Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background

Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.
Exploiting the Knowledge of Task Structure for Distributed Allocation

The aim of this paper is to evaluate the advantages in task allocation that derive from knowledge of the structure of a task, here modeled by an application graph. We will show how the information contained in the application graph can be embedded inside an allocator in order to guide its choices in a way that minimizes the overall response time of the task. We then propose two allocation algorithms which use knowledge of the application graph and measurement of the current system workload in a heuristic formulation and aim to minimize the task's response time. The presented algorithms, differing in the degree of detail with which they evaluate the effect of concurrence between modules allocated on the same host, have been implemented and evaluated in a real heterogeneous distributed system.
Economic Viability of Hardware Overprovisioning in Power-Constrained High Performance Computing

Recent research has established that hardware overprovisioning can improve system power utilization as well as job throughput in power-constrained, high-performance computing environments significantly. These benefits, however, may be associated with an additional infrastructure cost, making hardware overprovisioned systems less viable economically. It is thus important to conduct a detailed cost-benefit analysis before investing in such systems at a large-scale. In this paper, we develop a model to conduct this analysis and show that for a given, fixed infrastructure cost budget and a system power budget, it is possible for hardware overprovisioned systems to lead to a net performance benefit when compared to traditional, worst-case provisioned HPC systems.
A phenomics approach to the analysis of the influence of glutathione on leaf area and abiotic stress tolerance in Arabidopsis thaliana

Reduced glutathione (GSH) is an abundant low molecular weight plant thiol. It fulfills multiple functions in plant biology, many of which remain poorly characterized. A phenomics approach was therefore used to investigate the effects of glutathione homeostasis on growth and stress tolerance in Arabidopsis thaliana. Rosette leaf area was compared in mutants that are either defective in GSH synthesis (cad2, pad2, and rax1) or the export of γ-glutamylcysteine and GSH from the chloroplast (clt) and in wild-type plants under standard growth conditions and following exposure to a range of abiotic stress treatments, including oxidative stress, water stress, and high salt. In the absence of stress, the GSH synthesis mutants had a significantly lower leaf area than the wild type. Conversely, the clt mutant has a greater leaf area and a significantly reduced lateral root density than the wild type. These findings demonstrate that cellular glutathione homeostasis exerts an influence on root architecture and on rosette area. An impaired capacity to synthesize GSH or a specific depletion of the cytosolic GSH pool did not adversely affect leaf area in plants exposed to short-term abiotic stress. However, the negative effects of long-term exposure to oxidative stress and high salt on leaf area were less marked in the GSH synthesis mutants than the wild type. These findings demonstrate the importance of cellular glutathione homeostasis in the regulation of plant growth under optimal and stress conditions.
Direct laser writing in bio-inspired photonics

Direct laser writing (DLW) is a powerful tool toward the development of ultimate three-dimensional (3D) photonic devices. Because of the increasing demand for realising nano-geometries, the diffraction-limited resolution associated with DLW should be overcome to access the nanoscale. To meet this challenge, the concept of 3D nano printing, which is called super-resolution photoinduction-inhibition nanolithography (SPIN) [1-3], has been developed and this new technology enables us to break the diffraction barrier that has governed the optical instruments for over 140 years. The application of this technology in the optical data storage has allowed for the development of photonic big data storage with Petabyte capacity disks [4-7].
Co-creation of value or co-creation of experience? Interrogations in the field of cultural tourism

There is growing discussion among researchers relating to how consumers engage with producers to cocreate meanings, values, and experiences through consumption. This debate is particularly relevant in the field of tourism. We are in this research at the confluence of two major paradigms: Service Dominant Logic, and Consumer Culture Theory, Arnould (2007). Our goal is to examine and understand the concept of co-creation in the field of cultural tourism. How can we define the value? And how value emerges in the co-creation process? Finally is it about co-creation of value or rather co-creation of experience? This work presents a theoretical foundation and identified future research investigations.
International Conference on Strategic Innovative Marketing , IC-SIM 2014 , September 1-4 , 2014 , Madrid , Spain The complications and challenges of the work-family interface : A review paper

During the last few decades researchers have developed a genuine interest in the interaction of the work and family domains. This paper is an attempt to review the recent literature and to categorize the various outcomes produced by the relationship between work and family. In other words this review article assesses the consequences of the work-family interface through the perspective of conflict and facilitation, as argued in previous research. © 2015 The Authors. Published by Elsevier Ltd. Peer-review under responsibility of I-DASInstitute for the Dissemination of Arts and Science.
Research on voice codec algorithms of SIP phone based on embedded system

