Miracle-dz/UniFAR-FTUs huggingface dataset:
Isotope-labeled differential profiling of metabolites using N-benzoyloxysuccinimide derivatization coupled to liquid chromatography/high-resolution tandem mass spectrometry.

RATIONALE An isotopic labeling strategy based on derivatizing amine-containing metabolites has been developed using light ((12) C6 ) and heavy ((13) C6 ) N-benzoyloxysuccinimide reagents for semi-targeted metabolomic applications. METHODS Differentially labeled samples were combined and analyzed simultaneously by liquid chromatography/high-resolution tandem mass spectrometry (LC/HR-MS/MS) to compare relative amounts of amine-containing metabolites. The selectivity of the reaction was determined with model metabolites and was shown to also be applicable to thiol and phenol moieties. The potential for relative quantitation was evaluated in cell extracts and the method was then applied to quantify metabolic perturbations occurring in human cultured cells under normal vs. oxidative stress conditions. RESULTS A total of 279 derivatized features were detected in HL60 cell extracts, 77 of which yielded significant concentration changes upon oxidative stress treatment. Based on accurate mass measurements and MS/MS spectral matching with reference standard solutions, 10 metabolites were clearly identified. Derivatized compounds were found to have diagnostic fragment ions from the reagent itself, as well as structurally informative ions useful for metabolite identification. CONCLUSIONS This simple derivatization reaction can be applied to the relative quantitation of amine-, thiol- and phenol-containing compounds, with improved sensitivity and chromatographic peak shapes due to the increased hydrophobicity of polar metabolites not readily amenable to reversed-phase LC/MS analysis.
A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies

Side chain positioning is an important subproblem of the general protein-structure-prediction problem, with applications in homology modeling and protein design. The side chain positioning problem takes a fixed backbone and a protein sequence and predicts the lowest energy conformation of the protein's side chains on this backbone. We study a widely used version of the problem where the side chain positioning procedure uses a rotamer library and an energy function that can be expressed as a sum of pairwise terms. The problem is NP-complete; we show that it cannot even be approximated. In practice, it is tackled by a variety of general search techniques and specialized heuristics. Here, we propose formulating the side chain positioning problem as an instance of semidefinite programming (SDP). We introduce two novel rounding schemes and provide theoretical justification for their effectiveness under various conditions. We apply our method on simulated data, as well as on the computational redesign of two na.
The Modulatory Role of Spinally Located Histamine Receptors in the Regulation of the Blood Glucose Level in D-Glucose-Fed Mice

The possible roles of spinal histamine receptors in the regulation of the blood glucose level were studied in ICR mice. Mice were intrathecally (i.t.) treated with histamine 1 (H1) receptor agonist (2-pyridylethylamine) or antagonist (cetirizine), histamine 2 (H2) receptor agonist (dimaprit) or antagonist (ranitidine), histamine 3 (H3) receptor agonist (α-methylhistamine) or antagonist (carcinine) and histamine 4 (H4) receptor agonist (VUF 8430) or antagonist (JNJ 7777120), and the blood glucose level was measured at 30, 60 and 120 min after i.t. administration. The i.t. injection with α-methylhistamine, but not carcinine slightly caused an elevation of the blood glucose level. In addition, histamine H1, H2, and H4 receptor agonists and antagonists did not affect the blood glucose level. In D-glucose-fed model, i.t. pretreatment with cetirizine enhanced the blood glucose level, whereas 2-pyridylethylamine did not affect. The i.t. pretreatment with dimaprit, but not ranitidine, enhanced the blood glucose level in D-glucose-fed model. In addition, α-methylhistamine, but not carcinine, slightly but significantly enhanced the blood glucose level D-glucose-fed model. Finally, i.t. pretreatment with JNJ 7777120, but not VUF 8430, slightly but significantly increased the blood glucose level. Although histamine receptors themselves located at the spinal cord do not exert any effect on the regulation of the blood glucose level, our results suggest that the activation of spinal histamine H2 receptors and the blockade of spinal histamine H1 or H3 receptors may play modulatory roles for up-regulation and down-regulation, respectively, of the blood glucose level in D-glucose fed model.
HMM Parameter Learning for Japanese Morphological Analyzer

