Miracle-dz/UniFAR-FTUs huggingface dataset:
TCP Transcription Factors at the Interface between Environmental Challenges and the Plant’s Growth Responses

Plants are sessile and as such their reactions to environmental challenges differ from those of mobile organisms. Many adaptions involve growth responses and hence, growth regulation is one of the most crucial biological processes for plant survival and fitness. The plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) transcription factor family is involved in plant development from cradle to grave, i.e., from seed germination throughout vegetative development until the formation of flowers and fruits. TCP transcription factors have an evolutionary conserved role as regulators in a variety of plant species, including orchids, tomatoes, peas, poplar, cotton, rice and the model plant Arabidopsis. Early TCP research focused on the regulatory functions of TCPs in the development of diverse organs via the cell cycle. Later research uncovered that TCP transcription factors are not static developmental regulators but crucial growth regulators that translate diverse endogenous and environmental signals into growth responses best fitted to ensure plant fitness and health. I will recapitulate the research on TCPs in this review focusing on two topics: the discovery of TCPs and the elucidation of their evolutionarily conserved roles across the plant kingdom, and the variety of signals, both endogenous (circadian clock, plant hormones) and environmental (pathogens, light, nutrients), TCPs respond to in the course of their developmental roles.
INFLAMMATION RESPONSE OF MECHANICALLY EXPOSED PULP AFTER DIRECT PULP CAPPING WITH CALCIUM HYDROXIDE CEMENT AND PLATELET RICH PLASMA

Abstract During cavity preparation and the removal of caries dentine, it is possible to accidentally expose the dental pulp. Direct pulp capping may be indicated for maintaining pulp health and function. The direct pulp capping material that used in this study was platelet rich plasma (PRP). Platelet rich plasma is on autologous growth factor containing of platelet derived growth factor (PDGF), transforming growth factor-β (TGF-β), vascular endothelial growth factor (VEGF), insulin growth factor (IGF) and epidermal growth factor (EGF). The aim of this study was to evaluate inflammation response of pulp tissue following direct pulp capping with PRP. Thirty sound teeth from Sprague Dawley were used and divided into two groups: group 1 as a control, teeth were capped with calcium hydroxide/Ca(OH) 2 (n=15) and group 2 with PRP (n=15). After the 1 st , 7 th and 21 st days, respectively, 5 teeth of each group were processed for light microscopic examination. Inflammation responses were assessed by haematoxylin eosin. The result showed a similar inflammation response of Ca(OH) 2 (group 1) on the 1 st and 7 th days 40% necrose and 40% severe inflammation and the 21 st day 60% samples were severe inflammation. Inflammation response of PRP (group 2) on the 1 st day showed 40% necrose and 40% severe inflammation, on the 7 th day, 100% severe inflammation and on the 21 st day, 60% mild inflammation. After the 21 th day observation period, Kruskal Wallis test showed that inflammation response was not significant in both groups (p>0,05). In conclusion, PRP and Ca(OH) 2 as a direct pulp capping material had no different inflammation response. Key words: pulp capping, platelet rich plasma, inflammation response
Service Provider DevOps network capabilities and tools

This report provides an understanding of how the UNIFY Service Provider (SP)-DevOps concept can be applied and integrated with a combined cloud and transport network NFV architecture. Specifically, the report contains technical descriptions of a set of novel SP-DevOps tools and support functions that facilitate observability, troubleshooting, verification, and VNF development processes. The tools and support functions are described in detail together with their architectural mapping, giving a wider understanding of the SP-DevOps concept as a whole, and how SP-DevOps tools can be used for supporting orchestration and programmability in the UNIFY NFV framework. The concept is further exemplified in a case study for deployment and scaling of an Elastic Firewall.
Comparative Transcriptional Analysis of Loquat Fruit Identifies Major Signal Networks Involved in Fruit Development and Ripening Process

