the Rf-1 in combination with another Rf-QTL. Experiments were performed on Rf-1, Rf-3, Rf-4 and Rf-5 single congenics, and Rf-1+2, Rf-1+3, Rf-1+4, Rf-1+4 and Rf-1+5 double congenic rats. Susceptibility to the development of renal damage was assessed using four models, i.e. the two-kidney (2K) control situation, 2K with L-NAME induced hypertension, unilateral nephrectomy (UNX), and UNX with LNAME induced hypertension. Since previous studies showed that FHH rats have an impaired renal blood flow autoregulation, all congenic rats were tested for the presence of renal blood flow autoregulation. Besides these experiments we also tested the applicability of the remnant kidney model (RKM) to assess differences between the Rf-congenic strains. The outcome of the various physiological genomic studies presented in this thesis regarding the rat renal failure QTLs Rf-1 through Rf-5 led to the following conclusions: The Rf-1 region of the FHH contains one or more genes directly influencing renal susceptibility and impairing renal autoregulation. Whether these genes are the same needs to be further investigated. The direct effect of the Rf-2 region could not yet be tested. When the Rf-2 region is combined with the Rf-1 region, a significant increase in renal damage is seen when compared with Rf-1 alone. Furthermore, the Rf2 region, also harboring the blood pressure QTL Bpfh-1, increases blood pressure. The Rf-3 region contains genes directly influencing renal susceptibility. Renal damage susceptibility in Rf-3 single congenics is comparable to that of Rf-1 single congenics. When Rf-1 and Rf-3 are combined a significant synergistic interaction is present. The Rf-3 congenic rats do have a normal renal autoregulation. The mechanisms by which Rf-3 influences the development of renal damage still remains to be detected. Genes in the Rf-4 region do not directly influence renal susceptibility. However, when combined with Rf-1 a significant synergistic interaction is present. The Rf-4 congenic rats do have a normal autoregulation. The mechanisms by which Rf-4 indirectly influences the development of renal damage is still unknown and should be further investigated. The Rf-5 region does not contain genes that directly influence renal susceptibility. In addition, the Rf-5 region shows no synergistic interaction with the Rf-1 region. The RKM is not a very suitable model to analyze renal susceptibility in rats carrying Rf-regions of the FHH rats. The four models we used, especially the UNX and 2K+L-NAME model appear more suitable to assess differences in susceptibility to develop renal damage.
Flora, Life Form and Chorology of Winter and Rural Range Plants in the Northern Khorasan Province, Iran

Floristic studies are fundamental for the applied sciences such as rangelandmanagement and conservation. Unique ecological and climatic conditions in the NorthernKhorasan Province (NKP) make it a remarkable habitat for the floristic studies. Plant specieswere collected from 50 field sites, representing major habitats of winter and rural rangelands.Surveys were conducted during active growth periods in 2007 and 2008. Plant species wereidentified and their chorology and life form determined through laboratory examinations andby using reference books. Floristic surveys resulted in identification of 534 plant species,belonged to 315 genus and 68 families. Asteraceae, Poaceae and Fabaceae were respectivelythe most abundant plant families. Among the life forms, Hemicryptophytes, Therophytes,Chamaephytes, Phanerophytes and Geophytes included 45, 32, 9, 7 and 7% of the totalspecies, respectively. Irano-Turanian was the most dominant (65%) Chorotypes. Thedominance of Hemicryptophytes and Therophytes, as well as vast distribution ofChamaephytes, can be referred to the simultaneous effects of climate fluctuations andlivestock grazing on the flora of winter and rural rangelands in NKP.
Organisation et modulation du réseau neuronal de la respiration chez la lamproie

