Miracle-dz/UniFAR-FTUs huggingface dataset:
The Kinetic Profile of Intracellular Calcium Predicts Long-Term Potentiation and Long-Term Depression

Efficiency of synaptic transmission within the neocortex is regulated throughout life by experience and activity. Periods of correlated or uncorrelated presynaptic and postsynaptic activity lead to enduring changes in synaptic efficiency [long-term potentiation (LTP) and long-term depression (LTD), respectively]. The initial plasticity triggering event is thought to be a precipitous rise in postsynaptic intracellular calcium, with higher levels inducing LTP and more moderate levels inducing LTD. We used a pairing protocol in visual cortical brain slices from young guinea pigs with whole-cell recording and calcium imaging to compare the kinetic profiles of calcium signals generated in response to individual pairings along with the cumulative calcium wave and plasticity outcome. The identical pairing protocol applied to layer 2/3 pyramidal neurons results in different plasticity outcomes between cells. These differences are not attributable to variations in the conditioning protocol, cellular properties, inter-animal variability, animal age, differences in spike timing between the synaptic response and spikes, washout of plasticity factors, recruitment of inhibition, or activation of different afferents. The different plasticity outcomes are reliably predicted by individual intracellular calcium transients in the dendrites after the first few pairings. In addition to the differences in the individual calcium transients, the cumulative calcium wave that spreads to the soma also has a different profile for cells that undergo LTP versus LTD. We conclude that there are biological differences between like-type cells in the dendritic calcium signals generated by coincident synaptic input and spiking that determine the sign of the plasticity response after brief associations.
Use link-based clustering to improve Web search results

While Web search engines can retrieve information on the Web for a specific topic, users have to step a long ordered list in order to locate the needed information, which is often tedious and less efficient. We propose a new link-based clustering approach to cluster search results returned from Web search engines by exploring both co-citation and coupling. Unlike document clustering algorithms in IR that are based on common words/phrases shared among documents, our approach is based on common links shared by pages. We also extend the standard clustering algorithm, K-means, to make it more natural to handle noise and apply it to Web search results. By filtering some irrelevant pages, our approach clusters high quality pages in Web search results into semantically meaningful groups to facilitate users accessing and browsing. Preliminary experiments and evaluations are conducted to investigate its effectiveness. The experimental results show that link-based clustering of Web search results is promising and beneficial.
Place cells in the hippocampus: Eleven maps for eleven rooms

Significance The hippocampus is thought to store a large number of experiences that, despite their similarity, can be individually retrieved with minimal interference. Studies have shown that place cells in hippocampal area CA3 form statistically independent representations of pairs of environments. It has remained unclear, however, whether CA3 place cells maintain this independence when the number of environments is increased. We recorded activity from CA3 in 11 environments with nearly identical geometric features. Spatial firing patterns remained uncorrelated across all 55 pairs of environments, with minimal overlap in the populations of active cells. The data suggest that the capacity of the CA3 network is large and speak against extensive recurrence of spatial motifs across experiences. The contribution of hippocampal circuits to high-capacity episodic memory is often attributed to the large number of orthogonal activity patterns that may be stored in these networks. Evidence for high-capacity storage in the hippocampus is missing, however. When animals are tested in pairs of environments, different combinations of place cells are recruited, consistent with the notion of independent representations. However, the extent to which representations remain independent across larger numbers of environments has not been determined. To investigate whether spatial firing patterns recur when animals are exposed to multiple environments, we tested rats in 11 recording boxes, each in a different room, allowing for 55 comparisons of place maps in each animal. In each environment, activity was recorded from neuronal ensembles in hippocampal area CA3, with an average of 30 active cells per animal. Representations were highly correlated between repeated tests in the same room but remained orthogonal across all combinations of different rooms, with minimal overlap in the active cell samples from each environment. A low proportion of cells had activity in many rooms but the firing locations of these cells were completely uncorrelated. Taken together, the results suggest that the number of independent spatial representations stored in hippocampal area CA3 is large, with minimal recurrence of spatial firing patterns across environments.
Biochemical and Immunological Characterization of Toxoplasma gondii Macrophage Migration Inhibitory Factor*

