Miracle-dz/UniFAR-FTUs huggingface dataset:
Mosquito (Diptera: Culicidae) Diversity of a Forest-Fragment Mosaic in the Amazon Rain Forest

ABSTRACT To study the impact of Amazonian forest fragmentation on the mosquito fauna, an inventory of Culicidae was conducted in the upland forest research areas of the Biological Dynamics of Forest Fragments Project located 60 km north of Manaus, Amazonas, Brazil. The culicid community was sampled monthly between February 2002 and May 2003. CDC light traps, flight interception traps, manual aspiration, and net sweeping were used to capture adult specimens along the edges and within forest fragments of different sizes (1, 10, and 100 ha), in second-growth areas surrounding the fragments and around camps. We collected 5,204 specimens, distributed in 18 genera and 160 species level taxa. A list of mosquito taxa is presented with 145 species found in the survey, including seven new records for Brazil, 16 new records for the state of Amazonas, along with the 15 morphotypes that probably represent undescribed species. No exotic species [Aedes aegypti (L.) and Aedes albopictus (Skuse)] were found within the sampled areas. Several species collected are potential vectors of Plasmodium causing human malaria and of various arboviruses. The epidemiological and ecological implications of mosquito species found are discussed, and the results are compared with other mosquito inventories from the Amazon region.
A homing receptor-IgG chimera as a probe for adhesive ligands of lymph node high endothelial venules

The binding of lymphocytes to high endothelial venules (HEV) within peripheral lymph nodes (pln) is thought to be mediated by a lectinlike adhesion molecule termed the pln homing receptor (pln HR). The cloning and sequencing of cDNAs encoding both murine and human pln HR revealed that these adhesion molecules contain protein motifs that are homologous to C-type or calcium dependent lectin domains as well as to epidermal growth factor (egf) and complement-regulatory protein domains. We have produced a novel, antibody-like form of the murine HR by joining the extracellular region of the receptor to a human IgG heavy chain. This antibody-like molecule is capable of recognizing carbohydrates, blocking the binding of lymphocytes to pln HEV, and serving as a histochemical reagent for the staining of pln HEV. This murine HR-IgG chimera should prove useful in analyzing the distribution of the HR ligand(s) in normal as well as in inflammatory states.
Tumor and Stem Cell Biology Constitutive HER 2 Signaling Promotes Breast Cancer Metastasis through Cellular Senescence

Senescence, a terminal cell proliferation arrest, can be triggered by oncogenes. Oncogene-induced senescence is classically considered a tumor defense barrier. However, several findings show that, under certain circumstances, senescent cells may favor tumor progression because of their secretory phenotype. Here, we show that the expression in different breast epithelial cell lines of p95HER2, a constitutively active fragment of the tyrosine kinase receptor HER2, results in either increased proliferation or senescence. In senescent cells, p95HER2 elicits a secretome enriched in proteases, cytokines, and growth factors. This secretory phenotype is not a mere consequence of the senescence status and requires continuous HER2 signaling to be maintained. Underscoring the functional relevance of thep95HER2-induced senescence secretome,we show that p95HER2-induced senescent cells promote metastasis in vivo in a non–cell-autonomous manner. Cancer Res; 73(1); 450–8. 2012 AACR.
Micro-Halocline Enabled Nutrient Recycling May Explain Extreme Azolla Event in the Eocene Arctic Ocean

In order to understand the physicochemical mechanisms that could explain the massive growth of Azolla arctica in the Eocene Arctic Ocean, we carried out a laboratory experiment in which we studied the interacting effects of rain and wind on the development of salinity stratification, both in the presence and in the absence of a dense Azolla cover. Additionally, we carried out a mesocosm experiment to get a better understanding of the nutrient cycling within and beneath a dense Azolla cover in both freshwater and brackish water environments. Here we show that Azolla is able to create a windproof, small-scale salinity gradient in brackish waters, which allows for efficient recycling of nutrients. We suggest that this mechanism ensures the maintenance of a large standing biomass in which additional input of nutrients ultimately result in a further expansion of an Azolla cover. As such, it may not only explain the extent of the Azolla event during the Eocene, but also the absence of intact vegetative Azolla remains and the relatively low burial efficiency of organic carbon during this interval.
Experiments with a Multilanguage Non-Projective Dependency Parser

Parsing natural language is an essential step in several applications that involve document analysis, e.g. knowledge extraction, question answering, summarization, filtering. The best performing systems at the TREC Question Answering track employ parsing for analyzing sentences in order to identify the query focus, to extract relations and to disambiguate meanings of words.
An Axiomatic Account of Formal Argumentation