The neural control of breathing is currently investigated on multiple animal models such as frogs and rats. We have used the lamprey as an experimental model to characterize the brainstem neural networks involved in the genesis and modulation of the respiratory rhythm. We have first characterized a new population of respiratory neurons in the paratrigeminal respiratory group (pTRG). The pTRG is a region that was shown to be essential to respiratory rhythmogenesis in lampreys. We have shown that the pTRG contains a group of neurons with complex axonal arborisations, including bilateral projections to the motoneuron pools of the brainstem that activate gills, as well as bilateral projections connecting the pTRGs on the two sides of the brainstem. These results suggest that pTRG neurons could participate in the descending control of respiratory motoneurons as well as the bilateral synchrony of the respiratory rhythm. We have then studied the neural mechanisms by which respiration is increased during locomotion. We have shown that the mesencephalic locomotor region (MLR), in addition to its role in controlling locomotion, also increases breathing during locomotion. Neurons in the MLR are anatomically segregated, those projecting to the respiratory centers being located more dorsally. We have abolished the contribution of the dorsal part of the MLR to respiratory changes by injecting glutamate receptor blockers locally in semi-intact preparations. We have shown that during swimming episodes, a major part of the respiratory effect is dependent on the dorsal part of the MLR. Our results confirm that the respiratory rhythm is generated by a rostrolateral region in the pons of lampreys and show that connections from locomotor centers can
Integrative and FreeSpiroplasma citri oriCPlasmids: Expression of theSpiroplasma phoeniceumSpiralin inSpiroplasma citri

The replication region (oriC)oftheSpiroplasma citrichromosome has been recently sequenced, and a 2-kbp DNAfragmentwascharacterizedasanautonomouslyreplicatingsequence(F.Ye,J.Renaudin,J.M.Bove´,and F. Laigret, Curr. Microbiol. 29:23‐29, 1994). In the present studies, we have combined this DNA fragment, containing thednaAgene and theflankingdnaAboxes, with a ColE1-derivedEscherichia colireplicon and the Tet M determinant, which confers resistance to tetracycline. The recombinant plasmid, named pBOT1, was introducedintoS.citricells,inwhichitreplicated.PlasmidpBOT1wasshuttledfromE. colitoS.citriandback toE.coli. InS.citri,replicationofpBOT1didnotrequirethepresenceofafunctionaldnaAgeneontheplasmid. However, the dnaA box region downstream of the dnaA gene was essential. Upon passaging of the S. citri transformants, the plasmid integrated into the spiroplasmal host chromosome by recombination at the replication origin. The integration process led to duplication of the oriC sequences. In contrast to the integrative pBOT1, plasmid pOT1, which does not contain theE. colireplicon, was stably maintained as a free extrachromosomal element. Plasmid pOT1 was used as a vector to introduce intoS. citrithe G fragment of the cytadhesin P1 gene of Mycoplasma pneumoniae and the spiralin gene of Spiroplasma phoeniceum. The recombinant plasmids, pOTPG with the G fragment and pOTPS with the spiralin gene, were stably maintained in spiroplasmaltransformants.ExpressionoftheheterologousS. phoeniceumspiralininS.citriwasdemonstrated by Western immunoblotting.
Isolation of Cronobacter spp. Isolates from Infant Formulas and Their Survival in the Production Process of Infant Formula

FuS. � ,�GaoJ. ,�LiuY. ,�ChenH. �(2011):�Isolation of Cronobacter spp . isolates from infant formulas and their survival in the production process of infant formula. �CzechJ. �FoodSci. ,�29:�391-399. Overa�24-monthsurveillance, �threeCronobacterstrains, �NC041,�NC830,�andNC1006,�wereisolatedfrom �77�powder� infantformulas �(3.90%). �No Cronobacterwasdetectedinliquidmilk. �TheprevalenceofCronobacterintheprefinal� productandpackagedfinalproductwas �3.70%�and �4.35%,�respectively. �TheisolatedCronobacterstrainsweresub - jectedtoseverallethalchallengesincludingthepH, �drying, �disinfectant, �andsimulatedinfantformulasmanufactur - ingprocess �(SIFMP). �Theresultsindicatedthattheyexhibitedunusualresistancetothedrystressanddisinfectant. � InSIFMP,�Cronobacterisolateswereinoculatedintothreepossiblecontaminationentrypointsinvolvingthestages� priortoheating, � drying, � andfilling, � respectively. � NoCronobactercouldsurvivetheheating. � However, � ahighlevel� (10 5� CFU/ml) �ofCronobacterwasdetectedinthesamplesaftertheinoculationatthedryingpoint. �Furthermore, �the� survivalofCronobacterwasobservedduringthestorageat �10°Cafter �7�days. �Theresultssupportthehypothesisthat� Cronobactercontaminationoccursatthestagesofdryingandfilling, �andhighlighttheneedtoimprovethedisinfect - ingmeasuresinthemanufacturingprocess. �
The A9 Antigen Associated with Aggressive Human Squamous Carcinoma Is Structurally and Functionally Similar to the Newly Defined Integrin α6β4

