Miracle-dz/UniFAR-FTUs huggingface dataset:
Specialized Functional Diversity and Interactions of the Na,K-ATPase

Na,K-ATPase is a protein ubiquitously expressed in the plasma membrane of all animal cells and vitally essential for their functions. A specialized functional diversity of the Na,K-ATPase isozymes is provided by molecular heterogeneity, distinct subcellular localizations, and functional interactions with molecular environment. Studies over the last decades clearly demonstrated complex and isoform-specific reciprocal functional interactions between the Na,K-ATPase and neighboring proteins and lipids. These interactions are enabled by a spatially restricted ion homeostasis, direct protein-protein/lipid interactions, and protein kinase signaling pathways. In addition to its “classical” function in ion translocation, the Na,K-ATPase is now considered as one of the most important signaling molecules in neuronal, epithelial, skeletal, cardiac and vascular tissues. Accordingly, the Na,K-ATPase forms specialized sub-cellular multimolecular microdomains which act as receptors to circulating endogenous cardiotonic steroids (CTS) triggering a number of signaling pathways. Changes in these endogenous cardiotonic steroid levels and initiated signaling responses have significant adaptive values for tissues and whole organisms under numerous physiological and pathophysiological conditions. This review discusses recent progress in the studies of functional interactions between the Na,K-ATPase and molecular microenvironment, the Na,K-ATPase-dependent signaling pathways and their significance for diversity of cell function.
Design , Implementation and Evaluation of a Nursing Simulation : A Design and Development Research Study

The purpose of this study was to investigate the use of the Jeffries/National League for Nursing Framework for Designing, Implementing and Evaluating Simulations. The model was used to develop a simulation-based course to teach interprofessional communication to new graduate nurses in an acute care setting. Design and development research was employed to examine the phases of design, implementation, and evaluation. Findings revealed that the model generally functioned well in this context. Particular strengths were its emphasis on problem solving and recommendations for attending to fidelity. Identified weaknesses were inadequate guidance for designing and implementing student support and debriefing. Recommendations for strengthening the model include providing scaffolds to students during problem solving and a focus on the interrelationships of the design components in the model. Overall, designers would benefit from using the framework, supplementing it in areas where the model does not currently provide adequate guidance.
A WFST Framework for Single-Pass Multi-Stream Decoding

Combining disparate automatic speech recognition systems has long been an important strategy to improve recognition accuracy. Typically, each system requires a separate decoder; final results are derived by combining hypotheses from multiple lattices, necessitating multiple passes of decoding. We propose a novel Weighted Finite State Transducer (WFST) framework for integrating disparate systems. Our framework is different from the current popular system combination techniques in that the combination is done in one-pass decoding and allows the flexibility to combine systems at different levels of the decoding pipeline. Initial experiments with the framework achieved comparable performance as MBR-based combination which is reported to outperform ROVER and Confusion Network Combination (CNC). In this paper, we describe our methodology and present pilot study results for combining systems that use different sets of acoustic models, 1) gender-dependent GMM models, 2) MFCC and PLP features with GMM models, 3) MFCC, PLP and Filter Bank features with DNN models, and 4) SNR-specific DNN acoustic models. For each experiment, we also compared the computation time of the combined systems with their corresponding baseline systems. Our results show encouraging benefits of using the proposed framework to improve recognition performance while reducing computation time.
Satiation in Discounted Utility

In this paper, we propose a model of intertemporal choice that explicitly incorporates satiation due to previous consumption in the evaluation of the utility of current consumption. In the discounted utility (DU) model, the utility of consumption is evaluated afresh in each time period. In our model, the utility of current consumption represents an incremental utility from the past level. When the time interval between consumption periods is large, and there are, therefore, no carryover effects, our model coincides with the DU model. For short time intervals between consumption periods, the satiation due to previous consumption lowers the utility of current consumption. Several implications of our model are examined, and comparisons with the DU model and the habituation model are made.
Role of Intestinal Bacteria in Ileal Ulcer Formation in Rats Treated with a Nonsteroidal Antiinflammatory Drug

