Miracle-dz/UniFAR-FTUs huggingface dataset:
DnaK Protein Alleviates Toxicity Induced by Citrate-Coated Gold Nanoparticles in Escherichia coli

A number of previously reported studies suggest that synthetic gold nanoparticles (AuNPs) are capable of stabilising proteins against heat stress in vitro. However, it remains to be understood if AuNPs confer stability to proteins against cellular stress in vivo. Heat shock proteins (Hsps) are conserved molecules whose main role is to facilitate folding of other proteins (chaperone function). Hsp70 (called DnaK in prokaryotes) is one of the most prominent molecular chaperones. Since gold nanoparticles exhibit chaperone-like function in vitro, we investigated the effect of citrate-coated gold nanoparticles on the growth of E. coli BB1553 cells that possess a deleted dnaK gene. We further investigated the effects of the AuNPs on the solubility of the E. coli BB1553 proteome. E. coli BB1553 cells exposed to AuNPs exhibited cellular defects such as filamentation and plasma membranes pulled off the cell wall. The toxic effects of the AuNPs were alleviated by transforming the E. coli BB1553 cells with a construct expressing DnaK. We also noted that cells in which DnaK was restored exhibited distinct zones to which the nanoparticles were restricted. Our study suggests a role for DnaK in alleviating nanoparticle induced stress in E. coli.
When Scavengers Meet Industrial Wireless

Recent standardization efforts on industrial low-power wireless communication technologies clearly bet for the Time Slotted Channel Hopping (TSCH) medium access control (MAC) layer as it proved to achieve 99.999% reliability while ensuring deterministic behavior. Standards such as WirelessHART, ISA100.11a, and IEEE802.15. 4e rooted at the TSCH MAC layer are used to connect millions of industrial devices today, enabling the emergence of the Industrial Internet paradigm. At that point and due to the ultralow energy profile of TSCH networks, scavengers come into play, enabling autonomously powered control and monitoring systems on industries. However, putting these systems together requires a clear understanding of their behavior. Therefore, this paper presents a methodology and a model to reliably dimension scavenger properties to network requirements and application needs, allowing industries to optimize the adoption of that technologies while keeping technical risks low.
A new polynomial-time algorithm for linear programming

We present a new polynomial-time algorithm for linear programming. In the worst case, the algorithm requiresO(n3.5L) arithmetic operations onO(L) bit numbers, wheren is the number of variables andL is the number of bits in the input. The running-time of this algorithm is better than the ellipsoid algorithm by a factor ofO(n2.5). We prove that given a polytopeP and a strictly interior point a εP, there is a projective transformation of the space that mapsP, a toP′, a′ having the following property. The ratio of the radius of the smallest sphere with center a′, containingP′ to the radius of the largest sphere with center a′ contained inP′ isO(n). The algorithm consists of repeated application of such projective transformations each followed by optimization over an inscribed sphere to create a sequence of points which converges to the optimal solution in polynomial time.
DDMSVAR for Ox: a Software for Time Series Modeling with Duration Dependent Markov-Switching Vector Autoregressions

Duration dependent Markov-switching VAR (from now on DDMS-VAR) models are time series models with data generating process consisting in a mixture of two VAR processes, which switches according to a two-state Markov chain with transition probabilities depending on how long the process has been in a state. Interesting applications of this class of models have been carried out in business cycle analysis and in ﬁnance. In the present paper we introduce DDMSVAR for Ox, a software written by the author, for the analysis of time series by means of DDMS-VAR models. Possible uses of this software are shown through applications with real data
A fully integrated all-digital PLL based FM-radio Transmitter in 90 nm CMOS

A fully integrated FM-radio Transmitter (TX) is fabricated in 90 nm CMOS. It is based on an all-digital phase-locked-loop (ADPLL) and designed for co-integration in future nanoscale CMOS mobile applications. The in-band synthesizer phase noise is measured below −85 dBc/Hz for the loop bandwidth of 110 kHz. The 0.25 mm2 chip consumes 12.4 mW using a 1 V supply and provides 87 MHz to 108 MHz output frequency.
The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group

