Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutualism, Facilitation, and the Structure of Ecological Communities

Articles F acilitative, or positive, interactions are encounters between organisms that benefit at least one of the participants and cause harm to neither. Such interactions are considered " mutualisms " when both species derive benefit from the interaction. Positive interactions are ubiquitous: They may lie at the root of such diverse evolutionary phenomena as the origin of eukaryotic cells, the radiation of flowering plants, and the flourishing of coral reefs. Although a few ecologists have long recognized the importance of positive interactions in stressful environments (e.g., Clements 1916, Addicott 1984), ecological research on positive interactions is still far less common than that on other forms of interactions among species (Bronstein 1994a, Bruno and Bertness 2000). Consequently, positive interactions are rarely factored into models or even into thinking about factors impacting populations and communities. Recent empirical work and the conceptual models derived from this work (e.g., Bertness and Call-away 1994, Bruno and Bertness 2000) have helped refocus attention on the role of positive interactions among species, however, and scientists are beginning to better appreciate the importance of those interactions in the structuring of ecological communities. Simply by growing, many species alter the local environment. Trees cast shade on the forest floor, altering light and moisture regimes; corals form reefs, increasing habitat complexity and thereby providing habitat for countless other species. Many of the positive interactions that have emerged as important to community structure can be placed into this category of " habitat modification, " in which one individual (or species) alters local environmental conditions, often making a stressful habitat more hospitable for other individuals or species. I define stress broadly, as any extrinsic force that reduces the fitness of an individual or population. Stresses can be phys-Thus positive interactions occur when one organism makes the local environment more favorable for another either directly (such as by reducing thermal stress via shading or decreasing wind stress via baffling) or indirectly (such as by removing competitors or deterring predators of that species). Jones and colleagues (1997) have called this process " ecosystem engineering " and the species that modify the habitat " bioengineers. " Although these terms are useful metaphors for the critical role these species play in ecosystems, their use has stirred controversy because, for some, they imply conscious intent on the part of the species doing the " engineering. " Many habitat-modifying species form the basis on which the entire community …
Working Memory in Portuguese Children With Developmental Dyslexia

A Portuguese sample of 50 children with developmental dyslexia (DD) and 50 typical readers (TR) who were matched for age (8–12 years old) were tested on measures of working memory. Relative to the TR, the children with DD performed significantly worse on phonological loop (PL) and central executive (CE) tasks; however, they exhibited no impairments on visuospatial sketchpad (VSSP) tasks. After controlling for the influence of the PL, the group differences in CE tasks were no longer significant. The results of a receiver-operating characteristics curve analysis and a binary logistic regression analysis suggested that the PL and CE tasks (but not the VSSP tasks) were relevant variables for identifying children with DD. Hierarchical linear regression analyses showed that the PL and CE (Backward Digit Span only) tasks were significant predictors of reading and spelling abilities.
Core Stabilization Exercise Prescription, Part I

Context: Injury to the low back can cause significant pain and dysfunction, which can affect an athlete’s performance and result in time lost from sport. A common conservative treatment is therapeutic core stabilization exercises, which can address pain and musculoskeletal dysfunction in patients with low back pathology. Evidence Acquisition: MEDLINE and CINAHL were searched (from 1966 to March 2013) to identify relevant research. Keywords and keyword combinations searched included motor control exercise, segmental stabilization, core stabilization, transversus abdominis, multifidi, and low back pain. Results: There are 2 popular rehabilitation strategies to assess core function and promote core stabilization. Each has been developed based on biomechanical models of lumbar segmental stability and observed motor control dysfunction in patients with low back pain. Conclusion: Controversy exists among clinical and research groups as to the optimal strategy for an athlete with low back pain.
Novel miniaturized triplexer using Substrate Integrated technology

