Miracle-dz/UniFAR-FTUs huggingface dataset:
Calcium regulation of neuronal gene expression

Plasticity is a remarkable feature of the brain, allowing neuronal structure and function to accommodate to patterns of electrical activity. One component of these long-term changes is the activity-driven induction of new gene expression, which is required for both the long-lasting long-term potentiation of synaptic transmission associated with learning and memory, and the activitydependent survival events that help to shape and wire the brain during development. We have characterized molecular mechanisms by which neuronal membrane depolarization and subsequent calcium influx into the cytoplasm lead to the induction of new gene transcription. We have identified three points within this cascade of events where the specificity of genes induced by different types of stimuli can be regulated. By using the induction of the gene that encodes brain-derived neurotrophic factor (BDNF) as a model, we have found that the ability of a calcium influx to induce transcription of this gene is regulated by the route of calcium entry into the cell, by the pattern of phosphorylation induced on the transcription factor cAMP-response element (CRE) binding protein (CREB), and by the complement of active transcription factors recruited to the BDNF promoter. These results refine and expand the working model of activity-induced gene induction in the brain, and help to explain how different types of neuronal stimuli can activate distinct transcriptional responses.
Molecular Interactions of a Soluble Gibberellin Receptor, GID1, with a Rice DELLA Protein, SLR1, and Gibberellin[W]

GIBBERELLIN INSENSITIVE DWARF1 (GID1) encodes a soluble gibberellin (GA) receptor that shares sequence similarity with a hormone-sensitive lipase (HSL). Previously, a yeast two-hybrid (Y2H) assay revealed that the GID1-GA complex directly interacts with SLENDER RICE1 (SLR1), a DELLA repressor protein in GA signaling. Here, we demonstrated, by pull-down and bimolecular fluorescence complementation (BiFC) experiments, that the GA-dependent GID1–SLR1 interaction also occurs in planta. GA4 was found to have the highest affinity to GID1 in Y2H assays and is the most effective form of GA in planta. Domain analyses of SLR1 using Y2H, gel filtration, and BiFC methods revealed that the DELLA and TVHYNP domains of SLR1 are required for the GID1–SLR1 interaction. To identify the important regions of GID1 for GA and SLR1 interactions, we used many different mutant versions of GID1, such as the spontaneous mutant GID1s, N- and C-terminal truncated GID1s, and mutagenized GID1 proteins with conserved amino acids replaced with Ala. The amino acid residues important for SLR1 interaction completely overlapped the residues required for GA binding that were scattered throughout the GID1 molecule. When we plotted these residues on the GID1 structure predicted by analogy with HSL tertiary structure, many residues were located at regions corresponding to the substrate binding pocket and lid. Furthermore, the GA–GID1 interaction was stabilized by SLR1. Based on these observations, we proposed a molecular model for interaction between GA, GID1, and SLR1.
Exploring cross-language statistical machine translation for closely related South Slavic languages

This work investigates the use of crosslanguage resources for statistical machine translation (SMT) between English and two closely related South Slavic languages, namely Croatian and Serbian. The goal is to explore the effects of translating from and into one language using an SMT system trained on another. For translation into English, a loss due to cross-translation is about 13% of BLEU and for the other translation direction about 15%. The performance decrease for both languages in both translation directions is mainly due to lexical divergences. Several language adaptation methods are explored, and it is shown that very simple lexical transformations already can yield a small improvement, and that the most promising adaptation method is using a Croatian-Serbian SMT system trained on a very small corpus.
Bokode: imperceptible visual tags for camera based interaction from a distance

We show a new camera based interaction solution where an ordinary camera can detect small optical tags from a relatively large distance. Current optical tags, such as barcodes, must be read within a short range and the codes occupy valuable physical space on products. We present a new low-cost optical design so that the tags can be shrunk to 3mm visible diameter, and unmodified ordinary cameras several meters away can be set up to decode the identity plus the relative distance and angle. The design exploits the bokeh effect of ordinary cameras lenses, which maps rays exiting from an out of focus scene point into a disk like blur on the camera sensor. This bokeh-code or Bokode is a barcode design with a simple lenslet over the pattern. We show that a code with 15μm features can be read using an off-the-shelf camera from distances of up to 2 meters. We use intelligent binary coding to estimate the relative distance and angle to the camera, and show potential for applications in augmented reality and motion capture. We analyze the constraints and performance of the optical system, and discuss several plausible application scenarios.
A New Screen for Tuberculosis Drug Candidates Utilizing a Luciferase-Expressing Recombinant Mycobacterium bovis Bacillus Calmette-Guéren

