Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model

Access to nutrients is a key factor governing development, reproduction and ultimately fitness. Within social groups, contest-competition can fundamentally affect nutrient access, potentially leading to reproductive asymmetry among individuals. Previously, agent-based models have been combined with the Geometric Framework of nutrition to provide insight into how nutrition and social interactions affect one another. Here, we expand this modelling approach by incorporating evolutionary algorithms to explore how contest-competition over nutrient acquisition might affect the evolution of animal nutritional strategies. Specifically, we model tolerance of nutrient excesses and deficits when ingesting nutritionally imbalanced foods, which we term ‘nutritional latitude’; a higher degree of nutritional latitude constitutes a higher tolerance of nutritional excess and deficit. Our results indicate that a transition between two alternative strategies occurs at moderate to high levels of competition. When competition is low, individuals display a low level of nutritional latitude and regularly switch foods in search of an optimum. When food is scarce and contest-competition is intense, high nutritional latitude appears optimal, and individuals continue to consume an imbalanced food for longer periods before attempting to switch to an alternative. However, the relative balance of nutrients within available foods also strongly influences at what levels of competition, if any, transitions between these two strategies occur. Our models imply that competition combined with reproductive skew in social groups can play a role in the evolution of diet breadth. We discuss how the integration of agent-based, nutritional and evolutionary modelling may be applied in future studies to further understand the evolution of nutritional strategies across social and ecological contexts.
Experimental Evaluation of the Transport Mechanisms of PoIFN-α in Caco-2 Cells

For the development of an efficient intestinal delivery system for Porcine interferon-α (PoIFN-α), the understanding of transport mechanisms of which in the intestinal cell is essential. In this study, we investigated the absorption mechanisms of PoIFN-α in intestine cells. Caco-2 cells and fluorescein isothiocyanate-labeled (FITC)-PoIFN-α were used to explore the whole transport process, including endocytosis, intracellular trafficking, exocytosis, and transcytosis. Via various techniques, the transport pathways of PoIFN-α in Caco-2 cells and the mechanisms were clarified. Firstly, the endocytosis of PoIFN-α by Caco-2 cells was time, concentration and temperature dependence. And the lipid raft/caveolae endocytosis was the most likely endocytic pathway for PoIFN-α. Secondly, both Golgi apparatus and lysosome were involved in the intracellular trafficking of PoIFN-α. Thirdly, the treatment of indomethacin resulted in a significant decrease of exocytosis of PoIFN-α, indicating the participation of cyclooxygenase. Finally, to evaluate the efficiency of PoIFN-α transport, the transepithelial electrical resistance (TEER) value was measured to investigate the tight junctional integrity of the cell monolayers. The fluorescence microscope results revealed that the transport of PoIFN-α across the Caco-2 cell monolayers was restricted. In conclusion, this study depicts a probable picture of PoIFN-α transport in Caco-2 cells characterized by non-specificity, partial energy-dependency and low transcytosis.
BID-F1 and BID-F2 Domains of Bartonella henselae Effector Protein BepF Trigger Together with BepC the Formation of Invasome Structures

The gram-negative, zoonotic pathogen Bartonella henselae (Bhe) translocates seven distinct Bartonella effector proteins (Beps) via the VirB/VirD4 type IV secretion system (T4SS) into human cells, thereby interfering with host cell signaling [1], [2]. In particular, the effector protein BepG alone or the combination of effector proteins BepC and BepF trigger massive F-actin rearrangements that lead to the establishment of invasome structures eventually resulting in the internalization of entire Bhe aggregates [2], [3]. In this report, we investigate the molecular function of the effector protein BepF in the eukaryotic host cell. We show that the N-terminal [E/T]PLYAT tyrosine phosphorylation motifs of BepF get phosphorylated upon translocation but do not contribute to invasome-mediated Bhe uptake. In contrast, we found that two of the three BID domains of BepF are capable to trigger invasome formation together with BepC, while a mutation of the WxxxE motif of the BID-F1 domain inhibited its ability to contribute to the formation of invasome structures. Next, we show that BepF function during invasome formation can be replaced by the over-expression of constitutive-active Rho GTPases Rac1 or Cdc42. Finally we demonstrate that BID-F1 and BID-F2 domains promote the formation of filopodia-like extensions in NIH 3T3 and HeLa cells as well as membrane protrusions in HeLa cells, suggesting a role for BepF in Rac1 and Cdc42 activation during the process of invasome formation.
Systemic Inflammatory Response to Smoking in Chronic Obstructive Pulmonary Disease: Evidence of a Gender Effect

