Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Drought is one of the vitally critical environmental stresses affecting both growth and yield potential in rice. Drought resistance is a complicated quantitative trait that is regulated by numerous small effect loci and hundreds of genes controlling various morphological and physiological responses to drought. For this study, 270 rice landraces and cultivars were analyzed for their drought resistance. This was done via determination of changes in plant height and grain yield under contrasting water regimes, followed by detailed identification of the underlying genetic architecture via genome-wide association study (GWAS). We controlled population structure by setting top two eigenvectors and combining kinship matrix for GWAS in this study. Eighteen, five, and six associated loci were identified for plant height, grain yield per plant, and drought resistant coefficient, respectively. Nine known functional genes were identified, including five for plant height (OsGA2ox3, OsGH3-2, sd-1, OsGNA1, and OsSAP11/OsDOG), two for grain yield per plant (OsCYP51G3 and OsRRMh) and two for drought resistant coefficient (OsPYL2 and OsGA2ox9), implying very reliable results. A previous study reported OsGNA1 to regulate root development, but this study reports additional controlling of both plant height and root length. Moreover, OsRLK5 is a new drought resistant candidate gene discovered in this study. OsRLK5 mutants showed faster water loss rates in detached leaves. This gene plays an important role in the positive regulation of yield-related traits under drought conditions. We furthermore discovered several new loci contributing to the three investigated traits (plant height, grain yield, and drought resistance). These associated loci and candidate genes significantly improve our knowledge of the genetic control of these traits in rice. In addition, many drought resistant cultivars screened in this study can be used as parental genotypes to improve drought resistance of rice by molecular breeding.
Active pose SLAM with RRT*

We propose a novel method for robotic exploration that evaluates paths that minimize both the joint path and map entropy per meter traveled. The method uses Pose SLAM to update the path estimate, and grows an RRT* tree to generate the set of candidate paths. This action selection mechanism contrasts with previous approaches in which the action set was built heuristically from a sparse set of candidate actions. The technique favorably compares against the classical frontier-based exploration and other Active Pose SLAM methods in simulations in a common publicly available dataset.
Gaussian Processes for regression in channel equalization

Linear equalizers underperform in dispersive channels with additive white noise, because optimal decision functions are nonlinear. In this paper we present Gaussian Processes (GPs) for regression as new nonlinear equalizer for digital communication systems. GPs can be cast as nonlinear MMSE, a common criterion in digital communications. Unlike other nonlinear kernel based methods, such as kernel adaline or support vector machines, the solutions produced by GPs are analytical, and the hyperparameters can be readily learnt by maximum likelihood. Hence, we avoid cross-validation or noise estimation, and improve convergence speed. We present experimental results, over linear and nonlinear channel models, to show that GP-equalizers outperform linear and nonlinear state-of-the-art solutions.
Effects of agriculture, urbanization, and climate on water quality in the northern
Great Plains

The Qu'Appelle Valley drainage system provides water to a third of the population of the Canadian Great Plains, yet is plagued by poor water quality, excess plant growth, and periodic fish kills. Fossil algae (diatoms, pigments) and invertebrates (chironomids) in Pasqua Lake were analyzed by variance partitioning analysis (VPA) to determine the relative importance of climate, resource use, and urbanization as controls of aquatic community composition 1920‐1994. From fossil analyses, we identified three distinct biological assemblages in Pasqua Lake. Prior to agriculture (ca. 1776‐1890), the lake was naturally eutrophic with abundant cyanobacterial carotenoids (myxo‐xanthophyll, aphanizophyll), eutrophic diatoms (Stephanodiscus niagarae, Aulacoseira granulata, Fragilaria capucina/bidens), and anoxia‐tolerant chironomids (Chironomus). Principal components (PCA) and dissimilarity analyses demonstrated that diatom and chironomid communities did not vary significantly (P > 0.05) before European settlement. Communities changed rapidly during early land settlement (ca. 1890‐1930) before forming a distinct assemblage ca. 1930–1960 characterized by elevated algal biomass (inferred as β‐carotene), nuisance cyanobacteria, eutrophic Stephanodiscus hantzschii, and low abundance of deep‐water zoobenthos. Recent fossil assemblages (1977–1994) were variable and indicated water quality had not improved despite 3‐fold reduction in phosphorus from sewage. Comparison of fossil community change and continuous annual records of 83 environmental variables (1890–1994) using VPA captured 71–97% of variance in fossil composition using only 10‐14 significant factors. Resource use (cropland area, livestock biomass) and urbanization (nitrogen in sewage) were stronger determinants of algal and chironomid community change than were climatic factors (temperature, evaporation, river discharge). Landscape analysis of inferred changes in past algal abundance (as β‐carotene; ca. 1780‐1994) indicated that urban impacts declined with distance from point sources and suggested that management strategies will vary with lake position within the catchment.
Identification of miR-215 mediated targets/pathways via translational immunoprecipitation expression analysis (TrIP-chip)