Tuberculosis (TB) is a serious infectious disease caused by a bacterial pathogen. Mortality from tuberculosis was estimated at 1.5 million deaths worldwide in 2013. Development of new TB drugs is needed to not only to shorten the medication period but also to treat multi-drug resistant and extensively drug-resistant TB. Mycobacterium tuberculosis (Mtb) grows slowly and only multiplies once or twice per day. Therefore, conventional drug screening takes more than 3 weeks. Additionally, a biosafety level-3 (BSL-3) facility is required. Thus, we developed a new screening method to identify TB drug candidates by utilizing luciferase-expressing recombinant Mycobacterium bovis bacillus Calmette-Guéren (rBCG). Using this method, we identified several candidates in 4 days in a non-BSL-3 facility. We screened 10,080 individual crude extracts derived from Actinomyces and Streptomyces and identified 137 extracts which possessed suppressive activity to the luciferase of rBCG. Among them, 41 compounds inhibited the growth of both Mtb H37Rv and the extensively drug-resistant Mtb (XDR-Mtb) strains. We purified the active substance of the 1904–1 extract, which possessed strong activity toward rBCG, Mtb H37Rv, and XDR-Mtb but was harmless to the host eukaryotic cells. The MIC of this substance was 0.13 μg/ml, 0.5 μg/ml, and 2.0–7.5 μg/ml against rBCG, H37Rv, and 2 XDR-strains, respectively. Its efficacy was specific to acid-fast bacterium except for the Mycobacterium avium intracellular complex. Mass spectrometry and nuclear magnetic resonance analyses revealed that the active substance of 1904–1 was cyclomarin A. To confirm the mode of action of the 1904-1-derived compound, resistant BCG clones were used. Whole genome DNA sequence analysis showed that these clones contained a mutation in the clpc gene which encodes caseinolytic protein, an essential component of an ATP-dependent proteinase, and the likely target of the active substance of 1904–1. Our method provides a rapid and convenient screen to identify an anti-mycobacterial drug.
Evaluation of wildfire occurrence along high voltage power line by remote sensing data: A case study in Xianning, Hubei, China

In winter and spring, wildfire along the power line is the key hazard for State Grid Corporation of China in Hubei province. Remote sensing has been proved an effective technique for wildfire surveillance. This paper fused remote sensing data, meteorological data, and topography data to evaluate wildfire occurrence possibility along high voltage power line. According to the correlations among these factors, the Analytic Hierarchy Process (AHP) method was employed to evaluate these factors' weight and correlation function. The historical fire accidents along high voltage power lines in Xianning were used to validate the evaluation. The experimental results showed that the vegetation coverage, normalized difference vegetation index (NDVI) and precipitation are influential on wildfire accidents in this area. The evaluated wildfire occurrence results were used for the local company's routine fire patrol arrangement.
Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance

Objectives The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods. Methods Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied. Results Using a z score value of 3 as the cut-off, 98.11% - 100% (104-106/106) specificity and 100% (24/24) sensitivity and 99.06% - 100% (105-106/106) specificity and 100% (24/24) sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantly—p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively. Conclusions Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide.
Cognitive domains that predict time to diagnosis in prodromal Huntington disease

Background Prodromal Huntington's disease (prHD) is associated with a myriad of cognitive changes but the domains that best predict time to clinical diagnosis have not been studied. This is a notable gap because some domains may be more sensitive to cognitive decline, which would inform clinical trials. Objectives The present study sought to characterise cognitive domains underlying a large test battery and for the first time, evaluate their ability to predict time to diagnosis. Methods Participants included gene negative and gene positive prHD participants who were enrolled in the PREDICT-HD study. The CAG–age product (CAP) score was the measure of an individual's genetic signature. A factor analysis of 18 tests was performed to identify sets of measures or latent factors that elucidated core constructs of tests. Factor scores were then fit to a survival model to evaluate their ability to predict time to diagnosis. Results Six factors were identified: (1) speed/inhibition, (2) verbal working memory, (3) motor planning/speed, (4) attention–information integration, (5) sensory–perceptual processing and (6) verbal learning/memory. Factor scores were sensitive to worsening of cognitive functioning in prHD, typically more so than performances on individual tests comprising the factors. Only the motor planning/speed and sensory–perceptual processing factors predicted time to diagnosis, after controlling for CAP scores and motor symptoms. Conclusions The results suggest that motor planning/speed and sensory–perceptual processing are important markers of disease prognosis. The findings also have implications for using composite indices of cognition in preventive Huntington's disease trials where they may be more sensitive than individual tests.
Genetic algorithm-assisted joint quantised precoding and transmit antenna selection in multi-user multi-input multi-output systems

