Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of three cAMP‐dependent protein kinase (PKA) phosphorylation sites within the major intracellular domain of neuronal nicotinic receptor α4 subunits

This study determined whether all protein kinase A (PKA) and protein kinase C (PKC) phosphorylation sites on the α4 subunit of rat α4β2 neuronal nicotinic receptors could be localized to the M3/M4 cytoplasmic domain of the protein, and investigated specific amino acid substrates for the kinases through two‐dimensional phosphopeptide mapping and site‐directed mutagenesis. Experiments were conducted using α4β2 receptors expressed in Xenopus oocytes and a fusion protein corresponding to the M3/M4 cytoplasmic domain of α4 (α4333−594). When oocytes expressing α4β2 receptors were incubated with [32P]orthophosphate in order to label endogenous ATP stores, phosphorylation of α4 subunits was evident. Incubation of either immunoprecipitated receptors or the fusion protein with [32P]ATP and either PKA or PKC followed by trypsinization of the samples demonstrated that the kinases phosphorylated α4 subunits on multiple phosphopeptides, and that the phosphorylated full‐length α4 protein and fusion protein produced identical phosphopeptide maps. Site‐directed mutagenesis of Ser365, Ser472 and Ser491 to alanines in the fusion protein eliminated phosphopeptides phosphorylated by PKA, but not by PKC. Other mutations investigated, Ser470, Ser493, Ser517 and Ser590, did not alter the phosphopeptide maps. Results indicate that Ser365, Ser472 and Ser491 on neuronal nicotinic receptor α4 subunits are phosphorylated by PKA and are likely to represent post‐translational regulatory sites on the receptor.
Visualizing and Understanding Neural Machine Translation

While neural machine translation (NMT) has made remarkable progress in recent years, it is hard to interpret its internal workings due to the continuous representations and non-linearity of neural networks. In this work, we propose to use layer-wise relevance propagation (LRP) to compute the contribution of each contextual word to arbitrary hidden states in the attention-based encoder-decoder framework. We show that visualization with LRP helps to interpret the internal workings of NMT and analyze translation errors.
Acoustic Detail Guides Attention Allocation in a Selective Listening Task

The flexible allocation of attention enables us to perceive and behave successfully despite irrelevant distractors. How do acoustic challenges influence this allocation of attention, and to what extent is this ability preserved in normally aging listeners? Younger and healthy older participants performed a masked auditory number comparison while EEG was recorded. To vary selective attention demands, we manipulated perceptual separability of spoken digits from a masking talker by varying acoustic detail (temporal fine structure). Listening conditions were adjusted individually to equalize stimulus audibility as well as the overall level of performance across participants. Accuracy increased, and response times decreased with more acoustic detail. The decrease in response times with more acoustic detail was stronger in the group of older participants. The onset of the distracting speech masker triggered a prominent contingent negative variation (CNV) in the EEG. Notably, CNV magnitude decreased parametrically with increasing acoustic detail in both age groups. Within identical levels of acoustic detail, larger CNV magnitude was associated with improved accuracy. Across age groups, neuropsychological markers further linked early CNV magnitude directly to individual attentional capacity. Results demonstrate for the first time that, in a demanding listening task, instantaneous acoustic conditions guide the allocation of attention. Second, such basic neural mechanisms of preparatory attention allocation seem preserved in healthy aging, despite impending sensory decline.
Performance of rateless codes in half-duplex collaborative relay networks

Cooperative communications, where parallel relays forward information to a destination node, can greatly improve the energy efficiency and latency in ad-hoc networks. Communications using rateless codes, in which the source transmits an infinite number of parity bits to the destination until the receipt of an acknowledgement, provides a natural and efficient mechanism for accumulating information from multiple transmitting relays. One decode-and-forward protocol and one amplify-and-forward protocol both based on rateless codes are studied in this paper. The impact of the half-duplex constraint on the throughput of the system using rateless codes to harness spatial diversity and efficiently transmit information from a source to a destination is analyzed in our paper. Specially, the direct path from source to destination in a free-space path loss and small-scale Rayleigh environment is considered, which is often ignored in many other papers. Simulations show that the decode-and-forward protocol works more efficiently than the amplify-and-forward protocol.
Phenotypic heterogeneity and temporal expression of the capsular polysaccharide in Staphylococcus aureus