Argumentation theory has become an important topic in the field of AI. The basic idea is to construct arguments in favor and against a statement, to select the "acceptable" ones and, finally, to determine whether the statement can be accepted or not. Dung's elegant account of abstract argumentation (Dung 1995) may have caused some to believe that defining an argumentation formalism is simply a matter of determining how arguments and their defeat relation can be constructed from a given knowledge base. Unfortunately, things are not that simple; many straightforward instantiations of Dung's theory can lead to very unintuitive results, as is discussed in this paper. In order to avoid such anomalies, in this paper we are interested in defining some rules, called rationality postulates or axioms, that govern the well definition of an argumentation system. In particular, we define two important rationality postulates that any system should satisfy: the consistency and the closeness of the results returned by that system. We then provide a relatively easy way in which these quality postulates can be warranted by our argumentation system.
Silicate as regulating nutrient in phytoplankton competition

The development of phytoplankton communities was studied in floating enclosures. The enclosures were supplied with either surface water or water from 40 m depth. Nutrients with or without silicate were added in some of the experiments, while others recieved no artificial fertilization. It is shown that diatom dominance occurred irrespective of season if silicate concentration exceeded a threshold of approximately 2 PM. Flagellate dominance changed to diatom dominance within a few days after nutrient addition resulting in silicate concentrations above this threshold. Dominance of Phaeocystis sp. appeared on several occasions after the bloom of another species, but never at high silicate concentrations. The success of the diatom group seemed to be due to a high inherent growth rate at non-limiting silicate concentrations. Calculations indicated that the inherent growth rate for the diatom group had to be 5 to 50 % higher than for the flagellate group in order to explain the outcome of our experiments.
Women who smoke: are women more susceptible to tobacco-induced lung cancer?

The WHO estimates that lung cancer is the most frequent cancer in the world today and the global incidence of lung cancer is increasing at 0.5% per year due to the fact that the smoking epidemic continues to spread to developing countries. Lung cancer is strongly related to smoking. We know that ~85–90% of lung cancer patients are smokers. The cigarette epidemic is also becoming a serious issue in women’s health. Presently, ~47% of men and 12% of women worldwide aged 15 years and over are smokers. In many developed countries the smoking prevalence is about the same among women and men and may in several countries surpass the rate in men in the near future (1–3). In several countries, lung cancer has surpassed breast cancer and is now the leading cause of cancer deaths among women. For men in developed countries, the full effect of cigarette smoking can already be seen. For women in these countries, the peak of the tobacco epidemic has not yet arrived mainly due to a more recent spread of the habit to females. It is probable that the rate of lung cancer among females is increasing mainly because younger women smoke more. A question of great interest is in the younger generation of women that smoke as much as men, will their rates of lung cancer eventually becomes different from males? Is sex a possible factor in determining lung cancer risk? Recent results from both epidemiological and molecular studies may indicate a sex difference in the risk of developing lung cancer.
FISH and array‐CGH analysis of a complex chromosome 3 aberration suggests that loss of CNTN4 and CRBN contributes to mental retardation in 3pter deletions

Imbalances of 3p telomeric sequences cause 3p− and trisomy 3p syndrome, respectively, showing distinct, but also shared clinical features. No causative genes have been identified in trisomy 3p patients, but for the 3p− syndrome, there is growing evidence that monosomy for one or more of four genes at 3pter, CHL1, CNTN4, CRBN, and MEGAP/srGAP3, may play a causative role. We describe here an analysis of a complex chromosome 3p aberration in a severely mentally retarded patient that revealed two adjacent segments with different copy number gains and a distal deletion. The deletion in this patient included the loci for CHL1, CNTN4, and CRBN, and narrowed the critical segment associated with the 3p− syndrome to 1.5 Mb, including the loci for CNTN4 and CRBN. We speculate that the deletion contributes more to this patient's phenotype than the gains that were observed. We suggest that 3p− syndrome associated features are primarily caused by loss of CNTN4 and CRBN, with loss of CHL1 probably having an additional detrimental effect on the cognitive functioning of the present patient. © 2006 Wiley‐Liss, Inc.
A personality trait-based interactionist model of job performance.