The Mouse Genome Database (MGD) is a comprehensive community resource of mouse genetic and biological information populated both with data from published literature and with data electronically submitted from the research community. MGD stores genetic, physical and comparative mapping data, clones/probes/PCR information, and phenotype descriptions for genes, mutations and mouse strains. Supporting software for importation, analysis, display and distribution of mouse genetic data have been developed. User support is provided through dedicated staff providing documentation, training, and response to individual user queries. MGD is accessible over the Internet at URL http://www.informatics. jax.org.
[Analysis of the parental origin of MECP2 mutations in patients with Rett syndrome].

OBJECTIVE To identify the parental origin of methyl-CpG-binding protein 2 (MECP2) gene mutations in Chinese patients with Rett syndrome. METHODS Single nucleotide polymorphisms (SNPs) in intron 3 of the MECP2 gene were analyzed by PCR and sequencing in 115 patients with Rett syndrome. Then sequencing of the SNP region was performed for the fathers of the patients who had at least one SNP, to determine which allele was from the father. Then allele-specific PCR was performed and the products were sequenced to see whether the allele from father or mother harbored the mutation. RESULTS Seventy-six of the 115 patients had at least one SNP. Three hot SNPs were found in these patients. They were: IVS3+22C >G, IVS3+266C >T and IVS3+683C>T. Among the 76 cases, 73 had a paternal origin of MECP2 mutations, and the other 3 had a maternal origin. There were multiple types of MECP2 mutation of the paternal origin, including 4 frame shift, 2 deletion and 67 point (56C >T, 6C >G, 2A >G, 2G >T and 1A >T) mutations. The mutation types of the 3 patients with maternal origin included 2 frame shift and 1 point (C >T) mutation. CONCLUSION In Chinese RTT patients, the MECP2 mutations are mostly of paternal origin.
Sensor coverage with a multi-robot system

The present paper develops a novel strategy for the exploration of an unknown environment with a multi-robot system. It is required that the entire free space is covered by the sensors of the robots, with a certainty of 100%. Communication between the robots is restricted to line-of-sight and to a maximum interdistance between robots. Contrary to most exploration problems, the topographical properties of the space need not be mapped. An algorithm is presented that guides a group of N robots, scanning the free space for target objects. The group splits to pass obstacles of unknown size and shape. The decision of splitting the group takes a trade-off between group coherence and speed of advancing into account. A direct application of the algorithm is mine held clearance.
Characterization of the D-amino acid oxidase interactome

Schizophrenia is a psychiatric disorder affecting about 1% of the world's population and manifests itself as positive symptoms (eg. hallucinations), negative symptoms (eg. social withdrawal) in conjunction with cognitive impairments (eg. working memory). Evidence suggests that schizophrenia is, in part, a heritable disease. Candidate susceptibility genes implicate the glutamatergic neurotransmitter system, reinforcing clinical observations of N-methyl-D-aspartate receptor (NMDAR) hypofunction in schizophrenia. One of those genes, D-amino acid oxidase (DAO), is genetically associated with schizophrenia and its function includes degradation of D-serine, the NMDAR co-agonist. DAO is a candidate gene of high interest due to schizophrenic patients' manifestation of reduced D-serine levels, increased DAO expression and increased DAO activity. Despite mounting evidence for DAO involvement in schizophrenia, its regulation is poorly understood. Characterization of DAO may lead to a more thorough understanding of its function and biology and ultimately to the identification of novel targets for this disorder. To this end, DAO-specific antibodies were utilized to identify DAO-interacting proteins through co-immunoprecipitation from rat cerebellum, where DAO expression is especially high. Subsequent mass spectroscopy analysis of associating proteins yielded twenty-four putative DAO interactors. The most abundant and interesting interactors include known presynaptic active zone members such as bassoon (BSN) and piccolo (PCLO). The DAO interaction with BSN was confirmed through co-immunoprecipitation and both proteins were shown to localize in the presynaptic junction. These data suggest that BSN is a novel DAO interactor and defines a previously unappreciated localization of DAO perhaps as a result of a physiologically important interaction with BSN. Furthermore, BSN was found to partially inhibit DAO enzymatic activity in transiently transfected human embryonic kidney (Hek293) cells. Collectively these novel findings suggest that synaptic D-serine concentration may be under tight regulation by BSN via proximally localized DAO. DAO may thus play a role in modulating the functions of the presynaptic active zone via its interaction with BSN.
Lipid peroxidative stress and antioxidant defence status during ontogeny of rainbow trout (Oncorhynchus mykiss)