In this paper a novel multilayer triplexer is presented where a Substrate Integrated Waveguide (SIW) filter is integrated with Substrate Integrated Coaxial (SICx) filters in the same space for system miniaturization. It will be shown that low cross-coupling levels are achieved. The SIW and one SICx filters are designed using Composite Rigth Left Hand (CRLH) cells, while the other SICx filter is designed using hairpin resonators. Simulated and experimental results are shown with good agreement.
Characterization of saturable binding sites for rabies virus

A specific, saturable receptor for rabies virus was analyzed on cultured cells of neural or non-neural origin. Viral attachment kinetics were enhanced by DEAE-dextran, an effect which in turn enhanced the apparent infectivity of the virus inoculum. Under optimized conditions, the attachment of metabolically labeled ERA strain rabies virus obeyed the laws of mass action, whereby the amount of virus bound to cells varied proportionally with the concentration of cells or virus. Attachment was sensitive to changes of temperature and pH, did not require divalent cations such as Mg2+ or Ca2+, and occurred despite prior treatment of cells with proteolytic or sialic acid-specific enzymes. Saturation of the cell surface with rabies virus could be accomplished with 3 X 10(3) to 15 X 10(3) attached virions per cell. Competition for the rabies receptor occurred with rabies nonpathogenic variant virus, RV194 -2, and vesicular stomatitis virus. Reovirus type 3, another neurotropic virus, failed to inhibit rabies virus binding, and West Nile virus only slightly inhibited rabies virus binding, suggesting independent cellular receptors were recognized by these viruses. Isolated rabies virus glycoprotein failed to compete in an equivalent manner. However, solubilization of BHK-21 cells with octylglucoside yielded a chloroform-methanol-soluble extract which blocked rabies virus attachment. The binding inhibition activity of this extract was resistant to proteases but could be destroyed by phospholipases and neuraminidase, suggesting a phospholipid or glycolipid component at the receptor site. These data provide evidence for a rhabdovirus-common mechanism for cellular attachment to cells in culture.
Autocatalytic Maturation of the Tat-Dependent Halophilic Subtilase Nep Produced by the Archaeon Natrialba magadii

ABSTRACT Halolysins are subtilisin-like extracellular proteases produced by haloarchaea that possess unique protein domains and are salt dependent for structural integrity and functionality. In contrast to bacterial subtilases, the maturation mechanism of halolysins has not been addressed. The halolysin Nep is secreted by the alkaliphilic haloarchaeon Natrialba magadii, and the recombinant active enzyme has been synthesized in Haloferax volcanii. Nep contains an N-terminal signal peptide with the typical Tat consensus motif (GRRSVL), an N-terminal propeptide, the protease domain, and a C-terminal domain. In this study, we used Nep as a model protease to examine the secretion and maturation of halolysins by using genetic and biochemical approaches. Mutant variants of Nep were constructed by site-directed mutagenesis and expressed in H. volcanii, which were then analyzed by protease activity and Western blotting. The Tat dependence of Nep secretion was demonstrated in Nep RR/KK variants containing double lysine (KK) in place of the twin arginines (RR), in which Nep remained cell associated and the extracellular activity was undetectable. High-molecular-mass Nep polypeptides without protease activity were detected as cell associated and extracellularly in the Nep S/A variant, in which the catalytic serine 352 had been changed by alanine, indicating that Nep protease activity was needed for precursor processing and activation. Nep NSN 1-2 containing a modification in two potential cleavage sites for signal peptidase I (ASA) was not efficiently processed and activated. This study examined for the first time the secretion and maturation of a Tat-dependent halophilic subtilase.
OR I GI N A L A R T I CLE The Relationship Between Neuropeptides and Hormones in Starvation