Steady state mRNA expression profiling can identify the majority of miRNA targets. However, some translationally repressed miRNA targets are missed and thus not considered for functional validation. Therefore, analysis of mRNA translation can enhance miRNA target identification for functional studies. We have applied a unique approach to identify miRNA targets in a small number of cells. Actively translating mRNAs are associated with polyribosomes and newly synthesized peptide chains are associated with molecular chaperones such as HSP70s. Affinity capture beads were used to capture HSP70 chaperones associated with polyribosome complexes. The isolated actively translating mRNAs were used for high throughput expression profiling analysis. miR-215 is an important miRNA in colorectal cancer and loss of miR-215 is significantly associated with prognosis of this disease. miR-215 suppresses the expression of several key targets. We utilized the affinity capture approach to isolate miR-215 mediated mRNA target transcripts. This approach provides a unique way to identify targets regulated by non-coding RNAs and RNA binding proteins from a small number of cells.
A framework for integrative analysis of transcriptional and post-transcriptional gene regulation

Gene regulation is a complex biological phenomenon. A reliable analysis of this process requires the integration of several data sources in a rigorous pipeline. Here, we propose an approach for simultaneous modeling of transcriptional and post-transcriptional gene regulation over a Bayesian module network. The framework uses paired samples of mRNA and microRNA expressions and their sequence data to produce low-level regulatory circuits in addition to the co-regulated entities of mRNAs, microRNAs and transcription factors. The experiments performed on a real cancer dataset reveal that several biologically meaningful clusters and motifs can be inferred. The results lead to the generation of some testable biological hypotheses.
Physiological Tolerance Times while Wearing Explosive Ordnance Disposal Protective Clothing in Simulated Environmental Extremes

Explosive ordnance disposal (EOD) technicians are required to wear protective clothing to protect themselves from the threat of overpressure, fragmentation, impact and heat. The engineering requirements to minimise these threats results in an extremely heavy and cumbersome clothing ensemble that increases the internal heat generation of the wearer, while the clothing’s thermal properties reduce heat dissipation. This study aimed to evaluate the heat strain encountered wearing EOD protective clothing in simulated environmental extremes across a range of differing work intensities. Eight healthy males [age 25±6 years (mean ± sd), height 180±7 cm, body mass 79±9 kg, V˙O2max 57±6 ml.kg−1.min−1] undertook nine trials while wearing an EOD9 suit (weighing 33.4 kg). The trials involved walking on a treadmill at 2.5, 4 and 5.5 km⋅h−1 at each of the following environmental conditions, 21, 30 and 37°C wet bulb globe temperature (WBGT) in a randomised controlled crossover design. The trials were ceased if the participants’ core temperature reached 39°C, if heart rate exceeded 90% of maximum, if walking time reached 60 minutes or due to fatigue/nausea. Tolerance times ranged from 10–60 minutes and were significantly reduced in the higher walking speeds and environmental conditions. In a total of 15 trials (21%) participants completed 60 minutes of walking; however, this was predominantly at the slower walking speeds in the 21°C WBGT environment. Of the remaining 57 trials, 50 were ceased, due to attainment of 90% maximal heart rate. These near maximal heart rates resulted in moderate-high levels of physiological strain in all trials, despite core temperature only reaching 39°C in one of the 72 trials.
Activity-dependent BDNF release via endocytic pathways is regulated by synaptotagmin-6 and complexin