Evidence for situational specificity of personality-job performance relations calls for better understanding of how personality is expressed as valued work behavior. On the basis of an interactionist principle of trait activation (R. P. Tett & H. A. Guterman, 2000), a model is proposed that distinguishes among 5 situational features relevant to trait expression (job demands, distracters, constraints, releasers, and facilitators), operating at task, social, and organizational levels. Trait-expressive work behavior is distinguished from (valued) job performance in clarifying the conditions favoring personality use in selection efforts. The model frames linkages between situational taxonomies (e.g., J. L. Holland's [1985] RIASEC model) and the Big Five and promotes useful discussion of critical issues, including situational specificity, personality-oriented job analysis, team building, and work motivation.
Multi Kernel Learning with Online-Batch Optimization

In recent years there has been a lot of interest in designing principled classification algorithms over multiple cues, based on the intuitive notion that using more features should lead to better performance. In the domain of kernel methods, a principled way to use multiple features is the Multi Kernel Learning (MKL) approach. Here we present a MKL optimization algorithm based on stochastic gradient descent that has a guaranteed convergence rate. We directly solve the MKL problem in the primal formulation. By having a p-norm formulation of MKL, we introduce a parameter that controls the level of sparsity of the solution, while leading to an easier optimization problem. We prove theoretically and experimentally that 1) our algorithm has a faster convergence rate as the number of kernels grows; 2) the training complexity is linear in the number of training examples; 3) very few iterations are sufficient to reach good solutions. Experiments on standard benchmark databases support our claims.
Defense strategies for infrastructures with multiple systems of components

In several critical infrastructures correlations between the constituent systems represent certain vulnerabilities: disruptions to one may propagate to others and possibly to the entire infrastructure. The correlations between the systems are characterized in two ways in this paper: (i) the aggregate failure correlation function specifies the conditional failure probability of the infrastructure given the failure of an individual system, and (ii) the pairwise correlation function between two systems specifies the failure probability of one system given the failure of the other. The survival probabilities of individual systems satisfy first-order differential conditions that generalize the contest success functions and statistical independence conditions. We formulate a problem of ensuring the resilience of an infrastructure as a game between the provider and attacker; their utility functions are sums of infrastructure survival probability terms and cost terms, both expressed in terms of the numbers of system components attacked and reinforced. We derive Nash Equilibrium conditions and sensitivity functions that highlight the dependence of infrastructure resilience on the cost terms, correlation functions, and individual system survival probabilities. We apply these results to models of distributed cloud computing and energy grid infrastructures.
Tumor-promoting phorbol esters stimulate C3b and C3b' receptor-mediated phagocytosis in cultured human monocytes

Monocytes were isolated in high yield (approximately 80%) and purity (greater than 90%) by Percoll gradient centrifugation and incubated in Teflon culture vessels. Using this culture method, we routinely recovered 80% of the cells originally placed into culture. Studies of the C3b and C3b' receptors of these monocytes showed that the function of both receptors could be dramatically altered by treating the cells with tumor-promoting phorbol esters. Both C3b and C3b' receptors of human monocytes efficiently mediate attachment of erythrocytes coated with the corresponding ligands, but do not promote their ingestion. However, monocytes treated with phorbol myristate acetate (PMA) or phorbol didecanoate ingest C3b- and C3b'-coated erythrocytes. Phorbol esters that are inactive as tumor promoters do not stimulate C3 receptor-mediated phagocytosis. The ability of monocytes to respond to PMA by activation of C3 receptors is developmentally regulated. Freshly isolated monocytes do not take up C3b- or C3b'-coated erythrocytes in response to PMA, but after 3 d of culture they show strong PMA- stimulated uptake. The stimulatory effect of PMA on monocyte C3b and C3b' receptor function occurs within minutes, is stable for hours, is cycloheximide insensitive, and can be inhibited with colchicine. Several lines of evidence indicates that phagocytosis of C3b or C3b'- coated erythrocytes is specifically mediated by the monocytes' C3b and C3b' receptors. First, erythrocytes attached to monocytes with concanavalin A are not ingested when the monocytes are treated with PMA. Second, monocytes plated on IgG-bearing substrates lose Fc receptor activity on their nonadherent surfaces but retain the capacity to ingest C3b- or C3b'-coated erythrocytes after PMA treatment. Third, PMA-treated monocytes plated on C3b-coated surfaces lose C3b receptor activity on their nonadherent surfaces but retain the capacity to ingest C3b'-coated erythrocytes. Conversely, PMA-treated monocytes plated on C3b'-coated surfaces show reduced C3b' receptors activity on their nonadherent surfaces but retain the capacity to ingest C3b-coated erythrocytes.
Behavioral/systems/cognitive Functional Signal-and Paradigm-dependent Linear Relationships between Synaptic Activity and Hemodynamic Responses in Rat Somatosensory Cortex