We previously reported that altered expression of the A9 antigen (defined by monoclonal antibody UM-A9) is a predictive marker of early recurrence and progression of squamous cell carcinoma (SCC). In normal squamous cells A9 expression is limited to the site of contact with the basement membrane in vivo and the culture surface in vitro , whereas aggressive SCCs exhibit loss of polarity and increased intensity of A9 expression. The potential relationship of the A9 antigen to structures known to be involved in cell adhesion was analyzed by immunobiochemical and cell adhesion assay. UM-A9 precipitates a complex of protein chains reminiscent of the α and β heterodimer glycoproteins that characterize the integrin family of extracellular matrix receptors. Proteins were isolated from A9-positive cells using UM-A9 and well-defined antibodies specific for integrin α and β chains. UM-A9, anti-α6, and anti-β4 monoclonal antibodies (mAbs) all precipitated proteins with comparable electrophoretic mobilities. Furthermore, UM-A9 mAb precleared the SCC α6β4 integrin complex isolated with anti-α6 or anti-β4 mAbs but not that isolated by anti-β1 mAb. The isoelectric points of the A9 complex chains were consistent with those reported for α6 and β4. Three of the polypeptide chains (140, 175, and 205 kDa) precipitated by UM-A9 showed peptide homology to one another and to the β4 chain precipitated by mAb 439-9B. The A9/α6 subunit is composed of 125- and 30-kDa chains and was distinguished from β4 and β1 chains by its peptide map and isoelectric point. UM-A9 binds to an epitope common to the β4 subunits since in pulse-chase analysis the β4 species are precipitated at an early time point, whereas detection of α-subunit synthesis is detected during assembly of the mature complex. Immunoprecipitation and preclearing experiments demonstrated that in SCC the α6 subunit is associated primarily with the β4 species and not with the 130-kDa β1 subunit. In cell adhesion assays on extracellular matrix proteins, the α6-specific GoH3 mAb inhibited binding of SCC to laminin, suggesting that α6β4 may function as a laminin receptor in SCC. These data and our prior observations showing an association between altered A9 expression and early recurrence in SCC provide the first evidence that altered expression of α6β4 integrin is associated with the clinical behavior of human squamous cell carcinomas.
Analise experimental sobre a viabilidade de Escherichia coli em agua do mar

Five experiments were carried out in order to investigate the resistance of Escherichia coli strains isolated from Coco River and inoculated in sea water, stored in laboratory at environmental temperature. The strains of E. coli were incubated at 37 and 44.5 o C. The initial inocule (Ti) was of 166 x 109 CFU/ml. The time of each experiment was 168 h. Sea water resistant strains were counted at T0 (time which the inocule was introduced into the sea water), T1, T2, T24, T120 and T168h. Up to 168 h, for all experiments, it was possible to detect viable strains of E. coli. There was no statistically significantly difference (α = 0.05) between experiments, considering the strains were isolated from the same place and were treated on the same manner. Other factors, such as UV rays, may be more deleterious to the cell than salt concentration in sea water itself.
The Impact of the MERS Outbreak in Daily Lives: Sentiment Analysis of Korean Tweets using Time-series Methods