Session Initiation Protocol (SIP) as a new multimedia communicating and instant messaging protocol drew more and more attentions recently. The software and hardware architecture of SIP phone which based on ARM920T core is demonstrated in this paper. The comparison of three voice codec algorithms including PCM, SPEEX and iLBC are implemented by porting these algorithms to embedded SIP phone platform. After several experiments, the result indicates that voice quality (e.g. MOS and R value) almost varies depending on the bandwidth, which also fit for theoretical analysis perfectly. Brings forward an effective conclusion that iLBC speech codec have excellent performance in low bit rates and it is superior to PCM and SPEEX encoding in abominable packet loss conditions. The experimental results also demonstrate that the SIP phone is suitable for voice communication and it can meet practical engineering requirements well.
Updates on Mapping Quantitative Trait Loci QTL mapping in outbred populations : successes and challenges

Solberg Woods LC. QTL mapping in outbred populations: successes and challenges. Physiol Genomics 46: 81–90, 2014. First published December 10, 2013; doi:10.1152/physiolgenomics.00127. 2013. —Quantitative trait locus (QTL) mapping in animal populations has been a successful strategy for identifying genomic regions that play a role in complex diseases and traits. When conducted in an F2 intercross or backcross population, the resulting QTL is frequently large, often encompassing 30 Mb or more and containing hundreds of genes. To narrow the locus and identify candidate genes, additional strategies are needed. Congenic strains have proven useful but work less well when there are multiple tightly linked loci, frequently resulting in loss of phenotype. As an alternative, we discuss the use of highly recombinant outbred models for directly fine-mapping QTL to only a few megabases. We discuss the use of several currently available models such as the advanced intercross (AI), heterogeneous stocks (HS), the diversity outbred (DO), and commercially available outbred stocks (CO). Once a QTL has been finemapped, founder sequence and expression QTL mapping can be used to identify candidate genes. In this regard, the large number of alleles found in outbred stocks can be leveraged to identify causative genes and variants. We end this review by discussing some important statistical considerations when analyzing outbred populations. Fine-resolution mapping in outbred models, coupled with full genome sequence, has already led to the identification of several underlying causative genes for many complex traits and diseases. These resources will likely lead to additional successes in the coming years.
Clofarabine salvage therapy in refractory multifocal histiocytic disorders, including Langerhans cell histiocytosis, juvenile xanthogranuloma and Rosai–Dorfman disease

Existing therapies for recurrent or refractory histiocytoses, including Langerhans cell histiocytosis (LCH), juvenile xanthogranuloma (JXG), and Rosai–Dorfman disease (RDD), have limited effectiveness. We report our experience with using clofarabine as therapy in children with recurrent or refractory histiocytic disorders, including LCH (11 patients), systemic JXG (4 patients), and RDD (3 patients).
Anthropometric indices added the predictive ability of iron status in prognosis of atherosclerosis.

BACKGROUND Abnormal homeostasis of iron such as deficiency or overload is associated with the pathogenesis of cardiovascular disease (CVD). Another risk factor for CVD is obesity whose added predictive ability to iron status has been assessed by few study. This study aimed to eva¬luate the effect of adding anthropometric indices to a model based on iron status as risk factors of CVD. METHODS This cross-sectional study included 140 adult women aged 18-50 years randomly se-lected from Sheikhorrais Clinic that is one of the Tabriz University sub-specialized clinics in 2011. Anthropometric indices, carotid intima-media thickness (CIMT) and body iron status were measured by standard protocol, non-invasive ultrasound and concentrations of serum iron, ferri¬tin, TIBC (Total iron Binding Capacity) and complete blood cell counts (CBC), respectively. In¬tegrated discriminatory improvement index (IDI) and net reclassification improvement index (NRI) were used as the measures of added predictive ability of anthropometric measures to the iron statues. RESULTS IDI (SE) after adding Waist Circumference (WC), Waist to Heap Ratio (WHR), Waist to Height Ratio (WHtR), Body Mass Index (BMI) and Body fat (%) to base model was 0.12 (0.028), 0.09 (0.026), 0.12 (0.028), 0.07 (0.022) and 0.10 (0.026) respectively. The NRI (SE) was 0.10 (0.065) for WC, 0.03 (0.058) for WHR, 0.07 (0.067) for WHtR, 0.05 (0.067) for BMI, and 0.08 (0.064) for Body fat. CONCLUSIONS Anthropometric indices could significantly add to the predictive ability of the iron statues, with highest IDI when WC and WHtR were added to the base model. It suggests that by adding WC and WHtR to the iron status lead us to a more optimal model for predicting the ini¬tial stage of atherosclerosis.
Tracking Myocardial Motion From Cine DENSE Images Using Spatiotemporal Phase Unwrapping and Temporal Fitting

