Miracle-dz/UniFAR-FTUs huggingface dataset:
Enteric Salmonellosis Disrupts the Microbial Ecology of the Murine Gastrointestinal Tract

ABSTRACT The commensal microbiota protects the murine host from enteric pathogens. Nevertheless, specific pathogens are able to colonize the intestinal tract and invade, despite the presence of an intact biota. Possibly, effective pathogens disrupt the indigenous microbiota, either directly through pathogen-commensal interaction, indirectly via the host mucosal immune response to the pathogen, or by a combination of these factors. This study investigates the effect of peroral Salmonella enterica serovar Typhimurium infection on the intestinal microbiota. Since the majority of the intestinal microbiota cannot be cultured by conventional techniques, molecular approaches using 16S rRNA sequences were applied. Several major bacterial groups were assayed using quantitative PCR. Administration of either the 50% lethal dose (LD50) or 10× LD50 of Salmonella enterica serovar Typhimurium caused changes in the microbiota throughout the intestinal tract over the time course of infection. A 95% decrease in total bacterial number was noted in the cecum and large intestine with 10× LD50S. enterica serovar Typhimurium challenge at 7 days postinfection, concurrent with gross evidence of diarrhea. In addition, alterations in microbiota composition preceded the onset of diarrhea, suggesting the involvement of pathogen-commensal interactions and/or host responses unrelated to diarrhea. Microbiota alterations were not permanent and reverted to the microbiota of uninfected mice by 1 month postinfection. Infection with a Salmonella pathogenicity island 1 (SPI1) mutant did not result in microbiota alterations, while SPI2 mutant infections triggered partial changes. Neither mutant was capable of prolonged colonization or induction of mucosal inflammation. These data suggest that several Salmonella virulence factors, particularly those involved in the local mucosal host response, are required for disruption of the intestinal ecosystem.
The Relationship between the Curriculum and Content of Books & Using Educational Technology - A Meta-analysis

: The purpose of this study is to examine the relationship between the curriculum and contents of books and the use of Educational Technology by teachers and university professors in Iran through meta-analysis. An extensive search for relevant published and unpublished studies found 51 studies from 1993 to 2009, 8 research studies with inferential statistics were chosen. The results indicated that the curriculum and content of books had a lot of influences on not using Educational Technology and it was a big obstacle for using it
Combinatorics of Place Cell Coactivity and Hippocampal Maps

It is widely accepted that the hippocampal place cells' spiking activity produces a cognitive map of space. However, many details of this representation's physiological mechanism remain unknown. For example, it is believed that the place cells exhibiting frequent coactivity form functionally interconnected groups---place cell assemblies---that drive readout neurons in the downstream networks. However, the sheer number of coactive combinations is extremely large, which implies that only a small fraction of them actually gives rise to cell assemblies. The physiological processes responsible for selecting the winning combinations are highly complex and are usually modeled via detailed synaptic and structural plasticity mechanisms. Here we propose an alternative approach that allows modeling the cell assembly network directly, based on a small number of phenomenological selection rules. We then demonstrate that the selected population of place cell assemblies correctly encodes the topology of the environment in biologically plausible time, and may serve as a schematic model of the hippocampal network.
Answering search queries with CrowdSearcher

Web users are increasingly relying on social interaction to complete and validate the results of their search activities. While search systems are superior machines to get world-wide information, the opinions collected within friends and expert/local communities can ultimately determine our decisions: human curiosity and creativity is often capable of going much beyond the capabilities of search systems in scouting "interesting" results, or suggesting new, unexpected search directions. Such personalized interaction occurs in most times aside of the search systems and processes, possibly instrumented and mediated by a social network; when such interaction is completed and users resort to the use of search systems, they do it through new queries, loosely related to the previous search or to the social interaction. In this paper we propose CrowdSearcher, a novel search paradigm that embodies crowds as first-class sources for the information seeking process. CrowdSearcher aims at filling the gap between generalized search systems, which operate upon world-wide information - including facts and recommendations as crawled and indexed by computerized systems - with social systems, capable of interacting with real people, in real time, to capture their opinions, suggestions, emotions. The technical contribution of this paper is the discussion of a model and architecture for integrating computerized search with human interaction, by showing how search systems can drive and encapsulate social systems. In particular we show how social platforms, such as Facebook, LinkedIn and Twitter, can be used for crowdsourcing search-related tasks; we demonstrate our approach with several prototypes and we report on our experiment upon real user communities.
Sex-Dependent Correlations between the Personality Dimension of Harm Avoidance and the Resting-State Functional Connectivity of Amygdala Subregions

