Miracle-dz/UniFAR-FTUs huggingface dataset:
Docosahexaenoic Acid Supplementation Does Not Improve Western Diet-Induced Cardiomyopathy in Rats

Obesity increases risk for cardiomyopathy in the absence of hypertension, diabetes or ischemia. The fatty acid milieu, modulated by diet, may modify myocardial structure and function, lending partial explanation for the array of cardiomyopathic phenotypy. We sought to identify gross, cellular and ultrastructural myocardial changes associated with Western diet intake, and subsequent modification with docosahexaenoic acid (DHA) supplementation. Wistar and Sprague-Dawley (SD) rats received 1 of 3 diets: control (CON); Western (WES); Western + DHA (WES+DHA). After 12 weeks of treatment, echocardiography was performed and myocardial adiponectin, fatty acids, collagen, area occupied by lipid and myocytes, and ultrastructure were determined. Strain effects included higher serum adiponectin in Wistar rats, and differences in myocardial fatty acid composition. Diet effects were evident in that both WES and WES+DHA feeding were associated with similarly increased left ventricular (LV) diastolic cranial wall thickness (LVWcr/d) and decreased diastolic internal diameter (LVIDd), compared to CON. Unexpectedly, WES+DHA feeding was associated additionally with increased thickness of the LV cranial wall during systole (LVWcr/s) and the caudal wall during diastole (LVWca/d) compared to CON; this was observed concomitantly with increased serum and myocardial adiponectin. Diastolic dysfunction was present in WES+DHA rats compared to both WES and CON. Myocyte cross sectional area (CSA) was greater in WES compared to CON rats. In both fat-fed groups, transmission electron microscopy (TEM) revealed myofibril degeneration, disorganized mitochondrial cristae, lipid inclusions and vacuolation. In the absence of hypertension and whole body insulin resistance, WES+DHA intake was associated with more global LV thickening and with diastolic dysfunction, compared to WES feeding alone. Myocyte hypertrophy, possibly related to subcellular injury, is an early change that may contribute to gross hypertrophy. Strain differences in adipokines and myocardial fatty acid accretion may underlie heterogeneous data from rodent studies.
A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe

Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species.
A Disease Management Program Utilizing "Life Coaches" for Children with Asthma

An estimated 17 million Americans suffer from asthma, a costly disease accounting for 1.8 million emergency department visits and 10 million physician office visits annually [1]. Asthma is the most common chronic childhood disease, affecting more than 1 child in 20 and accounting for an annual loss of approximately 10 million school days per year [1]. Asthma-related hospitalization rates increased significantly during the past 2 decades even as overall hospitalization rates declined, particularly in children [2]. Further, asthma-related deaths increased 78% between 1980 and 1993 [1]. In 1998, the economic burden of asthma in the United States was estimated at $11.3 billion [1]. A number of disease management programs have been directed toward patients with asthma to improve their health status and reduce costs. Asthma disease management is a comprehensive, coordinated system of care that emphasizes prevention of exacerbations and complications and patient self-management education [3]. This article describes and presents preliminary data regarding the efficacy of Sentara Health Management’s asthma disease management program.
Changes in [Ca2+]i, [Na+]i and Ca2+ current in isolated rat ventricular myocytes following an increase in cell length.

Isolated rat ventricular myocytes were stretched using carbon fibres to investigate the mechanisms underlying the increase in contraction following stretch. 2. [Ca2+]i and [Na+]i were monitored using the fluorescent indicators fura‐2 and sodium‐binding benzofuran isophthalate, respectively. The L‐type Ca2+ current was recorded simultaneously with contraction using the perforated patch‐clamp technique. 3. Mechanical stretch caused an immediate increase in contraction, followed by a slow increase. Contraction was prolonged immediately after the stretch, but did not change during the slow phase. 4. The Ca2+ transient did not change immediately after the stretch. The slow increase in contraction was accompanied by an increase in the amplitude of the Ca2+ transient. However, diastolic [Ca2+]i did not change significantly following stretch. 5. [Na+]i did not change significantly either immediately, or during the slow increase in contraction, after the stretch. 6. The L‐type Ca2+ current was not significantly altered either by mechanical loading of the cell with carbon fibres or by stretching the cell. 7. These results suggest that: (1) the rapid increase in contraction following a stretch is due to an increase in myofilament Ca2+ sensitivity rather than to changes in the L‐type Ca2+ current or [Na+]i; and (2) a slow increase in the Ca2+ transient underlies the slow increase in contraction in isolated myocytes, but is not caused by either an increase in diastolic [Ca2+]i or a change in [Na+]i (and hence Ca2+ influx via Na(+)‐Ca2+ exchange) or a change in myofilament Ca2+ sensitivity.
Sound-producing sand avalanches P