The role of intestinal bacteria in induction and repression of ulcer formation in the ileum of rats treated with one of the nonsteroidal antiinflammatory drugs (NSAIDs), 5‐bromo‐2‐(4‐fluorophenyl)‐3‐(4‐methylsulfonylphenyl) thiophene (BFMeT), was examined in this study. BFMeT was administered by intragastric gavage once at doses of 500‐1,500 mg/kg of body weight to Wistar rats treated with and without antibiotics (bacitracin, neomycin, streptomycin), germ‐free rats and gnotobiotic rats, and 72 hr later their gastrointestinal tracts were examined for ulcer formation. A single oral administration of BFMeT induced ileal ulcers in specific pathogen‐free rats. However, the rats given antibiotics to reduce the intestinal bacteria had no ulcers. BFMeT‐treated germ‐free rats and gnotobiotic rats mono‐associated with Bifidobacterium adolescentis or Lactobacillus acidophilus also had no intestinal ulcers. However, the drug induced ileal ulcers in gnotobiotic rats mono‐associated with Eubacterium limosum or Escherichia coli. An overnight culture of B. adolescentis or L. acidophilus or yogurt containing Bifidobacterium breve and Streptococcus thermophilus, when given as drinking water, inhibited ulcer formation in the ileum of rats treated with BFMeT. Gram staining of the ileal contents of normal rats revealed that 97.4% of the stained microorganisms were Gram‐positive rods and only 1.2% were Gram‐negative rods. In the group of rats with ulcers induced by BFMeT, the Gram‐positive rods decreased by 56.4% and the Gram‐negative rods including Escherichia coli, Klebsiella, Proteus and Bacteroides increased by 37.3%. However, in the group of rats administered the Bifidobacterium culture, the Lactobacillus culture or yogurt, the percentages of the Gram‐negative rods were decreased. Although Lactobacillus was a major bacterium in the ileum of normal rats, the Gram‐negative facultatively anaerobic rods E. coli, Klebsiella and Proteus were increased in the ulcerated ileum of rats treated with BFMeT, suggesting that these bacteria are associated with ulcer formation in rats treated with NSAIDs, and that Lactobacillus and Bifidobacterium inhibit it by repressing the growth of ulcer‐inducing bacteria.
Multiple PEX genes are required for proper subcellular distribution and stability of Pex5p, the PTS1 receptor: evidence that PTS1 protein import is mediated by a cycling receptor

PEX5 encodes the type-1 peroxisomal targeting signal (PTS1) receptor, one of at least 15 peroxins required for peroxisome biogenesis. Pex5p has a bimodal distribution within the cell, mostly cytosolic with a small amount bound to peroxisomes. This distribution indicates that Pex5p may function as a cycling receptor, a mode of action likely to require interaction with additional peroxins. Loss of peroxins required for protein translocation into the peroxisome (PEX2 or PEX12) resulted in accumulation of Pex5p at docking sites on the peroxisome surface. Pex5p also accumulated on peroxisomes in normal cells under conditions which inhibit protein translocation into peroxisomes (low temperature or ATP depletion), returned to the cytoplasm when translocation was restored, and reaccumulated on peroxisomes when translocation was again inhibited. Translocation inhibiting conditions did not result in Pex5p redistribution in cells that lack detectable peroxisomes. Thus, it appears that Pex5p can cycle repeatedly between the cytoplasm and peroxisome. Altered activity of the peroxin defective in CG7 cells leads to accumulation of Pex5p within the peroxisome, indicating that Pex5p may actually enter the peroxisome lumen at one point in its cycle. In addition, we found that the PTS1 receptor was extremely unstable in the peroxin-deficient CG1, CG4, and CG8 cells. Altered distribution or stability of the PTS1 receptor in all cells with a defect in PTS1 protein import implies that the genes mutated in these cell lines encode proteins with a direct role in peroxisomal protein import.
Quantitative assessment of foot structure in rheumatoid arthritis by a foot digitizer: Detection of deformities even in the absence of erosions

Foot involvement is a major feature in rheumatoid arthritis (RA), leading to structural deformities. Methods to allow a 3‐dimensional (3‐D) evaluation of foot structure in RA to be applicable in daily clinical practice have not been evaluated. This study assessed the use of a foot digitizer, a noninvasive 3‐D scanner collecting objective quantitative data of the feet, to evaluate the presence of foot structure abnormalities in an RA outpatient cohort.
Contribution of α2-adrenoceptors and Y1 neuropeptide Y receptors to the blunting of sympathetic vasoconstriction induced by systemic hypoxia in the rat