This paper presents a method to apply Hidden Markov Model (HMM) to parameter learning for Japanese morphological analyzer. We especially emphasize how the following two information sources affect the results of the parameter learning: 1) The initial value of parameters, i.e., the initial probabilities and 2) some grammatical constraints that hold in Japanese sentences independently of any domain. First and foremost, a simple application of HMM to Japanese corpus does not give a satisfactory results since word boundaries are not clear in Japanese texts because of lack of word separators. The first results of the experiments show that initial probabilities learned from correct tagged corpus affects greatly to the results and that a small tagged corpus is enough for the initial probabilities. The second result is that the incorporation of simple grammatical constraints works well in the improvements of the results. The final result gives that the total performance of the HMM-based parameter learning achieves almost the same level as the human developed rule-based Japanese morphological analyzer.
Constant density spanners for wireless ad-hoc networks

An important problem for wireless ad hoc networks has been todesign overlay networks that allow time- and energy-efficientrouting. Many local-control strategies for maintaining such overlaynetworks have already been suggested, but most of them are based onan oversimplified wireless communication model. In this paper, we suggest a model that is much more general thanprevious models. It allows the path loss of transmissions tosignificantly deviate from the idealistic unit disk model and doesnot even require the path loss to form a metric. Also, our model isapparently the first proposed for algorithm design that does notonly model transmission and interference issues but also aims atproviding a realistic model for physical carrier sensing. Physicalcarrier sensing is needed so that our protocols do not require<i>any</i> prior information (not even an estimate onthe number of nodes) about the wireless network to runefficiently. Based on this model, we propose a local-control protocol forestablishing a constant density spanner among a set of mobilestations (or <i>nodes</i>) that are distributed in anarbitrary way in a 2-dimensional Euclidean space. More precisely,we establish a backbone structure by efficiently electing clusterleaders and gateway nodes so that there is only a constant numberof cluster leaders and gateway nodes within the transmission rangeof any node and the backbone structure satisfies the properties ofa topological spanner. Our protocol has the advantage that it is locallyself-stabilizing, i.e., it can recover from <i>any</i>initial configuration, even if adversarial nodes participate in it,as long as the honest nodes sufficiently far away from adversarialnodes can in principle form a single connected component.Furthermore, we only need constant size messages and a constantamount of storage at the nodes, irrespective of the distribution ofthe nodes. Hence, our protocols would even work in extremesituations such as very simple wireless devices (like sensors) in ahostile environment.
Semantic Recognition of a Data Structure in Big-Data

Data governance is a subject that is becoming increasingly important in business and government. In fact, good governance data allows improved interactions between employees of one or more organizations. Data quality represents a great challenge because the cost of non-quality can be very high. Therefore the use of data quality becomes an absolute necessity within an organization. To improve the data quality in a Big-Data source, our purpose, in this paper, is to add semantics to data and help user to recognize the Big-Data schema. The originality of this approach lies in the semantic aspect it offers. It detects issues in data and proposes a data schema by applying a semantic data profiling.
Dual x-tree wavelet image coding

The lack of directional selectivity has harmed the performance of traditional discrete wavelet transform based image coding, especially when the original image includes multidirectional textures. To offer a better compression ability for multidirectional textural images, a novel wavelet image coding scheme, called dual x-tree wavelet image coding is proposed in this paper. First, the 2-D dual-tree discrete wavelet transform (DDWT) is performed on the input image. Then the noise shaping procedure is exerted on the transform coefficients to get their sparse representation. Finally, an improved x-tree image coding algorithm is applied to encode the coefficients. Different from the common used noise shaping, we adopt a pruning phase to the procedure to make the coefficients better fit our dual x-tree encoder. To make good use of the strong correlation between two wavelet trees produced from DDWT, the dual wavelet trees are jointly encoded to improve the coding performance. Simulation results have demonstrated that the proposed algorithm achieves about 0.5dB gain over state-of-the-arts for multidirectional textural image at low bitrate.
Influence of the temperature and uniaxial pressure on the elastic properties of synthetic diamond single crystal