Background Tobacco smoking is the main risk factor of chronic obstructive pulmonary disease (COPD) but not all smokers develop the disease. An abnormal pulmonary and systemic inflammatory response to smoking is thought to play a major pathogenic role in COPD, but this has never been tested directly. Methods We studied the systemic biomarker and leukocyte transcriptomic response (Affymetrix microarrays) to smoking exposure in 10 smokers with COPD and 10 smokers with normal spirometry. We also studied 10 healthy never smokers (not exposed to smoking) as controls. Because some aspects of COPD may differ in males and females, and the inflammatory response to other stressors (infection) might be different in man and women, we stratified participant recruitment by sex. Differentially expressed genes were validated by q-PCR. Ontology enrichment was evaluated and interaction networks inferred. Results Principal component analysis identified sex differences in the leukocyte transcriptomic response to acute smoking. In both genders, we identified genes that were differentially expressed in response to smoking exclusively in COPD patients (COPD related signature) or smokers with normal spirometry (Smoking related signature), their ontologies and interaction networks. Conclusions The use of an experimental intervention (smoking exposure) to investigate the transcriptomic response of peripheral leukocytes in COPD is a step beyond the standard case-control transcriptomic profiling carried out so far, and has facilitated the identification of novel COPD and Smoking expression related signatures which differ in males and females.
EXPLOITING CAUSAL STRUCTURE TO CONTROL RETRIEVAL AND REFITTING DURING PLAN REUSE

The ability to reuse existing plans to solve new planning problems can enable a domain‐independent planner to improve its average case efficiency by exploiting the problem distribution and avoiding repetition of planning effort. The pay‐off from plan reuse, however, crucially depends on finding effective solutions to two important underlying control problems: (i) controlling the retrieval of an appropriate plan and mapping to be reused in a new situation, and (ii) controlling the modification (refitting) of the retrieved plan so as to minimize perturbation to the applicable parts of the plan. This paper is concerned with the development of efficient domain‐independent solutions to these two problems. For the retrieval, it provides a domain independent similarity metric that utilizes the plan causal dependency structure to estimate the utility of reusing a given plan in a new problem situation. For the refitting, it presents a minimum‐conflict heuristic, again based on the causal dependency structure of the plan, to conservatively control the modification. The paper also discusses the implementation and evaluation of these strategies within the PRIAR plan modification framework.
Saturated throughput analysis of the IEEE 802.11b DCF mode in a slow Rayleigh fading channel

In this paper we analyze the saturated throughput of the IEEE802.11b DCF mode in a quasi-static Rayleigh fading channel. Considering the saturated throughput as a random variable we evaluate its cumulative distribution function (CDF). This function is obtained for an IEEE802.11b WLAN working on a slow Rayleigh fading environment. Based on the obtained results the effect of the system parameters on the saturated throughput is discussed.
Study on the Relationships between Intrinsic Functional Connectivity of the Default Mode Network and Transient Epileptic Activity

