Miracle-dz/UniFAR-FTUs huggingface dataset:
MINK and TNIK Differentially Act on Rap2-Mediated Signal Transduction to Regulate Neuronal Structure and AMPA Receptor Function

Misshapen/NIKs (Nck-interacting kinases)-related kinase (MINK) and closely related TRAF2/Nck-interacting kinase (TNIK) are proteins that specifically bind to activated Rap2 and are thus hypothesized to relay its downstream signal transduction. Activated Rap2 has been found to stimulate dendritic pruning, reduce synaptic density and cause removal of synaptic AMPA receptors (AMPA-Rs) (Zhu et al., 2005; Fu et al., 2007). Here we report that MINK and TNIK are postsynaptically enriched proteins whose clustering within dendrites is bidirectionally regulated by the activation state of Rap2. Expression of MINK and TNIK in neurons is required for normal dendritic arborization and surface expression of AMPA receptors. Overexpression of a truncated MINK mutant unable to interact with Rap2 leads to reduced dendritic branching and this MINK-mediated effect on neuronal morphology is dependent upon Rap2 activation. While similarly truncated TNIK also reduces neuronal complexity, its effect does not require Rap2 activity. Furthermore, Rap2-mediated removal of surface AMPA-Rs from spines is entirely abrogated by coexpression of MINK, but not TNIK. Thus, although both MINK and TNIK bind GTP-bound Rap2, these kinases employ distinct mechanisms to modulate Rap2-mediated signaling. MINK appears to antagonize Rap2 signal transduction by binding to activated Rap2. We suggest that MINK interaction with Rap2 plays a critical role in maintaining the morphological integrity of dendrites and synaptic transmission.
On the use of genetic algorithms in database client clustering

In conventional two-tier client-server databases, clients access and modify shared data resident in a common server. As the number of clients increases, the centralized database server can become a performance bottleneck. In order to overcome this scalability problem, a three-tier client-server configuration has been proposed that features the partitioning of clients into logical clusters. Here, the objective is to maximize the data sharing among the clients in each cluster. We propose a genetic algorithm to create such client clusters and evaluate two different techniques for generating the initial solution populations. We compare the performance of the two-tier and three-tier configurations with respect to the transaction turnaround times and object response times. Our experimental results indicate that the clustered architecture can offer improved performance over its two-tier counterpart.
Pharmacokinetics of etravirine , raltegravir and darunavir / ritonavir in treatment experienced patients

Etravirine is an enzyme inducer and could lower the concentration of combined drugs. Ten HIV-1infected patients with multiple treatment failure received raltegravir (400mg, twice daily) and darunavir/ritonavir (600/100mg, twice daily). Addition of etravirine (200 mg, twice daily) leads to a significant increase in raltegravir and darunavir trough concentrations (405 vs. 118 and 3837 vs. 2241 ng/ml) and darunavir area under the curve (AUC12h) (50 083 vs. 36 277 ng h/ml). All pharmacokinetic parameters appeared to be highly variable regardless to the addition of etravirine.
The unstructured C-terminus of the τ subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the α subunit

The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by τC16 derivatives for binding to α gave values of KD of 7 μM for the α−τC16Δ7 complex. Low-level expression of the genes encoding τC16 and τC16▵7, but not τC16Δ11, is lethal to E. coli. Suppression of this lethal phenotype enabled selection of mutations in the 3′ end of the τC16 gene, that led to defects in α binding. The data suggest that the unstructured C-terminus of τ becomes folded into a helix–loop–helix in its complex with α. An N-terminally extended construct, τC24, was found to bind DNA in a salt-sensitive manner while no binding was observed for τC16, suggesting that the processivity switch of the replisome functionally involves Domain IV of τ.
On the Analysis of CMMN Expressiveness: Revisiting Workflow Patterns

Traditional business process modeling languages use an imperative style to specify all possible execution flows, leaving little flexibility to process operators. Such languages are appropriate for low-complexity, high-volume, mostly automated processes. However, they are inadequate for case management, which involves low-volume, high- complexity, knowledge-intensive work processes of today's knowledge workers. OMG's Case Management Model and Notation (CMMN), which uses a declarative style to specify constraints placed at a process execution, aims at addressing this need. To the extent that typical case management situations do include at least some measure of imperative control, it is legitimate to ask whether an analyst working exclusively in CMMN can comfortably model the range of behaviors s/he is likely to encounter. This paper aims at answering this question by trying to express the extensive collection of Workflow Patterns in CMMN. Unsurprisingly, our study shows that the workflow patterns fall into three categories: 1) the ones that are handled by CMMN basic constructs, 2) those that rely on CMMN's engine capabilities and 3) the ones that cannot be handled by current CMMN specification. A CMMN tool builder can propose patterns of the second category as companion modeling idioms, which can be translated behind the scenes into standard CMMN. The third category is problematic, however, since its support in CMMN tools will break model interoperability.
On the relationship between capacity and distance in an underwater acoustic communication channel