Harm avoidance (HA) is a personality dimension involving the tendency to respond intensely to signals of aversive stimuli. Many previous neuroimaging studies have associated HA scores with the structural and functional organization of the amygdala, but none of these studies have evaluated the correlation between HA score and amygdala resting-state functional connectivity (rsFC). Moreover, the amygdala is not a homogeneous structure, and it has been divided into several structurally and functionally distinct subregions. Investigating the associations between HA score and properties of subregions of the amygdala could greatly improve our understanding of HA. In the present study, using a large sample of 291 healthy young adults, we aimed to uncover correlations between HA scores and the rsFCs of each amygdala subregion and to uncover possible sex-based differences in these correlations. We found that subregions of the amygdala showed different rsFC patterns, which contributed differently to individual HA scores. More specifically, HA scores were correlated with rsFCs between the laterobasal amygdala subregion and temporal and occipital cortices related to emotional information input, between the centromedial subregion and the frontal cortices associated with emotional output control, and between the superficial subregion and the frontal and temporal areas involved in both functions. Moreover, significant gender-based differences were uncovered in these correlations. Our findings provide a more detailed model of association between HA scores and amygdala rsFC, extend our understanding of the connectivity of subregions of the amygdala, and confirm sex-based differences in HA associations.
Stochastic First- and Zeroth-Order Methods for Nonconvex Stochastic Programming

In this paper, we introduce a new stochastic approximation (SA) type algorithm, namely the randomized stochastic gradient (RSG) method, for solving an important class of nonlinear (possibly nonconvex) stochastic programming (SP) problems. We establish the complexity of this method for computing an approximate stationary point of a nonlinear programming problem. We also show that this method possesses a nearly optimal rate of convergence if the problem is convex. We discuss a variant of the algorithm which consists of applying a post-optimization phase to evaluate a short list of solutions generated by several independent runs of the RSG method, and show that such modification allows to improve significantly the large-deviation properties of the algorithm. These methods are then specialized for solving a class of simulation-based optimization problems in which only stochastic zeroth-order information is available.
Biological Alchemy: Engineering Bone and Fat From Fat-Derived Stem Cells

Adipose tissue contains a population of pluripotent stem cells capable of differentiating along multiple mesenchymal cell lineages. In this study the authors isolated these fat-derived stem cells successfully from Lewis rats and induced differentiation along adipogenic and osteogenic lineages in vitro and in vivo. Induction was stimulated by exposing stem cells to lineage-specific induction factors. Adipocyte-inducing media contained dexamethasone, insulin, and isobutyl-methylxanthine. Osteoblast inducing media contained dexamethasone, &bgr;-glycerophosphate, and ascorbic acid. Undifferentiated stem cells were maintained in minimal essential media alpha and fetal bovine serum. At 10 days, cells cultured in adipogenic media differentiated into adipocytes in vitro, as evidenced by positive Oil red O staining of lipid vacuoles. At 21 days, cells cultured in osteogenic media differentiated into osteoblasts in vitro as demonstrated by Alizarin red staining of a calcified extracellular matrix and immunohistochemical staining for osteocalcin. Differentiated cells were seeded at a density of 5 × 106 cells onto 15 × 15-mm polyglycolic acid grafts and implanted subcutaneously into three groups of Lewis rats: Group I contained undifferentiated stem cell grafts, group II contained adipocyte grafts, and group III contained osteoblast grafts. At weeks 4 and 8, in vivo fat formation was demonstrated in group II rats, as confirmed by Oil red O staining. At 8 weeks, group III rats demonstrated in vivo bone formation, as confirmed by the presence of osteocalcin on immunohistochemistry and the characteristic morphology of bone on hematoxylin–eosin staining. Group I rats demonstrated no in vivo bone or fat formation at either time interval. These results demonstrate the ability to isolate pluripotent stem cells from adipose tissue, to induce their differentiation into osteoblasts and adipocytes in vitro, and to form bone and fat subsequently in vivo. This is the first published report of in vivo bone formation from fat-derived stem cells. These cells may eventually serve as a readily available source of autologous stem cells for the engineering of bone and fat.
On the Feasibility of the Link Abstraction in Wireless Mesh Networks

