Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice

The digestive tract of mammals and other animals is colonized by trillions of metabolically-active microorganisms. Changes in the gut microbiota have been associated with obesity in both humans and laboratory animals. Dietary modifications can often modulate the obese gut microbial ecosystem towards a more healthy state. This phenomenon should preferably be studied using dietary ingredients that are relevant to human nutrition. This study was designed to evaluate the influence of whole-wheat, a food ingredient with several beneficial properties, on gut microorganisms of obese diabetic mice. Diabetic (db/db) mice were fed standard (obese-control) or whole-wheat isocaloric diets (WW group) for eight weeks; non-obese mice were used as control (lean-control). High-throughput sequencing using the MiSeq platform coupled with freely-available computational tools and quantitative real-time PCR were used to analyze fecal bacterial 16S rRNA gene sequences. Short-chain fatty acids were measured in caecal contents using quantitative high-performance liquid chromatography photo-diode array analysis. Results showed no statistical difference in final body weights between the obese-control and the WW group. The bacterial richness (number of Operational Taxonomic Units) did not differ among the treatment groups. The abundance of Ruminococcaceae, a family containing several butyrate-producing bacteria, was found to be higher in obese (median: 6.9%) and WW-supplemented mice (5.6%) compared to lean (2.7%, p = 0.02, Kruskal-Wallis test). Caecal concentrations of butyrate were higher in obese (average: 2.91 mmol/mg of feces) but especially in WW-supplemented mice (4.27 mmol/mg) compared to lean controls (0.97 mmol/mg), while caecal succinic acid was lower in the WW group compared to obese but especially to the lean group. WW consumption was associated with ∼3 times higher abundances of Lactobacillus spp. compared to both obese and lean control mice. Analysis of weighted UniFrac distances revealed a distinctive clustering of lean microbial communities separately from both obese and WW-supplemented mice (p = 0.001, ANOSIM test). Predictive metagenome analysis revealed significant differences in several metabolic features of the microbiota among the treatment groups, including carbohydrate, amino acids and vitamin metabolism (p < 0.01, Kruskal-Wallis test). However, obese and WW groups tended to share more similar abundances of gene families compared to lean mice. Using an in vivo model of obesity and diabetes, this study suggests that daily WW supplementation for eight weeks may not be enough to influence body weight or to output a lean-like microbiome, both taxonomically and metabolically. However, WW-supplementation was associated with several statistically significant differences in the gut microbiome compared to obese controls that deserve further investigation.
Determinants of RNA Binding and Translational Repression by the Bicaudal-C Regulatory Protein*

Background: Bicaudal-C RNA binding proteins are important translational repressors in many different biological contexts. Results: A minimal site for RNA binding and translation repression by Bicaudal-C was identified. Conclusion: The RNA binding site for Bicaudal-C forms a stem-loop structure important for binding and translational repression. Significance: This will facilitate the identification of Bicaudal-C binding sites in other mRNAs. Bicaudal-C (Bic-C) RNA binding proteins function as important translational repressors in multiple biological contexts within metazoans. However, their RNA binding sites are unknown. We recently demonstrated that Bic-C functions in spatially regulated translational repression of the xCR1 mRNA during Xenopus development. This repression contributes to normal development by confining the xCR1 protein, a regulator of key signaling pathways, to specific cells of the embryo. In this report, we combined biochemical approaches with in vivo mRNA reporter assays to define the minimal Bic-C target site within the xCR1 mRNA. This 32-nucleotide Bic-C target site is predicted to fold into a stem-loop secondary structure. Mutational analyses provided evidence that this stem-loop structure is important for Bic-C binding. The Bic-C target site was sufficient for Bic-C mediated repression in vivo. Thus, we describe the first RNA binding site for a Bic-C protein. This identification provides an important step toward understanding the mechanisms by which evolutionarily conserved Bic-C proteins control cellular function in metazoans.
DNA adduct formation in relation to lymphocyte mutations and lung tumor induction in F344 rats treated with the environmental pollutant 1,6-dinitropyrene.