Background: Toxoplasma gondii possesses proteins that can modulate host immune responses. TgMIF is a homologue of mammalian macrophage migration inhibitory factor. Results: TgMIF possesses tautomerase but not oxidoreductase activity. It can stimulate ERK MAPK and IL-8 production. Conclusion: TgMIF is capable of modulating host molecules. Significance: The study identifies immunomodulatory activity of TgMIF consistent with a role for sustaining parasite survival. Macrophage migration inhibitory factor (MIF) is a proinflammatory molecule in mammals that, unusually for a cytokine, exhibits tautomerase and oxidoreductase enzymatic activities. Homologues of this well conserved protein are found within diverse phyla including a number of parasitic organisms. Herein, we produced recombinant histidine-tagged Toxoplasma gondii MIF (TgMIF), a 12-kDa protein that lacks oxidoreductase activity but exhibits tautomerase activity with a specific activity of 19.3 μmol/min/mg that cannot be inhibited by the human MIF inhibitor ISO-1. The crystal structure of the TgMIF homotrimer has been determined to 1.82 Å, and although it has close structural homology with mammalian MIFs, it has critical differences in the tautomerase active site that account for the different inhibitor sensitivity. We also demonstrate that TgMIF can elicit IL-8 production from human peripheral blood mononuclear cells while also activating ERK MAPK pathways in murine bone marrow-derived macrophages. TgMIF may therefore play an immunomodulatory role during T. gondii infection in mammals.
Carbon-Nitrogen Interactions in Terrestrial Ecosystems in Response to Rising Atmospheric Carbon Dioxide

AbstractInteractions involving carbon (C) and nitrogen (N) likely modulate terrestrial ecosystem responses to elevated atmospheric carbon dioxide (CO2) levels at scales from the leaf to the globe and from the second to the century. In particular, response to elevated CO2 may generally be smaller at low relative to high soil N supply and, in turn, elevated CO2 may influence soil N processes that regulate N availability to plants. Such responses could constrain the capacity of terrestrial ecosystems to acquire and store C under rising elevated CO2 levels. This review highlights the theory and empirical evidence behind these potential interactions. We address effects on photosynthesis, primary production, biogeochemistry, trophic interactions, and interactions with other resources and environmental factors, focusing as much as possible on evidence from long-term field experiments.
The development of number processing and its relation to other parietal functions in early childhood

The project has explored the developmental trajectories of several cognitive functions related to different brain regions: parietal cortex (quantity manipulation, finger gnosis, visuo-spatial memory and grasping abilities) and occipito-temporal cortex (face and object processing), in order to investigate their contributions to the acquisition of formal arithmetic in the first year of schooling. We tested preschooler, first grader and adult subjects, using correlational cross-sectional and longitudinal approaches. Results show that anatomical proximity is a strong predictor of behavioural correlations and of segregation between dorsal and ventral streams’ functions. This observation is particularly prominent in children: within parietal functions, there is a progressive separation across functions during development. During preschool age, presymbolic and symbolic number systems follow distinct developmental trajectories that converge during the first year of primary school. Indeed a possible cause of this phenomenon could be due to the refinement of the numerosity acuity during the acquisition of symbolic knowledge for numbers. Among the tested parietal functions, we observe a strong association between the numerical and the finger domain, especially in children. In preschoolers, finger gnosis is strongly associated with non-symbolic quantity processing, while in first graders it links up to symbolic mental arithmetic. This finding may reflect a pre-existing anatomical connection between the cortical regions supporting the quantity and finger-related functions in early childhood. In contrast, first graders exhibit a finger-arithmetic association more influenced by functional factors and cultural-based strategies (e.g. finger counting). Longitudinal data has allowed us to individuate which cognitive functions measured in kindergarteners predicts better the success in mental arithmetic in the first year of school. Results show that finger gnosis, as well as quantity and space–related abilities all concur at shaping the success in mental calculation in first graders. These results are important because, primarily, they are the first to observe a strong relation between visuo-spatial, finger and quantity related abilities in young children, and, secondly, because the longitudinal design provides strong evidence for a causal link between these functions and the success in formal arithmetic. These results suggest that educational programs should include training in each of these cognitive domains in mathematic classes. Finally, specific applications of these findings can be found within the domain of educational neuroscience and for the rehabilitation of children with numerical deficits (dyscalculia).
Improving retrieval feedback with multiple term-ranking function combination