The results of experimental studies on the propagation of bulk acoustic waves (10-200MHz) in a synthetic diamond single crystal under the influence of uniaxial pressure and temperature have been presented. Obtained data on second and third order elastic constants were used to calculate the anisotropy of the acoustic waves propagation characteristics in diamond under the pressure application. The peculiarities of wave propagation have been discussed.
Mechanisms of transactivation by nuclear factor of activated T cells-1

Nuclear factor of activated T cells-family proteins (NFAT1/NFATp, NFATc, NFAT3, and NFAT4/NFATx/NFATc3) play a key role in the transcription of cytokine genes and other genes during the immune response. We have defined the mechanisms of transactivation by NFAT1. NFAT1 possesses two transactivation domains whose sequences are not conserved in the other NFAT-family proteins, and a conserved DNA- binding domain that mediates the recruitment of cooperating nuclear transcription factors even when it is expressed in the absence of other regions of the protein. The activity of the NH2-terminal transactivation domain is modulated by an adjacent regulatory region that contains several conserved sequence motifs represented only in the NFAT family. Our results emphasize the multiple levels at which NFAT- dependent transactivation is regulated, and predict significant differences in the architecture of cooperative transcription complexes containing different NFAT-family proteins.
Surveying the motivations of groups of learners in highly-technical STEM MOOCs

Highly technical STEM MOOCs have recently become widely available, but little is known about the motivations of the various groups of learners participating. In this work, we perform a detailed survey of 1,624 learners to examine their motivations in detail. These learners exhibited overall high levels of intrinsic motivation, but varied in their extrinsic motivation, according to their current position as students, workers, or unemployed individuals. Students generally reported the highest levels of extrinsic motivation compared to other groups (p<;0.001). The results from this analysis indicate that additional factors about learners in each group, such as their course participation and performance, should be examined in future work to help better understand the various needs of those enrolling in highly technical STEM MOOCs.
Molded Vascularized Neo-ossicle Formation in Silicone Chambers

Vascularized bone grafts generally achieve their aims but are not used frequently owing to donor site morbidity and limited supply. To bioengineer an alternate vascularized bone graft, we developed a novel silicone bone reactor capable of producing vascularized neo-ossicles when appropriate osteoprecursor elements are included in the implanted chambers. Requirements for ossicle production were assessed in the model, including osteoprogenitor cells (donor bone marrow), osteoinductive signals (rhBMP2 or demineralized bone matrix), and osteoconductive matrix (Collagraft®). Ossicle production required patency of the vascular pedicle, and for samples not containing cancellous isograft, donor marrow viability and an osteoinductive signal. Ossicles were produced without the need for an implanted osteoinductive matrix. Bone production and maturation time course were similar in chambers containing cancellous isograft, marrow/rhBMP2, and marrow/demineralized bone matrix. The demineralized bone matrix group had delayed early bone production, and the rhBMP2 group had lower final bone area. All groups had central osteolysis in the vascularized neo-ossicles. We believe the approach is promising for selected applications.
Excessive Signal Transduction of Gain-of-Function Variants of the Calcium-Sensing Receptor (CaSR) Are Associated with Increased ER to Cytosol Calcium Gradient