Epidemiological studies suggest an association between exposure to diesel emissions and an increased incidence of lung and bladder cancer in humans. Of the compounds associated with diesel emissions, 1,6-dinitropyrene is a particularly potent mutagen and carcinogen. In these experiments we administered [4,5,9,10-3H]1,6-dinitropyrene (30 or 100 micrograms) directly to the lungs of F344 rats according to a protocol known to induce lung tumors and characterized the DNA adducts present in the target tissue. In addition, we examined the adducts present in spleen lymphocytes and assayed for the induction of mutations at the hypoxanthine-guanine phosphoribosyltransferase locus in these cells, as measured by the frequency of 6-thioguanine-resistant (TGr) T-lymphocytes. Adduct formation was detected in both lung and spleen lymphocyte DNA, with the extent of binding being dose-dependent in the lymphocytes but not the lung. 32P-Postlabeling analyses indicated the formation of a major DNA adduct, N-(deoxyguanosin-8-yl)-1-amino-6- nitropyrene, in both tissues. 1,6-Dinitropyrene treatment resulted in a dose-dependent increase in TGr T-lymphocytes, with the increase being detected for at least 21 weeks after treatment. These data indicate that 1,6-dinitropyrene is metabolically activated by nitroreduction to form DNA adducts in both the target tissue and spleen lymphocytes and that a tumorigenic dose results in a significant induction of TGr T-lymphocytes. ImagesFIGURE 2.
A novel all-optical transport network with time-shared wavelength channels

High-speed and high-capacity transport networks are necessary for providing future broadband services and multimedia applications. Optical networks, such as wavelength-routed networks and optical switching networks, are the most popular solutions. However, the limited electronic switching capability constrains the scalability of the multihop wavelength routed networks, while the difficulty and complexity of implementing efficient optical buffers and optical contention resolution schemes constrains the development of optical switching networks. This paper proposes a new architecture for the optical transport networks based on time-wavelength-space routers (TWSRs). The TWSR is equipped without optical buffers and optical contention resolution devices. A connection is established by constructing a time-slot based lightpath (ts-lightpath) between source TWSR and destination TWSR. The paper also proposes a heuristic algorithm for the problem of establishing the set of efficient ts-lightpaths for a given set of connection requests. The effectiveness of the proposed network architecture with the heuristic algorithm is demonstrated by simulation.
Phosphorylation of Eukaryotic Translation Initiation Factor 2 Mediates Apoptosis in Response to Activation of the Double-stranded RNA-dependent Protein Kinase*

The interferon-inducible, double-stranded (ds) RNA-dependent serine/threonine protein kinase (PKR) plays a role in viral pathogenesis, cell growth, and differentiation and is implicated as a tumor suppressor gene. Expression of atrans-dominant negative, catalytically inactive mutant PKR protected NIH3T3 cells from apoptosis in response to either treatment with tumor necrosis factor α (TNFα), serum deprivation. In cells expressing mutant PKR, TNFα, but not dsRNA induced transcription from a nuclear factor κ B-dependent promoter, demonstrating specificity for dsRNA in signaling through the PKR pathway. Serum or platelet-derived growth factor addition to serum-deprived mutant PKR-expressing cells induced transcription of the early response genes c-fos and c-jun, indicating that the immediate early response signaling was intact. Overexpression of wild-type PKR in a transient DNA transfection system was sufficient to induce apoptosis. TNFα-induced apoptosis correlated with increased phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF-2α), the primary physiological substrate of the PKR. Furthermore, forced expression of a nonphosphorylatable S51A mutant eIF-2α partially protected cells from TNFα-induced apoptosis, and expression of a S51D mutant eIF-2α, a mutant that mimics phosphorylated eIF-2α, was sufficient to induce apoptosis. Taken together, these studies identify a novel requirement for PKR in stress-induced apoptosis that is mediated through eIF-2α phosphorylation.
Reaction Textures of Retrograde Pressure-Temperature-Deformation Paths from Granulites of Schirmacher Hills, East Antarctica