In this article we consider methods for automatic query expansion from top retrieved documents (i.e., retrieval feedback) that make use of various functions for scoring expansion terms within Rocchio's classical reweighting scheme. An analytical comparison shows that the retrieval performance of methods based on distinct term-scoring functions is comparable on the whole query set but differs considerably on single queries, consistent with the fact that the ordered sets of expansion terms suggested for each query by the different functions are largely uncorrelated. Motivated by these findings, we argue that the results of multiple functions can be merged, by analogy with ensembling classifiers, and present a simple combination technique based on the rank values of the suggested terms. The combined retrieval feedback method is effective not only with respect to unexpanded queries but also to any individual method, with notable improvements on the system's precision. Furthermore, the combined method is robust with respect to variation of experimental parameters and it is beneficial even when the same information needs are expressed with shorter queries.
Alterations in Cortical Thickness and White Matter Integrity in Mild Cognitive Impairment Measured by Whole-Brain Cortical Thickness Mapping and Diffusion Tensor Imaging

BACKGROUND AND PURPOSE: Mild cognitive impairment (MCI) is a risk factor for Alzheimer disease and can be difficult to diagnose because of the subtlety of symptoms. This study attempted to examine gray matter (GM) and white matter (WM) changes with cortical thickness analysis and diffusion tensor imaging (DTI) in patients with MCI and demographically matched comparison subjects to test these measurements as possible imaging markers for diagnosis. MATERIALS AND METHODS: Subjects with amnestic MCI (n = 10; age, 72.2 ± 7.1 years) and normal cognition (n = 10; age, 70.1 ± 7.7 years) underwent DTI and T1-weighted MR imaging at 3T. Fractional anisotropy (FA), apparent diffusion coefficient (ADC), and cortical thickness were measured and compared between the MCI and control groups. We evaluated the diagnostic accuracy of 2 methods, either in combination or separately, using binary logistic regression and nonparametric statistical analyses for sensitivity, specificity, and accuracy. RESULTS: Decreased FA and increased ADC in WM regions of the frontal and temporal lobes and corpus callosum (CC) were observed in patients with MCI. Cortical thickness was decreased in GM regions of the frontal, temporal, and parietal lobes in patients with MCI. Changes in WM and cortical thickness seemed to be more pronounced in the left hemisphere compared with the right hemisphere. Furthermore, the combination of cortical thickness and DTI measurements in the left temporal areas improved the accuracy of differentiating MCI patients from control subjects compared with either measure alone. CONCLUSIONS: DTI and cortical thickness analyses may both serve as imaging markers to differentiate MCI from normal aging. Combined use of these 2 methods may improve the accuracy of MCI diagnosis.
An analysis of queries intended to search information for children

Query logs contain valuable information about the behavior, interests, and preferences of the users. The analysis of this information can give insight in their interaction and search behavior. In this paper, we analyze queries and groups of queries intended to find information that is suitable for children by using a large-scale query log. The aim of the analysis it twofold: (i) To identify differences in the query space, content space, user sessions, and user click behavior. (ii) To enhance the query log by including annotations of queries, sessions and actions. The paper presents plans to use this resource for further research on information retrieval for children. We found statistically significant differences between the set of general purpose queries, and the set of children queries. We show that many of these differences are consistent with small-scale research studies in which children were observed while using web search engines.
Capacity credit evaluation: A literature review

The amount of conventional resources (mainly thermal) that could be 'replaced' by renewable production, without making the system less reliable is defined as the capacity credit of the renewable plant(s). For any proper assessment of the capacity credit, it is primordial to be able to assess the reliability of the power system network. Ideally, the reliability of the network before the introduction of DGs should be the same, if not better, than after their introduction. This paper discusses the methods used to evaluate capacity credit and provides links to several studies performed mostly in and around Europe and the US. Because the majority of these methods use reliability indices to quantify the reliability with and without wind, it is important to include reliability metrics in the discussion. The sole aim of this paper is to provide a database of most of the available literature to the topic and discuss some of the better attempts.
Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae

