Miracle-dz/UniFAR-FTUs huggingface dataset:
Two-stage Activation for α5β1Integrin Binding to Surface-adsorbed Fibronectin*

By analyzing the functional binding of α5β1 integrin to adsorbed fibronectin in intact cells, we demonstrate that integrin activation results in linear increases in adhesion strength as a function of ligand density, suggesting that modulation of the receptor-ligand interaction is the dominant mechanism for adhesion during the initial stages of adhesion and that cooperative binding contributes little to initial adhesion strength. Using this experimental framework, we show the existence of three distinct activation states for α5β1integrin binding to adsorbed fibronectin for both passive, antibody-induced and active, cell-controlled activation. During the initial phase of adhesion, α5β1 integrin is activated in an energy-dependent process from the nonbinding ground state to an intermediate state in which the receptor binds fibronectin and provides significant mechanical coupling. In later stages of adhesion maturation, α5β1integrin is activated to a higher binding state, which provides significant increases in adhesion strength compared with the intermediate state. These multiple binding states most likely result from different integrin conformations and reflect distinct interactions between α5β1 and sites on adsorbed fibronectin. Multiple activation states for α5β1 suggest the existence of distinct stages in adhesion signaling and strengthening and can provide a versatile mechanism for the regulation of adhesive interactions.
In situ and in vitro analysis of germ and stem cell marker-positive cells in the postnatal ovary of the common marmoset monkey (Callithrix jacchus)

Oogonia are the proliferating diploid germ cells within the female gonad giving rise to oocytes. Oocytes are the meiotic female germ cell stages. In humans, almost all oogonia enter meiosis between weeks 9 and 22 of prenatal development. As a consequence, neonatal human ovaries generally lack oogonia. The same was found in neonatal ovaries of the rhesus monkey, a representative of the old world monkeys (Catarrhini). In the present study we used the common marmoset monkey (Callithrix jacchus) as a representative of the new world monkeys (Platyrrhini). In the first part of the study we could show that the neonatal marmoset monkey ovary has an extremely immature histological appearance compared with human and rhesus monkey ovaries. It contains numerous oogonia expressing the pluripotency factors OCT4A, SALL4, and LIN28. These cells also express the proliferation marker Ki-67, which has previously been shown in human ovary to be restricted to fetal premeiotic germ cells. Together, these data demonstrate the primitiveness of the neonatal marmoset ovary compared with human. This part of the study may introduce the marmoset monkey as a suitable non-human primate model to experimentally study aspects of primate primitive gonad development, follicle assembly, and germ cell biology in vivo. In the second part of the study we aimed at culturing marmoset female germline stem cells (FGSCs) from neonatal ovaries. We successfully established ovarian cell cultures for more than 20 passages and 5 months. Importantly, comparative transcriptome analysis of the early passages with reference samples including native neonatal ovary and embryonic stem cells revealed a lack of germ cell and pluripotency genes indicating the immediate loss of the typical germ cell populations in culture. However, from passage 4 onwards, the cultured cells produced oocyte-like cells under a specific cell culture condition, while oocyte-like cells did not develop under embryonic stem cell conditions. Oocyte-like cells were free-floating, approximately 50 µm in diameter and strongly expressed several germ cell markers. The cultured ovarian cells did not develop treratoma or ovarian-like tissues after transplantation into immuno-deficient mice. In summary, our novel primate ovarian cell culture initially lacked germ cells, but then recovered germ cell expression and produced oocyte-like cells. This suggests the presence of FGSCs in the cultures. However, their identity needs to be determined, but we hypothesize that FGSCs lack the typical germ cell signature. The presence of functional FGSCs in the postnatal primate ovary of the common marmoset monkey could have important implications for the development of possible novel strategies for the protection and preservation of human female fertility during the treatment of cancer and other conditions using chemo- and radiation therapy.
Geographic variation in reproductive traits and trade-offs between size and number of eggs of the Chinese cobra (Naja atra)

