Miracle-dz/UniFAR-FTUs huggingface dataset:
J Domain-Independent Regulation of the Rb Family by Polyomavirus Large T Antigen

ABSTRACT The ability of polyomavirus large T antigen (LT) to promote cell cycling, to immortalize primary cells, and to block differentiation has been linked to its effects on tumor suppressors of the retinoblastoma susceptibility (Rb) gene family. Our previous studies have shown that LT requires an intact N-terminal DnaJ domain, in addition to an Rb binding site, for activation of simple E2F-containing promoters and stimulation of cell cycle progression. Here we show that some LT effects dependent on interaction with the Rb family are largely DnaJ independent. In differentiating C2C12 myoblasts, overexpression of LT caused apoptosis. Although this activity of LT completely depended on Rb binding, LTs with mutations in the J domain remained able to kill. Comparisons of Rb− and J− LTs revealed additional differences. Wild-type but not Rb− LT activated the cyclin A promoter under serum starvation conditions. Genetic analysis of the promoter linked the Rb requirement to an E2F site in the promoter. LTs with mutations in the J domain were still able to activate the promoter. Finally, J mutant LTs caused changes in phosphorylation of both pRb and p130. In the case of p130, Thr-986 was shown to be a site that is regulated by J mutant LT. Taken together, these observations reveal that LT regulation of Rb function can be separated into both DnaJ-dependent and DnaJ-independent pathways.
Expanding genomics of mycorrhizal symbiosis

The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.
Lähdekieli kielenoppimisen apuna

Kaivapalu, Annekatrin Contribution L1 to foreign language acquisition Jyvaskyla: University of Jyvaskyla, 2005, 348 p. (Jyvaskyla Studies in Humanities ISSN 1459-4331; 44) ISBN 951-39-2391-6 Diss. This study investigates the effect of Estonian as the mother tongue on the acquisition of Finnish, a closely related language, with particular regard to plural inflection of Finnish nouns. The aims of the study are to determine the essential nature of first language influence on morphology, what constrains it and how it interacts with other factors, and to assess the positive influence of a closely related source language. The subjects of this study were two test groups, one of 30 Estonian high school students and the other of 30 Russian high-school students. The data were gathered by means of written and oral inflection tests. First of all learners were asked to inflect 30 context-free words in the partitive, illative and elative plural. The second task of the test was designed to elicit the same plural forms of the test words in written narratives. In order to determine how written and oral processing differ from each other, some of the Estonianand some of the Russian-speaking subjects were given the task of inflecting context-free words orally a few weeks before the written test. Another source of data consisted of the tape-recorded comments of the learners while performing this task. The study concludes that the source language has an important role among the factors influencing the inflection of plural forms of Finnish nouns. As predicted, the positive influence of source language morphology is at its greatest in the case of words with the same or a very similar stem and inflection in the source and target languages. The influence of the source language acts in conjunction with other factors in the inflectional process of target language in different ways in different contexts and on different occasions. The choice of processing strategy also depends, at least partly, on the particular source language and the level of learner’s target language skills. In closely related languages such as Finnish and Estonian the influence of the source language on inflectional morphology is considerably more positive than former studies have argued.
Distinctive Glial and Neuronal Interfacing on Nanocrystalline Diamond

Direct electrode/neuron interfacing is a key challenge to achieve high resolution of neuronal stimulation required for visual prostheses. Neuronal interfacing on biomaterials commonly requires the presence of glial cells and/or protein coating. Nanocrystalline diamond is a highly mechanically stable biomaterial with a remarkably large potential window for the electrical stimulation of tissues. Using adult retinal cell cultures from rats, we found that glial cells and retinal neurons grew equally well on glass and nanocrystalline diamond. The use of a protein coating increased cell survival, particularly for glial cells. However, bipolar neurons appeared to grow even in direct contact with bare diamond. We investigated whether the presence of glial cells contributed to this direct neuron/diamond interface, by using purified adult retinal ganglion cells to seed diamond and glass surfaces with and without protein coatings. Surprisingly, these fully differentiated spiking neurons survived better on nanocrystalline diamond without any protein coating. This greater survival was indicated by larger cell numbers and the presence of longer neurites. When a protein pattern was drawn on diamond, neurons did not grow preferentially on the coated area, by contrast to their behavior on a patterned glass. This study highlights the interesting biocompatibility properties of nanocrystalline diamond, allowing direct neuronal interfacing, whereas a protein coating was required for glial cell growth.
Information Research in Leisure: Implications from an Empirical Study of Backpackers