Rationale: Simultaneous recording of electroencephalogram and functional MRI (EEG–fMRI) is a powerful tool for localizing epileptic networks via the detection of hemodynamic changes correlated with interictal epileptic discharges (IEDs). fMRI can be used to study the long-lasting effect of epileptic activity by assessing stationary functional connectivity during the resting-state period [especially, the connectivity of the default mode network (DMN)]. Temporal lobe epilepsy (TLE) and idiopathic generalized epilepsy (IGE) are associated with low responsiveness and disruption of DMN activity. A dynamic functional connectivity approach might enable us to determine the effect of IEDs on DMN connectivity and to better understand the correlation between DMN connectivity changes and altered consciousness. Method: We studied dynamic changes in DMN intrinsic connectivity and their relation to IEDs. Six IGE patients (with generalized spike and slow-waves) and 6 TLE patients (with unilateral left temporal spikes) were included. Functional connectivity before, during, and after IEDs was estimated using a sliding window approach and compared with the baseline period. Results: No dependence on window size was observed. The baseline DMN connectivity was decreased in the left hemisphere (ipsilateral to the epileptic focus) in TLEs and was less strong but remained bilateral in IGEs. We observed an overall increase in DMN intrinsic connectivity prior to the onset of IEDs in both IGEs and TLEs. After IEDs in TLEs, we found that DMN connectivity increased before it returned to baseline values. Most of the DMN regions with increased connectivity before and after IEDs were lateralized to the left hemisphere in TLE (i.e., ipsilateral to the epileptic focus). Conclusion: Results suggest that DMN connectivity may facilitate IED generation and may be affected at the time of the IED. However, these results need to be confirmed in a larger independent cohort.
Gratifications and Seeding Behavior of Online Adolescents

Several studies indicate that only a small minority of Web 2.0 users actively participates, while the minority do not contribute at all. This article investigates whether a similar division applies for adolescents' Internet behavior. Using Szuprowicz’ (1995) typology of interactivity, we distinguish different types of user-generated content (UGC): media, narrative, and metadata UGC. Our results show a 20%–80% division between high- and low-frequency seeders. Furthermore, we utilize the uses-and-gratifications paradigm to investigate how these high- and low-frequency seeders differ in their overall gratifications obtained by WWW use. Although the gratifications' rank orders are identical for all groups, their magnitudes differ significantly. Finally, this article focuses on how these WWW gratifications can predict seeding, while controlling for socio-demographics and usage frequency.
This new whole: An exploration into the factors of self-authorship in college students

Title of proposed thesis: THIS NEW WHOLE: AN EXPLORATION INTO THE FACTORS OF SELF-AUTHORSHIP IN COLLEGE STUDENTS James Robert Neumeister, Master of Arts, 2007 Thesis directed by: Dr. Susan R. Komives, Professor Department of Counseling and Personnel Services College Student Personnel Program Over the past few years, self-authorship has become one of the most promising concepts and theories to emerge in college student development literature (Baxter Magolda, 2001b; Kegan, 1994). Despite an increasing amount of scholarship on this topic, the understanding of self-authorship remains incomplete, especially with regard to a clear comprehension of its structure, dimensions, and components. Using an exploratory factor analysis with oblique rotation to study the responses of over 3,500 college students at 52 institutions of higher education on 89 variables associated with self-authorship, this investigation identified eight, highly intercorrelated factors or lines of development associated with self-authorship: (1) Interdependence; (2) Engaging Diverse Views; (3) Dissonance and Change; (4) Cognitive Complexity; (5) Engaged Responsibility; (6) Personal and Communal Efficacy; (7) Congruence; and (8) Openness to New Ideas and Experiences. Implications of these results are outlined for current self-authorship theory, higher education policy and practice, and future research.
CoBWeb-a crawler for the Brazilian Web

One of the key components of current Web search engines is the document collector. The paper describes CoBWeb, an automatic document collector whose architecture is distributed and highly scalable. CoBWeb aims at collecting large amounts of documents per time period while observing operational and ethical limits in the crawling process. CoBWeb is part of the SIAM (Information Systems in Mobile Computing Environments) search engine which is being implemented to support the Brazilian Web. Thus, several results related to the Brazilian Web are presented.
The Role of C-Reactive Protein and the SOFA Score as Parameter for Clinical Decision Making in Surgical Patients during the Intensive Care Unit Course