We collected gravid Chinese cobras (Naja atra) from one island (Dinghai) and three mainland (Yiwu, Lishui and Quanzhou) populations in south-eastern China to study geographical variation in female reproductive traits and the trade-off between the size and number of eggs. We then conducted an common experiment on cobras from two of the four populations to further identify factors contributing to the observed trade-offs. The mean size (snout–vent length) of the smallest five reproductive females increased with increasing latitude. Oviposition occurred between late June and early August, with females from the warmer localities laying eggs earlier than those from the colder localities. Maternal size was a major determinant of the reproductive investment in all populations, with larger females producing not only more but also larger eggs. Clutch size was more variable than egg size within and among populations. The observed geographical variation in clutch size, egg size, clutch mass and post-oviposition body condition was not a simple consequence of variation in maternal size among populations, because interpopulation differences in these traits were still evident when the influence of maternal size was removed. The upper limit to reproductive investment was more likely to be set by the space availability in the island population, but by the resource availability in the three mainland populations. Trade-offs between size and number of eggs were detected in all populations, with females that had larger clutches for their size having smaller eggs. Egg size at any given level of relative fecundity differed among populations, primarily because of interpopulation differences in the resource availability rather than the space availability. Except for the timing date of oviposition and the mean size of the smallest five reproductive females, all other examined traits did not vary in a geographically continuous trend. The common garden experiment, which standardized environmental factors, synchronized the timing date of oviposition, but it did not modify the conclusion drawn from the gravid females collected from the field. The observed geographical variation in the female reproductive traits could be attributed to the consequence of the effects of either proximate or ultimate factors. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 27–40.
Human Cytomegalovirus Inhibits IFN-α-Stimulated Antiviral and Immunoregulatory Responses by Blocking Multiple Levels of IFN-α Signal Transduction

The type I IFNs represent a primordial, tightly regulated defense system against acute viral infection. IFN-α confers resistance to viral infection by activating a conserved signal transduction pathway that up-regulates direct antiviral effectors and induces immunomodulatory activities. Given the critical role of IFN-α in anti-human cytomegalovirus (HCMV) immunity and the profound ability of HCMV to escape the host immune response, we hypothesized that HCMV blocks IFN-α-stimulated responses by disrupting multiple levels of the IFN-α signal transduction pathway. We demonstrate that HCMV inhibits IFN-α-stimulated MHC class I, IFN regulatory factor-1, MxA and 2′,5-oligoadenylate synthetase gene expression, transcription factor activation, and signaling in infected fibroblasts and endothelial cells by decreasing the expression of Janus kinase 1 and p48, two essential components of the IFN-α signal transduction pathway. This investigation is the first to report inhibition of type I IFN signaling by a herpesvirus. We propose that this novel immune escape mechanism is a major means by which HCMV is capable of escaping host immunity and establishing persistence.
Red blood cell indices of rainbow trout Oncorhynchus mykiss (Walbaum) in aquaculture

A direct non-parametric method was used to calculate reference (physiological) haematology values for farmed 10–12-month rainbow trout of the Kamloops strain (mean weight: 330±131 g) with respect to red blood cell counts (RBCc), haematocrit values (Hct), haemoglobin concentrations (Hb), mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH) and mean corpuscular haemoglobin concentrations (MCHC). The fish in the selected reference group (n=798) were given dry pelleted diets that contained 37–47% crude protein, 7–18% crude fat and 108–300-mg vitamin E, 1.08–5-mg folic acid, 0.018–0.05-mg vitamin B12, 48–64.5-mg iron, 4.5–8.4-mg copper and 0.18–0.24-mg selenium supplied per kg of diet. Ethoxyquin and butylhydroxytoluol were used to protect the fat component against oxidation. The fish were kept at a stocking density of 50kg per cubic metre in tanks provided with running freshwater (dissolved oxygen 8.4–11.5 mg L−1, with O2 saturation of 77–98%) at an ambient temperature of 0.2–16°C. Blood was sampled between September and November at a photoperiod of 9–13 h:11–15 h (light:dark). Reference ranges for the preceding haematological indices were as follows in immature females (males): RBCc, 0.77–1.42T L−1 (T – tera, 1012) (0.98–1.55T L−1); Hct, 0.304–0.502 (0.34–0.546); Hb, 54–93 g L−1 (59–97 g L−1); MCV, 282–469 fL (279–434 fL); MCH, 51–86 pg (47–78 pg); MCHC, 0.15–0.22 (0.15–0.2). In males, values for RBCc, Hct and Hb were significantly higher (P=0.01 and 0.0000 respectively) and those for MCV, MCH and MCHC were significantly lower (P=0.01 and 0.0002 respectively) than in immature females. Nutritional and environmental factors affecting erythropoiesis in trout and some correlations between haematological (RBCc, Hb, Hct) and biochemical indices of the blood plasma (total protein, cholesterol) are discussed.
Measurement Models for Brand Performance -a literature review