This study examines the correlation between sentiments in tweets and the number of passengers in the subway as the social index during the MERS outbreak in South Korea. The observation that motivated this study in the social context was that people tended to avoid their social lives outdoors by the fear of being infected during the situation. Two time-series datasets were processed for the purpose of getting rid of seasonal patterns. The result showed that they are correlated with each other with 169 hours. It indicates that the sentiments in social media can be a good way of mirroring people’s behaviors ahead of time.
Phenotypic spectrum associated with mutations of the mitochondrial polymerase γ gene. Commentary

Mutations in the gene coding for the catalytic subunit of the mitochondrial DNA (mtDNA) polymerase γ (POLGI) have recently been described in patients with diverse clinical presentations, revealing a complex relationship between genotype and phenotype in patients and their families. POLGI was sequenced in patients from different European diagnostic and research centres to define the phenotypic spectrum and advance understanding of the recurrence risks. Mutations were identified in 38 cases, with the majority being sporadic compound heterozygotes. Eighty-nine DNA sequence changes were identified, including 2 predicted to alter a splice site, I predicted to cause a premature stop codon and 13 predicted to cause novel amino acid substitutions. The majority of children had a mutation in the linker region, often 1399G-A (A467T), and a mutation affecting the polymerase domain. Others had mutations throughout the gene, and 11 had 3 or more substitutions. The clinical presentation ranged from the neonatal period to late adult life, with an overlapping phenotypic spectrum from severe encephalopathy and liver failure to late-onset external ophthalmoplegia, ataxia, myopathy and isolated muscle pain or epilepsy. There was a strong gender bias in children, with evidence of an environmental interaction with sodium valproate. POLGI mutations cause an overlapping clinical spectrum of disease with both dominant and recessive modes of inheritance. 1399G-A (A467T) is common in children, but complete POLGI sequencing is required to identify multiple mutations that can have complex implications for genetic counselling.
Quantifying and Engineering Protein Dynamics in Bacteria

Genetically identical cells can display heterogeneity in their level of proteins due to stochastic gene expression. Such noise has been found to be widespread across biology, and can have a tremendous impact by allowing cells to access different phenotypes. However, the timescales of these fluctuations matter: slow fluctuations are potentially much more potent whereas if fluctuations are corrected rapidly they are relatively innocuous. Many simple mechanisms in cells – such as gene cascades, time-averaging to suppress fluctuations and epigenetic modifications – can create slow fluctuations. Quantifying protein dynamics remains a technical challenge as it requires measuring gene expression of long time series under constant growth conditions, and thus the timescales of fluctuations in gene expression remain largely unknown. By using a newly developed microfluidic device – to follow hundreds of cells for hundreds of cell divisions under constant growth conditions – we quantify the timescale of fluctuations of∼ 50 transcriptional reporters and∼10 translational reporters in Escherichia coli. All reporters show a strikingly similar and surprising behavior: an exponential decorrelation with a half-life of one generation. We show that the discrepancy with previous studies can be explained by artifacts arising from calculating autocorrelation functions with short time series or non-uniform growth conditions. The general absence of slow fluctuations in cells opens up the question of how difficult it is to
Análise das práticas de produtores em sistemas de produção leiteiros e seus resultados na produção e qualidade do leite

There was carried a research with 18 dairy systems aiming typify these farms concerning their zootechnical conduct and comparing that against the production and quality indicators of the milk as a product. The study was placed in northwest Parana state region, in five municipalities. Data was obtained using DRP – Fast Participative Diagnosis, by means of an interview. Milk was sampled in each farm and analyzed as follows. Data analysis was made using a multivariate techniques Multilple Correspondence Analysis and Cluster’s Analysis. Were obtained four homogeneous groups (clusters) concerning to conduct that influenced (p<0,05) the quality and production indicators of the milk. This was obtained using analysis of variance with clusters as factors and milk variables as response variables. There were identified four distinct dairy farmer profiles. These concerning to: general structure of the dairy system, technologic level and possibility of continuity of dairy farming related to farmer’s age. The actions of technical assistance must be adequate to those profiles but not homogenized, like is usual in our context, for reach many dairy farms as possible and make these production systems.