Linear relationships between synaptic activity and hemodynamic responses are critically dependent on functional signal etiology and paradigm. To investigate these relationships, we simultaneously measured local field potentials (FPs) and optical intrinsic signals in rat somatosensory cortex while delivering a small number of electrical pulses to the hindpaw with varied stimulus intensity, number, and interstimulus interval. We used 570 and 610 nm optical signals to estimate cerebral blood volume (CBV) and oxygenation, respectively. The spatiotemporal evolution patterns and trial-by-trial correlation analyses revealed that CBV-related optical signals have higher fidelity to summed evoked FPs (⌺FPs) than oxygenation-derived signals. CBV-related signals even correlated with minute ⌺FP fluctuations within trials of the same stimulus condition. Furthermore, hemodynamic signals (CBV and late oxygenation signals) increased linearly with ⌺FP while varying stimulus number, but they exhibited a threshold and steeper gradient while varying stimulus intensity, suggesting insufficiency of the homogeneity property of linear systems and the importance of spatiotemporal coherence of neuronal population activity in hemodynamic response formation. These stimulus paradigm-dependent linear and nonlinear relationships demonstrate that simple subtraction-based analyses of hemodynamic signals produced by complex stimulus paradigms may not reflect a difference in ⌺FPs between paradigms. Functional signal-and paradigm-dependent linearity have potentially profound implications for the interpretation of perfusion-based functional signals.
Encephalomyocarditis Virus Disrupts Stress Granules, the Critical Platform for Triggering Antiviral Innate Immune Responses

ABSTRACT In response to stress, cells induce ribonucleoprotein aggregates, termed stress granules (SGs). SGs are transient loci containing translation-stalled mRNA, which is eventually degraded or recycled for translation. Infection of some viruses, including influenza A virus with a deletion of nonstructural protein 1 (IAVΔNS1), induces SG-like protein aggregates. Previously, we showed that IAVΔNS1-induced SGs are required for efficient induction of type I interferon (IFN). Here, we investigated SG formation by different viruses using green fluorescent protein (GFP)-tagged Ras-Gap SH3 domain binding protein 1 (GFP-G3BP1) as an SG probe. HeLa cells stably expressing GFP-G3BP1 were infected with different viruses, and GFP fluorescence was monitored live with time-lapse microscopy. SG formations by different viruses was classified into 4 different patterns: no SG formation, stable SG formation, transient SG formation, and alternate SG formation. We focused on encephalomyocarditis virus (EMCV) infection, which exhibited transient SG formation. We found that EMCV disrupts SGs by cleavage of G3BP1 at late stages of infection (>8 h) through a mechanism similar to that used by poliovirus. Expression of a G3BP1 mutant that is resistant to the cleavage conferred persistent formation of SGs as well as an enhanced induction of IFN and other cytokines at late stages of infection. Additionally, knockdown of endogenous G3BP1 blocked SG formation with an attenuated induction of IFN and potentiated viral replication. Taken together, our findings suggest a critical role of SGs as an antiviral platform and shed light on one of the mechanisms by which a virus interferes with host stress and subsequent antiviral responses.
The AC-OK Cooccurring Screen: Reliability, Convergent Validity, Sensitivity, and Specificity

The principal barriers to universal screening for the cooccurring disorders of mental illness and substance abuse are training, time, cost, and a reliable and valid screen. Although many of the barriers to universal screening still remain intact, the lack of a cooccurring screen that is effective and can be administered in a cost efficient way is no longer an obstacle. This study examined the reliability, factor structure, and convergent validity of the 15-item AC-OK Cooccurring Screen. A total of 2,968 AC-OK Cooccurring Screens administrated to individuals who called or went to one of the nine participating mental health and substance abuse treatment facilities were administrated and analyzed. Principal axis factor (PAF) analysis was used in the confirmatory factor analysis to identify the common variance among the items in the scales while excluding unique variance. Cronbach's Alpha was used to establish internal consistency (reliability) of each subscale. Finally, the findings from the AC-OK Cooccurring Screen were compared to individual scores on two standardized reference measures, the addiction severity index and the Client assessment record (a measure of mental health status) to determine sensitivity and specificity. This analysis of the AC-OK Cooccurring Screen found the subscales to have excellent reliability, very good convergent validity, excellent sensitivity, and sufficient specificity to be highly useful in screening for cooccurring disorders in behavioral health settings. In this study, the AC-OK Cooccurring Screen had a Cronbach's Alpha of . 92 on the substance abuse subscale and a Cronbach's Alpha of . 80 on the mental health subscale.
Using text processing techniques to automatically enrich a domain ontology

Though the utility of domain Ontologies is now widely acknowledgedin an increasing number of domains, several barriers must beovercome before Ontologies become practical and useful tools. Acritical issue is the task of identifying, defining, and enteringthe concept definitions. In case of large and complex applicationdomains this task can be lengthy, costly, and controversial (sincedifferent persons may have different points of view about the sameconcept). To reduce time, cost (and, sometimes, harsh discussions)it is highly advisable to refer, in constructing or updating anontology, to the documents available in the field. In this paper wedescribe OntoLearn, a text-mining tool devised to improvehuman productivity during the process of ontology construction.