Sound-producing sand grains constitute one of nature’ s more puzzling and least understood physical phenomena. They occur naturally in two distinct types: booming and squeaking sands. Although both varieties of sand produce unexpectedly pure acoustic emissions when sheared, they diŒer in their frequency range and duration of emission, as well as the environment in which they tend to be found. Large-scale slumping events on dry booming dunes can produce acoustic emissions that can be heard up to 10 km away and which resemble hums, moans, drums, thunder, foghorns or the drone of low̄ ying propeller aircraft. These analogies emphasize the uniqueness of the phenomenon and the clarity of the produced sound. Although reports of these sands have existed in the literature for over one thousand years, a satisfactory explanation for either type of acoustic emission is still unavailable.
A new-type THz null-ellipsometer based on quasi-optical transmission line and components

Ellipsometry is a set of noncontact and nondestructive experimental techniques for studying physical properties and structural parameters of various materials and systems [1-3]. Ellipsometry is based on the phenomena of radiation polarization state change at reflecting from a surface. At present, extension of the probing radiation frequency-range is one of the major development lines of ellipsometric experimental technique. Each spectral interval requires specific elements and design though general configuration remains the same.
The Effect of Familiarity on Face Adaptation

Face aftereffects can provide information on how faces are stored by the human visual system (eg Leopold et al, 2001 Nature Neuroscience 4 89 – 94), but few studies have used robustly represented (highly familiar) faces. In this study we investigated the influence of facial familiarity on adaptation effects. Participants were adapted to a series of distorted faces (their own face, a famous face, or an unfamiliar face). In experiment 1, figural aftereffects were significantly smaller when participants were adapted to their own face than when they were adapted to the other faces (ie their own face appeared significantly less distorted than a famous or unfamiliar face). Experiment 2 showed that this ‘own-face’ effect did not occur when the same faces were used as adaptation stimuli for participants who were unfamiliar with them. Experiment 3 replicated experiment 1, but included a pre-adaptation baseline. The results highlight the importance of considering facial familiarity when conducting research on face aftereffects.
Individual-based simulation of the clustering behaviour of epidermal growth factor receptors.

This paper describes ongoing work on a project to simulate the behaviour of epidermal growth factor receptors. These are structures which can be found on the surface of cells in the body, which receive and process chemical signals concerned with cell growth. We describe the implementation of a program which simulates the stimulation and clustering behaviour of these structures, discuss how we scale up this simulation so that we can simulate a whole cell on a tractable timescale, and discuss ongoing work in which we are calibrating our simulation against results from experiments.
Exploration and Exploitation in Visuomotor Prediction of Autonomous Agents

This paper discusses various techniques to let an agent learn how to predict the effects of its own actions on its sensor data autonomously, and their usefulness to apply them to visual sensors. An Extreme Learning Machine is used for visuomotor prediction, while various autonomous control techniques that can aid the prediction process by balancing exploration and exploitation are discussed and tested in a simple system: a camera moving over a 2D greyscale image.
High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes

The global transcriptional regulator H-NS selectively silences bacterial genes associated with pathogenicity and responses to environmental insults. Although there is ample evidence that H-NS binds preferentially to DNA containing curved regions, we show here that a major basis for this selectivity is the presence of a conserved sequence motif in H-NS target transcriptons. We further show that there is a strong tendency for the H-NS binding sites to be clustered, both within operons and in genes contained in the pathogenicity-associated islands. In accordance with previously published findings, we show that these motifs occur in AT-rich regions of DNA. On the basis of these observations, we propose that H-NS silences extensive regions of the bacterial chromosome by binding first to nucleating high-affinity sites and then spreading along AT-rich DNA. This spreading would be reinforced by the frequent occurrence of the motif in such regions. Our findings suggest that such an organization enables the silencing of extensive regions of the genetic material, thereby providing a coherent framework that unifies studies on the H-NS protein and a concrete molecular basis for the genetic control of H-NS transcriptional silencing.
Kidney Bean: A Major Sensitizer among Legumes in Asthma and Rhinitis Patients from India

