Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of energy restriction and physical exercise intervention on phenotypic flexibility as examined by transcriptomics analyses of mRNA from adipose tissue and whole body magnetic resonance imaging

Overweight and obesity lead to changes in adipose tissue such as inflammation and reduced insulin sensitivity. The aim of this study was to assess how altered energy balance by reduced food intake or enhanced physical activity affect these processes. We studied sedentary subjects with overweight/obesity in two intervention studies, each lasting 12 weeks affecting energy balance either by energy restriction (~20% reduced intake of energy from food) in one group, or by enhanced energy expenditure due to physical exercise (combined endurance‐ and strength‐training) in the other group. We monitored mRNA expression by microarray and mRNA sequencing from adipose tissue biopsies. We also measured several plasma parameters as well as fat distribution with magnetic resonance imaging and spectroscopy. Comparison of microarray and mRNA sequencing showed strong correlations, which were also confirmed using RT‐PCR. In the energy restricted subjects (body weight reduced by 5% during a 12 weeks intervention), there were clear signs of enhanced lipolysis as monitored by mRNA in adipose tissue as well as plasma concentration of free‐fatty acids. This increase was strongly related to increased expression of markers for M1‐like macrophages in adipose tissue. In the exercising subjects (glucose infusion rate increased by 29% during a 12‐week intervention), there was a marked reduction in the expression of markers of M2‐like macrophages and T cells, suggesting that physical exercise was especially important for reducing inflammation in adipose tissue with insignificant reduction in total body weight. Our data indicate that energy restriction and physical exercise affect energy‐related pathways as well as inflammatory processes in different ways, probably related to macrophages in adipose tissue.
Sodium deprivation alters neural responses to gustatory stimuli

The effects of sodium deprivation for 10 d, a period sufficient to induce sodium appetite, on gustatory nerve discharges in rats were determined. Chorda tympani responses to concentration series of sodium chloride, sucrose, hydrochloric acid, and quinine hydrochloride were recorded and analyzed without the experimenter knowing the animal's deprivation condition. After deprivation, both whole nerve and single nerve fiber responses to sodium chloride were smaller; NaCl-best fibers, those more responsive to sodium chloride than to sucrose, hydrochloric acid, or quinine, were most affected. Thresholds had not changed; however, slopes of the stimulus-response functions for sodium chloride were lowered. Comparable changes in responses to the other stimuli did not occur. These results were discussed with respect to a possible relationship between changes in sodium chloride responsivity and changes in sodium intake, differences between methods of inducing sodium appetite, coding of taste quality and intensity, and mechanisms which might effect the responsivity change.
Pathological CNS Autoimmune Disease Triggered by Traumatic Spinal Cord Injury: Implications for Autoimmune Vaccine Therapy

Lymphocytes respond to myelin proteins after spinal cord injury (SCI) and may contribute to post-traumatic secondary degeneration. However, there is increasing evidence that autoreactive T-lymphocytes may also convey neuroprotection and promote functional recovery after CNS injury. To clarify the role of myelin autoreactive lymphocytes after SCI, we performed contusion injuries in the thoracic spinal cord of transgenic (Tg) mice in which >95% of all CD4+ T-lymphocytes are reactive with myelin basic protein (MBP). We observed significantly impaired recovery of locomotor and reflex function in Tg mice compared with non-Tg (nTg) littermates. Measures of functional impairment in Tg mice correlated with significantly less white matter at the injury site, and morphometric comparisons of injured Tg and nTg spinal cords revealed increased rostrocaudal lesion expansion (i.e., secondary degeneration) in Tg mice. Rostrocaudal to the impact site in SCI–nTg mice, demyelination was restricted to the dorsal funiculus, i.e., axons undergoing Wallerian degeneration. The remaining white matter appeared normal. In contrast, lymphocytes were colocalized with regions of demyelination and axon loss throughout the white matter of SCI–Tg mice. Impaired neurological function and exacerbated neuropathology in SCI–Tg mice were associated with increased intraspinal production of proinflammatory cytokine mRNA; neurotrophin mRNA was not elevated. These data suggest that endogenous MBP-reactive lymphocytes, activated by traumatic SCI, can contribute to tissue injury and impair functional recovery. Any neuroprotection afforded by myelin-reactive T-cells is likely to be an indirect effect mediated by other non-CNS-reactive lymphocytes. Similar to the Tg mice in this study, a subset of humans that are genetically predisposed to autoimmune diseases of the CNS may be adversely affected by vaccine therapies designed to boost autoreactive lymphocyte responses after CNS trauma. Consequently, the safe implementation of such therapies requires that future studies define the mechanisms that control T-cell function within the injured CNS.
On the Tabletop: Tangibles for Creative Problem Solving and Learning