In the modern, increasingly flat world, many individuals have seen an increase in the amount of leisure time they have available. This leisure time is used for different purposes, often including travel and tourism. Among the many types of travel and tourism, backpack or budget travelling is becoming more and more popular. This increasingly common leisure activity presumably involves intensive information search activities.This study places the backpackers' search for travel information in an everyday life information seeking (ELIS) perspective. The search for information by backpackers can be seen as a three-stage information search process. In each stage, depending on the type of task, backpackers use various information resources for different purposes. Such sources may be used for more than one purpose and in more than one information search stage. However, their relative importance varies depending on the characteristics of the source of information and the information search stage in which the source is being used.In this article I suggest that studies of leisure information behaviors and leisure activities show theoretical and practical value for both the information seeking public and the information science community. We also suggest that library and information science scholars and practice communities direct attention and research resources to leisure research in general, and the concept of serious leisure and its structured information acquisition and sharing activities in particular.
IgE-dependent cytokine production by human peripheral blood mononuclear phagocytes.

These studies demonstrate the IgE-dependent production of IL-1 beta and TNF-alpha by circulating blood monocytes. IL-1 beta production was demonstrated biologically as the stimulation of proliferation of the cloned IL-1-dependent murine T cell line D10.G4. 1 in the presence of a submitogenic concentration of PHA. In a representative experiment, 3H-thymidine uptake increased from 57826 cpm in the presence of supernatants obtained from unstimulated cells to 200774 cpm with supernatants from monocytes stimulated by IgE/alpha IgE immune complexes. By ELISA, IgE complexes increased IL-1 beta production from 0.54 +/- 0.06 ng (per 10(6) monocytes) to 2.60 +/- 0.62 ng (p less than 0.01; mean of eight experiments) and TNF-alpha production from 0.17 +/- 0.10 ng to 3.00 +/- 0.54 ng (p less than 0.01; mean of four experiments). No IL-1 alpha secretion was observed. RNA hybridization analysis demonstrated that IL-1 beta production represented de novo synthesis of the cytokine. Stimulated RNA production was observed after a minimal 1/2-h incubation and was maximal at 2 h. The IgE-dependent secretion of these pro-inflammatory cytokines by mononuclear phagocytic cells may contribute to the inflammation characteristic of allergic responses.
A Multiscale Graph Theoretical Approach to Gene Regulation Networks: A Case Study in Atrial Fibrillation

The changes in between gene expression correlation structure induced in heart tissue by atrial fibrillation are studied by means of a graph theoretical approach. As expected by general statistical mechanics principles, the disease increases the general connectivity of the gene regulation network; the multiscale character of the analysis allows us to get both a general appreciation of regulation network connectivity and the sketching of a biological interpretation of the studied disease. The presence of a still largely unknown, scale invariant, global correlation field encompassing the entire genome is demonstrated as well.
Two capsular polysaccharides enable Bacillus cereus G9241 to cause anthrax‐like disease

Bacillus cereus G9241 causes an anthrax‐like respiratory illness in humans; however, the molecular mechanisms of disease pathogenesis are not known. Genome sequencing identified two putative virulence plasmids proposed to provide for anthrax toxin (pBCXO1) and/or capsule expression (pBC218). We report here that B. cereus G9241 causes anthrax‐like disease in immune‐competent mice, which is dependent on each of the two virulence plasmids. pBCXO1 encodes pagA1, the homologue of anthrax protective antigen, as well as hasACB, providing for hyaluronic acid capsule formation, two traits that each contribute to disease pathogenesis. pBC218 harbours bpsX‐H, B. cereus exo‐polysaccharide, which produce a second capsule. During infection, B. cereus G9241 elaborates both hasACB and bpsX‐H capsules, which together are essential for the establishment of anthrax‐like disease and the resistance of bacilli to phagocytosis. A single nucleotide deletion causes premature termination of hasA translation in Bacillus anthracis, which is known to escape phagocytic killing by its pXO2 encoded poly‐d‐γ‐glutamic acid (PDGA) capsule. Thus, multiple different gene clusters endow pathogenic bacilli with capsular material, provide for escape from innate host immune responses and aid in establishing the pathogenesis of anthrax‐like disease.
Marburgvirus Genomics and Association with a Large Hemorrhagic Fever Outbreak in Angola