Loquat (Eriobotrya japonica Lindl.) is an important non-climacteric fruit and rich in essential nutrients such as minerals and carotenoids. During fruit development and ripening, thousands of the differentially expressed genes (DEGs) from various metabolic pathways cause a series of physiological and biochemical changes. To better understand the underlying mechanism of fruit development, the Solexa/Illumina RNA-seq high-throughput sequencing was used to evaluate the global changes of gene transcription levels. More than 51,610,234 high quality reads from ten runs of fruit development were sequenced and assembled into 48,838 unigenes. Among 3256 DEGs, 2304 unigenes could be annotated to the Gene Ontology database. These DEGs were distributed into 119 pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A large number of DEGs were involved in carbohydrate metabolism, hormone signaling, and cell-wall degradation. The real-time reverse transcription (qRT)-PCR analyses revealed that several genes related to cell expansion, auxin signaling and ethylene response were differentially expressed during fruit development. Other members of transcription factor families were also identified. There were 952 DEGs considered as novel genes with no annotation in any databases. These unigenes will serve as an invaluable genetic resource for loquat molecular breeding and postharvest storage.
Motion planning in urban environments

We present the motion planning framework for an autonomous vehicle navigating through urban environments. Such environments present a number of motion planning challenges, including ultrareliability, high‐speed operation, complex intervehicle interaction, parking in large unstructured lots, and constrained maneuvers. Our approach combines a model‐predictive trajectory generation algorithm for computing dynamically feasible actions with two higher level planners for generating long‐range plans in both on‐road and unstructured areas of the environment. In the first part of this article, we describe the underlying trajectory generator and the on‐road planning component of this system. We then describe the unstructured planning component of this system used for navigating through parking lots and recovering from anomalous on‐road scenarios. Throughout, we provide examples and results from “Boss” an autonomous sport utility vehicle that has driven itself over 3,000 km and competed in, and won, the DARPA Urban Challenge. © 2008 Wiley Periodicals, Inc.
Effect of Cold Plasma Treatment on Surface Roughness and Bonding Strength of Polymeric Substrates

For an effective application of polymers, it is essential to have good adhesion behaviour to ensure good mechanical properties and durable components. Unfortunately, in general terms, polymers are characterized by high chemical inertness, which leads to very low surface energy values and, consequently, poor adhesive properties; this is particularly true for polyolefins. In this study, the effects of low pressure plasma treatment on surface roughness of polyethylene and polypropylene samples and on shear properties of adhesive bonded joints based on these substrates have been investigated. In particular, the optimization of three plasma process parameters, exposure time, voltage and working gas, were studied performing roughness measurement, contact angle evaluation and lap-shear tests. The experimental results show that the optimized plasma process may remarkably change the surface morphology, increasing wettability properties of the surfaces and shear strength of the bonded joints. These good properties remain almost unchanged even after some days of storage in the laboratory.
Exploiting Latent Semantic Relations in Highly Linked Hypertext for Information Retrieval in Wikis

Good hypertext writing style mandates that link texts clearly indicate the nature of the link target. While this guideline is routinely ignored in HTML, the lightweight markup languages used by wikis encourage or even force hypertext authors to use semantically appropriate link texts. This property of wiki hypertext makes it an ideal candidate for processing with latent semantic analysis, a factor analysis technique for finding latent transitive relations among naturallanguage documents. In this study, we design, implement, and test an LSA-based information retrieval system for wikis. Instead of a full-text index, our system indexes only link texts and document titles. Nevertheless, its precision exceeds that of a popular full-text search engine, and is comparable to that of PageRank-based systems such as Google.
Stacked Convolutional and Recurrent Neural Networks for Music Emotion Recognition

This paper studies the emotion recognition from musical tracks in the 2-dimensional valence-arousal (V-A) emotional space. We propose a method based on convolutional (CNN) and recurrent neural networks (RNN), having significantly fewer parameters compared with the state-of-the-art method for the same task. We utilize one CNN layer followed by two branches of RNNs trained separately for arousal and valence. The method was evaluated using the 'MediaEval2015 emotion in music' dataset. We achieved an RMSE of 0.202 for arousal and 0.268 for valence, which is the best result reported on this dataset.
Independent Evolutionary Origin of fem Paralogous Genes and Complementary Sex Determination in Hymenopteran Insects