The objective of the present study was to characterise some important antioxidant enzymes and their relationships with retinoids and lipid peroxidation during rainbow trout (Oncorhynchus mykiss) early development. Eggs were incubated at 7°C until the swim-up stage whereupon fry were fed two semi-purified diets with 0 % (CO) and 8 % (OX) oxidised lipid respectively for 2 months at 17°C. The activities and gene expression of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) were determined as well as the levels of retinoids, F2-isoprostanes and lipid-soluble fluorescent products (LSFP) at various developmental stages. Only SOD had a detectable activity in embryos which increased during development and was linked with an increase of mitochondrial (SOD2) and cytosolic (SOD1) gene expression. SOD1 and SOD2 mRNA were more abundant in fry fed OX than in fry fed CO. CAT activity and gene expression also increased during development and were higher in fry fed OX compared with fry fed CO. Activity of Se-dependent GPX (Se-GPX) increased during development. The gene expression of cytosolic Se-GPX (GPX1) increased from hatching to 2-month-fed fry. Both phospholipid-hydroperoxide GPX and GPX1 genes were more expressed in fry fed OX than in fry fed CO. Retinoids decreased during development and, by 2 months, were lowered in fry fed OX compared with those fed CO. The levels of LSFP were higher in fry fed OX compared with fry fed CO. The present study demonstrates that antioxidant defence systems are active all through the development of rainbow trout and modulated by feeding oxidised lipid.
Unified Theory of Source Coding: Part II -- Multiterminal Problems

Since the publication of Shannon's theory of one terminal source coding, a number of interesting extensions have been derived by researchers such as Slepian-Wolf, Wyner, Ahlswede-K\"{o}rner, Wyner-Ziv and Berger-Yeung. Specifically, the achievable rate or rate-distortion region has been described by a first order information-theoretic functional of the source statistics in each of the above cases. At the same time several problems have also remained unsolved. Notable two terminal examples include the joint distortion problem, where both sources are reconstructed under a combined distortion criterion, as well as the partial side information problem, where one source is reconstructed under a distortion criterion using information about the other (side information) available at a certain rate (partially). In this paper we solve both of these open problems. Specifically, we give an infinite order description of the achievable rate-distortion region in each case. In our analysis we set the above problems in a general framework and formulate a unified methodology that solves not only the problems at hand but any two terminal problem with noncooperative encoding. The key to such unification is held by a fundamental source coding principle which we derive by extending the typicality arguments of Shannon and Wyner-Ziv. Finally, we demonstrate the expansive scope of our technique by re-deriving known coding theorems. We shall observe that our infinite order descriptions simplify to the expected first order in the known special cases.
Parameterized Runtime Analyses of Evolutionary Algorithms for the Planar Euclidean Traveling Salesperson Problem