Background The prevalence of IgE mediated food allergies has increased over the last two decades. Food allergy has been reported to be fatal in highly sensitive individuals. Legumes are important food allergens but their prevalence may vary among different populations. The present study identifies sensitization to common legumes among Indian population, characterizes allergens of kidney bean and establishes its cross reactivity with other legumes. Methodology Patients (n = 355) with history of legume allergy were skin prick tested (SPT) with 10 legumes. Specific IgE (sIgE) and total IgE were estimated in sera by enzyme-linked immunosorbent assay. Characterization of kidney bean allergens and their cross reactivity was investigated by immunobiochemical methods. Identification of major allergens of kidney bean was carried out by mass spectrometry. Principal Findings Kidney bean exhibited sensitization in 78 (22.0%) patients followed by chickpea 65 (18.0%) and peanut 53 (15%). SPT positive patients depicted significantly elevated sIgE levels against different legumes (r = 0.85, p<0.0001). Sera from 30 kidney bean sensitive individuals exhibited basophil histamine release (16–54%) which significantly correlated with their SPT (r = 0.83, p<0.0001) and sIgE (r = 0.99, p<0.0001). Kidney bean showed eight major allergens of 58, 50, 45, 42, 40, 37, 34 and 18 kDa on immunoblot and required 67.3±2.51 ng of homologous protein for 50% IgE inhibition. Inhibition assays revealed extensive cross reactivity among kidney bean, peanut, black gram and pigeon pea. nLC-MS/MS analysis identified four allergens of kidney bean showing significant matches with known proteins namely lectin (phytohemagglutinin), phaseolin, alpha-amylase inhibitor precursor and group 3 late embryogenesis abundant protein. Conclusion/Significance Among legumes, kidney bean followed by chick pea and peanut are the major allergic triggers in asthma and rhinitis patients in India. Kidney bean showed eight major allergens and cross reacted with other legumes. A combination of SPT, sIgE and histamine release assay is helpful in allergy diagnosis.
Autism-Associated Insertion Mutation (InsG) of Shank3 Exon 21 Causes Impaired Synaptic Transmission and Behavioral Deficits

SHANK3 (also known as PROSAP2) is a postsynaptic scaffolding protein at excitatory synapses in which mutations and deletions have been implicated in patients with idiopathic autism, Phelan–McDermid (aka 22q13 microdeletion) syndrome, and other neuropsychiatric disorders. In this study, we have created a novel mouse model of human autism caused by the insertion of a single guanine nucleotide into exon 21 (Shank3G). The resulting frameshift causes a premature STOP codon and loss of major higher molecular weight Shank3 isoforms at the synapse. Shank3G/G mice exhibit deficits in hippocampus-dependent spatial learning, impaired motor coordination, altered response to novelty, and sensory processing deficits. At the cellular level, Shank3G/G mice also exhibit impaired hippocampal excitatory transmission and plasticity as well as changes in baseline NMDA receptor-mediated synaptic responses. This work identifies clear alterations in synaptic function and behavior in a novel, genetically accurate mouse model of autism mimicking an autism-associated insertion mutation. Furthermore, these findings lay the foundation for future studies aimed to validate and study region-selective and temporally selective genetic reversal studies in the Shank3G/G mouse that was engineered with such future experiments in mind.
Playful Geospatial Data Acquisition by Location-based Gaming Communities

The success of Web 2.0 communities demonstrates that the users of an information service are willing to participate in the content creation process on a voluntary basis. In this paper we adapt this idea to the task of collecting geographic data by player communities of location-based games. We identify three types of geographic data that players can collect as part of the game experience: (1) data about the localization/communication network, (2) data about the geographic environment, and (3) related non-geographic information. Furthermore, we present game design patterns that permit to gather all three types of data. The approach is illustrated with the Geogame “CityExplorer”. First empirical results are reported from the evaluation of geographic data acquired over a one-year period with two Geogames, “GeoTicTacToe” and “CityPoker”.
High-resolution studies of chromatin arrays and their salt-dependent compaction

Compaction of long DNA molecules into the small cell nucleus is accomplished through an elaborate structure called chromatin. This DNA-protein complex is a hallmark of the nucleus of the eukaryotic cell and unravelling its structural details is mandatory for a better understanding of all DNA-involving processes, especially for full comprehension of transcription, recombination and replication. The structure of the basic chromatin unit, the nucleosome, is well known since the end of the last century. In contrast, despite strong experimental e orts, many questions concerning the DNA packing at higher levels are still open. In particular, whether a highly ordered structure, often-times referred to as the 30 nm bre , exists in vivo is the cause for an ongoing controversy in the scienti c community. In last decades, development of the molecular biology tools allowed to produce chromatin and nucleosomal arrays from recombinant proteins, introducing a model structure for chromatin experiments in vitro. In this PhD thesis I establish protocols for preparing human recombinant nucleosome arrays. Furthermore, I employ various single-molecule and high-resolution microscopy methods to investigate the structure of chromatin arrays under di erent sodium chloride concentrations. The results provided by Atomic Force Microscopy (AFM), a cutting-edge tool for high-resolution imaging of DNA-protein complexes, turned out to be especially valuable. Here, I present results from high-resolution AFM of non-cross-linked chromatin arrays in liquid, under di erent salt concentrations. A detailed statistical analysis of the imaging data reveals that the array compaction is salt-dependent, however in a non-monotonic fashion. Nevertheless, the presented data do not provide any support for the existence of regular chromatin bres for the investigated arrays. Instead, they show chromatin arrays as highly dynamic structures, strongly in uenced by NaCl concentration. These studies shed a new light upon chromatin and thus contribute to a deeper understanding of the mechanisms of DNA condensation.
JHU/APL Onto-Mapology Results for OAEI 2006