Introduction C-reactive Protein (CRP) is used next to clinical scoring systems to recognize critically ill patients prone to develop complications on the Intensive Care Unit (ICU). The purpose of this study is to assess the predictive value of CRP as parameter for clinical deterioration and/or clinical decision making as ordering diagnostic procedures or performing (re)interventions. Also, we wanted to determine the value of CRP in early detection of surgical complications in the critically ill general surgical patient in the ICU and its interpretation in adjunct to a clinical scoring system, the Sequential Organ Failure Assessment Score. Materials and Methods In our prospective observational study, 174 general surgical patients admitted into the Intensive Care Unit were included. We evaluated the Sequential Organ Failure Assessment Score (SOFA) and daily measured the C-reactive protein (CRP) concentrations. All events (diagnostic or therapeutic interventions) and surgical complications were registered. Then the relationship between SOFA score, CRP concentrations, events and complications were studied. Results Each 10% increase in CRP resulted in a 3.5% increase in the odds of an event (odds ratio 1.035, 95% CI: 1.004–1.068; p = 0.028). However, an increase in CRP levels did not lead to a higher odds of complication (OR 0.983, 95% CI: 0.932–1.036; p = 0.52). When adjusting for the SOFA score the effect of CRP on the probability of a first event remained significant (OR 1.033, 95% CI: 1.001–1.065; p = 0.046), and again did not significantly affect the complication probability (OR 0.980, 95% CI: 0.929–1.035; p = 0.46). Conclusions An increase in C-reactive protein is a poor parameter for early detection of complications in the critically ill surgical patient in the ICU by means of diagnostic procedures or therapeutic (re)-interventions.
PHASE SYNCHRONIZATION EFFECTS IN A LATTICE OF NONIDENTICAL ROSSLER OSCILLATORS

We study phase synchronization in a chain of weakly coupled chaotic oscillators. In the synchronous state, the phases of oscillators are locked, while the amplitudes remain chaotic. We demonstrate that the coexistence of several clusters of mutually synchronized elements and global synchronization of all oscillators is possible. Two mechanisms of the transition to global synchronization are shown. The dynamics of spatiotemporal defects is discussed for the cases of phase-coherent and funnel Ro ̈ssler scillators. @S1063-651X~97! 01803-7#
Fortified-Descent Simplicial Search Method: A General Approach

We propose a new simplex-based direct search method for unconstrained minimization of a real-valued function f of n variables. As in other methods of this kind, the intent is to iteratively improve an n-dimensional simplex through certain reflection/expansion/contraction steps. The method has three novel features. First, a user-chosen integer $\bar m_k$ specifies the number of "good" vertices to be retained in constructing the initial trial simplices---reflected, then either expanded or contracted---at iteration k. Second, a trial simplex is accepted only when it satisfies the criteria of fortified descent, which are stronger than the criterion of strict descent used in most direct search methods. Third, the number of additional function evaluations needed to check a trial reflected/expanded simplex for fortified descent can be controlled. If one of the initial trial simplices satisfies the fortified-descent criteria, it is accepted as the new simplex; otherwise, the simplex is shrunk a fraction of the way toward a best vertex and the process is restarted, etc., until either a trial simplex is accepted or the simplex effectively has shrunk to a single point. We prove several theoretical properties of the new method. If f is continuously differentiable, bounded below, and uniformly continuous on its lower level set and we choose $\bar m_k$ with the same value at all iterations k, then every cluster point of the generated sequence of iterates is a stationary point. The same conclusion holds if the function is continuously differentiable, bounded below, and we choose $\bar m_k=1$ at all iterations k.
Predictors of chronic obstructive pulmonary disease exacerbation reduction in response to daily azithromycin therapy.