Significance Brain-derived neurotrophic factor (BDNF) is a secreted neurotrophin known to mediate activity-dependent synaptic plasticity. Endogenously synthesized BDNF is normally stored and transported in dense core vesicles and secreted at synapses in response to activity. However, secreted BDNF may also be endocytosed by neurons and transported within neuronal cytoplasm in the form of endosomes. By monitoring the endocytosed BDNF bound to fluorescent quantum dots (BDNF-QDs), we found that endocytosed BDNF-QDs could be preferentially localized to postsynaptic sites in cultured hippocampal neurons and became exocytosed in response to synaptic activity. This synaptic release of endocytic BDNF requires a synaptotagmin isoform distinct from that regulates the secretion of dense core vesicles, and may serve as a source for activity-dependent secretion of synaptic BDNF. Brain-derived neurotrophic factor (BDNF) is known to modulate synapse development and plasticity, but the source of synaptic BDNF and molecular mechanisms regulating BDNF release remain unclear. Using exogenous BDNF tagged with quantum dots (BDNF-QDs), we found that endocytosed BDNF-QDs were preferentially localized to postsynaptic sites in the dendrite of cultured hippocampal neurons. Repetitive neuronal spiking induced the release of BDNF-QDs at these sites, and this process required activation of glutamate receptors. Down-regulating complexin 1/2 (Cpx1/2) expression eliminated activity-induced BDNF-QD secretion, although the overall activity-independent secretion was elevated. Among eight synaptotagmin (Syt) isoforms examined, down-regulation of only Syt6 impaired activity-induced BDNF-QD secretion. In contrast, activity-induced release of endogenously synthesized BDNF did not depend on Syt6. Thus, neuronal activity could trigger the release of endosomal BDNF from postsynaptic dendrites in a Cpx- and Syt6-dependent manner, and endosomes containing BDNF may serve as a source of BDNF for activity-dependent synaptic modulation.
Energy efficiency of optically backhauled LTE: A case study

Nowadays, we are witnesses of fast penetration of high data-rate cellular networks such as the Long Term Evolution (LTE). With increasing average access data rates in mobile networks, also the requirements on networks providing backhaul for the wireless infrastructure are increasing. New radio interfaces are already capable of providing hundreds of Mbps over a single radio link between a base station and a user, which means that the future backhaul network should be able to provide a connection to base station sites in the order of Gbps. As optical access networks are able to provide a very high bandwidth practically almost independent on distance as well as high energy efficiency, it seems that a combination of mobile wireless access with optical access networks is a very promising integrated approach for a sustainable and efficient next generation ubiquitous access network. Wireless cellular and optical wired access networks provide synergies and complementary features. The main benefits of using a kind of wireless access are mobility and ubiquity while optical access networks provide high data rates, low power consumption and robustness. In this paper, we investigate various options for deploying LTE in urban areas with a particular emphasis on energy efficiency. For the purpose of evaluation, we apply an access network model to estimate both power consumption and achievable access data rates for various deployment scenarios and show results of a case study for the city of Vienna. The considered deployment scenarios are assessed regarding their potential for improving energy efficiency.
CREATING ATMOSPHERE IN 3 D GEOVISUALIZATION A USER STUDY OF VISUAL MEANS

Abtract: 3D geovisualization is based on virtual reality technology and are thus capable of introducing aesthetic elements in a scene for instance for commercial applications that are based on geographic information. In this paper visual and aesthetic elements are introduced in a tourist model, representing the downtown area of Aalborg, Denmark. A group of subjects and experts are invited to evaluate the model. The result of the evaluation shows clearly that users react differently on different elements in the model, suggesting that they are powerful means of communication and indicating a relevance in commercial applications. On the other hand they can be imprecise means if they manipulate the whole scene, as in this case where the creation of the same atmosphere is not relevant for all tourist attractions in the represented area.
Experimental Studies on SAT-Based ATPG for Gate Delay Faults

The clock rate of modern chips is still increasing and at the same time the gate size decreases. As a result, already slight variations during the production process may cause a functional failure. Therefore, dynamic fault models like the gate delay fault model are becoming more important. Meanwhile classical algorithms for test pattern generation reach their limits regarding run time and memory needs. In this work, a SAT-based approach to calculate test patterns for gate delay faults is presented. The basic transformation is explained in detail. The application to industrial circuits - where multi-valued logic has to be considered - is studied and experimental results are reported.
Parts that add up to a whole : a framework for the analysis of tables

Managing the buffering of data along arcs is a critical part of compiling a synchronous dataflow (SDF) program. This paper shows how dataflow properties can be analyzed at compile-time to make buffering more efficient. Since the target code corresponding to each node of an SDF graph is normally obtained from a hand-optimized library of predefined blocks, the efficiency of data transfer between blocks is often the limiting factor in how closely an SDF compiler can approximate meticulous manual coding. Furthermore, in the presence of large sample-rate changes, straightforward buffering techniques can quickly exhaust limited on-chip data memory, necessitating the use of slower external memory. The techniques presented in this paper address both of these problems in a unified manner.
Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi. nlm.nih. gov.
Effective Dropout Prevention and College Attendance Programs for Latino Students.