Bacteria respond to ever‐changing environments through several adaptive strategies. This includes mechanisms leading to a high degree of phenotypic variability within a genetically homogeneous population. In Staphylococcus aureus, the capsular polysaccharide (CP) protects against phagocytosis, but also impedes adherence to endothelial cells and/or matrix proteins. We analysed the regulation of core biosynthesis genes (capA‐P) necessary for CP synthesis using single‐cell assays (immunofluorescence and promoter‐activity). In persistent human carriers, we found a distinct subpopulation of nasal S. aureus to be CP positive. In vitro, cap expression is also heterogeneous and strongly growth‐phase dependent. We asked whether this peculiar expression pattern (earlyOff/lateHeterogen) is orchestrated by the quorum system Agr. We show that the Agr‐driven effector molecule RNAIII promotes cap expression largely via inactivation of the repressor Rot. High NaCl, deletion of CodY or Sae also resulted in higher cap expression but did not change the earlyOFF/lateHeterogen expression pattern. Activity of the quorum system itself is largely homogenous and does not account for the observed heterogeneity of cap expression or the strictly growth phase dependent expression. Our findings are in contrast to the prevailing view that quorum sensing is the main driving force for virulence gene expression when bacterial cell densities increase.
Maesaquinone: A Novel Inhibitor of Plant Mitochondrial Respiratory Enzymes That React with Ubiquinone

The effect of maesaquinone, 2‐(14‐nonadecenyl)‐3,6‐dihydroxy5‐methyl‐1,4‐benzoquinone, on plant mitochondrial respiration has been investigated. In mitochondria isolated from thermogenic Arum maculatum spadices, this compound inhibits both cytochrome and alternative pathway activities. Kinetic analyses reveal that this inhibition is the result of potent effects of maesaquinone on the alternative oxidase (ID50 <0.3θM) and complex III (ID50 <5θM). Succinate dehydrogenase and external NADH dehydrogenase are also inhibited, albeit to a lesser extent (∼30% at 1 θM). These data suggest that maesaquinone specifically affects the interaction of the respective enzymes with ubiquinone.
Soaking increases the efficacy of supplemental microbial phytase in a low-phosphorus corn-soybean meal diet for growing pigs.

Sixty-three crossbred barrows averaging 18.7 kg initial BW were used in a 6-wk study of the effects of soaking on the efficacy of supplemental microbial phytase (Natuphos, BASF) in a low-P corn-soybean meal diet. The basal corn-soybean meal diet contained . 06% available P, . 32% total P, and . 55% Ca with no added inorganic P. The basal diet was supplemented with 0, 250, or 500 phytase units (PU)/kg of diet. The diet was fed dry or soaked (2 parts water:1 part diet and mixed for 2 h at 30 degrees C before feeding) in a 3 x 2 factorial arrangement. A positive control diet was supplemented with inorganic P and provided . 23% available P, . 48% total P, and . 60% Ca. Pigs were individually penned and fed their respective diets to appetite in four equal meals daily. There were no soaking x phytase interactions (P > .1 to .6) for growth performance criteria. Daily gain and gain/feed ratio were increased (P < .01) by soaking and increased linearly (P < .01) by phytase. Daily feed intake was increased linearly (P < .01) by phytase. There were soaking x phytase quadratic interactions (P < .01) for apparent P absorption criteria because soaking the 250 PU/kg diet increased P absorption similar to that obtained with the 500 PU/kg diet fed dry. Apparent P absorption criteria were increased by soaking (P < .01) and were increased linearly (P < .001) and quadratically (P < .03) by phytase. Phytase reduced fecal P excretion 37 to 40% with dry feeding (P < .03) and 48 to 49% with soaking (P < .01).
On the application of orthogonal transformation for the design and analysis of feedforward networks