This study presents a simple and efficient genetic algorithm-assisted approach for joint quantised precoding and transmit antenna selection based on the criterion of maximum capacity. The objective is to alleviate the effect of multi-user interference and to reduce hardware costs, such as the cost of radio frequency chains associated with antennas in the downlink of multi-input multi-output systems with limited feedback. To avoid the enormous search effort required by existing approaches, the authors propose a novel variant of the conventional genetic algorithm, called the hybrid genetic algorithm, in which each chromosome is divided into a bit string for precoding vector selection and an integer string for transmit antenna selection. In addition, new crossover and mutation operations are employed to accommodate these new chromosomes. The results of simulations show that the performance of the proposed approach is close to that of the exhaustive search method, but its computational complexity is substantially lower.
Synaptic transmission and plasticity require AMPA receptor anchoring via its N-terminal domain

AMPA-type glutamate receptors (AMPARs) mediate fast excitatory neurotransmission and are selectively recruited during activity-dependent plasticity to increase synaptic strength. A prerequisite for faithful signal transmission is the positioning and clustering of AMPARs at postsynaptic sites. The mechanisms underlying this positioning have largely been ascribed to the receptor cytoplasmic C-termini and to AMPAR-associated auxiliary subunits, both interacting with the postsynaptic scaffold. Here, using mouse organotypic hippocampal slices, we show that the extracellular AMPAR N-terminal domain (NTD), which projects midway into the synaptic cleft, plays a fundamental role in this process. This highly sequence-diverse domain mediates synaptic anchoring in a subunit-selective manner. Receptors lacking the NTD exhibit increased mobility in synapses, depress synaptic transmission and are unable to sustain long-term potentiation (LTP). Thus, synaptic transmission and the expression of LTP are dependent upon an AMPAR anchoring mechanism that is driven by the NTD. DOI: http://dx.doi. org/10.7554/eLife.23024. 001
Subcellular Localization Screening of Colletotrichum higginsianum Effector Candidates Identifies Fungal Proteins Targeted to Plant Peroxisomes, Golgi Bodies, and Microtubules

The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum, encodes a large inventory of putative secreted effector proteins that are sequentially expressed at different stages of plant infection, namely appressorium-mediated penetration, biotrophy and necrotrophy. However, the destinations to which these proteins are addressed inside plant cells are unknown. In the present study, we selected 61 putative effector genes that are highly induced in appressoria and/or biotrophic hyphae. We then used Agrobacterium-mediated transformation to transiently express them as N-terminal fusions with fluorescent proteins in cells of Nicotiana benthamiana for imaging by confocal microscopy. Plant compartments labeled by the fusion proteins in N. benthamiana were validated by co-localization with specific organelle markers, by transient expression of the proteins in the true host plant, Arabidopsis thaliana, and by transmission electron microscopy-immunogold labeling. Among those proteins for which specific subcellular localizations could be verified, nine were imported into plant nuclei, three were imported into the matrix of peroxisomes, three decorated cortical microtubule arrays and one labeled Golgi stacks. Two peroxisome-targeted proteins harbored canonical C-terminal tripeptide signals for peroxisome import via the PTS1 (peroxisomal targeting signal 1) pathway, and we showed that these signals are essential for their peroxisome localization. Our findings provide valuable information about which host processes are potentially manipulated by this pathogen, and also reveal plant peroxisomes, microtubules, and Golgi as novel targets for fungal effectors.
A tale of two cities : local government, community events and social capital building : a thesis presented in partial fulfilment of the requirements for the degree of Master of Business Studies (Communication) at Massey University, Wellington, New Zealand

i Acknowledgements iii Table of contents iv Introduction 1 Background to research project 1 Research questions and objectives 3 Local government in New Zealand 4 The research setting 6 Key guiding documents 7 Events portfolio 8 Events resources for event organisers 9 Literature review 12 Background 12 Definition: Event 13 Mega and major events 13 Festivals 17 Community events 19 Event objectives & strategic planning 21 Stakeholders 29 Event organisers & the host community 35 Social capital 37 Social capital & events 43 Impacts 47 Social impacts 49 Social impact measures 53 Economic impacts 57 Methodology 60 Participants 60 Selection & recruitment 61 Data collection 63
Orbitronics — Harnessing metal insulator phase transition in 1T-MoSe2