RATIONALE Daily azithromycin decreases acute exacerbations of chronic obstructive pulmonary disease (AECOPD), but long-term side effects are unknown. OBJECTIVES To identify the types of exacerbations most likely to be reduced and clinical subgroups most likely to benefit from azithromycin, 250 mg daily, added to usual care. METHODS Enrollment criteria included irreversible airflow limitation and AECOPD requiring corticosteroids, emergency department visit, or hospitalization in the prior year or use of supplemental oxygen. Recurrent events and cumulative incidence analyses compared treatment received for AECOPD by randomization group, stratified by subgroups of interest. Cox proportional hazards models estimated treatment effects in subgroups adjusted for age, sex, smoking status, FEV1% predicted, concomitant COPD medications, and oxygen use. MEASUREMENTS AND MAIN RESULTS Azithromycin was most effective in reducing AECOPD requiring both antibiotic and steroid treatment (n = 1,113; cumulative incidence analysis, P = 0.0002; recurrent events analysis, P = 0.002). No difference in treatment response by sex (P = 0.75), presence of chronic bronchitis (P = 0.19), concomitant inhaled therapy (P = 0.29), or supplemental oxygen use (P = 0.23) was observed. Older age and milder Global Initiative for Chronic Obstructive Lung Disease stage were associated with better treatment response (P = 0.02 and 0.04, respectively). A significant interaction between treatment and current smoking was seen (P = 0.03) and azithromycin did not reduce exacerbations in current smokers (hazard ratio, 0.99; 95% confidence interval, 0.71-1.38; P = 0.95). CONCLUSIONS Azithromycin is most effective in preventing AECOPD requiring both antibiotic and steroid treatment. Adjusting for confounders, we saw no difference in efficacy by sex, history of chronic bronchitis, oxygen use, or concomitant COPD therapy. Greater efficacy was seen in older patients and milder Global Initiative for Chronic Obstructive Lung Disease stages. We found little evidence of treatment effect among current smokers. Clinical trial registered with www.clinicaltrials. gov (NCT0011986 and NCT00325897).
OntoLabel - data labeling for deep web using WordNet

Wrappers are used to extract relevant information from the deep web, align, tabulate, and label these data for the users to recognize the contents simply and quickly. Existing wrappers use DOM Tree and visual cue to label data. These wrappers use several sets of heuristic rules to determine the label for a particular data, which may not be applicable to certain groups of data with words which are nearly similar in meaning. In this paper, we propose an ontological wrapper for labeling data using existing lexical database for English, WordNet. Our wrapper could label a wide range of data records without using any specific assumptions for the data structure. Instead of examining data structure and layout, our wrapper assigns label using the contents of the data. Experimental results show that our wrapper could label data records with high accuracy.
Functional specialization among insect chitinase family genes revealed by RNA interference

The biological functions of individual members of the large family of chitinase-like proteins from the red flour beetle, Tribolium castaneum (Tc), were examined by using gene-specific RNAi. One chitinase, TcCHT5, was found to be required for pupal–adult molting only. A lethal phenotype was observed when the transcript level of TcCHT5 was down-regulated by injection of TcCHT5-specific dsRNA into larvae. The larvae had metamorphosed into pupae and then to pharate adults but did not complete adult eclosion. Specific knockdown of transcripts for another chitinase, TcCHT10, which has multiple catalytic domains, prevented embryo hatch, larval molting, pupation, and adult metamorphosis, indicating a vital role for TcCHT10 during each of these processes. A third chitinase-like protein, TcCHT7, was required for abdominal contraction and wing/elytra extension immediately after pupation but was dispensable for larval–larval molting, pupation, and adult eclosion. The wing/elytra abnormalities found in TcCHT7-silenced pupae were also manifest in the ensuing adults. A fourth chitinase-like protein, TcIDGF4, exhibited no chitinolytic activity but contributed to adult eclosion. No phenotypic effects were observed after knockdown of transcripts for several other chitinase-like proteins, including imaginal disk growth factor IDGF2. These data indicate functional specialization among insect chitinase family genes, primarily during the molting process, and provide a biological rationale for the presence of a large assortment of chitinase-like proteins.
Comparison and selection of protease and lipase sources from visceral organs of three tuna species

Tuna viscera accounts for 7-8% of body weight and its value is still underutilized. This paper investigated on the influence of three tuna species and their individual visceral organ on the activities of three enzymes in tuna viscera. Results revealed that visceral enzymes of yellowfin tuna (Thunnus albacares) possessed the highest protease activity (3.09 U.mg -1 protein) and lipase activity (0.05 U.mg -1 protein) compared to those of skipjack tuna (Katsuwonus pelamis) and tonggol tuna (Thunnus albacares). None of them contained amylolytic activity. Among the individual visceral organ (stomach, liver, pancreas, spleen), spleen was the best source for protease (0.723 U.mg -1 protein) while pancreas gave the highest value of lipase activity (0.03 U.mg -1 protein).