In humans, gain-of-function mutations of the calcium-sensing receptor (CASR) gene are the cause of autosomal dominant hypocalcemia or type 5 Bartter syndrome characterized by an abnormality of calcium metabolism with low parathyroid hormone levels and excessive renal calcium excretion. Functional characterization of CaSR activating variants has been so far limited at demonstrating an increased sensitivity to external calcium leading to lower Ca-EC50. Here we combine high resolution fluorescence based techniques and provide evidence that for the efficiency of calcium signaling system, cells expressing gain-of-function variants of CaSR monitor cytosolic and ER calcium levels increasing the expression of the Sarco-Endoplasmic Reticulum Calcium-ATPase (SERCA) and reducing expression of Plasma Membrane Calcium-ATPase (PMCA). Wild-type CaSR (hCaSR-wt) and its gain-of-function (hCaSR-R990G; hCaSR-N124K) variants were transiently transfected in HEK-293 cells. Basal intracellular calcium concentration was significantly lower in cells expressing hCaSR-wt and its gain of function variants compared to mock. In line, FRET studies using the D1ER probe, which detects [Ca2+]ER directly, demonstrated significantly higher calcium accumulation in cells expressing the gain of function CaSR variants compared to hCaSR-wt. Consistently, cells expressing activating CaSR variants showed a significant increase in SERCA activity and expression and a reduced PMCA expression. This combined parallel regulation in protein expression increases the ER to cytosol calcium gradient explaining the higher sensitivity of CaSR gain-of-function variants to external calcium. This control principle provides a general explanation of how cells reliably connect (and exacerbate) receptor inputs to cell function.
Statistical Monitoring of Service Levels and Staffing Adjustments for Call Centers

Call centers are an indispensable part of many businesses, and their economic role is important and fast growing. To remain competitive, call centers must provide high‐quality services while keeping the number of agents and hence labor costs down. It is thus vital to monitor the service level (SL), which is a common measure of the quality of service, and make suitable staffing adjustments. In this paper, we describe an engineering process control strategy to monitor SL. Staffing is adjusted according to changes in SL. An exponentially weighted moving average for SL based on upper and lower limits is determined from historical data and employed to monitor changes in SL during different time intervals so as to keep the frequency of adjustments to a minimum. Only if SL exceeds its lower or upper limit do we increase or decrease the number of agents for a given interval. Numerical tests show that we can strike a balance between SL and staffing by using our proposed method. Copyright © 2016 John Wiley & Sons, Ltd.
Bottleneck Routing Games in Communication Networks

We consider routing games where the performance of each user is dictated by the worst (bottleneck) element it employs. We are given a network, finitely many (selfish) users, each associated with a positive flow demand, and a load-dependent performance function for each network element; the social (i.e., system) objective is to optimize the performance of the worst element in the network (i.e., the network bottleneck). Although we show that such "bottleneck" routing games appear in a variety of practical scenarios, they have not been considered yet. Accordingly, we study their properties, considering two routing scenarios, namely when a user can split its traffic over more than one path (splittable bottleneck game) and when it cannot (unsplittable bottleneck game). First, we prove that, for both splittable and unsplittable bottleneck games, there is a (not necessarily unique) Nash equilibrium. Then, we consider the rate of convergence to a Nash equilibrium in each game. Finally, we investigate the efficiency of the Nash equilibria in both games with respect to the social optimum; specifically, while for both games we show that the price of anarchy is unbounded, we identify for each game conditions under which Nash equilibria are socially optimal.
Controlled Contention: Balancing Contention and Reservation in Multicore Application Scheduling

One of the benefits of multiprogramming in conventional systems is to allow effective use of resources. For example, when one application blocks for I/O, another can use the available CPU time, improving throughput and performance. In a multithreaded environment, contention for resources can lead to substantial interference between applications: an application with dependencies can suffer if a thread holding critical dependency is not scheduled in time. In the HPC community, this problem is often addressed by reservation-based schedulers such as Gang scheduling. However, such schedulers cannot reap the benefits of resource multiplexing leading to underutilization of the resources and lower overall throughput of the system. In this paper, we explore the trade off between contention and reservation in multithreaded application scheduling on multicourse systems. We show that neither approach is optimal under all conditions. We propose Controlled Contention (CC) -- a scheduling algorithm that allows controlled contention for resources, allowing the benefits of contention while supporting limited reservation to reduce interference. CC provides around 25% improvement in relative speedup over the Completely Fair Scheduler (CFS). We also show that CC can significantly benefit from application-level interference management while providing fairness that is not possible to achieve with application-level adaptation alone. The combined approach (CC with application-level adaptation)provides an average of 21% improvement in throughput, 35% improvement in relative speedup and 36% reduction in energy for the application mixes we consider.
Experiment on MIMO cognitive radio using Tx/Rx beamforming