The objective behind Tangible User Interfaces (TUIs) is to allow users to interact with computers through familiar tangible objects, thereby taking advantage of the richness of the tactile world combined with the power of computer-based simulations. TUIs “give physical form to digital information, employing physical artifacts both as representations and controls for computational media”. They lend themselves well to collaboration around intelligent tables, or what we call tabletop interaction.
Improving Semantic Composition with Offset Inference

Count-based distributional semantic models suffer from sparsity due to unobserved but plausible co-occurrences in any text collection. This problem is amplified for models like Anchored Packed Trees (APTs), that take the grammatical type of a co-occurrence into account. We therefore introduce a novel form of distributional inference that exploits the rich type structure in APTs and infers missing data by the same mechanism that is used for semantic composition.
Whole Exome Sequencing Reveals Genetic Predisposition in a Large Family with Retinitis Pigmentosa

Next-generation sequencing has become more widely used to reveal genetic defect in monogenic disorders. Retinitis pigmentosa (RP), the leading cause of hereditary blindness worldwide, has been attributed to more than 67 disease-causing genes. Due to the extreme genetic heterogeneity, using general molecular screening alone is inadequate for identifying genetic predispositions in susceptible individuals. In order to identify underlying mutation rapidly, we utilized next-generation sequencing in a four-generation Chinese family with RP. Two affected patients and an unaffected sibling were subjected to whole exome sequencing. Through bioinformatics analysis and direct sequencing confirmation, we identified p.R135W transition in the rhodopsin gene. The mutation was subsequently confirmed to cosegregate with the disease in the family. In this study, our results suggest that whole exome sequencing is a robust method in diagnosing familial hereditary disease.
Tissue distribution of adenosine receptor mRNAs in the rat

1 A degree of ambiguity and uncertainty exists concerning the distribution of mRNAs encoding the four cloned adenosine receptors. In order to consolidate and extend current understanding in this area, the expression of the adenosine receptors has been examined in the rat by use of in situ hybridisation and the reverse transcription‐polymerase chain reaction (RT‐PCR). 2 In accordance with earlier studies, in situ hybridisation revealed that the adenosine A1 receptor was widely expressed in the brain, whereas A2A receptor mRNA was restricted to the striatum, nucleus accumbens and olfactory tubercle. In addition, A1 receptor mRNA was detected in large striatal cholinergic interneurones, 26% of these neurones were also found to express the A2A receptor gene. Central levels of mRNAs encoding adenosine A2B and A3 receptors were, however, below the detection limits of in situ hybridisation. 3 The more sensitive technique of RT‐PCR was then employed to investigate the distribution of adenosine receptor mRNAs in the central nervous system (CNS) and a wide range of peripheral tissues. As a result, many novel sites of adenosine receptor gene expression were identified. A1 receptor expression has now been found in the heart, aorta, liver, kidney, eye and bladder. These observations are largely consistent with previous functional data. A2A receptor mRNA was detected in all brain regions tested, demonstrating that expression of this receptor is not restricted to the basal ganglia. In the periphery A2A receptor mRNA was also found to be more widely distributed than generally recognised. The ubiquitous distribution of the A2B receptor is shown for the first time, A2B mRNA was detected at various levels in all rat tissues studied. Expression of the gene encoding the adenosine A3 receptor was also found to be widespread in the rat, message detected throughout the CNS and in many peripheral tissues. This pattern of expression is similar to that observed in man and sheep, which had previously been perceived to possess distinct patterns of A3 receptor gene expression in comparison to the rat. 4 In summary, this work has comprehensively studied the expression of all the cloned adenosine receptors in the rat, and in so doing, resolves some of the uncertainty over where these receptors might act to control physiological processes mediated by adenosine.
Feature Extraction Based on Speech Attractors in the Reconstructed Phase Space for Automatic Speech Recognition Systems