Numerous techniques for ontology alignment and mapping have appeared in the literature, but there has been little discussion on the use of formal semantics for the task. Typical solutions apply multiple techniques to produce their results. We demonstrate that a hybrid solution that brings together a number of matching techniques yields the best results. An essential component of any ontology mapping solution is the ability for users to interact with the system and manipulate intermediate and final results. We introduce Onto-Mapology; an approach to ontology mapping that integrates techniques based on string/text matching, structure/graph matching, and semantic (rulebased/ logic-based) matching. After the initial design, development, testing and evaluation we applied Onto-Mapology to the OAEI 2006 test cases with encouraging results.
Fluctuations in Uncertainty

This review article tries to answer four questions: (i) what are the stylized facts about uncertainty over time; (ii) why does uncertainty vary; (iii) do fluctuations in uncertainty matter; and (iv) did higher uncertainty worsen the Great Recession of 2007-2009? On the first question both macro and micro uncertainty appears to rise sharply in recessions. On the second question the types of exogenous shocks like wars, financial panics and oil price jumps that cause recessions appear to directly increase uncertainty, and uncertainty also appears to endogenously rise further during recessions. On the third question, the evidence suggests uncertainty is damaging for short-run investment and hiring, but there is some evidence it may stimulate longer-run innovation. Finally, in terms of the Great Recession, the large jump in uncertainty in 2008 potentially accounted for about one third of the drop in GDP.
Effect of Bradykinin Receptor Antagonists on Vincristine- and Streptozotocin-Induced Hyperalgesia in a Rat Model of Chemotherapy-Induced and Diabetic Neuropathy

The role of bradykinin receptor blockade in the development of neuropathies caused by diabetes mellitus and vincristine was examined. The effects of a potent and selective B1 receptor antagonist (des-Arg10-HOE 140) as well as a specific antagonist of B2 receptors (HOE 140) were investigated. Both agents significantly decreased hyperalgesia caused otherwise by vincristine. In a diabetic neuropathy model, both agents almost completely suppressed hyperalgesia in the first 10 days of the study. However, from day 11 after administration of streptozotocin, the action of des-Arg10-HOE 140 was significantly weaker than that of HOE 140. The results of the study suggest involvement of both B1 and B2 receptors in transmission of nociceptive stimuli in the vincristine-induced as well as diabetic neuropathy model.
The exploration/exploitation trade-off in Reinforcement Learning for dialogue management

Conversational systems use deterministic rules that trigger actions such as requests for confirmation or clarification. More recently, Reinforcement Learning and (Partially Observable) Markov Decision Processes have been proposed for this task. In this paper, we investigate action selection strategies for dialogue management, in particular the exploration/exploitation trade-off and its impact on final reward (i.e. the session reward after optimization has ended) and lifetime reward (i.e. the overall reward accumulated over the learner's lifetime). We propose to use interleaved exploitation sessions as a learning methodology to assess the reward obtained from the current policy. The experiments show a statistically significant difference in final reward of exploitation-only sessions between a system that optimizes lifetime reward and one that maximizes the reward of the final policy.
Threshold Certificate-based Encryption

Certificate-based encryption (CBE) is a new asymmetric encryption paradigm which combines traditional public-key encryption (PKE) and identity based encryption (IBE) while preserving some of their most attractive features. CBE provides an efficient implicit certificate mechanism to eliminate third-party queries for the certificate status and to simply the certificate revocation problem. Therefore, CBE can be used to construct an efficient PKI requiring fewer infrastructures. In addition, it also solves the key escrow problem and key distribution problem inherent in IBE. In this paper, we introduce a new notion called Threshold Certificate-Based Encryption (TCBE) to overcome the limitations of CBE due to the using of sole master key in the system. It preserves the advantages of CBE such as implicit certificate and no private key escrow. At the same time it inherits the properties of threshold encryption. We first formalize the definition and security model for TCBE. Then we propose a concrete TCBE scheme and prove it to be CCA-secure under the Decisional Bilinear Diffie-Hellman assumption in the standard model.