ABSTRACT In March 2005, the Centers for Disease Control and Prevention (CDC) investigated a large hemorrhagic fever (HF) outbreak in Uige Province in northern Angola, West Africa. In total, 15 initial specimens were sent to CDC, Atlanta, Ga. , for testing for viruses associated with viral HFs known to be present in West Africa, including ebolavirus. Marburgvirus was also included despite the fact that the origins of all earlier outbreaks were linked directly to East Africa. Surprisingly, marburgvirus was confirmed (12 of 15 specimens) as the cause of the outbreak. The outbreak likely began in October 2004 and ended in July 2005, and it included 252 cases and 227 (90%) fatalities (report from the Ministry of Health, Republic of Angola, 2005), making it the largest Marburg HF outbreak on record. A real-time quantitative reverse transcription-PCR assay utilized and adapted during the outbreak proved to be highly sensitive and sufficiently robust for field use. Partial marburgvirus RNA sequence analysis revealed up to 21% nucleotide divergence among the previously characterized East African strains, with the most distinct being Ravn from Kenya (1987). The Angolan strain was less different (∼7%) from the main group of East African marburgviruses than one might expect given the large geographic separation. To more precisely analyze the virus genetic differences between outbreaks and among viruses within the Angola outbreak itself, a total of 16 complete virus genomes were determined, including those of the virus isolates Ravn (Kenya, 1987) and 05DRC, 07DRC, and 09DRC (Democratic Republic of Congo, 1998) and the reference Angolan virus isolate (Ang1379v). In addition, complete genome sequences were obtained from RNAs extracted from 10 clinical specimens reflecting various stages of the disease and locations within the Angolan outbreak. While the marburgviruses exhibit high overall genetic diversity (up to 22%), only 6.8% nucleotide difference was found between the West African Angolan viruses and the majority of East African viruses, suggesting that the virus reservoir species in these regions are not substantially distinct. Remarkably few nucleotide differences were found among the Angolan clinical specimens (0 to 0.07%), consistent with an outbreak scenario in which a single (or rare) introduction of virus from the reservoir species into the human population was followed by person-to-person transmission with little accumulation of mutations. This is in contrast to the 1998 to 2000 marburgvirus outbreak, where evidence of several virus genetic lineages (with up to 21% divergence) and multiple virus introductions into the human population was found.
The Auditory Comprehension of Unaccusative Verbs in Aphasia

Some persons with aphasia, particularly those diagnosed with a Broca’s aphasia, exhibit a delayed time course of lexical activation in canonically ordered S-V-O sentences (Ferrill et al., 2012) and delayed re-activation of displaced arguments in sentences that contain syntactic dependencies (Love et al., 2008). These patterns support the Delayed Lexical Activation (DLA) hypothesis: Lexical activation is delayed relative to the normal case, and thus lexical activation and syntactic operations are de-synchronized; that is, lexical access is too slow for normally fast-acting syntactic operations. This delay in lexical access leads to what appear to be syntactic comprehension deficits in aphasia. In the current study we further examined lexical activation during sentence comprehension in persons with aphasia by using unaccusative verbs. Unaccusative verbs are a type of intransitive verb with a single argument that is base generated in object position and displaced to the surface subject position, leaving behind a copy or trace (‘gap’) of the movement (see, for example, Burzio, 1986), as in: 1. The girl vanished Thus there is a syntactic dependency between the two positions. When encountering sentences that contain syntactic dependencies (e.g., object relatives, Wh-questions) neurologically unimpaired individuals immediately reactivate the displaced argument at the gap (Shapiro et al., 1999; Love et al., 2008). In contrast to this immediate reactivation, prior findings indicate that neurologically unimpaired individuals do not reactivate the displaced argument in similar sentences with unaccusative verbs until 750ms downstream from the gap (Friedmann et al., 2008). This built-in delay observed with unaccusative verbs in neurologically healthy participants provides a unique opportunity to further examine lexical delays in individuals with Broca’s aphasia. Importantly, individuals with Broca’s aphasia may have unaccusative verb deficits. Previous research has found that persons with aphasia have difficulty producing unaccusative verbs. Offline truth-value judgment tasks with intransitive sentences containing unaccusative verbs do not reveal comprehension deficits (Lee & Thompson, 2004). However, in a sentence-picture matching task, McAllister et al. (2009) found lower accuracy for intransitive sentences that contained unaccusative verbs than transitive sentences. We entertain the following hypothesis: The delayed lexical access routines better synchronize with the delay of reactivating the argument of unaccusatives, suggesting that individuals with Broca’s aphasia should evince a pattern like that of unimpaired individuals. Alternatively, participants with Broca’s aphasia might show activation even further downstream from the gap, given that in other sentence constructions containing syntactic dependencies they exhibit a delayed pattern of reactivation compared to neurologically unimpaired individuals.
Active versus passive transportation to school–differences in screen time, socio-economic position and perceived environmental characteristics in adolescent girls