A retrograde path inferred for the Schirmacher Hills granulites involves near ITD path following post-peak granulite facies metamorphism (M1/D1), preserved only in enclaves, followed by near IBC path, M3, post dating M2/D2 granulites facies metamorphism and deformation. Final uplift and cooling of the terrain occurred in the upper amphibolite facies metamorphic conditions, M4, syntectonic with respect to D3 deformation and emplacement of large volume of syntectonic granitoids. Fluids released during cooling and crystallization of these granitoids probably caused the large scale retrogression of granulite facies rocks to amphibolite facies gneisses.
Temozolomide in metastatic breast cancer (MBC): a phase II trial of the National Cancer Institute of Canada - Clinical Trials Group (NCIC-CTG).

BACKGROUND Temozolomide is an oral alkylating agent that crosses the blood-brain barrier, and has preclinical activity in breast cancer. This phase II trial sought to determine the activity and toxicity of temozolomide in metastatic breast cancer (MBC). Temozolomide was administered in a dose dense schedule of 150 mg/m(2) on days 1-7 and 15-21 in a 28-day cycle. MATERIALS AND METHODS Patients had unidimensional disease for response assessment by RECIST criteria, up to two prior chemotherapy regimens for MBC, and may have had brain metastases if radiation was not expected to be required within 4 weeks. RESULTS Nineteen women were entered on the study. All were evaluable for toxicity and 18 were evaluable for response. The median age was 54 years; 14 had prior chemotherapy for MBC and 12 had prior hormones. Sites of disease included bone, brain, liver and lung. Treatment was well tolerated with 14/19 receiving >90% planned dose intensity. Common grade 1-3 drug-related effects included nausea, fatigue, vomiting, anorexia and skin rash. Grade 3-4 hematologic toxicities included granulocytopenia and thrombocytopenia. Of the 18 evaluable patients, there were no objective responses; three had stable disease and 15 progressive disease. CONCLUSIONS No responses to temozolomide were documented in these heavily pretreated women with extensive MBC including brain metastases.
A middle Eocene seep deposit with silicified fauna from the Humptulips Formation in western Washington State, USA.

Carbonate blocks with silicified fossils were recovered from a newly recognized cold seep deposit, the Satsop Weatherwax site, in the basal Humptulips Formation, along the West Fork of Satsop River in Washington State, USA. The petrography and the stable carbon isotope signature of the carbonate, with values as low as -43.5‰, indicate that these carbonate blocks formed at an ancient methane seep. The fossils recovered from this block include five vesicomyid specimens, two fragments of a thyasirid, five specimens of the peltospirid Depressigyra , two specimens of the hyalogyrinid Hyalogyrina , 25 specimens of the neritimorph Thalassonerita eocenica, and three limpet specimens of two different species. Five species can be described as new: Nuculana acutilineata (Nuculanoidea), Desbruyeresia belliatus (Provannidae), Provanna fortis (Provannidae), Orbitestella dioi (Orbitestellidae), and Leptochiton terryiverseni (Polyplacophora). Other fossils recovered from this site are numerous serpulid tubes, echinoid spines, one brachiopod fragment and two neogastropods. Almost all species recovered belong to extant genera and the fauna has a modern character, but are different from species found in younger seeps in Washington State. This is the first record of an orbitestellid from an ancient cold seep deposit, the first fossil provannids from the Humptulips Formation, and the first fossil record of Desbruyeresia from North America.
Local approximation schemes for ad hoc and sensor networks