In this paper, a feature extraction (FE) method is proposed that is comparable to the traditional FE methods used in automatic speech recognition systems. Unlike the conventional spectral‐based FE methods, the proposed method evaluates the similarities between an embedded speech signal and a set of predefined speech attractor models in the reconstructed phase space (RPS) domain. In the first step, a set of Gaussian mixture models is trained to represent the speech attractors in the RPS. Next, for a new input speech frame, a posterior‐probability‐based feature vector is evaluated, which represents the similarity between the embedded frame and the learned speech attractors. We conduct experiments for a speech recognition task utilizing a toolkit based on hidden Markov models, over FARSDAT, a well‐known Persian speech corpus. Through the proposed FE method, we gain 3.11% absolute phoneme error rate improvement in comparison to the baseline system, which exploits the mel‐frequency cepstral coefficient FE method.
Evolving full oblique decision trees

This paper presents a novel algorithm for induction of full oblique decision trees (EFTI). Proposed algorithm is based on special, single individual evolutionary algorithm, which evolves full decision tree by modifying its structure and node coefficients during the evolution process. EFTI algorithm is particularly well suited to be used in embedded applications, because it uses much less computational resources when compared with existing full DT inference algorithms. Performance of proposed EFTI algorithm, in terms of accuracy and tree sizes of evolved decision trees, has been studied and compared with nine previously proposed decision tree building algorithms, using selected datasets from the standard UCI Machine Learning Repository database. Results of conducted experiments suggest that proposed EFTI algorithm generally generates significantly smaller decision trees than the ones produced by previously proposed algorithms, while retaining the classification accuracy.
Automatic analysis of flourescence labeled neurites in microscope images

Microscope imaging technologies have turned out to yield an indispensable tool in modern biomedical research. Combined with fluorescence labeling techniques they not only provide new perspectives on tissues and cells as a whole, but also on processes at the cellular level, and will be one important experimental technique of systems biology. To handle this steadily increasing amount of image data, in this paper we propose a new and fully automatic approach for neurite segmentation and protein quantification. Our technique combines three phases of automatic neuron cell localization, neurite segmentation and protein analysis. In the second stage active contour models based on hierarchical gradient vector flow fields are employed, enabling precise neurite segmentation despite inhomogeneous texture. Neurite segmentation results as well as protein quantification profiles from a set of test images demonstrate the appropriateness of our approach for practical biomedical research.
Towards formal knowledge intelligibility at the semiotic level

Exchange of formalised knowledge through computers is developing fast. It is assumed that using knowledge will increase the efficiency of the systems by providing a better understanding of exchanged information. However, intelligibility is by no way ensured by the use of a semantically defined language. This statement of interest explains why and calls for the involvement of the semioticians for tackling this problem.
What's in the container? Classifying object contents from vision and touch

Robots operating in household environments need to interact with food containers of different types. Whether a container is filled with milk, juice, yogurt or coffee may affect the way robots grasp and manipulate the container. In this paper, we concentrate on the problem of identifying what kind of content is in a container based on tactile and/or visual feedback in combination with grasping. In particular, we investigate the benefits of using unimodal (visual or tactile) or bimodal (visual-tactile) sensory data for this purpose. We direct our study toward cardboard containers with liquid or solid content or being empty. The motivation for using grasping rather than shaking is that we want to investigate the content prior to applying manipulation actions to a container. Our results show that we achieve comparable classification rates with unimodal data and that the visual and tactile data are complimentary.
Merging Databases Under Constraints