Path loss of an underwater acoustic communication channel depends not only on the transmission distance, but also on the signal frequency. As a result, the useful bandwidth depends on the transmission distance, a feature that distinguishes an underwater acoustic system from a terrestrial radio one. This fact influences the design of an acoustic network: a greater information throughput is available if messages are relayed over multiple short hops instead of being transmitted directly over one long hop.We asses the bandwidth dependency on the distance using an analytical method that takes into account physical models of acoustic propagation loss and ambient noise. A simple, single-path time-invariant model is considered as a first step. To assess the fundamental bandwidth limitation, we take an information-theoretic approach and define the bandwidth corresponding to optimal signal energy allocation -- one that maximizes the channel capacity subject to the constraint that the transmission power is finite. Numerical evaluation quantifies the bandwidth and the channel capacity, as well as the transmission power needed to achieve a pre-specified SNR threshold, as functions of distance. These results lead to closed-form approximations, which may become useful tools in the design and analysis of acoustic networks.
Multivariate amortized resource analysis

We study the problem of automatically analyzing the worst-case resource usage of procedures with several arguments. Existing automatic analyses based on amortization, or sized types bound the resource usage or result size of such a procedure by a sum of unary functions of the sizes of the arguments. In this paper we generalize this to arbitrary multivariate polynomial functions thus allowing bounds of the form mn which had to be grossly overestimated by m2+n2 before. Our framework even encompasses bounds like ∗i,j≤n m_i mj where the mi are the sizes of the entries of a list of length n. This allows us for the first time to derive useful resource bounds for operations on matrices that are represented as lists of lists and to considerably improve bounds on other super-linear operations on lists such as longest common subsequence and removal of duplicates from lists of lists. Furthermore, resource bounds are now closed under composition which improves accuracy of the analysis of composed programs when some or all of the components exhibit super-linear resource or size behavior. The analysis is based on a novel multivariate amortized resource analysis. We present it in form of a type system for a simple first-order functional language with lists and trees, prove soundness, and describe automatic type inference based on linear programming. We have experimentally validated the automatic analysis on a wide range of examples from functional programming with lists and trees. The obtained bounds were compared with actual resource consumption. All bounds were asymptotically tight, and the constants were close or even identical to the optimal ones.
On the impossibility of basing trapdoor functions on trapdoor predicates

We prove that, somewhat surprisingly, there is no black-box reduction of (poly-to-one) trapdoor functions to trapdoor predicates (equivalently, to public-key encryption schemes). Our proof follows the methodology that was introduced by R. Impagliazzo and S. Rudich (1989), although we use a new, weaker model of separation.
Development of microsatellite markers for identifying Brazilian Coffea arabica varieties

Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of nineteen commercially important Brazilians and six interspecific hybrids of Coffea arabica, Coffea canephora and Coffealiberica. The set used comprised 52 newly developed SSR markers derived from microsatellite enriched libraries, 56 designed on the basis of coffee SSR sequences available from public databases, 6 already published, and 13 universal chloroplast microsatellite markers. Only 22 were polymorphic, these detecting 2-7 alleles per marker, an average of 2.5. Based on the banding patterns generated by polymorphic SSR loci, the set of twenty-five coffee varieties were clustered into two main groups, one composed of only Brazilian varieties, and the other of interspecific hybrids, with a few Brazilians. Color mutants could not be separated. Clustering was in accordance with material genealogy thereby revealing high similarity.
BEE-SMART - A Natural Language Interface For Knowledge Retrieval and Service Execution over the Semantic Web2

Semantic Web technologies allow for a simplified way to represent machine perishable knowledge over Web and have significant implications in extending Web capabilities beyond our current imagination. However, in order to bring its unprecedented power to Web users, we need an intuitive, easy to use interface to retrieve knowledge and execute services over the Web. In this paper we describe a system BEE-SMART, which provides a natural language interface to sophisticated Semantic Web technologies. Broadly the system facilitates users with a) Simple Chat b) Knowledge Query c) Semantic Service Execution interfaces. The system was developed by the graduate students at University of Missouri under guidance of Dr. Yugyung Lee.
An Assessment of the Methodological Quality of Published Network Meta-Analyses: A Systematic Review