Displacement encoding with stimulated echoes (DENSE) encodes myocardial tissue displacement into the phase of the MR image. Cine DENSE allows for rapid quantification of myocardial displacement at multiple cardiac phases through the majority of the cardiac cycle. For practical sensitivities to motion, relatively high displacement encoding frequencies are used and phase wrapping typically occurs. In order to obtain absolute measures of displacement, a two-dimensional (2-D) quality-guided phase unwrapping algorithm was adapted to unwrap both spatially and temporally. Both a fully automated algorithm and a faster semi-automated algorithm are proposed. A method for computing the 2-D trajectories of discrete points in the myocardium as they move through the cardiac cycle is introduced. The error in individual displacement measurements is reduced by fitting a time series to sequential displacement measurements along each trajectory. This improvement is in turn reflected in strain maps, which are derived directly from the trajectories. These methods were validated both in vivo and on a rotating phantom. Further measurements were made to optimize the displacement encoding frequency and to estimate the baseline strain noise both on the phantom and in vivo. The fully automated phase unwrapping algorithm was successful for 767 out of 800 images (95.9%), and the semi-automated algorithm was successful for 786 out of 800 images (98.3%). The accuracy of the tracking algorithm for typical cardiac displacements on a rotating phantom is 0.24plusmn0.15mm. The optimal displacement encoding frequency is in the region of 0.1 cycles/mm, and, for 2 scans of 17-s duration, the strain noise after temporal fitting was estimated to be 2.5plusmn3. 0% at end-diastole, 3.1plusmn3. 1% at end-systole, and 5.3plusmn5. 0% in mid-diastole. The improvement in intra-myocardial strain measurements due to temporal fitting is apparent in strain histograms, and also in identifying regions of dysfunctional myocardium in studies of patients with infarcts
Plasma Biomarkers of Inflammation, the Kynurenine Pathway, and Risks of All-Cause, Cancer, and Cardiovascular Disease Mortality

We aimed to evaluate 10 biomarkers related to inflammation and the kynurenine pathway, including neopterin, kynurenine:tryptophan ratio, C-reactive protein, tryptophan, and 6 kynurenines, as potential predictors of all-cause and cause-specific mortality in a general population sample. The study cohort was participants involved in a community-based Norwegian study, the Hordaland Health Study (HUSK). We used Cox proportional hazards models to assess associations of the biomarkers with all-cause mortality and competing-risk models for cause-specific mortality. Of the 7,015 participants, 1,496 deaths were recorded after a median follow-up time of 14 years (1998–2012). Plasma levels of inflammatory markers (neopterin, kynurenine:tryptophan ratio, and C-reactive protein), anthranilic acid, and 3-hydroxykynurenine were positively associated with all-cause mortality, and tryptophan and xanthurenic acid were inversely associated. Multivariate-adjusted hazard ratios for the highest (versus lowest) quartiles of the biomarkers were 1.19–1.60 for positive associations and 0.73–0.87 for negative associations. All of the inflammatory markers and most kynurenines, except kynurenic acid and 3-hydroxyanthranilic acid, were associated with cardiovascular disease (CVD) mortality. In this general population, plasma biomarkers of inflammation and kynurenines were associated with risk of all-cause, cancer, and CVD mortality. Associations were stronger for CVD mortality than for mortality due to cancer or other causes.
A compositional DRS-based formalism for NLP applications

This paper describes and discusses the formalism which forms the backbone of semantic processing in the Verbmobil spoken dialogue translation project. In the first part, the theoretical core of the formalism is presented: lambda-DRT, a compositional version of Discourse Representation Theory. The main part describes the implementation of lambda-DRT, as a worked out semantic representation language for the Verbmobil project, which is designed to meet the special requirements of the application. Finally, we discuss future extensions and modications of the formalism.
Task Scheduling using Modified PSO Algorithm in Cloud Computing Environment

Task scheduling problem is one of the most important steps in using cloud computing environment capabilities. Different experiments show that although having an optimum solution is almost impossible but having a sub-optimal solution using heuristic algorithms seems possible. In this paper three heuristic approaches for task scheduling on cloud environment have been compared with each other. These approaches are PSO algorithm, genetic algorithm and modified PSO algorithm for efficient task scheduling. In all these three algorithms the goal is to generate an optimal schedule in order to minimize completion time of task execution.
Transcriptional Profiling of Mycobacterium Tuberculosis During Infection: Lessons Learned