We present two local approaches that yield polynomial-time approximation schemes (PTAS) for the Maximum Independent Set and Minimum Dominating Set problem in unit disk graphs. The algorithms run locally in each node and compute a <i>(1+ε)</i>-approximation to the problems at hand for any given <i>ε > 0</i>. The time complexity of both algorithms is <i>O(T<inf>MIS</inf> + log<sup>*</sup>! n/ε<sup>O(1)</sup>)</i>, where <i>T<inf>MIS</inf></i> is the time required to compute a maximal independent set in the graph, and n denotes the number of nodes. We then extend these results to a more general class of graphs in which the maximum number of pair-wise independent nodes in every <i>r</i>-neighborhood is at most polynomial in <i>r</i>. Such <i>graphs of polynomially bounded growth</i> are introduced as a more realistic model for wireless networks and they generalize existing models, such as unit disk graphs or coverage area graphs.
Modular Organization of Excitatory Circuits between Neurons of the Spinal Superficial Dorsal Horn (Laminae I and II)

Neural circuitry of the spinal superficial dorsal horn (SDH) (laminae I and II) and its relationship to pain and other somatosensory phenomena remain poorly understood. To gain information on this issue, synaptic connections between identified SDH neurons were studied in rat spinal cord slices by simultaneous whole-cell recordings from pairs of cells. Both excitatory and inhibitory connections were noted. This report focuses on the observed excitatory linkages. Synaptic excitatory connections between SDH neurons proved highly selective and consistently were unidirectional. Two patterns repeatedly appeared (for neuron classification, see Materials and Methods) (Grudt and Perl, 2002). Lamina II central neurons, with dorsal root (DR) C-fiber input, monosynaptically excited lamina II vertical neurons with DR Aδ input. Lamina II outer vertical neurons with DR Aδ input monosynaptically excited lamina I neurons. Some of the postsynaptic lamina I cells were shown to project rostrally. In contrast to the usual case for connected neurons, in unconnected pairs, primary afferent input to the same type of neuron proved closely similar. Together, these observations indicate that the neural circuitry in the SDH, including its substantia gelatinosa (lamina II), has an explicit organization in which particular combinations of neurons comprise modules arranged to modify and transmit sensory information arriving from Aδ and C primary afferent fibers.
Living with acquired brain injury: Self-concept as mediating variable in the adjustment process

Sequelae of acquired brain injury (ABI) require adjustment processes in which survivors must strive to regain subjective well-being (SWB) in the face of chronic impairment. The current study investigates whether the self-concept of achievement mediates this process. Thirty-five post-acute patients with ABI were assessed neuropsychologically for performance in memory, attention, concept formation and reasoning. Data concerning subjective complaints in applied cognition, self-concept, and SWB were collected. Patients rated their self-concept more negatively compared to a normative sample. Effects of subjective complaints in applied cognition on SWB were mediated by the self-concept of achievement. Contrary to expectations, objective cognitive deficits demonstrated no independent significant relationship to self-concept of achievement or SWB in multiple regression modelling when subjective complaints in applied cognition were considered simultaneously. The findings highlight the necessity of considering patients' subjective complaints and self-concepts to improve rehabilitative progress. Potential implications for neuropsychological rehabilitation are discussed.
Optimal Search on Some Game Trees

It is proved that the dlrecUonal algorithm for solving a game tree is optimal, in the sense of average run trine, for balanced trees (a family containing all uniform trees). This result implies that the alpha-beta pruning method is asymptotJcally opttmal among all game searching algorithms. Categones and Subject Descriptors. 1 2.8 [Artificial Intelligence] Problem Solving, Control Methods and Search--graph and tree search strategies General Terms' None Addmonal
Overexpression of human fibroblast growth factor 2 stimulates cell proliferation in an ex vivo model of articular chondrocyte transplantation

Genetically engineered chondrocytes could be used to enhance cartilage repair. Fibroblast growth factor 2 (FGF‐2) is a mitogen for chondrocytes and may be a candidate for gene transfer approaches to stimulate chondrocyte proliferation. In the present study, we tested the hypothesis that human FGF‐2 (hFGF‐2) gene transfer into articular chondrocytes modulates cell proliferation in an ex vivo model of chondrocyte transplantation.
Segmenting echocardiography images using B-Spline snake and active ellipse model