The primary signal of sex determination in the honeybee, the complementary sex determiner (csd) gene, evolved from a gene duplication event from an ancestral copy of the fem gene. Recently, other paralogs of the fem gene have been identified in several ant and bumblebee genomes. This discovery and the close phylogenetic relationship of the paralogous gene sequences led to the hypothesis of a single ancestry of the csd genetic system of complementary sex determination in the Hymenopteran insects, in which the fem and csd gene copies evolved as a unit in concert with the mutual transfers of sequences (concerted evolution). Here, we show that the paralogous gene copies evolved repeatedly through independent gene duplication events in the honeybee, bumblebee, and ant lineage. We detected no sequence tracts that would indicate a DNA transfer between the fem and the fem1/csd genes between different ant and bee species. Instead, we found tracts of duplication events in other genomic locations, suggesting that gene duplication was a frequent event in the evolution of these genes. These and other evidences suggest that the fem1/csd gene originated repeatedly through gene duplications in the bumblebee, honeybee, and ant lineages in the last 100 million years. Signatures of concerted evolution were not detectable, implicating that the gene tree based on neutral synonymous sites represents the phylogenetic relationships and origins of the fem and fem1/csd genes. Our results further imply that the fem1 and csd gene in bumblebees, honeybees, and ants are not orthologs, because they originated independently from the fem gene. Hence, the widely shared and conserved complementary sex determination mechanism in Hymenopteran insects is controlled by different genes and molecular processes. These findings highlight the limits of comparative genomics and emphasize the requirement to study gene functions in different species and major hymenopteran lineages.
Theoretical analysis and numerical simulation of inter-modal four-wave-mixing in few mode fibers

Analogous to single-mode fiber, nonlinear effects may eventually limit the information capacity in next generation long-haul few-mode fiber (FMF) transmission systems. In this paper, we theoretically and numerically investigate inter-modal four-wave mixing (IM-FWM) among up to four spatial modes in FMFs. Different forms of multi-mode non-linear Schrödinger equation (MM-NLSE) for two, three and four spatial modes are derived, along with up to six types of wave/mode distributions and their corresponding phase matching conditions. We analyze the mixed effects of differential mode group delay (DMGD), chromatic dispersion (CD), random mode coupling (RMC) and wavelength separation upon IM-FWM efficiency in FMF.
Adaptive selective sidelobe canceller beamformer with applications in radio astronomy

We propose a new algorithm for parameter estimation that is applicable when many array are used to detect the incoming signals. This adaptive beamformer can be used in applications, most notably radio-astronomy and synthetic aperture array, where moving arrays are used for measuring the incoming signals. We demonstrate a significant improvement in performance compared with currently used methods for situations with strong interfering sources.
Transparency, Efficiency and the Distribution of Economic Welfare in Pass-Through Investment Trust Games

We design an experiment to examine behavior and welfare in a multi-level trust game representing a pass through investment in an intermediated market. In a repeated game, an investor invests via an intermediary who lends to a borrower. A pre-experiment one-shot version of the game serves as a baseline and to type each subject. We alter the transparency of exchanges between non-adjacent parties. We find transparency of the exchanges between the investor and intermediary does not significantly affect welfare. However, transparency regarding exchanges between the intermediary and borrower promotes trust on the part of the investor, increasing welfare. Further, this has asymmetric effects: borrowers and intermediaries achieve greater welfare benefits than investors. We discuss implications for what specific aspects of financial market transparency may facilitate more efficiency.
B-Cell Development and Differentiation During HIV Infection: Tolerance Versus Immunity

Early after HIV infection, B-cell homeostasis is disrupted which results in autoantibody production and auto- immunity. The systemic inflammation induced during chronic HIV infection relaxes B-cell tolerance mechanisms that normally suppress this autoimmune pathology. Tolerance to self antigens is established during the development of B cells; however, rare, broadly neutralizing antibodies to HIV cross-react with host cellular antigens, suggesting that mechanisms of B-cell tolerance limit protective humoral responses to HIV. The association between HIV infection, induction of autoantibody and the emergence of neutralizing antibodies directed at HIV suggests that protective humoral immune re- sponses may only occur after B-cell tolerance control mechanisms are relaxed. In this review, we focus on mechanisms that promote a diverse repertoire of antibody specificities during mouse and human B-cell development. Furthermore, we discuss mecha- nisms of tolerance that purge the B-cell repertoire of self- reactive clones and, as a consequence, limit the recognition of pathogens which express "host-like" antigens. In addition, we explore mechanisms that can be used by pathogens to subvert immune recognition, including the elicitation of autoantibody. We discuss the "tolerance hypothesis" of Hay- nes et al. (5) as a potential mode of immune evasion utilized by HIV to subvert neutralizing B-cell responses. B-CELL DEVELOPMENT
Statistical Study of Solar X-Ray Jets Observed with the YOHKOH Soft X-Ray Telescope