The problem of integrating information from conflicting sources comes up in many current applications, such as cooperative information systems, heterogeneous databases, and multiagent systems. We model this by the operation of merging first-order theories. We propose a formal semantics for this operation and show that it has desirable properties, including abiding by majority rule in case of conflict and syntax independence. We apply our semantics to the special case when the theories to be merged represent relational databases under integrity constraints. We then present a way of merging databases that have different or conflicting schemas caused by problems such as synonyms, homonyms or type conflicts mentioned in the schema integration literature.
Warfarin and aspirin in patients with heart failure and sinus rhythm.

BACKGROUND It is unknown whether warfarin or aspirin therapy is superior for patients with heart failure who are in sinus rhythm. METHODS We designed this trial to determine whether warfarin (with a target international normalized ratio of 2.0 to 3.5) or aspirin (at a dose of 325 mg per day) is a better treatment for patients in sinus rhythm who have a reduced left ventricular ejection fraction (LVEF). We followed 2305 patients for up to 6 years (mean [±SD], 3.5±1.8). The primary outcome was the time to the first event in a composite end point of ischemic stroke, intracerebral hemorrhage, or death from any cause. RESULTS The rates of the primary outcome were 7.47 events per 100 patient-years in the warfarin group and 7.93 in the aspirin group (hazard ratio with warfarin, 0.93; 95% confidence interval [CI], 0.79 to 1.10; P=0.40). Thus, there was no significant overall difference between the two treatments. In a time-varying analysis, the hazard ratio changed over time, slightly favoring warfarin over aspirin by the fourth year of follow-up, but this finding was only marginally significant (P=0.046). Warfarin, as compared with aspirin, was associated with a significant reduction in the rate of ischemic stroke throughout the follow-up period (0.72 events per 100 patient-years vs. 1.36 per 100 patient-years; hazard ratio, 0.52; 95% CI, 0.33 to 0.82; P=0.005). The rate of major hemorrhage was 1.78 events per 100 patient-years in the warfarin group as compared with 0.87 in the aspirin group (P<0.001). The rates of intracerebral and intracranial hemorrhage did not differ significantly between the two treatment groups (0.27 events per 100 patient-years with warfarin and 0.22 with aspirin, P=0.82). CONCLUSIONS Among patients with reduced LVEF who were in sinus rhythm, there was no significant overall difference in the primary outcome between treatment with warfarin and treatment with aspirin. A reduced risk of ischemic stroke with warfarin was offset by an increased risk of major hemorrhage. The choice between warfarin and aspirin should be individualized. (Funded by the National Institute of Neurological Disorders and Stroke; WARCEF ClinicalTrials.gov number, NCT00041938.).
The range of PaO2 variation determines the severity of oxygen-induced retinopathy in newborn rats.