Objective To assess the methodological quality of published network meta-analysis. Design Systematic review. Methods We searched the medical literature for network meta-analyses of pharmaceuticals. We assessed general study characteristics, study transparency and reproducibility, methodological approach, and reporting of findings. We compared studies published in journals with lower impact factors with those published in journals with higher impact factors, studies published prior to January 1st, 2013 with those published after that date, and studies supported financially by industry with those supported by non-profit institutions or that received no support. Results The systematic literature search identified 854 citations. Three hundred and eighteen studies met our inclusion criteria. The number of network meta-analyses has grown rapidly, with 48% of studies published since January 2013. The majority of network meta-analyses were supported by a non-profit institution or received no support (68%). We found considerable inconsistencies among reviewed studies. Eighty percent reported search terms, 61% a network diagram, 65% sufficient data to replicate the analysis, and 90% the characteristics of included trials. Seventy percent performed a risk of bias assessment of included trials, 40% an assessment of model fit, and 56% a sensitivity analysis. Among studies with a closed loop, 69% examined the consistency of direct and indirect evidence. Sixty-four percent of studies presented the full matrix of head-to-head treatment comparisons. For Bayesian studies, 41% reported the probability that each treatment was best, 31% reported treatment ranking, and 16% included the model code or referenced publicly-available code. Network meta-analyses published in higher impact factors journals and those that did not receive industry support performed better across the assessment criteria. We found few differences between older and newer studies. Conclusions There is substantial variation in the network meta-analysis literature. Consensus among guidelines is needed improve the methodological quality, transparency, and consistency of study conduct and reporting.
The sensitive to freezing3 mutation of Arabidopsis thaliana is a cold-sensitive allele of homomeric acetyl-CoA carboxylase that results in cold-induced cuticle deficiencies

The sfr3 mutation causes freezing sensitivity in Arabidopsis thaliana. Mapping, sequencing, and transgenic complementation showed sfr3 to be a missense mutation in ACC1, an essential gene encoding homomeric (multifunctional) acetyl-CoA carboxylase. Cuticle permeability was compromised in the sfr3 mutant when plants were grown in the cold but not in the warm. Wax deposition on the inflorescence stem of cold-grown sfr3 plants was inhibited and the long-chain components of their leaf cuticular wax were reduced compared with wild-type plants. Thus, freezing sensitivity of sfr3 appears, from these results, to be due to cuticular deficiencies that develop during cold acclimation. These observations demonstrated the essential role of the cuticle in tolerance to freezing and drought.
The Topology Construction Power Control Algorithm Based on Birthday Paradox

Now, power control is an emphasis of application of Ad Hoc network. It can be used in MAC layer, network layer and application layer. Using power control in topology construction of Ad Hoc can control the connectivity of network and save the nodes' energy well. This paper provides an APCTC algorithm using birthday paradox theory to control the nodes alternate among transmitting status and dormancy status and listen status. This algorithm is based on distributed power control based topology construction, and it can reduce the energy consumption of nodes with the precondition of ensuring connectivity of network. At the end of this paper, the simulation is done for APCTC algorithm and the result is provided.
Art of expertise in stroke telemedicine: imaging and the collaterome.

See related article, p 740. Expertise in stroke telemedicine leverages advanced technology with the art of medical decision-making garnered from clinical experience in acute stroke. The Pre-Hospital Acute Neurological Therapy and Optimization of Medical Care in Stroke (PHANTOM-S) investigators demonstrate the profound effect that specialized stroke prehospital triage may have on stroke care, much as stroke unit care changed the nature of stroke management many years ago.1 The group elegantly studied the role of a stroke ambulance, the Stroke Emergency Mobile (STEMO), equipped with a computed tomographic (CT) scanner, point-of-care laboratory testing, and specialized personnel, in the delivery of appropriate patients to stroke units based on this novel framework for prehospital care. They previously reported an increased rate of intravenous thrombolysis in patients with ischemic stroke and a reduced time to treatment using the STEMO.2,3 This previous groundbreaking work on prehospital thrombolysis awaits broader validation in analyses of long-term clinical outcomes and overall costs, yet such analyses focus on a relatively small fraction of potential patients triaged with telemedicine in the field. Perhaps more importantly than measuring time to thrombolysis of patients with ischemic stroke, in this recent article, they demonstrated the effect of such telemedicine expertise on patients with both ischemic and hemorrhagic stroke. STEMO lead to improved delivery of patients with …
Fourier and wavelet spectral analysis of EMG signals in maximal constant load dynamic exercise