There is evidence that sympathetically evoked vasoconstriction in skeletal muscle is blunted in systemic hypoxia, but the mechanisms underlying this phenomenon are not clear. In Saffan‐anaesthetized Wistar rats, we have studied the role of α2‐adrenoceptors and neuropeptide Y (NPY) Y1 receptors in mediating vasoconstriction evoked by direct stimulation of the lumbar sympathetic chain by different patterns of impulses in normoxia (N) and systemic hypoxia (H: breathing 8% O2). Patterns comprised 120 impulses delivered in bursts over a 1 min period at 40 or 20 Hz, or continuously at 2 Hz. Hypoxia attenuated the evoked increases in femoral vascular resistance (FVR) by all patterns, the response to 2 Hz being most affected (40 Hz bursts: N = 3.25 ± 0.75 arbitrary resistance units (RU); H = 1.14 ± 0.29 RU). Yohimbine (Yoh, α2‐adrenoceptor antagonist) or BIBP 3226 (Y1‐receptor antagonist) did not affect baseline FVR. In normoxia, Yoh attenuated the responses evoked by high frequency bursts and 2 Hz, whereas BIBP 3226 only attenuated the response to 40 Hz (40 Hz bursts: N + Yoh = 2.1 ± 0.59 RU; N + BIBP 3226 = 1.9 ± 0.4 RU). In hypoxia, Yoh did not further attenuate the evoked responses, but BIBP 3226 further attenuated the response to 40 Hz bursts. These results indicate that neither α2‐adrenoceptors nor Y1 receptors contribute to basal vascular tone in skeletal muscle, but both contribute to constrictor responses evoked by high frequency bursts of sympathetic activity. We propose that in systemic hypoxia, the α2‐mediated component represents about 50% of the sympathetically evoked constriction that is blunted, whereas the contribution made by Y1 receptors is resistant. Thus we suggest the importance of NPY in the regulation of FVR and blood pressure increases during challenges such as systemic hypoxia.
The A930G Polymorphism of P22phox (CYBA) Gene but Not C242T Variation Is Associated with Hypertension: A Meta-Analysis

Background Recently, it has been reported that the A930G and C242T polymorphisms within p22phox (CYBA) gene are involved in the pathogenesis of hypertension. However, the results remain controversial. Furthermore, no previous meta-analysis has been conducted to evaluate the relationship between the A930G and C242T polymorphisms and hypertension. Therefore, we performed this meta-analysis to clarify these controversies. Objective and Methods All of the included articles were retrieved from the PubMed and Embase databases, as well as the CNKI, CBM, Chongqing VIP and Wan Fang databases according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Odds ratios (OR) with corresponding 95% confidence intervals (CI) were used to assess the strength of the association. Accounting for heterogeneity, a fixed or random effects model was respectively adopted. Heterogeneity was checked using the Q test and the I2 statistic. A cumulative meta-analysis was conducted to estimate the tendency of pooled OR. Funnel plots and Egger’s tests were performed to test for possible publication bias. Results Five articles on A930G with 2003 cases/2434 controls and eight articles on C242T with 2644 cases/1967 controls were identiﬁed. A signiﬁcant association of A930G polymorphisms with the risk of hypertension was found in the dominant model (OR=0.59, 95% CI: 0.38–0.92, p=0.021) and allelic model (OR=0.66, 95% CI: 0.46–0.95, p=0.024). In the stratified analysis, a signiﬁcant association could be found among the hospital-based and population-based studies. However, no evidence of a significant association of the C242T polymorphism with hypertension was found in the overall analysis and subgroup analysis. Conclusions This meta-analysis indicates that the A930G polymorphism, but not the C242T variation, might be a protective factor for hypertension.
Synaptotagmin IV Does Not Alter Excitatory Fast Synaptic Transmission or Fusion Pore Kinetics in Mammalian CNS Neurons