A well-refuted model considering every dimension of brand performance is yet to evolve. Existing brand performance models explains two important premiseconsumer brand equity driven measure of brand performance and Firm based brand performance, whereby it excludes many more dimensions and applies to limited category of brands. To identify any of such gaps in the existing conceptual theory that which is yet desired, is the objective of this paper. Listing of all brand performance models and identifying its scope and application value it provides to further its relevance in bringing a specified metric to define brand performance is the purpose. Major results from the point at further research direction such as making the model application value
Increasing participation in a mobile app study: the effects of a sequential mixed-mode design and in-interview invitation

In this paper we examine two potential ways of increasing participation in app-based data collection: 1) inviting respondents to the mobile app study within an interview rather than by post, and 2) offering a browser-based alternative to the mobile app. We use experimental data from Spending Study 2, collected on the Understanding Society Innovation Panel and on an online access panel managed by Lightspeed UK. The results suggest that inviting respondents to an app study within a face-to-face interview increases participation, but does not bring in different types of participants. In contrast the browser-based alternative can both increase participation and reduce biases in who participates.
Laying the foundations of evolutionary and systematic studies in crickets (Insecta, Orthoptera): a multilocus phylogenetic analysis

Orthoptera have been used for decades for numerous evolutionary questions but several of its constituent groups, notably crickets, still suffer from a lack of a robust phylogenetic hypothesis. We propose the first phylogenetic hypothesis for the evolution of crickets sensu lato, based on analysis of 205 species, representing 88% of the subfamilies and 71% tribes currently listed in the database Orthoptera Species File (OSF). We reconstructed parsimony, maximum likelihood and Bayesian phylogenies using fragments of 18S, 28SA, 28SD, H3, 12S, 16S, and cytb (~3600 bp). Our results support the monophyly of the cricket clade, and its subdivision into two clades: mole crickets and ant‐loving crickets on the one hand, and all the other crickets on the other (i.e. crickets sensu stricto). Crickets sensu stricto form seven monophyletic clades, which support part of the OSF families, “subfamily groups”, or subfamilies: the mole crickets (OSF Gryllotalpidae), the scaly crickets (OSF Mogoplistidae), and the true crickets (OSF Gryllidae) are recovered as monophyletic. Among the 22 sampled subfamilies, only six are monophyletic: Gryllotalpinae, Trigonidiinae, Pteroplistinae, Euscyrtinae, Oecanthinae, and Phaloriinae. Most of the 37 tribes sampled are para‐ or polyphyletic. We propose the best‐supported clades as backbones for future definitions of familial groups, validating some taxonomic hypotheses proposed in the past. These clades fit variously with the morphological characters used today to identify crickets. Our study emphasizes the utility of a classificatory system that accommodates diagnostic characters and monophyletic units of evolution. Moreover, the phylogenetic hypotheses proposed by the present study open new perspectives for further evolutionary research, especially on acoustic communication and biogeography.
Reflections on “What is Ecosystem Management?”

I review 10 dominant themes of ecosystem management described in the paper “What is Ecosystem Management? ” (Grumbine 1994a) based on feedback received from managers actively implementing ecosystem management projects in the field. My emphasis is on practical advice from working professionals for working professionals. Key points include the importance of managing for ecological integrity, the need for social as well as scientific data, suggestions for implementing cooperation strategies and conservation partnerships, a pragmatic definition of adaptive management, and first steps toward changing the structure of natural resource organizations. As ecosystem management evolves, the pressure for change within traditional resource management agencies appears to be reaching a critical point.
Genotypic and pathogenic characterization of Newcastle Disease Viruses isolated from domestic ducks in China.