Orthogonal transformation, which can lead to compaction of information, has been used in two ways to optimize on the size of feedforward networks: 1) through the selection of optimum set of time-domain inputs, and the optimum set of links and nodes within a neural network (NN); and 2) through the orthogonalization of the data to be used in NN's, in case of processes with periodicity. The proposed methods are efficient and are also extremely robust numerically. The singular value decomposition (SVD) and QR with column pivoting factorization (QRcp) are the transformations used. SVD mainly serves as the null space detector; QRcp coupled with SVD is used for subset selection, which is one of the main operations on which the design of the optimal network is based. SVD has also been used to devise a new approach for the assessment of the convergence of the NN's, which is an alternative to the conventional output error analysis.
Multiclass Microarray Data Classification Based on SA-ECOC

Multiclass microarray data analysis is a hard task because of the small sample size problem along with heavy data overlapping among classes. In this paper, we propose a new algorithm to tackle it, called as Self-Adjusting Error Correcting Output Codes (SA-ECOC) method. This algorithm generates diverse code matrices based on different feature subset by a data complexity (DC) measure at first, then all columns are gathered to form a column pool. Our algorithm constructs an effective code matrix by picking up columns from the pool, and an iterative algorithm optimizes the matrix with a proposed criterion called as Distance Interval (DI). We compare our method with other well-known ECOC coding methods on the cancer microarray data, and the results confirm the effectiveness of our algorithm.
Electrical Characterization of Screen-Printed Circuits on the Fabric

Fabrication methods of planar printed circuits on fabrics are introduced and their electrical characteristics are measured and analyzed. Wet patterning method like screen printing as well as dry process of sputtering are used to fabricate the patterned film electrodes on various types of fabrics. The minimum width of the patterns is 0.2 mm for screen printing and 0.1 mm for gold sputtering, and the typical sheet resistance is 134 m ¿/¿. Fabrication methods of capacitors of 1 pF-1 nF and inductors of 500 nH-1 ¿H at 10 MHz on the fabrics are also introduced. Bonding and packaging of silicon chip directly on the fabric circuit board are proposed and their mechanical properties are investigated. The ac impedance of the transmission line is measured as 201-215 ¿ with variation, and the time-domain reflectometry profile shows that the -3 dB frequency of the printed transmission line of 15 cm on the fabric is 80 MHz. A complete system composed of a fabric capacitor sensor input, a controller system-on-a-chip, and an LED array display is implemented on the fabric and its operation is demonstrated successfully.
Proceedings of the 2016 ICML Workshop on Human Interpretability in Machine Learning (WHI 2016)

This is the Proceedings of the 2016 ICML Workshop on Human Interpretability in Machine Learning (WHI 2016), which was held in New York, NY, June 23, 2016. Invited speakers were Susan Athey, Rich Caruana, Jacob Feldman, Percy Liang, and Hanna Wallach.
Dimethyl Sulfoxide and Ethanol Elicit Increased Amyloid Biogenesis and Amyloid-Integrated Biofilm Formation in Escherichia coli

ABSTRACT Escherichia coli directs the assembly of functional amyloid fibers termed “curli” that mediate adhesion and biofilm formation. We discovered that E. coli exhibits a tunable and selective increase in curli protein expression and fiber assembly in response to moderate concentrations of dimethyl sulfoxide (DMSO) and ethanol. Furthermore, the molecular alterations resulted in dramatic functional phenotypes associated with community behavior, including (i) cellular agglutination in broth, (ii) altered colony morphology, and (iii) increased biofilm formation. Solid-state nuclear magnetic resonance (NMR) spectra of intact pellicles formed in the presence of [13C2]DMSO confirmed that DMSO was not being transformed and utilized directly for metabolism. Collectively, the chemically induced phenotypes emphasize the plasticity of E. coli's response to environmental stimuli to enhance amyloid production and amyloid-integrated biofilm formation. The data also support our developing model of the extracellular matrix as an organized assembly of polymeric components, including amyloid fibers, in which composition relates to bacterial physiology and community function.
Pricing Multiple Products with the Multinomial Logit and Nested Logit Models: Concavity and Implications