PURPOSE This study was conducted to determine the potential influence of PaO2 fluctuation on the retinal neovascular response known to occur in newborn rats exposed to hyperoxic conditions. As an inherent corollary, the authors also defined the relationship between the fraction of inspired oxygen (FiO2) and the arterial blood oxygen tension (PaO2) in newborn rats. METHODS Experiment 1 was composed of several oxygen-exposure protocols in which atmospheres of 10% oxygen concentration were alternated with different higher levels of ambient oxygen (50%, 40%, 30%, and room air). In experiment 2, two alternating oxygen concentrations were made to converge toward room air (20.9% oxygen) with each successive group of four treatment groups. These included another group exposed to alternating 50% and 10% oxygen, a group exposed to alternating 45% and 12.5% oxygen concentrations, one exposed to alternating concentrations of 40% and 15% oxygen, and a final group exposed to 35% and room air oxygen concentrations. In each case, oxygen was alternated between the two exposure concentrations every 24 hours. The term delta FiO2 is used to designate the difference in the two oxygen concentrations to which a treatment group was subjected, applying the units of fraction of inspired oxygen (i.e., delta FiO2 = 0.4 for the exposure to alternating 50% and 10% oxygen). At birth, litters of albino rats were placed in each of these environments for 13 or 14 days, after which PaO2 and retinal vascular development were assessed in some rats. The remainder were removed to room air for 4 days before the incidence and severity of abnormal neovascularization were measured. RESULTS PaO2 and FiO2 were directly and linearly correlated (r2 = 0.998). In experiment 1, the extent of retinal vascular development on removal from oxygen was a linear function of delta FiO2. Retinal neovascularization subsequently occurred in all rats exposed to alternating 50% and 10% or 40% and 10% oxygen concentrations, but only a third of the 30% and 10% exposure group, indicating a minimum threshold for proliferative disease at delta FiO2 = 0.2. In experiment 2, retinal avascularity also increased linearly with increasing delta FiO2. There was a threshold for neovascularization between the exposure to alternating 45% and 12.5% oxygen and the 40% and 15% oxygen exposure (100% versus 4.8% incidence of neovascularization), indicating a requirement of < or = 12.5% oxygen episodes to stimulate a consistent proliferative response. CONCLUSIONS These results suggest that PaO2 fluctuation and degree of hypoxia may have more influence on proliferative retinal disease in newborn rats than the extended hyperoxia that has historically received greater attention. Experimental designs that address the inherent differences in pulmonary function between intrinsically healthy animals and compromised premature infants are of substantial value to our understanding of the pathogenesis of retinopathy of prematurity.
Reversal of reflex-induced myocardial ischemia by median nerve stimulation: a feline model of electroacupuncture.

BACKGROUND Acupuncture is reported to reduce myocardial ischemia, arrhythmias, and hypertension. To investigate the physiological mechanisms underlying these observations, a model of reflex-induced, reversible myocardial ischemia was developed to test the effects of median nerve stimulation as a surrogate for electroacupuncture. METHODS AND RESULTS Chloralose-anesthetized cats were instrumented to measure arterial blood pressure, left ventricular pressure, left ventricular dP/dt, heart rate, left anterior descending (LAD) coronary blood velocity, and regional wall motion. The LAD artery either was partially occluded or a small diagonal branch was ligated. Subsequently, transient reflex activation of the cardiovascular system was evoked by application of bradykinin (typically 1 microg/mL) to the gallbladder, which significantly increased myocardial oxygen demand (double product), left ventricular dP/dt, and coronary blood velocity and caused ischemia-induced regional dysfunction, evidenced by significant (P<.05) reduction in normalized wall thickening (10.7+/-4.2% versus -23.6+/-2.9%; control versus ischemia; n=7). However, when median nerves were stimulated with low frequency (5 Hz) to mimic electroacupuncture, bradykinin-induced change in normalized wall thickening was significantly improved (-23.6+/-2.9% versus 9.8+/-4.9%; ischemia versus median nerve stimulation, P<.05) and remained augmented > or = 1 hour. Results were similar in partial and complete occlusion groups. Significant improvement in wall thickening was associated with unchanged increment of coronary blood velocity and significantly diminished increments of double product and diastolic blood pressure. CONCLUSIONS These results suggest that stimulation of the median nerve to mimic electroacupuncture diminishes regional myocardial ischemia triggered by a sympathetically mediated increase in cardiac oxygen demand. The mechanism of this effect is related to reduction in cardiac oxygen demand, secondary to a diminished pressor response. These data provide the first documentation of the physiological mechanisms underlying the possible beneficial effect of electroacupuncture in the context of restricted coronary blood flow and augmented myocardial oxygen demand.