In this work, we reveal a remarkable orbital ordering texture associated with a Peierls distortion that leads to metal-insulator phase transition (MIT) in 1T molybdenum diselenide (MoSe2). The metallic conductivity in this MIT is realized by an isotropically distributed Mo t2g orbitals whereas splitting of both t2g and eg orbitals near the Fermi level opens a bandgap in distorted semiconducting phase. Our results also indicate that a stacking of two orbitally ordered layers allows triggering of phase transition by external perturbations such as, vertical pressure and vertical electric field.
Untangling cloth

Deficient cloth-to-cloth collision response is the most serious shortcoming of most cloth simulation systems. Past approaches to cloth-cloth collision have used history to decide whether nearby cloth regions have interpenetrated. The biggest pitfall of history-based methods is that an error anywhere along the way can give rise to persistent tangles. This is a particularly serious issue for production character animation, because characters' bodies routinely self-intersect, for instance in the bend of an elbow or knee, or where the arm or hand rests against the body. Cloth that becomes pinched in these regions is often forced into jagged self-intersections that defeat history-based methods, leaving a tangled mess when the body parts separate. This paper describes a history-free cloth collision response algorithm based on global intersection analysis of cloth meshes at each simulation step. The algorithm resolves tangles that arise during pinching as soon as the surrounding geometry permits, and also resolves tangled initial conditions. The ability to untangle cloth after pinching is not sufficient, because standard cloth-solid collision algorithms handle pinches so poorly that they often give rise to visible flutters and other simulation artifacts during the pinch. As a companion to the global intersection analysis method, we present a cloth-solid collision algorithm called collision flypapering, that eliminates these artifacts. The two algorithms presented have been used together extensively and successfully in a production animation environment.
Income Redistribution Effects in the Presence of Region-Specific Factors

This paper examines the effect of changes in factor endowments on income Distribution in a four-factor, there-commodity model, in which two of the factors are region-specific while the other two are inter-regionally and inter-sectorally mobile. We provide an intermediate run model which bridges the gap between the Heckscher-Ohlin-Samuelson and the specific factor models, and which yields Results which differ from both these models. A simple derivation of factor Friendship patterns is made possible by exploiting the properties of the GNP Function. The procedure used may be applied to any n-commodity, (n+1)-factor Model. [F20]
A virtual instrument for time-frequency analysis

A virtual instrument for time-frequency analysis is presented. Its realization is based on an order recursive approach to the time-frequency signal analysis. Starting from the short time Fourier transform and using the S-method, a distribution having the auto-terms concentrated as high as in the Wigner distribution, without cross-terms, may be obtained. The same relation is used in a recursive manner to produce higher order time-frequency representations without cross-terms. Thus, the introduction of this new virtual instrument for time-frequency analysis may be of help to the scientists and practitioners in signal analysis. Application of the instrument is demonstrated on several simulated and real data examples.
Strictly-Localized Construction of Near-Optimal Power Spanners for Wireless Ad-Hoc Networks

We present a strictly-localized distributed algorithm that, given a wireless ad-hoc network modeled as a unit disk graph in the plane, constructs a planar power spanner of whose degree is bounded by and whose stretch factor is bounded by , where is an integer parameter and ! is the power exponent constant. For the same degree bound , the stretch factor of our algorithm significantly improves the previous best bounds by Song et al. and Kanj and Perkovic. We show that this bound is near-optimal by proving that the slightly smaller stretch factor of " # $ % &(') is unattainable for the same degree bound . In contrast to previous algorithms by Song et al. and by Kanj and Perkovic, the presented algorithm is strictly localized: the construction of the power spanner depends solely on the local structure and does not require information propagation. As a consequence, the algorithm is highly scalable and robust. Moreover, on a graph with * points and + edges the algorithm exchanges no more than ,+messages and has a local processing time of ,. / 01.2 435,*6/ 01* at a node of degree . Finally, while the algorithm is efficient and easy to implement in practice, it relies on deep insights on the geometry of unit disk graphs and novel techniques that are of independent interest.
Protecting distributed software upgrades that involve message-passing

We present in this paper an extension of the message-driven confidence-driven framework that we developed for onboard guarded software upgrading. The purpose of this work is to provide the framework with the capability of protecting distributed software upgrades that involve message-passing interface changes. To achieve this goal, we propose an approach to clustering the components involved in software upgrades and those involved in message-passing interface changes, such that from outside the cluster all those components can be perceived collectively as one virtual low-confidence component. Moreover, we develop a confidence-driven mechanism that enables combined use of sender- and receiver-side message logging for efficient, fine-grained error containment and recovery. The paper provides a detailed algorithm description.