Outdoor community mesh networks based on IEEE 802.11 have seen tremendous growth in the recent past. The current understanding is that wireless link performance in these settings is inherently unpredictable, due to multipath delay spread. Consequently, researchers have focused on developing intelligent routing techniques to achieve the best possible performance. In this paper, we are specifically interested in mesh networks in rural locations. We first present detailed measurements to show that the PHY layer in these settings is indeed stable and predictable. There is a strong correlation between the error rate and the received signal strength. We show that interference, and not multipath fading, is the primary cause of unpredictable performance. This is in sharp contrast with current widespread knowledge from prior studies. Furthermore, we corroborate our view with a fresh analysis of data presented in these prior studies. While our initial measurements focus on 802.11b, we then use two different PHY technologies as well, operating in the 2.4-GHz ISM band: 802.11g and 802.15. 4. These show similar results too. Based on our results, we argue that outdoor rural mesh networks can indeed be built with the link abstraction being valid. This has several design implications, including at the MAC and routing layers, and opens up a fresh perspective on a wide range of technical issues in this domain.
Multiuser Detection for Uplink DS-CDMA Amplify-and-Forward Relaying Systems

We consider the uplink of a cooperative DS-CDMA communication system, where each user communicates with the base station through a direct link and with the help of relays. A multiuser detection approach for the joint estimation of spatial signatures, channel gains and transmitted symbols of all the users is proposed. Such an approach is derived from a trilinear tensor model for the received signal that combines the source-destination and relay-destination links. The proposed multiuser receiver provides an extension of the traditional trilinear DS-CDMA receiver to cooperative relaying systems, by including the users' relay-assisted links into the trilinear model. Moreover, in contrast to a previous work by the authors, where the relays of a cluster transmit over orthogonal channels, the proposed receiver operates in a more attractive scenario where all the relays simultaneously transmit towards the base station without requiring orthogonal codes. Simulation results illustrate the performance of the proposed receiver in comparison with alternative approaches.
Effects of Synaptic Weight Diffusion on Learning in Decision Making Networks

When animals repeatedly choose actions from multiple alternatives, they can allocate their choices stochastically depending on past actions and outcomes. It is commonly assumed that this ability is achieved by modifications in synaptic weights related to decision making. Choice behavior has been empirically found to follow Herrnstein's matching law. Loewenstein & Seung (2006) demonstrated that matching behavior is a steady state of learning in neural networks if the synap-tic weights change proportionally to the covariance between reward and neural activities. However, their proof did not take into account the change in entire synaptic distributions. In this study, we show that matching behavior is not necessarily a steady state of the covariance-based learning rule when the synaptic strength is sufficiently strong so that the fluctuations in input from individual sensory neurons influence the net input to output neurons. This is caused by the increasing variance in the input potential due to the diffusion of synaptic weights. This effect causes an undermatching phenomenon, which has been observed in many behavioral experiments. We suggest that the synaptic diffusion effects provide a robust neural mechanism for stochastic choice behavior.
Bernstein type's concentration inequalities for symmetric Markov processes