We consider the problem of pricing multiple differentiated products with the nested logit model and, as a special case, the multinomial logit model. We prove that concavity of the total profit function with respect to market share holds even when price sensitivity may vary with products. We use this result to analytically compare the optimal monopoly solution to oligopolistic equilibrium solutions. To demonstrate further applications of the concavity result, we consider several multiperiod dynamic models that incorporate the pricing of multiple products in the context of inventory control and revenue management, and establish structural results of the optimal policies.
Blunted Fasting-Induced Hypothalamic Activation and Refeeding Hyperphagia in Late-Onset Obesity

Hormonal and metabolic factors signal the status of energy balance to hypothalamic nuclei. Obesity is characterized by neuronal, metabolic and hormonal alterations. We therefore hypothesized that hypothalamic responses to challenges of energy balance may differ between lean and obese animals. To test this, we compared c-Fos expression in the hypothalamic arcuate (ARC) and paraventricular nuclei (PVN) and the lateral hypothalamic area (LHA) of mice (1-year-old) with late-onset obesity (LOO) and of lean controls under different feeding conditions. Fourteen hours of fasting induced high c-Fos expression in neuropeptide-Y-positive ARC neurons, in the PVN and in the rostral LHA in lean but not in LOO mice. c-Fos expression in melanin-concentrating hormone (MCH) and orexin-containing neurons in the caudal LHA was not affected by fasting. LOO mice showed fasting hyperinsulinemia, hyperleptinemia, elevated fasting blood glucose and an attenuated hyperphagic response during refeeding. Moreover, the anorectic response to leptin and hypoglycemic response to insulin were reduced in LOO mice. We conclude that adiposity blunts the neuronal responses to metabolic challenges in hypothalamic centers which control feeding behavior and energy balance. Elevated blood glucose may be one factor that suppresses hypothalamic responsiveness in obese mice. A similar impact of hyperinsulinemia and hyperleptinemia in LOO mice is also likely although under the current experimental conditions responsiveness to some effects of these hormones appeared to be reduced.
Learning Predictive Leading Indicators for Forecasting Time Series Systems with Unknown Clusters of Forecast Tasks

We present a new method for forecasting systems of multiple interrelated time series. The method learns the forecast models together with discovering leading indicators from within the system that serve as good predictors improving the forecast accuracy and a cluster structure of the predictive tasks around these. The method is based on the classical linear vector autoregressive model (VAR) and links the discovery of the leading indicators to inferring sparse graphs of Granger causality. We formulate a new constrained optimisation problem to promote the desired sparse structures across the models and the sharing of information amongst the learning tasks in a multi-task manner. We propose an algorithm for solving the problem and document on a battery of synthetic and real-data experiments the advantages of our new method over baseline VAR models as well as the state-of-the-art sparse VAR learning methods.
Relative Direction Change - A Topology-based Metric for Layout Stability in Treemaps

This paper presents a topology-based metric for layout stability in treemaps—the Relative Direction Change (RDC). The presented metric considers the adjacency and arrangement of single shapes in a treemap, and allows for a rotation-invariant description of layout changes between two snapshots of a dataset depicted with treemaps. A user study was conducted that shows the applicability of the Relative Direction Change in comparison and addition to established layout metrics, such as Average Distance Change (ADC) and Average Aspect Ratio (AAR), with respect to human perception of treemaps. This work contributes to the establishment of a more precise model for the replicable and reliable comparison of treemap layout algorithms.
Regulators of synaptic transmission: Roles in the pathogenesis and treatment of epilepsy