Synaptotagmin IV (Syt IV) is a brain-specific isoform of the synaptotagmin family, the levels of which are strongly elevated after seizure activity. The dominant hypothesis of Syt IV function states that Syt IV upregulation is a neuroprotective mechanism for reducing neurotransmitter release. To test this hypothesis in mammalian CNS synapses, Syt IV was overexpressed in cultured mouse hippocampal neurons, and acute effects on fast excitatory neurotransmission were assessed. We found neurotransmission unaltered with respect to basal release probability, Ca2+ dependence of release, short-term plasticity, and fusion pore kinetics. In contrast, expression of a mutant Syt I with diminished Ca2+ affinity (R233Q) reduced release probability and altered the Ca2+ dependence of release, thus demonstrating the sensitivity of the system to changes in neurotransmission resulting from changes to the Ca2+ sensor. Together, these data refute the dominant model that Syt IV functions as an inhibitor of neurotransmitter release in mammalian neurons.
Flux Weakening Mechanism of Interior Permanent Magnet Synchronous Machines With Segmented Permanent Magnets

The flux weakening mechanism of interior permanent magnet synchronous machines with segmented permanent magnets (PMs) in the rotor is studied in this paper. Air gap flux density with and without segments are analyzed and compared, based on both analytical and finite element methods. Frozen permeability technique is used to separate the PM component flux density in iron bridges at load condition, to find out the influence of demagnetizing current on flux variation. Design parameters are optimized to improve the field weakening capability. A novel explanation is proposed to explain the improvement effect of the flux weakening capability by magnet segmentation.
Piloting Computer Science Education Week in Mexico

Computer Science Education Week activities, featuring online? programming tools embedded with tutorials, report large participation numbers. However, to truly broaden participation, activities need to be made accessible in international contexts. In 2014, Tecnológico de Monterrey and Instituto de Innovación y Transferencia de Tecnología de Nuevo León, modified the Scalable Game Design CS Ed Week activity to include a Mexican feasibility pilot study. The goal of the pilot was to broaden participation in Computer Science in Mexico by creating interest and demand in further activities, including launching of 2015 Mexico CS Ed Week. This paper reviews the initial results of this 2014 pilot, including the discussion of the unique challenges faced in this context, and examines efforts to make this activity more accessible and successful. In addition to pilot data highlighting future activity improvements, initial retention results show that despite challenges, Mexican students were able to effectively use the modified activity to create games on par with U.S. students.
Histological Features of the Gastrointestinal Tract of Wild Indonesian Shortfin Eel, Anguilla bicolor bicolor (McClelland, 1844), Captured in Peninsular Malaysia

This study was conducted to record the histological features of the gastrointestinal tract of wild Indonesian shortfin eel, Anguilla bicolor bicolor (McClelland, 1844), captured in Peninsular Malaysia. The gastrointestinal tract was segmented into the oesophagus, stomach, and intestine. Then, the oesophagus was divided into five (first to fifth), the stomach into two (cardiac and pyloric), and the intestine into four segments (anterior, intermediate, posterior, and rectum) for histological examinations. The stomach had significantly taller villi and thicker inner circular muscles compared to the intestine and oesophagus. The lamina propria was thickest in stomach, significantly when compared with oesophagus, but not with the intestine. However, the intestine showed significantly thicker outer longitudinal muscle while gastric glands were observed only in the stomach. The histological features were closely associated with the functions of the different segments of the gastrointestinal tract. In conclusion, the histological features of the gastrointestinal tract of A. b. bicolor are consistent with the feeding habit of a carnivorous fish.
Synchrotron diffraction measurement of residual stresses in friction stir welded 5383-H321 aluminium butt joints and their modification by fatigue cycling