In order to determine the prevalence of Newcaste Disease Virus (NDV) in ducks in Guangdong province of China, 10 NDVs were isolated in domestic ducks. Eight isolates were pathogenic as determined by MDT, ICPI and cleavage site of F protein. The F genes of 10 isolates were sequenced, all the genes and their deduced amino acids were compared with 32 reference strains. 5 isolates were clustered in genotype VII (VIId), 3 isolates were classified as genotype IX and 2 isolates were classified as genotype. The subgenotype VIId isolates possessed the motif 112R-R-Q-K-R-F117, and the genotype IX isolates possessed the motif 112R-R-Q-R-R-F117. The 8 NDV isolates exhibited a high ICPI, they were classified as velogenic type of NDVs and were collected between the years of 2006 and 2010. The genotype I isolates possessing the motif 112G-K-Q-G-R-L117 were collected in 2005, they were exhibited a low ICPI and were classified as lentogenic type of NDVs. The NDVs of subgenotype VII are now dominant and have been implicated in most of the recent ND outbreaks in duck farms in Guangdong province. These findings provide data on genetics and molecular evolution of NDV in ducks in China and emphasize importance of NDV surveillance for improving of strategies for the control of the disease.
Estudo in silico das bases moleculares responsáveis pela reatividade cruzada entre epitopos virais restritos ao alelo HLA-A*02:01

8 Capítulo I: Introdução e Objetivos . 9 1 Introdução: . 10 1.1 Resposta imune humoral e resposta imune celular . 11 1.2 Região do MHC e a família gênica do HLA . 12 1.3 Estrutura do MHC-I . 14 1.4 Rota de apresentação de peptídeos endógenos . 15 1.5 Reconhecimento pelos linfócitos T citotóxicos . 18 1.6 Memória imunológica . 19 1.7 Imunidade heteróloga e reatividade cruzada . 20 1.8 O Vírus da Hepatite C (HCV) . 23 1.9 Desenvolvimento de vacinas anti-HCV . 25 1.10 A Bioinformática e suas aplicações à Imunologia . 27 1.11 Predição da estrutura tridimensional de complexos pMHC . 29 2 Objetivos: . 32 3 Capítulo II : Structural Allele-Specific Patterns Adopted by Epitopes in The MHC-I Cleft and Reconstruction of MHC:Peptide Complexes to Cross-Reactivity Assessment Artigo Completo Publicado na Revista PLoS One . 33 4 Capítulo III : Structural in Silico Analysis of Cross-Genotype-Reactivity Among Naturally Occurring HCV NS3-1073-Variants in The Context Of HLA-A*02:01 Allele Artigo Completo Aceito para Publicação na Revista Molecular Immunology . 51 5 Capítulo IV: Discussão geral . 78 6 Referências . 95 7 Anexos . 100 7.1 Anexo 1: Errata submetida ao sitio da revista PLoS One. 101 7.2 Anexo 2: Versão editada da figura 4 (capítulo II). 102 7.3 Anexo 3: Tabela com os valores preditos para a afinidade de ligação ao MHC-I. 103 7.4 Anexo 4: Valores de ASA para os peptídeos selecionados. 103 7.5 Anexo 5: Parâmetros das simulações (arquivos mdp). 104
Response of mungbean (Vigna radiata L., Wilczek) to gibberellic acid (GA3) rates and varying irrigation frequencies

An attempt was made to investigate the response of mungbean local cultivar to irrigation frequencies and for improving its drought resistance capability by the application of 0, 100 and 200mg/l GA3. Results showed that irrigating mungbean plants every 8 days drastically reduced plant height (46.8%), internodes length (32.1%), number leaves per plant (64.3%), leaf area per plant 9158.5%), leaf area index (179.3%), inflorescence number per plant (119%) pod length (22.6%), pod number per plant (117%), seed number per pod (23.8), biomass yield (74.6%), yield (91.3%) and seed yield per plant (83.7%). However, this treatment highly increased number first fruiting node (180.1%) and weight of 1000 seeds (11.5%). Treatments can be ordered due to their importance as below: 2days > 4days > 6days > 8days. Yield was linearly responded to irrigation frequencies and it can be estimated by the following equation: Y = 131.252 – 5.233 X, where (r 2 =13). Mash plants treated by (200 mg.l -1 GA3) substantially increased plant height (11.7%). However, treated plants highly reduced yield (12.5%) and harvest index (8.2%). However, other detected traits revealed non unequivocal differences with that of untreated plants. Yield showed linear response to GA3 rates and it could be estimated from the below formula: Y = 114.698 – 0.064 X, where (r 2 =2.4). 200 mg.l -1 GA3 treated plants irrigated every 2 days appeared the most potent dual interaction treatment. Since it exhibited the highest values in terms of plant height (52.33 cm), internodes length (6.19), inflorescence number per plant (13), pod length 5.83 cm), pod number per plant (29), seed
ColMiner: uma ferramenta de apoio ao gerenciamento das comunicações em um ambiente de issue tracking