Infection with Mycobacterium tuberculosis, the causative agent of tuberculosis, is considered one of the biggest infectious disease killers worldwide. A significant amount of attention has been directed toward revealing genes involved in the virulence and pathogenesis of this air-born pathogen. With the advances in technologies for transcriptional profiling, several groups, including ours, took advantage of DNA microarrays to identify transcriptional units differentially regulated by M. tuberculosis within a host. The main idea behind this approach is that pathogens tend to regulate their gene expression levels depending on the host microenvironment, and preferentially express those needed for survival. Identifying this class of genes will improve our understanding of pathogenesis. In our case, we identified an in vivo expressed genomic island that was preferentially active in murine lungs during early infection, as well as groups of genes active during chronic tuberculosis. Other studies have identified additional gene groups that are active during macrophage infection and even in human lungs. Despite all of these findings, one of the lingering questions remaining was whether in vivo expressed transcripts are relevant to the virulence, pathogenesis, and persistence of the organism. The work of our group and others addressed this question by examining the contribution of in vivo expressed genes using a strategy based on gene deletions followed by animal infections. Overall, the analysis of most of the in vivo expressed genes supported a role of these genes in M. tuberculosis pathogenesis. Further, these data suggest that in vivo transcriptional profiling is a valid approach to identify genes required for bacterial pathogenesis.
Structural requirements of double-stranded RNA for the activation of 2',5'-oligo(A) polymerase and protein kinase of interferon-treated HeLa cells.

Addition of double-stranded RNA (dsRNA) to extracts of interferon-treated HeLa cells results in the synthesis of 2’,8-oligo(A) from ATP and in the phosphorylation of a ribosome-associated protein of M, = 72,000. Previously described assays were used to investigate the structural requirements of dsRNA for the activation of these two enzymatic activities. Poly(CG) with different ratios of C/G was synthesized with polynucleotide phosphorylase. These polynucleotides were either annealed with poly(1) to form mismatched dsRNA or digested with ribonuclease T1 to produce smaller polynucleotides. Polymers with an average of one mismatch every eight nucleotides failed to activate the 2’,5’-oligo(A) polymerase and protein kinase, whereas polymers with a mismatch every 45 nucleotides were fully active. The polynucleotides obtained by T1 digestion of poly(CG) were fractionated by gel filtration into discrete size polymers. These sized polynucleotides were annealed with high molecular weight poly(1) and assayed for activation of 2’,5’-oligo(A) polymerase and protein kinase. These enzymes could not be activated by dsRNA containing poly(C) shorter than 30 nucleotides. Maximal activation was obtained with dsRNA containing poly(C) longer than 65 to 80 nucleotides. A similar size requirement for activation was observed with dsRNA formed with poly(A) and poly(U) of known length. These results indicate that a relatively long stretch of base pairs, uninterrupted by either a mismatch or a discontinuity in one of the complementary strands, is required for the activation of the two enzymes studied. These structural characteristics are similar to those previously shown to be required for the induction of interferon by dsRNA.
Human pose estimation based on human limbs

Modeling the relationship among human joints is one of the most important components in human pose estimation. Previous methods usually define this relationship as geometric constraints on the relative location of two neighboring joints. In this definition, the local image appearance of the region connecting two neighboring joints is ignored. In fact, this image appearance, called human limb, plays an important role in human joint localization in human visual system. To make full use of this local image appearance, we propose to solve a new task: human limb detection. We combine it with human joint localization in one deep convolutional neural network. After getting coarse results, we employ a graphical model to remove false positive detections. Besides, shallow and deep features are combined in this model. We evaluate our method on the FLIC and LSP datasets. The experiments results show the effectiveness of our method.
A Multi-View Clustering Method for Community Discovery Integrating Links and Tags

Community discovery is a popular research problem in the realm of complex network analysis and many methods have been proposed to solve it. However, most of the existing methods only consider the usage of links information and ignore tags information of complex networks. As a result, the quality of their discovered communities is often poor owing to the sparse and noisy data existing in links information. Actually, both links and tags contain noisy but complementary information with each other. In this paper, we propose a multi-view clustering method for community discovery, which is based on multi-view Nonnegative Matrix Factorization (NMF) model and can provide a unified framework to integrate links and tags information. Its key idea is to build a joint NMF process with the constraint that pushes community indicator matrices of links view and tags view towards a common consensus matrix, which can uncover the common latent community structure shared by links view and tags view. Under the optimization framework of multiplicative update rules, we devise the corresponding community discovery algorithm, which can be used to obtain higher quality communities. We conduct extensive experiments on several real datasets and the results demonstrate the effectiveness of our method.