This paper presents two-dimensional information on the residual stresses in 8 mm 5383-H321 aluminium plates joined by double pass (DP) friction stir welding (FSW). It considers the inherent variability in residual stress magnitudes along 0.5 m lengths of weld pass, and their modification under a sequence of applied fatigue loads. This represents one of a planned series of experiments aimed at illuminating the effects of fatigue cycling on residual stress fields. In this particular case, the magnitudes of the bending fatigue loads (R = 0.1) were chosen to correlate with the measured proof strengths of the weld metal (approximately 160 MPa) and the parent plate (approximately 260-270 MPa). In four-point bend S-N tests at R = 0.1 on 40 mm wide FS welded specimens of this alloy and plate thickness, these peak stress levels correspond to lives of around 10 5 cycles and 10 7 cycles, respectively. Results from the work indicate that significant variability exists among welded plates in peak compressive stress magnitudes (a range of perhaps -50 MPa to -140 MPa), although peak tensile stresses were relatively low and more consistent (from around 0 to 30 MPa). Fatigue loading accentuates the peak-to-valley stress change and causes an overall translation of the stresses to become more positive. Peak tensile stresses increase several-fold during fatigue cycling.
Resampling-Based Approaches to Study Variation in Morphological Modularity

Modularity has been suggested to be connected to evolvability because a higher degree of independence among parts allows them to evolve as separate units. Recently, the Escoufier RV coefficient has been proposed as a measure of the degree of integration between modules in multivariate morphometric datasets. However, it has been shown, using randomly simulated datasets, that the value of the RV coefficient depends on sample size. Also, so far there is no statistical test for the difference in the RV coefficient between a priori defined groups of observations. Here, we (1), using a rarefaction analysis, show that the value of the RV coefficient depends on sample size also in real geometric morphometric datasets; (2) propose a permutation procedure to test for the difference in the RV coefficient between a priori defined groups of observations; (3) show, through simulations, that such a permutation procedure has an appropriate Type I error; (4) suggest that a rarefaction procedure could be used to obtain sample-size-corrected values of the RV coefficient; and (5) propose a nearest-neighbor procedure that could be used when studying the variation of modularity in geographic space. The approaches outlined here, readily extendable to non-morphometric datasets, allow study of the variation in the degree of integration between a priori defined modules. A Java application – that will allow performance of the proposed test using a software with graphical user interface – has also been developed and is available at the Morphometrics at Stony Brook Web page (http://life.bio.sunysb.edu/morph/).
Approximate methods for sequential decision making using expert advice

We consider a game theoretic approach for sequentially choosing decisions by combining the suggestions of a fixed number of experts. Since the optimal decision making strategy is often computationally expensive, we present a methodology for obtaining approximate strategies with provably good performance. These methods are applicable to any decision problem with bounded payoff function, are computationally feasible, and arise naturally as approximations to the exact solution. We illustrate the ideas by applying our results to the problem of predicting a sequence of letters drawn from a finite alphabet with the goal being to minimize the number of mistakes made.
Cooperation over frequency-selective fading relay channels

We study information-rate calculations and coded cooperation strategies for relay channels with frequency-selective (FS) fading. We develop suitable channel trellises for the multiaccess and broadcast parts of the relay channel, and employ simulation-based techniques to calculate (approximate) ergodic information-rate bounds with FS Rayleigh fading. Our results show that frequency selectivity provides higher information rates than flat fading when the fading coefficients are known at the receiver, however, the improvement becomes marginal with increasing number of channel taps (when the overall signal to noise ratio is kept constant). Furthermore, we develop a distributed turbo-coding strategy and several decode-and-forward type detection/decoding schemes to ensure successful cooperative communication where the source and the relay may transmit simultaneously. We show that with suitable coding and iterative decoding, one can approach the approximate information-rate limits closely, and that detection schemes based on MMSE criterion provide a good performance/complexity trade-off.
Rigorous analysis of heuristics for NP-hard problems

The known NP-hardness results imply that for many combinatorial optimization problems there are no efficient algorithms that find an optimal solution, or even a near optimal solution, on every instance. A heuristic for an NP-hard problem is a polynomial time algorithm that produces optimal or near optimal solutions on some input instances, but may fail on others. The study of heuristics involves both an algorithmic issue (the design of the heuristic algorithm) and a conceptual challenge, namely, how does one evaluate the quality of a heuristic. Current methods for evaluating heuristics include experimental evidence, hand wavingarguments, and rigorous analysis of the performance of the heuristic on some wide (in a sense that depends on the context) classes of inputs. This talk is concerned with the latter method. On the conceptual side, several frameworks that have been used in order to model the classes of inputs of interest (including random models, semi-random models, smoothed analysis) will be discussed. On the algorithmic side, several algorithmic techniques and principles of analysis that are often useful in these frameworks will be presented.