Frequency domain analyses of changes in electromyographic (EMG) signals over time are frequently used to assess muscle fatigue. Fourier based approaches are typically used in these analyses, yet Fourier analysis assumes signal stationarity, which is unlikely during dynamic contractions. Wavelet based methods of signal analysis do not assume stationarity and may be more appropriate for joint time-frequency domain analysis. The purpose of this study was to compare Short-Time Fourier Transform (STFT) and Continuous Wavelet Transform (CWT) in assessing muscle fatigue in maximal constant load dynamic exercise (100% Wmax). The results of this study indicate that CWT and STFT analyses give similar fatigue estimates (slope of median frequency) in maximal constant load dynamic exercise (P>0.05). However, the results of the variance was significantly lower for at least one of the muscles studied in CWT compared to STFT (P<0.05) indicating more variability in the EMG signal analysis using STFT. Thus, the stationarity assumption may not be the sole factor responsible for affecting the Fourier based estimates.
Reconstruction in the Labelled Stochastic Block Model

The labelled stochastic block model is a random graph model representing networks with community structure and interactions of multiple types. In its simplest form, it consists of two communities of approximately equal size, and the edges are drawn and labelledat random with probability depending on whether their two endpoints belong to the same community or not. It has been conjectured in [1] that correlated reconstruction (i.e., identification of a partition correlated with the true partition into the underlying communities) would be feasible if and only if a model parameter exceeds a threshold. We prove one half of this conjecture, i.e., reconstruction is impossible when below the threshold. In the positive direction, we introduce a weighted graph to exploit the label information. With a suitable choice of weight function, we show that when above the threshold by a specific constant, reconstruction is achieved by (1) minimum bisection, (2) a semidefinite relaxation of minimum bisection, and (3) a spectral method combined with removal of edges incident to vertices of high degree. Furthermore, we show that hypothesis testing between the labelled stochastic block model and the labelled Erdos-Renyi random graph model exhibits a phase transition at the conjectured reconstruction threshold.
A cathepsin F-like peptidase involved in barley grain protein mobilization, HvPap-1, is modulated by its own propeptide and by cystatins

Among the C1A cysteine proteases, the plant cathepsin F-like group has been poorly studied. This paper describes the molecular and functional characterization of the HvPap-1 cathepsin F-like protein from barley. This peptidase is N-glycosylated and has to be processed to become active by its own propeptide being an important modulator of the peptidase activity. The expression pattern of its mRNA and protein suggest that it is involved in different proteolytic processes in the barley plant. HvPap-1 peptidase has been purified in Escherichia coli and the recombinant protein is able to degrade different substrates, including barley grain proteins (hordeins, albumins, and globulins) stored in the barley endosperm. It has been localized in protein bodies and vesicles of the embryo and it is induced in aleurones by gibberellin treatment. These three features support the implication of HvPap-1 in storage protein mobilization during grain germination. In addition, a complex regulation exerted by the barley cystatins, which are cysteine protease inhibitors, and by its own propeptide, is also described
Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries1[W][OA]

Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare ‘Haruna Nijo’) under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.
System-level power optimization: techniques and tools

This tutorial surveys design methods for energy-efficient system-level design. We consider electronic sytems consisting of a hardware platform and software layers. We consider the three major constituents of hardware that consume energy, namely computation, communication, and storage units, and we review methods of reducing their energy consumption. We also study models for analyzing the energy cost of software, and methods for energy-efficient software design and compilation.This survery is organized around three main phases of a system design: conceptualization and modeling design and implementation, and runtime management. For each phase, we review recent techniques for energy-efficient design of both hardware and software.
The Integration of TESLA and FLUTE over Satellite Networks

Researches on multicast has explored security challenges faced by group communications. Multicast transport protocols and multicast security protocols need to work closely to provide reliable and secure multicast services. However, there has been comparatively little work carried out to specify how exactly the two technologies can work together efficiently. In this paper, authors present an example of partially integrating the Timed Efficient Stream Loss-Tolerant Authentication (TESLA) protocol and the File Delivery over Unidirectional Transport (FLUTE) protocol. TESLA provides source authorization and data integrity for multicast groups while FLUTE ensures reliability of the multicast transmission. This paper proposes a loose synchronization mechanism for a unidirectional transmission environment, suited to satellite networks. The proposed algorithm was implemented on a testbed with multicast tunnel between University of Surrey and University of Aberdeen and the results are presented in this paper.