A comunicacao e um dos pilares do trabalho colaborativo e tem sido abordada na literatura como um dos fatores criticos que impactam os resultados de um projeto de software. No entanto, ha uma falta de ferramentas computacionais para suportar a analise de comunicacao. Este artigo apresenta o ColMiner, uma ferramenta capaz de medir a qualidade da comunicacao em um ambiente de rastreamento de problemas atraves do calculo da relevância dos comentarios da questao para o tema principal da discussao (relevância tematica). Sua finalidade e identificar falhas no processo de comunicacao. A abordagem da analise de comunicacao utiliza algumas tecnicas de mineracao de texto baseadas no uso de graficos para representar o conteudo textual dos comentarios. Para validar a abordagem, as relevâncias calculadas pelo ColMiner sao comparadas com aquelas definidas manualmente por alguns desenvolvedores. Por fim, o trabalho apresenta as principais funcionalidades do ColMiner, destacando o suporte ao gerenciamento de comunicacoes em projetos de software e discutindo algumas ameacas a validade.
Reducing death by electrocution of the white stork Ciconia ciconia

Anthropogenic changes have strongly influenced the biodiversity of Europe. In the last 50 years electric power‐line networks have become a conspicuous part of the European landscape, and have strongly influenced the survival of some bird species. When they were constructed it was known, at least locally, that these lines and their support structures would cause fatalities in the white stork Ciconia ciconia. Annually thousands of white storks die in collision with, and through electrocution by, power lines, and these are important causes of their mortality. Using data collected in central Poland we show that technical modifications to electricity poles are an effective way to assist stork conservation and may, at least locally, reduce mortality by electrocution to zero. Because the white stork is an icon of nature conservation, we believe that public utilities and power‐line companies will more readily focus on protecting this species; while indirectly aiding wider bird conservation. Furthermore, since contact with power‐lines results in a break in energy transmission, these modifications also positively benefit both energy consumers and power companies.
Sistema de monitoreo de crecimiento de lunares para la detección temprana de cáncer de piel tipo melanoma basado en dispositivos móviles Android

Melanoma skin cancer is highly curable if it is detected in early stages. Melanoma can arise in moles exposed to UV radiation for extended periods of time, changing its color, shape and size. In this paper, we present a monitoring system for mole’s growth and appearance as an alert for possible malignant melanoma. First, we segment moles in the image taken by the mobile device by using ﬁlters in the YCbCr color space. Then, we remove residual noise in the image and calculate the mole area. Finally, the photograph, as well as the capture date and the area
Establishment and characterization of urine-resistance cell sub-strain of human bladder cancer

Abstract Background: Metastasis of tumor implantation includes a series of processes from detachment from the primary tumor to formation of the implanted metastase. Tumor cells survival in urine is a necessary condition for metastasis. Adaptation to urine is essential for this. Objective: Establish a urine-resistant cell sub-strain of human bladder cancer cell line (ET cell lines), and study different characteristics compared to parent cells. Methods: EJ cell lines were cultured in nutrient medium. Urine-resistance cell sub-strain (EJ-U) was harvested after prolonged culture by gradually increasing the concentration of urine. Gen chip was used to detect the genome series of EJ and EJ-U and to analyze the difference of gene expression. Results: EJ-U in urine had a higher survival rate after 24 hours in urine compared with EJ. The EJ-U had almost the same growth velocity with EJ, and they had the analogous growth curves. The time-duration for EJ-U to survive was longer than EJ in urine. In gene ontology analysis, 272 significant different genes were found. Conclusion: EJ-U cell sub-strain was more adaptable than its parent cell lines EJ. The different genes may explain the reason why bladder cancer cells could survive for a long time in urine.