Objective: The aims of this study were (1) to assess the relationships between transport to and from school (active vs. passive), sedentary behaviours, measures of socio-economic position and perceived environmental variables, and (2) to determine which, if any, variables were predictors of active transportation. Methods: The sample comprised 705 girls with mean age of 14.7 (SD = 1.6) years old. Questionnaires were used to describe travel mode to school and to estimate weekly television and computer use (screen time). Girls were assigned to active transportation (AT) or passive transportation (PT) groups depending on whether they walked or bicycled (AT) to and from school or travelled by car or bus (PT). Screen time was determined by the number of hours they reported watching television and using computers in the week preceding the examination, including weekends. Socio-economic position was established by parental occupation and educational level. A questionnaire assessed Perceived Neighbourhood Environments. Results: No statistically significant differences were seen for screen time between travel groups. Occupational status of both mother (r = −0.17) and father (r = −0.15) and father's educational level (r = −0.10) were significantly and negatively associated with AT, while street connectivity (r = 0.10) was positively and significantly associated with AT. Logistic regression analysis showed that the likelihood of active commuting decreased by around 50% with increasing father's occupation (odds ratio (OR) = 0.51; p ≤ 0.05) and father's education (OR = 0.52; p ≤ 0.05) from low to middle socio-economic position groups. Further, the data showed that girls who agreed that ‘there are many four-way intersections in my neighbourhood’ were more likely to be active (OR = 1.63; p ≤ 0.05). Conclusion: The data of this study showed that lower socio-economic position is associated with active commuting to school and that street connectivity is a predictor of active transportation in adolescent girls.
Partial orientation and local structural learning of causal networks for prediction

For a prediction problem of a given target feature in a large causal network under external interventions, we propose in this paper two partial orientation and local structural learning (POLSL) approaches, Local-Graph and PCD-by-PCD (where PCD denotes Parents, Children and some Descendants). The POLSL approaches are used to discover the local structure of the target and to orient edges connected to the target without discovering a global causal network. Thus they can greatly reduce computational complexity of structural learning and improve power of statistical tests. This approach is stimulated by the challenge problems proposed in IEEE World Congress on Computational Intelligence (WCCI2008) competition workshop. For the cases with and without external interventions, we select difierent feature sets to build prediction models. We apply the L1 penalized logistic regression model to the prediction. For the case with noise and calibrant features in microarray data, we propose a two-stage fllter to correct global and local patterns of noise.
Fiscal challenges to monetary dominance in the euro area: a theoretical perspective

The government debt and banking turmoil that persists in several euro area countries begs the question of why countries such as the United States or Japan, which do not have less debt, have not been affected by the same problems. To shed light on this question, two forms of monetary dominance should be distinguished. According to the first (soft, or preventive) form of monetary dominance, the government adjusts its fiscal policy so as to avoid having to choose between a default or debt monetisation. In the second case (hard form of monetary dominance), in the extreme situation where this choice has to be made, the monetary authorities let the government default rather than monetising the debt. We show that hard monetary dominance may reduce the probability of fiscal adjustment and, if it is not perfectly credible, may increase the probability of inflation.
Ultrastructural characterization of the new NG97ht human‐derived glioma cell line using two different electron microscopy technical procedures

On the basis of transmission electron microscopy observations in tumor cell lines, oncologists have made innumerous diagnostic and therapeutical progresses. Following this path, the UNICAMP immunopathologies laboratory established the NG97 cell line derived from a human astrocytoma grade III, which when injected to the athymic nude mouse flank developed a grade IV astrocytoma. In this study, we focused on ultrastructural characterization of the NG97 cells after being recovered from xenotransplant (NG97ht). These cells in culture were assayed by two different electron microscopy procedures to characterize ultrastructures related to grade IV astrocytomas and to observe their structures through cell subcultivation. Additionally, comparative morphological descriptions of different cell passages in these technical procedures could be a useful tool for improving electron microscopy cell lineage protocols. Results from many cell passage observations showed ultrastructural similarities, which suggest malignant and glioblastoma phenotypes. In the first procedure, NG97ht cells were harvested and then incorporated into agarose before subjecting them to electron microscopy protocols, whereas in the second one, monolayer cells grew first on cover slides. Comparison among protocols revealed that organelles, cytoplasmatic extensions, spatial conformation of filopodia, and cell attachment to substrate were more preserved in the second procedure. Furthermore, in this latter procedure, a unique ellipsoidal structure was observed, which was already described when dealing with gliosarcoma cell line elsewhere. Therefore, these analyses demonstrated a morphological characterization of a new NG97ht cell line using electron transmission microscopy. Moreover, it has been shown that the second procedure provides more detailed information compared with the first. Microsc. Res. Tech, 2009. © 2008 Wiley‐Liss, Inc.