This paper reviews research related to effective secondary school programs aimed at dropout prevention and increasing college enrollment rates for at-risk Latino youth. The review identifies programs that have demonstrated a significant impact on dropout rates, college attendance, school performance, or related outcomes in rigorous evaluations; that are replicable across a broad range of secondary schools; and that have been successfully evaluated among or at least frequently applied to schools serving Latino students. Two dropout prevention programs and four college attendance programs were identified as meeting the criteria: the Coca-Cola Valued Youth Program, the Achievement for Latinos through Academic Success (ALAS) program, Upward Bound, SCORE, Project Advancement Via Individual Determination (AVID), and Project GRAD. Also included are brief analyses of nine college attendance/dropout prevention programs in California that did not meet the criteria of the review, but that are used on a fairly broad scale with Latino students. While successful program interventions vary considerably, common program themes include creating meaningful relationships between students and teachers and among students, connecting students to an attainable future, giving students help with specific courses as well as more generic study strategies, recognizing students for academic efforts, and providing activities to increase parental involvement. Contains 45 references and information on program contacts. (LP) ******************************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. ******************************************************************************** Effective Dropout Prevention and College Attendance Programs for Latino Students Olatokunbo S. Fashola Robert E. Slavin Johns Hopkins University
A Synoptic Climatology of Episodic, Subseasonal Retractions of the Pacific Jet

AbstractTwenty-eight years of NCEP–NCAR reanalysis data are employed in a composite analysis of the structure and evolution of the large-scale circulation associated with rapid, subseasonal, westward retractions of the Northern Hemisphere Pacific jet. Nineteen Pacific jet retractions are identified in the dataset. The salient characteristics of these transitions are presented, emphasizing the structure and evolution of anomalies in the zonal wind, upper-tropospheric geopotential height, sea level pressure (SLP), and tropopause potential vorticity (PV). The composite analysis demonstrates that as the jet retracts, a transition from a dominant negative anomaly to a dominant positive anomaly across the North Pacific in both the 500-hPa geopotential height and SLP fields occurs in ~10 days. The resulting anticyclonic anomalies are sprawling and intense with SLP anomalies of nearly 20 hPa and 500-hPa geopotential height anomalies of more than 200 m. The vertical superposition of these upper- and lower-level an.
A Comparison Of Two Competitive Fitness Functions

Competitive fitness is the assessment of an individual's fitness in the context of competition with other individuals in the evolutionary system. This commonly takes one of two forms: one-population competitive fitness, where competition is solely between individuals in the same population; and N-population competitive fitness, often termed competitive coevolution. In this paper we discuss common topologies for one-population competitive fitness functions, then test the performance of two such topologies, Single-Elimination Tournament and K-Random Opponents, on four problem domains. We show that neither of the extremes of K-Random Opponents (Round Robin and Random-Pairing) gives the best results when using limited computational resources. We also show that while Single-Elimination Tournament usually outperforms variations of K-Random Opponents in noise-free problems, it can suffer from premature convergence in noisy domains.
Detect DDoS Attack Using Border Gateways and Edge Routers

The system is design to implement an identification and classification algorithm for tracing DDoS attack and multicast attack information to a edge router using cyclical deterministic packet marking (CDPM) method. Edge router registry stores the received packet IP source address and mark the packet. An Identification and classification algorithm implemented on Border gateway. An algorithm based on received packet and path variation. Border gateways analyze the packet path and number of request received from particular source address. And classify the packet if attacker multicast the attack packet information to edge router and intermediate router or if legitimate packet the border gateway allow to use server. Finally edge router can update their registry and block the attacker IP source address from home network itself. In our proposed model we identify an attack source and multicast the information to an edge router.
Conceptual Integration Networks

Conceptual integration—“blending”—is a general cognitive operation on a par with analogy, recursion, mental modeling, conceptual categorization, and framing. It serves a variety of cognitive purposes. It is dynamic, supple, and active in the moment of thinking. It yields products that frequently become entrenched in conceptual structure and grammar, and it often performs new work on its previously entrenched products as inputs. Blending is easy to detect in spectacular cases but it is for the most part a routine, workaday process that escapes detection except on technical analysis. It is not reserved for special purposes, and is not costly. In blending, structure from input mental spaces is projected to a separate, “blended” mental space. The projection is selective. Through completion and elaboration, the blend develops structure not provided by the inputs. Inferences, arguments, and ideas developed in the blend can have effect in cognition, leading us to modify the initial inputs and to change our view of the corresponding situations. Blending operates according to a set of uniform structural and dynamic principles. It additionally observes a set of optimality principles.
Hybrid Grammars for Discontinuous Parsing

We introduce the concept of hybrid grammars, which are extensions of synchronous grammars, obtained by coupling of lexical elements. One part of a hybrid grammar generates linear structures, another generates hierarchical structures, and together they generate discontinuous structures. This formalizes and generalizes some existing mechanisms for dealing with discontinuous phrase structures and non-projective dependency structures. Moreover, it allows us to separate the degree of discontinuity from the time complexity of parsing.