In this paper, a fully automated method for segmenting Left Ventricle (LV) in echocardiography images is proposed. A new method named active ellipse model is developed to automatically find the best ellipse inside the LV chamber without intervention of any specialist. A modified B-Spline Snake algorithm is used to segment the LV chamber in which the initial contour is formed by the predefined ellipse. As a result of using active ellipse model, the segmentation is extricated from dealing with gaps within myocardium boundary which are highly problematic in echocardiography image segmentation. Based on the results obtained from different studies, the proposed method is faster and more accurate than previous approaches. Our method is evaluated on 20 sets of echocardiography images of patients; and acquired results (92.30±4.45% dice's coefficient) indicate the proposed method has remarkable performance.
Work-related symptoms and dose-response relationships for personal exposures and pulmonary function among woodworkers.

BACKGROUND Four sawmills, a wood chipping mill, and five joineries in New South Wales, Australia, were studied for the effects of personal exposure to wood dust, endotoxins. (1-->3)-beta-D-glucans, Gram-negative bacteria, and fungi on lung function among woodworkers. METHODS Personal inhalable and respirable dust sampling was carried out. The lung function tests of workers were conducted before and after a workshift. RESULTS The mean percentage cross-shift decrease in lung function was markedly high for woodworkers compared with the controls. Dose-response relationships among personal exposures and percentage cross-shift decrease in lung function and percentage predicted lung function were more pronounced among joinery workers compared with sawmill and chip mill workers. Woodworkers had markedly high prevalence of regular cough, phlegm, and chronic bronchitis compared with controls. Significant associations were found between percentage cross-shift decrease in FVC and regular phlegm and blocked nose among sawmill and chip mill workers. Both joinery workers and sawmill and chip mill workers showed significant relationships between percentage predicted lung function (FVC, FEV1, FEV1/FVC, FEF25-75%) and respiratory symptoms. CONCLUSIONS Wood dust and biohazards associated with wood dust are potential health hazards and should be controlled.
The High-Yield Spread as a Predictor of Real Economic Activity: Evidence of a Financial Accelerator for the United States

Previous studies find that the interest rate term spread predicts real U.S. economic activity. We show that this relationship breaks down for the 1990s and suggest that its earlier success was due to high and volatile inflation. We find, however, that the high-yield spread (HYS) between “junk bond” and government bond yields predicts real activity during the 1990s – especially high levels of the HYS. We also find that the HYS works through both the demand and the supply side of the economy. We interpret our findings as supportive of a financial accelerator mechanism.
Learning Boolean read-once formulas with arbitrary symmetric and constant fan-in gates

A formula is read-once if each variable appears on at most a single input. Angluin, Hellerstein, and Karpinski have shown that boolean formulas with AND, OR, and NOT gates are exactly identifiable in polynomial time using membership and equivalence queries [AHK89]. Hancock and Hellerstein have generalized this to allow a wider subclass of symmetric basis functions [HH91]. We show a polynomial time algorithm in this model for identifying read-once formulas whose gates compute arbitrary functions of fan-in <italic>k</italic> or less for some constant <italic>k</italic> (i.e. any <italic>f :{0,1}<supscrpt>1≤c≤k</supscrpt> → {0,1})</italic>. We further show that if there is a polynomial time membership and equivalence query algorithm to identify read-once formulas over some set of functions <italic>B</italic> that meets certain technical conditions, then there is also such an algorithm to identify read-once formulas over <italic>B&ugr;{f:{0,1}<supscrpt>1≤c≤k</supscrpt> → {0,1}}</italic>. Finally, we extend the previous results to show that there is a polynomial time identification algorithm for read-once formulas over the basis of <italic>all</italic> symmetric functions (and hence also over the union of arbitrary symmetric and arbitrary constant fan-in gates). Given standard cryptographic assumptions, none of these results are possible for read-twice formulas.