The conservation of hox genes as well as their genomic organization across the phyla suggests that this system of anterior–posterior axis formation arose early during evolution and has come under strong selection pressure. Studies in the split Hox cluster of Drosophila have shown that proper expression of hox genes is dependent on chromatin domain boundaries that prevent inappropriate interactions among different types of cis-regulatory elements. To investigate whether boundary function and their role in regulation of hox genes is conserved in insects with intact Hox clusters, we used an algorithm to locate potential boundary elements in the Hox complex of mosquito, Anopheles gambiae. Several potential boundary elements were identified that could be tested for their functional conservation. Comparative analysis revealed that like Drosophila, the bithorax region in A. gambiae contains an extensive array of boundaries and enhancers organized into domains. We analysed a subset of candidate boundary elements and show that they function as enhancer blockers in Drosophila. The functional conservation of boundary elements from mosquito in fly suggests that regulation of hox genes involving chromatin domain boundaries is an evolutionary conserved mechanism and points to an important role of such elements in key developmentally regulated loci.
Misconceived Relationships between Logical Positivism and Quantitative Research: An Analysis in the Framework of Ian Hacking.

Although quantitative research methodology is widely applied by social scientists, there is a common misconception that quantitative research is based upon logical positivism. This misconception leads to misguided disputes between qualitative and quantitative researchers. This article points out that the polarities between the two are unnecessary, and the richness and continuity of “research traditions” is therefore proposed as a replacement for the incommensurability in the Kuhnian “paradigm. ” Further, this article examines the relationship between quantitative research and eight major notions of logical positivism: (a) verification, (b) pro-observation, (c) anti-cause, (d) downplaying explanation, (e) anti-theoretical entities, (f) anti-metaphysics, (g) logical analysis and (h) frequentist probability. It is argued that the underlying philosophy of modern quantitative research does not subscribe to logical positivism. Associating an outdated philosophy with quantitative research may discourage social science researchers from applying this research approach. Researchers and students should be encouraged to keep an open mind to different methodologies because mixed methods have the potential to achieve the goals of convergent validity and completeness.
Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa

Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host‐plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near‐simultaneous radiation events, coupled with shifts in host‐plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene – early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation‐associated changes in climate and sea level.
Autonomous interface agents

Two branches of the trend towards “agents” that are gaining currency are inre~ace agents, software that actively assists a user in operating an interactive interface, and autonomous agents, software that takes action without user intervention and operates concurrently, either while the user is idle or taking other actions. These two branches are related, but not identical, and are often lumped together under the single term “agent”. Much agent work can be classified as either being an interface agent, but not autonomous, or as an autonomous agent, but not operating directly in the interface. We show why it is important to have agents that are both interface agents and autonomous agents. We explore some design principles for such agents, and illustrate these principles with a description of Letizia, an autonomous interface agent that makes real-time suggestions for Web pages that a user might be interested in browsing.
Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

Significance The spindle assembly checkpoint (SAC) works as a surveillance mechanism to ensure accurate segregation of genetic materials during cell division. Protein kinase monopolar spindle 1 (Mps1) plays a key role in SAC, but the mechanism of Mps1 action in chromosome segregation remains elusive. In this study, we identified a previously undefined structural determinant of Mps1 named “IRK” (internal region for kinetochore localization) and demonstrated its functional importance in accurate kinetochore–microtubule attachment. Mechanistically, a dynamic hierarchical interaction between Mps1 and the nuclear division cycle 80 complex (Ndc80C) orchestrates accurate mitosis, because persistent association of inactive Mps1 with Ndc80C via the IRK perturbs correct kinetochore–microtubule attachment. Our results provide a new mechanistic insight into the spatiotemporal dynamics of Mps1 activity at the kinetochore in mitosis. The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.