OBJECTIVES: Some hormonal disturbances were demonstrated in starvation. Leptin, NPY and galanin play an important role in the control of appetite and in the mechanism of hormone release. METHODS: In order to evaluate the effect of starvation on the relationship between leptin, neuropeptide Y (NPY) galanin and pituitary and gonadal hormones release, plasma leptin, NPY and galanin as well as serum LH, FSH, prolactin (PRL), estradiol, progesterone levels in non-starved female rats (in diestrus) and after 72 hrs of starvation were measured with RIA methods. Effects of leptin, NPY and galanin administration on pituitary and gonadal hormones were investigated in vivo and in vitro experiments. RESULTS: Plasma leptin, NPY and galanin as well as serum estradiol and progesterone concentrations were signifi cantly lower in starved rats as compared with non-starved rats. However serum prolactin level was signifi cantly higher in starved rats. Opposite effects after leptin and NPY administration on hormone release in vivo and in vitro experiments were observed in non-starved rats. However, in starved rats we did not fi nd changes in pituitary and gonadal hormones release after leptin, NPY and galanin injection or the hormonal response was blunted. CONCLUSIONS: 1) The disturbances in neuropeptides activity and in hormones release were observed in starvation. 2) Leptin, NPY and galanin have direct and indirect effects on pituitary and gonadal hormones release. 3) In starvation the hormonal response to leptin, NPY and galanin is impaired.
ZnO Nanorod-Based Ultraviolet Photodetector Prepared on Patterned Sapphire Substrates

A patterned sapphire substrate with a submicron hole array structure was used to fabricate ZnO nanorod (NR) array by low-temperature hydrothermal method. A ZnO seed layer was spin-coated using sol-gel process and then etched to form separated seed islands. Different concentrations of zinc acetate in the hydrothermal solution were performed for ZnO NR synthesis to investigate ultraviolet (UV) photo-response properties. The ZnO NRs synthesized on the patterned substrates were oriented at various inclined angles. The diameter of the NRs increased and their surface-to-volume ratio decreased as the concentrations of zinc acetate increased from 0.01 to 0.04 M. X-ray diffraction and photoluminescence analyses showed that the NRs synthesized at a higher zinc acetate concentration had better crystal quality and fewer defects. The current–voltage characteristics of the ZnO NR-based metal-semiconductor-metal photodetectors exhibited a linear relationship, suggesting an Ohmic contact between NRs and Al electrodes. The UV response, defined by the resistance ratio (Rdark/RUV), of the photodetectors increased with the decreasing zinc acetate concentration from 0.04 to 0.01 M. Compared to traditional vertically aligned NR array on plain substrates, the proposed ZnO NR-based photodetector on the patterned substrates achieved improved UV responses, and the average increment for samples of 0.01–0.04 M was 145%.
Mapping processing strategies in learning from expository text: an exploratory eye tracking study followed by a cued recall

This study starts from the observation that current empirical research on students’ processing strategies in higher education has mainly focused on the use of self-report instruments to measure students’ general preferences towards processing strategies. In contrast, there is a rather limited use of more direct and online observation techniques to uncover differences in processing strategies at a task specific level. We based our study on one of the most influential studies in the domain of Students’ Approaches to Learning (SAL) (Marton, Dahlgren, Saljo, & Svensson, 1975). In our exploratory experiment we used eye tracking followed by a cued recall to investigate how students use processing strategies in learning from expository text. Nineteen university students participated in the experiment. Results suggested that students in the deep condition did not look longer at the essentials in the text compared with students in the surface condition, but that they processed them in a more deep way. In our sample, students in the surface condition looked longer at facts and details and also reported repeating these facts and details more often. We suggest that the combination of eye tracking followed by a cued recall is a promising tool to investigate students’ processing strategies since not all differences in processing strategies are reflected in overt eye movement behaviour. The current methodology allows researchers in the domain of SAL to complement and extend the present knowledge base that has accumulated through years of research with self-report questionnaires and interviews on students’ general preferences towards processing strategies.
Young Maltese children's ideas about plants

Fifty Maltese children, 25 in the second year of pre-school (4 years olds) and 25 in the first year of compulsory education (5 years old), were interviewed about their knowledge of plants. Analysis showed that they had a restricted understanding of the term, meaning something small, with a thin stalk, leaves and a flower. Trees, cacti and nettles were not classified as plants. Children's knowledge was observed to increase with age. Parents were identified as the main source of knowledge; schools were rarely mentioned. Maltese teachers should be made aware of children's limited knowledge about plants and they need to use readily available resources in schools to expose pre-school children to the plants in their immediate surroundings.
Computational methods for Gene Orthology inference