Using the method of transportation-information inequality introduced in [A. Guillin et al., Probab. Theory Related Fields, 144 (2009), pp. 669--695], we establish Bernstein-type concentration inequalities for empirical means of functions of the Markov process $(\int_0^t g(X_s)\,ds)/t$ where $g$ is an unbounded observable of the symmetric Markov process $(X_t)$. Three approaches are proposed: a functional inequalities approach, a Lyapunov function method, and an approach through the Lipschitzian norm of the solution to the Poisson equation. Several applications and examples are studied.
Suzaku Spectroscopy of an X-Ray Reflection Nebula and a New Supernova Remnant Candidate in the SgrB1 Region

We made a 100 ks observation of the Sagittarius (Sgr) B1 region at (l, b) = (0.5, -0.1) near to the Galactic center (GC) with the Suzaku/XIS. Emission lines of S XV, Fe I, Fe XXV, and Fe XXVI were clearly detected in the spectrum. We found that the Fe XXV and Fe XXVI line emissions smoothly distribute over the Sgr B1 and B2 regions connecting from the GC. This result suggests that the GC hot plasma extends at least up to the Sgr B region with a constant temperature. There are two diffuse X-ray sources in the observed region. One of the two (G0.42-0.04) is newly discovered, and exhibits a strong S XV Ka emission line, suggesting a candidate for a supernova remnant located in the GC region. The other one (M0.51-0.10), having a prominent Fe I Ka emission line and a strongly absorbed continuum, is likely to be an X-ray reflection nebula. There is no near source bright enough to irradiate M0.51-0.10. However, the Fe I Ka emission can be explained if Sgr A* was ~ 10^6 times brighter 300 years ago, the light travel time for 100 pc to M0.51-0.10, than it is at present.
Two Heuristic Algorithms for Test Point Selection in Analog Circuit Diagnoses

The paper presents a heuristic approach to the prob lem of analog circuit diagnosis. Different optimiza tion techniques in the field of test point selection are discussed. Two new algorithms: SALTO and COSMO have been introduced. Both searching procedures have been implemented in a form of the expert system in PROLOG language. The proposed methodologies have bee n exemplified on benchmark circuits. The obtained r esults have been compared to the others achieved by different a pproaches in the field and the benefits of the prop osed methodology have been emphasized. The inference engine of the heuristic algorithms has been presented and the expert system knowledge-base construction discussed.
Central corneal thickness. Ocular correlations in normal eyes and those with primary angle-closure glaucoma.

In recent papers (Lowe, I968, I969a) it was shown that in normal eyes, lens position and thickness were coordinated with axial length and radius of corneal curvature, whereas in eyes with primary angle-closure glaucoma these correlations were lacking. Throughout adult life, lenses increase in thickness at the same rate in normal eyes and those with angle-closure glaucoma, but no change could be shown in axial length or mean radius of corneal curvature. The present paper describes investigations to determine whether central corneal thickness is correlated with axial length and radius of corneal curvature, whether central corneal thickness changes with age, and whether corneal thickness has any special effect in producing the shallow anterior chamber which is the distinguishing feature of eyes with primary angle-closure glaucoma.
1 " Dynamics of Rules and Resources : Three New Field Experiments on Water , Forests and Fisheries " 1