Spatial spectrum sharing with MIMO cognitive radio is efficient and attractive for wireless systems with limited communication resources. MIMO cognitive radio is a kind of cognitive radios using MIMO beamforming techniques to avoid interference to other nodes. There are many theoretical works on this topic but validation of the algorithm on real hardware has not been realized. Most of these works assume perfect CSI though it is always obtained with errors in practice, especially CSIT. It is known that MIMO beamforming techniques are sensitive to CSI errors and their performance might severely be degraded in practice. Despite the fact that cognitive radio with MIMO beamforming techniques is powerful in terms of spatial efficiency as shown by theoretical results, the feasibility of such systems in real environment have never been studied before. Therefore, we attempt to provide the first implementation of a MIMO cognitive radio system using Tx/Rx beamforming and prove the feasibility by measuring its throughput performance. In this paper, we will explain our implementation and measurement results. In the measurement, we measure achievable throughput of both primary and secondary system. As a result, we found that this system works effectively when transmit power of primary nodes is large enough while that of the secondary nodes is relatively small.
Philosophy in the flesh

"We are neural beings," states Berkeley cognitive scientist George Lakoff. "Our brains take their input from the rest of our bodies. What our bodies are like and how they function in the world thus structures the very concepts we can use to think. We cannot think just anything only what our embodied brains permit. " His new book Philosophy In The Flesh, coauthored by Mark Johnson, makes the following points: "The mind is inherently embodied. Thought is mostly unconscious. Abstract concepts are largely metaphorical. " Lakoff believes that new empirical evidence concerning these finding of cognitive science have taken us over the epistemological divide: we are in a new place and our philosophical assumptions are all up for grabs. He and Johnson write: "When taken together and considered in detail, these three findings from the science of the mind are inconsistent with central parts of Western philosophy, and require a thorough rethinking of the most popular current approaches, namely, Anglo-American analytic philosophy and postmodernist philosophy. " According to Lakoff, metaphor appears to be a neural mechanism that allows us to adapt the neural systems used in sensory-motor activity to create forms of abstract reason. "If this is correct, as it seems to be," he says, "our sensory-motor systems thus limit the abstract reasoning that we can perform. Anything we can think or understand is shaped by, made possible by, and limited by our bodies, brains, and our embodied interactions in the world. This is what we have to theorize with. " He then raises the interesting question: "Is it adequate to understand the world scientifically? -JB
Enumeration schemes for words avoiding permutations

The enumeration of permutation classes has been accomplished with a variety of techniques. One wide-reaching method is that of enumeration schemes, introduced by Zeilberger and extended by Vatter. In this paper we further extend the method of enumeration schemes to words avoiding permutation patterns. The process of finding enumeration schemes is programmable and allows for the automatic enumeration of many classes of pattern-avoiding words. 1 Background The enumeration of permutation classes has been accomplished by many beautiful techniques. One natural extension of permutation classes is pattern-avoiding words. Our concern in this paper is not attractive methods for counting individual classes, but rather developing a systematic technique for enumerating many classes of words. Four main techniques with wide success exist for the systematic enumeration of permutation classes. These are generating trees, insertion coding, substitution decomposition, and enumeration schemes. In this paper we adapt the method of enumeration schemes, first introduced for permutations by Zeilberger [5] and extended by Vatter [4] to the case of enumerating pattern-restricted words. Definition 1. Let [k] n denote the set of words of length n in the alphabet {1,. ,k}, and let w 2 [k] n ,w = w1 ···wn. The reduction of w, denoted by red(w), is the unique word of length n obtained by replacing the i th smallest entries of w with i,