Parameterized runtime analysis seeks to understand the influence of problem structure on algorithmic runtime. In this paper, we contribute to the theoretical understanding of evolutionary algorithms and carry out a parameterized analysis of evolutionary algorithms for the Euclidean traveling salesperson problem (Euclidean TSP). We investigate the structural properties in TSP instances that influence the optimization process of evolutionary algorithms and use this information to bound their runtime. We analyze the runtime in dependence of the number of inner points k. In the first part of the paper, we study a EA in a strictly black box setting and show that it can solve the Euclidean TSP in expected time where A is a function of the minimum angle between any three points. Based on insights provided by the analysis, we improve this upper bound by introducing a mixed mutation strategy that incorporates both 2-opt moves and permutation jumps. This strategy improves the upper bound to . In the second part of the paper, we use the information gained in the analysis to incorporate domain knowledge to design two fixed-parameter tractable (FPT) evolutionary algorithms for the planar Euclidean TSP. We first develop a EA based on an analysis by M. Theile, 2009, ”Exact solutions to the traveling salesperson problem by a population-based evolutionary algorithm,” Lecture notes in computer science, Vol. 5482 (pp. 145–155), that solves the TSP with k inner points in generations with probability . We then design a EA that incorporates a dynamic programming step into the fitness evaluation. We prove that a variant of this evolutionary algorithm using 2-opt mutation solves the problem after steps in expectation with a cost of for each fitness evaluation.
Power Optimal Signaling for Fading Multi-Access Channel in Presence of Coding Gap

In a multi-access fading channel, dynamic allocation of bandwidth, transmission power and rates is an important aspect to counter the detrimental effect of time-varying nature of the channel. Most of the existing work on dynamic resource allocation assumes capacity achieving codes for various signaling schemes like TDMA, FDMA, CDMA and successive decoding. For the capacity achieving codes, the rate achievable by the user is log(1 + SNR), where SNR denotes the signal to noise ratio of the user at the receiver side. However, codes that are used in practice have a finite gap to capacity, i.e., the achievable rate is log(1 + SNR/Γ) Γ > 1. The exact value of Γ depends on the coding strategy and the desired bit error rate. Many existing resource allocation techniques that are optimal for capacity achieving codes perform sub-optimally in presence of the coding gap. For example, successive decoding does not always minimize the sum power required for providing the desired rate to each of the users for Γ > 1. The problem of minimizing the sum power while guaranteeing the required rate to each of the users is important for both real-time and non real-time applications, and is addressed here. We obtain the resource allocation that is optimal for the above problem in presence of the coding gap.
Phosphorylation of Yeast Hexokinase 2 Regulates Its Nucleocytoplasmic Shuttling*

Background: Nucleocytoplasmic transport of Hxk2 is mediated by the α/β-importins (Kap60/Kap95) and the Xpo1(Crm1) exportin. Results: Hxk2 phosphorylation affects its subcellular localization and its interaction with karyopherins Kap60 and Xpo1. Conclusion: The shuttling back and forth of Hxk2 between the nucleus and the cytoplasm is regulated by phosphorylation and dephosphorylation of serine 14. Significance: Regulating the subcellular distribution of Hxk2 represents a novel physiological function mediated by Snf1 and Glc7-Reg1 proteins. Nucleocytoplasmic shuttling of Hxk2 induced by glucose levels has been reported recently. Here we present evidence that indicates that Hxk2 nucleocytoplasmic traffic is regulated by phosphorylation and dephosphorylation at serine 14. Moreover, we identified the protein kinase Snf1 and the protein phosphatase Glc7-Reg1 as novel regulatory partners for the nucleocytoplasmic shuttling of Hxk2. Functional studies revealed that, in contrast to the wild-type protein, the dephosphorylation-mimicking mutant of Hxk2 retains its nuclear localization in low glucose conditions, and the phosphomimetic mutant of Hxk2 retains its cytoplasmic localization in high glucose conditions. Interaction experiments of Hxk2 with Kap60 and Xpo1 indicated that nuclear import of the S14D mutant of Hxk2 is severely decreased but that the export is significantly enhanced. Conversely, nuclear import of the S14A mutant of Hxk2 was significantly enhanced, although the export was severely decreased. The interaction of Hxk2 with Kap60 and Xpo1 was found to occur in the dephosphorylated and phosphorylated states of the protein, respectively. In addition, we found that Hxk2 is a substrate for Snf1. Mutational analysis indicated that serine 14 is a major in vitro and in vivo phosphorylation site for Snf1. We also provide evidence that dephosphorylation of Hxk2 at serine 14 is a protein phosphatase Glc7-Reg1-dependent process. Taken together, this study establishes a functional link between Hxk2, Reg1, and Snf1 signaling, which involves the regulation of Hxk2 nucleocytoplasmic shuttling by phosphorylation-dephosphorylation of serine 14.
On fuzzy logic control of PV/T based reverse Osmosis desalination plant