Most common-pool resource experiments, inspired by the ground-breaking work of Ostrom, Gardner and Walker (1994), involve a typical structure of a static non-linear social dilemma with a rival but nonexcludable good that is extracted by a number of players. However there are specific ecological features of relevant common-pool resources that can be incorporated into an experimental design and tested in the field or the lab. Stock effects, spatial effects or vertical downstream externalities are issues that natural scientists and economists have studied in forests, fisheries or watershed management although experimental works on these ecological aspects are rather scarce. We designed three resource specific games to capture particular characteristics of common-pool resources and apply them in six villages in Thailand and Colombia. In each village we recruited 60 people and conducted three games. A water irrigation game capturing the downstream externalities and collective action problem of provision and appropriation stages where all players need to contribute to a public project that produces water which is then extracted sequentially by each of the players starting with the one located upstream, leaving the remaining water to the next player downstream, and so on. In our forestry game players start with a number of standing trees that can be cut by any of the players; in any round each player can extract between zero and a fixed number of trees. The remaining trees regrow at a certain rate and the resulting trees are then left for the next round for individual extraction. The game ends at a maximum number of rounds or when no trees are left. Finally, the fisheries game involves two possible fishing sites that can have high or low levels of stock. Each player needs to decide where to fish between the two sites and her individual effort of fishing. Depending on the aggregate level of fishing effort in each site, the stock level will change for the following round and will determine the fishing returns. All games involve a social dilemma where individual interests clash with the socially optimal outcome. Lessons can be derived regarding the design of better resource management rules and a better understanding of how resource specific dynamics affect the social dilemmas in commonpool resources. 1 The authors wish to thank the NSF grant within the HUMAN AND SOCIAL DYNAMICS PROGRAM for their funding. More details about the research project can be found in: http://www.public. asu.edu/~majansse/dor/nsfhsd.htm 2
Stratigraphic hierarchy of organic carbon–rich siltstones in deep-water facies, Brushy Canyon Formation (Guadalupian), Delaware Basin, West Texas

The first systematic test for a predictive relationship between organic carbon content and stratigraphic hierarchy in a deep-water slope to basin-floor deposit was performed. The studied section includes the Pipeline Shale, the Brushy Canyon Formation, and the lower part of the Cherry Canyon Formation of the Delaware Mountain Group, West Texas. This interval represents one large-scale, 3rd-order genetic sequence within which 4th- and 5th-order stratigraphic cycles are recognized. Samples of fine-grained facies throughout the section were collected from outcrop and analyzed for organic carbon content and hydrogen index. Degree of pyritization was also determined for a subset of the samples. The results indicate that organic enrichment is closely correlated to the stratigraphic hierarchy at the 3rd-, 4th-, and 5th-order levels. The data suggest that quantity and quality of preserved organic matter are controlled by changes in bulk sedimentation rate (dilution vs. condensation), which affect organic matter inputs to the sediment, as well as the balance between (1) burial and preservation of organic matter and (2) its degradation on the sea floor during times of sediment starvation.
Porphyromonas endodontalis in chronic periodontitis: a clinical and microbiological cross-sectional study

Abstract Background Although previous studies have shown the presence of Porphyromonas endodontalis in chronic periodontitis associated with periapical lesions, the occurrence of this pathogen in diseased periodontal sites without periapical lesions has been poorly investigated. Objective The aims of this study were to quantify P. endodontalis in patients with chronic periodontitis without periapical lesions, to evaluate the potential correlation of P. endodontalis with Porphyromonas gingivalis and Tannerella forsythia, and to evaluate the ability of periodontal treatment to reduce these pathogens. Design Patients with generalized chronic periodontitis were selected by recording clinical attachment level (CAL), probing depth (PD), and bleeding on probing (BOP). Subgingival samples from 30 diseased nonadjacent sites (CAL ≥ 5 mm, PD between 5 and 7 mm and positive BOP) and 30 healthy nonadjacent sites (PD ≤ 3 mm and negative BOP) were collected and subjected to microbial analysis by quantitative polymerase chain reaction (qPCR) The variables of age, PD, CAL and BOP of all individuals were analyzed using the paired t-test (GrapPad Prism5®). Data of bacteria quantification were subjected to a normality test (D'Agostino-Pearson Test). For bacterial correlation analysis, the Spearman correlation was used. Results Our results showed that diseased sites had significantly higher levels of P. endodontalis compared to healthy sites, similar to the results obtained for P. gingivalis and T. forsythia. The numbers of all bacterial species were reduced significantly after mechanical periodontal treatment. P. endodontalis was significantly correlated with the presence of T. forsythia and P. gingivalis in the diseased group. Conclusion Our results suggest that there is a high prevalence of P. endodontalis, P. gingivalis and T. forsythia in periodontitis sites and that mechanical periodontal treatment is effective at reducing the pathogens studied.