Accurate inference of orthologous genes is a pre-requisite for most comparative genomics studies, and is also important for functional annotation of new genomes. Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis, or some combination of these approaches. The most direct tree-based methods typically rely on the comparison of an individual gene tree with a species tree. Once the two trees are accurately constructed, orthologs are straightforwardly identified by the definition of orthology as those homologs that are related by speciation, rather than gene duplication, at their most recent point of origin. Although ideal for the purpose of orthology identification in principle, phylogenetic trees are computationally expensive to construct for large numbers of genes and genomes, and they often contain errors, especially at large evolutionary distances. Moreover, in many organisms, in particular prokaryotes and viruses, evolution does not appear to have followed a simple 'tree-like' mode, which makes conventional tree reconciliation inapplicable. Other, heuristic methods identify probable orthologs as the closest homologous pairs or groups of genes in a set of organisms. These approaches are faster and easier to automate than tree-based methods, with efficient implementations provided by graph-theoretical algorithms enabling comparisons of thousands of genomes. Comparisons of these two approaches show that, despite conceptual differences, they produce similar sets of orthologs, especially at short evolutionary distances. Synteny also can aid in identification of orthologs. Often, tree-based, sequence similarity- and synteny-based approaches can be combined into flexible hybrid methods.
Assessing the associations of sodium intake with long-term all-cause and cardiovascular mortality in a hypertensive cohort.

BACKGROUND Although higher sodium intake is known to increase blood pressure, its association with cardiovascular mortality is less established. We examined the association of baseline sodium intake in a hypertensive cohort with all-cause and cardiovascular mortality over a mean follow-up of 18.6 years. METHODS Three thousand five hundred five subjects were participants in a worksite hypertension program. Sodium intake was estimated by 24-hour urine excretion. Mortality data were obtained from the U.S. National Death Index. Unadjusted and multivariable-adjusted associations between sodium quartiles (quartile I (QI) to quartile IV (QIV)) and mortality were assessed using Cox models. RESULTS Estimated mean ± SD sodium intake was 130±69 mmol overall (55±20 mmol in QI; 220±56 mmol in QIV). Baseline systolic blood pressure did not vary significantly between groups. Last available mean systolic blood pressure was highest in QI and lowest in QIV (137±16 vs. 134±14 mm Hg; P = 0.009). Overall there were 1,013 deaths (399 cardiovascular). Unadjusted models exhibited significant inverse relationships between sodium and mortality outcomes. In adjusted models, sodium intake was not significantly associated with cardiovascular mortality (QI vs. QIV: hazard ratio (HR) = 1.00; 95% confidence interval (CI) = 0.71-1.42; P = 0.99). A borderline significant direct association with all-cause mortality was observed (QI vs. QIV: HR = 0.81; 95% CI = 0.66-1.00; P = 0.05) driven partly by noncardiovascular deaths. CONCLUSIONS Our study found no significant association between sodium intake and cardiovascular outcomes, although a significant association with all-cause mortality was observed. Although these findings suggest that sodium may not have a strong relationship with cardiovascular mortality, the inconsistent results cast doubt on whether a single measurement can reliably predict mortality over a prolonged follow-up period.
Latency, without persistence, of murine cytomegalovirus in the spleen and kidney