Synaptic transmission is the communication between a presynaptic and a postsynaptic neuron, and the subsequent processing of the signal. These processes are complex and highly regulated, reflecting their importance in normal brain functioning and homeostasis. Sustaining synaptic transmission depends on the continuing cycle of synaptic vesicle formation, release, and endocytosis, which requires proteins such as dynamin, syndapin, synapsin, and synaptic vesicle protein 2A. Synaptic transmission is regulated by diverse mechanisms, including presynaptic modulators of synaptic vesicle formation and release, postsynaptic receptors and signaling, and modulators of neurotransmission. Neurotransmitters released presynaptically can bind to their postsynaptic receptors, the inhibitory γ‐aminobutyric acid (GABA)ergic receptors or the excitatory glutamate receptors. Once released, glutamate activates a variety of postsynaptic receptors including α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid (AMPA), N‐methyl‐D‐aspartate (NMDA), kainate, and metabotropic receptors. The activation of the receptors triggers downstream signaling cascades generating a vast array of effects, which can be modulated by a numerous auxiliary regulatory subunits. Moreover, different neuropeptides such as neuropeptide Y, brain‐derived neurotrophic factor (BDNF), somatostatin, ghrelin, and galanin, act as regulators of diverse synaptic functions and along with the classic neurotransmitters. Abnormalities in the regulation of synaptic transmission play a critical role in the pathogenesis of numerous brain diseases, including epilepsy. This review focuses on the different mechanisms involved in the regulation of synaptic transmission, which may play a role in the pathogenesis of epilepsy: the presynaptic modulators of synaptic vesicle formation and release, postsynaptic receptors, and modulators of neurotransmission, including the mechanism by which drugs can modulate the frequency and severity of epileptic seizures.
Examining the repeatable battery for the assessment of neuropsychological status: factor analytic studies in an elderly sample.

OBJECTIVE The Repeatable Battery for the Assessment of Neuropsychological Status (RBANS), a recently developed cognitive assessment instrument, has been shown to be useful with a variety of neuropsychiatric conditions, but its factor structure has not been examined. METHOD Using 824 community-dwelling elders, the RBANS was examined with confirmatory and exploratory factor analyses. RESULTS The existing structure of the RBANS was not supported; however, a two-factor solution was. CONCLUSIONS Clinicians and researchers using the RBANS should be cautious when interpreting this measure with its existing structure.
A modified spatial spread spectrum method for digital image watermarking

Spread spectrum is one of the most effective approaches for digital image watermarking because it satisfies the imperceptiveness, robustness as well as security requirements. Unfortunately, this method may be affected by interference from the cover image and completely fails in the case of having no watermark in the tested image. In addition, some proposed improvements to eliminate this interference are invalid for spatial image watermarking which obtains a low cost and is easy to adapt to real-time applications. This paper proposes a modified spatial spread spectrum method to overcome these disadvantages. By removing the mean value in the tested image, the proposed method reduces the interference and achieves a better error probability. Moreover, by using a flexible threshold in the detector, our method can work successfully even if the tested image is pure. We not only analyze and derive the closed-form expressions for the optimal threshold and the error probability, but also investigate various images and some common image attacks including noise, compression and filtering.
Research on Brain-Computer Interface Technology Based on Steady State Visual Evoked Potentials

A Brain-Computer Interface (BCI) system based on Steady State Visual Evoked Potentials (SSVEP) was presented in this paper to realize four-direction motion control of a small ball on the computer screen. The system mainly included five parts of visual stimulator, electroencephalogram (EEG) amplifier, EEG acquisition, EEG processing and machine human interface on the computer screen. The system utilized wavelet packet decomposition technology and linear classifier to obtain the features of SSVEP and converted them to the control commands. Comparing with FFT method , the wavelet packet technology can achieve better performance.The experimental results have proved the effectiveness of the system. The realization of the system can provide a new way to enhance the human capability to control external device.
Regulation of spo0H, an early sporulation gene in bacilli

The construction of lacZ fusions in frame with the spo0H gene of Bacillus licheniformis enabled us to study the expression of this gene under various growth conditions and in various genetic backgrounds. spo0H was expressed during vegetative growth, but the levels increased during early stationary phase and then decreased several hours later. Expression of the gene was not repressed by glucose, but was induced by decoyinine, an inhibitor of guanine nucleotide biosynthesis, which can induce sporulation. Of those tested, the only spo0 gene required for the expression of spo0H was spo0A, and this requirement was eliminated by the abrB mutation, a partial suppressor of spo0A function. spo0H-lacZ expression was much higher in a strain with a deletion in the spo0H gene.
A Braille Recognition System by the Mobile Phone with Embedded Camera

It has been suggested that blind and visually impaired people may have difficulty reading Braille that is widely set in the public place according to barrier free policy of the government. This paper describes a new system that recognizes Braille characters from a photo taken by a mobile phone with embedded camera. The photo is dealt with by a Java program developed by "DoJa I-appli tool kit " to supply a real time reply.