Reverse Osmosis desalination process supplied by Photovoltaic Thermal collectors presents a practical method for water desalination [1]. It is shown that the control of the circulated fluid rate ameliorates the system productivity. Photovoltaic Thermal collector combines between heat and electric energy production. In addition, the fluid flow rate variation inside the collector ducts decreases photovoltaic cells temperature. Feed water temperature is increased by the produced heat in order to improve the Reverse Osmosis unit productivity. The system control serves also to prevent overheating Photovoltaic cells and stored water in the boiler. In this paper, a Fuzzy Logic Controller is designed to achieve these objectives. The controller effectiveness is validated using LABVIEW.
An Efficient Chart-based Algorithm for Partial-Parsing of Unrestricted Texts

We present an efficient algorithm for chart-based phrase structure parsing of natural language that is tailored to the problem of extracting specific information from unrestricted texts where many of the words are unknown and much of the text is irrelevant to the task. The parser gains algorithmic efficiency through a reduction of its search space. As each new edge is added to the chart, the algorithm checks only the topmost of the edges adjacent to it, rather than all such edges as in conventional treatments. The resulting spanning edges are insured to be the correct ones by carefully controlling the order in which edges are introduced so that every final constituent covers the longest possible span. This is facilitated through the use of phrase boundary heuristics based on the placement of function words, and by heuristic rules that permit certain kinds of phrases to be deduced despite the presence of unknown words. A further reduction in the search space is achieved by using semantic rather than syntactic categories on the terminal and nonterminal edges, thereby reducing the amount of ambiguity and thus the number of edges, since only edges with a valid semantic interpretation are ever introduced.
Perisomatic Voltage-Gated Sodium Channels Actively Maintain Linear Synaptic Integration in Principal Neurons of the Medial Superior Olive

Principal neurons of the medial superior olive (MSO) compute azimuthal sound location by integrating phase-locked inputs from each ear. While previous experimental and modeling studies have proposed that voltage-gated sodium channels (VGSCs) play an important role in synaptic integration in the MSO, these studies appear at odds with the unusually weak active backpropagation of action potentials into the soma and dendrites. To understand the spatial localization and biophysical properties of VGSCs, we isolated sodium currents in MSO principal neurons in gerbil brainstem slices. Nucleated and cell-attached patches revealed that VGSC density at the soma is comparable to that of many other neuron types, but channel expression is largely absent from the dendrites. Further, while somatic VGSCs activated with conventional voltage dependence (V1/2 = −30 mV), they exhibited an unusually negative range of steady-state inactivation (V1/2 = −77 mV), leaving ∼92% of VGSCs inactivated at the resting potential (approximately −58 mV). In current-clamp experiments, non-inactivated VGSCs were sufficient to amplify subthreshold EPSPs near action potential threshold, counterbalancing the suppression of EPSP peaks by low voltage-activated potassium channels. EPSP amplification was restricted to the perisomatic region of the neuron, and relatively insensitive to preceding inhibition. Finally, computational modeling showed that the exclusion of VGSCs from the dendrites equalizes somatic EPSP amplification across synaptic locations and lowered the threshold for bilateral versus unilateral excitatory synaptic inputs. Together, these findings suggest that the pattern of sodium channel expression in MSO neurons contributes to these neurons' selectivity for coincident binaural inputs.