It is not known if murine cytomegalovirus (MCMV) establishes a state of molecular latency independent of low-level persistent infection. The presence of low levels of infectious MCMV distinguishes persistence from molecular latency. Thus, the distinction between persistence and latency has depended on the sensitivity of plaque assays for detecting low levels of infectious virus in tissue of previously infected mice. To determine whether MCMV establishes molecular latency or remains persistent, we developed two assays for detecting low levels of MCMV in tissue. Using prolonged in vitro culture of virus with either mouse embryonic fibroblasts or the murine 3T12 fibroblast cell line, we reproducibly detected a single PFU of MCMV. Inclusion of undiluted sonicated tissue in this assay decreased sensitivity by up to 100-fold. However, sensitivity was improved to 1 PFU of MCMV when sonicated tissue was appropriately diluted. Severe combined immunodeficient (SCID) mice were also used to detect MCMV in sonicated tissue. Infection of SCID mice with a single PFU of MCMV killed two of eight SCID mice, and the 50% lethal dose of MCMV in SCID mice was 2 to 3 PFU. Applying these two methods, we detected infectious virus in 0 of 34 spleens, 1 of 34 kidneys, and 0 of 37 salivary glands from latently infected mice. Spleens and kidneys assessed for persistent virus contained MCMV DNA by PCR and reactivated after 10 to 50 days in explant cultures. Latently infected kidney cells reactivated after adoptive transfer to SCID mice. Quantitation of the MCMV genome by PCR showed that latently infected spleens without detectable infectious MCMV contained about 3,000,000 copies of the MCMV genome. These results demonstrate that MCMV latency in spleen and kidney exists in the absence of low-level persistent infection. Use of assays with defined sensitivity for detection of MCMV in tissue provides a basis for evaluation of cytomegalovirus gene expression in the spleen and kidney during molecular latency.
Auto-parallelizing stateful distributed streaming applications

Streaming applications transform possibly infinite streams of data and often have both high throughput and low latency requirements. They are comprised of operator graphs that produce and consume data tuples. The streaming programming model naturally exposes task and pipeline parallelism, enabling it to exploit parallel systems of all kinds, including large clusters. However, it does not naturally expose data parallelism, which must instead be extracted from streaming applications. This paper presents a compiler and runtime system that automatically extract data parallelism for distributed stream processing. Our approach guarantees safety, even in the presence of stateful, selective, and user-defined operators. When constructing parallel regions, the compiler ensures safety by considering an operator's selectivity, state, partitioning, and dependencies on other operators in the graph. The distributed runtime system ensures that tuples always exit parallel regions in the same order they would without data parallelism, using the most efficient strategy as identified by the compiler. Our experiments using 100 cores across 14 machines show linear scalability for standard parallel regions, and near linear scalability when tuples are shuffled across parallel regions.
Sources and characteristics of Web temporal locality

Temporal locality of reference in Web request streams emerges from two distinct phenomena: the long-term popularity of Web documents and the short-term temporal correlations of references. We show that the commonly-used distribution of inter-request times is predominantly determined by the power law governing the long-term popularity of documents. This inherent relationship tends to disguise the existence of short-term temporal correlations. We propose a new and robust metric that enables accurate characterization of that aspect of temporal locality. Using this metric, we characterize the locality of reference in a number of representative proxy cache traces. Our findings show that there are measurable differences between the degrees (and sources) of temporal locality across these traces.
A Biochemical Calculus Based on Strategic Graph Rewriting

When modeling interactions between molecules or proteins, the behaviour of a protein is given by its functional domains that determine which other protein it can bind to or interact with and these domains are usually abstracted as sites that can be bound or free, visible or hidden. Hence a protein is characterized by the collection of interaction sites on its surface and proteins can bind to each other forming molecular complexes. Based on such structures, we considered port graphs [1] which are graphs with ports and with multiple edges and loops attached to ports of nodes. Molecular complexes are port graphs where each port is connected to at most one other port. Such restricted port graphs are called molecular graphs and their ports are called sites. We illustrate below a molecular graph G representing the initial state of the system modeling a fragment of the EGFR signaling cascade [12, 14]. The protagonists of this model are three types of proteins: the signal EGF, the receptor EGFR, and the adapter SHC . The molecular graph G′ represents a state of the system where two signal proteins are already bound forming a dimer binding in turn a receptor. A node is graphically represent as a box with an unique identifier and a name placed outside the box. A site is represented as a filled, empty, or slashed circle on the surface of the box if its state is respectively bound, free, or hidden.