From a statistical study of 100 X-ray jets, found from the database of full Sun images taken with the Soft X-ray Telescope (SXT) aboard Yohkoh during the period between November 1991 and April 1992, we found the following characteristics: 1) Most of the jets are associated with small flares (microflare — subflare) at their footpoints. 2) The length of jet ranges from a few ×104 km to a few ×105 km. 3) The apparent velocity ranges from ~ 10 km/s to 1000 km/s and the well observed apparent velocity of jet is about 200 km/s. 4) The lifetime ranges from a few min to ~ 10 hours and the distribution of lifetimes is a power law. 5) We found that the shape of the X-ray jet can be classified into about 5 distinct types; 43% of jet have constant widths, and 33% of the jet appear to be converging. 6) About two thirds (64%) of the jets appear in or near active regions (AR). When a jet is ejected from a bright point like feature in an AR, it occurs to the west (86%). 7) A clear gap (> 104 km) is seen between the exact footpoint of the jet and the brightest part of the associated flare in 27% of the jets. 8) The X-ray intensity along an X-ray jet often shows an exponential decrease with distance from the footpoint. 9) This exponential intensity distribution holds from the early phase to the decay phase.
APP interacts with LRP4 and agrin to coordinate the development of the neuromuscular junction in mice

ApoE, ApoE receptors and APP cooperate in the pathogenesis of Alzheimer’s disease. Intriguingly, the ApoE receptor LRP4 and APP are also required for normal formation and function of the neuromuscular junction (NMJ). In this study, we show that APP interacts with LRP4, an obligate co-receptor for muscle-specific tyrosine kinase (MuSK). Agrin, a ligand for LRP4, also binds to APP and co-operatively enhances the interaction of APP with LRP4. In cultured myotubes, APP synergistically increases agrin-induced acetylcholine receptor (AChR) clustering. Deletion of the transmembrane domain of LRP4 (LRP4 ECD) results in growth retardation of the NMJ, and these defects are markedly enhanced in APP−/−;LRP4ECD/ECD mice. Double mutant NMJs are significantly reduced in size and number, resulting in perinatal lethality. Our findings reveal novel roles for APP in regulating neuromuscular synapse formation through hetero-oligomeric interaction with LRP4 and agrin and thereby provide new insights into the molecular mechanisms that govern NMJ formation and maintenance. DOI: http://dx.doi. org/10.7554/eLife.00220. 001
Metabolomics technology and bioinformatics

Metabolomics is the global analysis of all or a large number of cellular metabolites. Like other functional genomics research, metabolomics generates large amounts of data. Handling, processing and analysis of this data is a clear challenge and requires specialized mathematical, statistical and bioinformatics tools. Metabolomics needs for bioinformatics span through data and information management, raw analytical data processing, metabolomics standards and ontology, statistical analysis and data mining, data integration and mathematical modelling of metabolic networks within a framework of systems biology. The major approaches in metabolomics, along with the modern analytical tools used for data generation, are reviewed in the context of these specific bioinformatics needs.
Optimal Update with Multistep Out-of-Sequence Measurements in Target Tracking

In centralized multisensor tracking systems, there are out-of-sequence measurement (OOSM) problems frequently arising due to different time delays in communication links and varying pre-processing times at the sensor. Such OOSM arrivals can induce "negative-time measurement update" problem, which is quite common in real multisensor tracking systems. Recently, the optimal update with multistep OOSMs denoted as algorithm Zl was presented. However, this paper shows the optimality of algorithm Zl is true only in simple OOSM scenario and discretized continuous-time model (DCM) of the process noise. Otherwise it is not optimal. A new optimal OOSM filtering algorithm with multistep OOSMs based on information filter is presented, which is independent of the discrete time model of the process noise and is optimal for different OOSM scenarios. It is shown that the performance of the new optimal algorithm is better than that of algorithm Zl by numerical results.
Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells

A major challenge in computational biology is constraining free parameters in mathematical models. Adjusting a parameter to make a given model output more realistic sometimes has unexpected and undesirable effects on other model behaviors. Here, we extend a regression-based method for parameter sensitivity analysis and show that a straightforward procedure can uniquely define most ionic conductances in a well-known model of the human ventricular myocyte. The model's parameter sensitivity was analyzed by randomizing ionic conductances, running repeated simulations to measure physiological outputs, then collecting the randomized parameters and simulation results as “input” and “output” matrices, respectively. Multivariable regression derived a matrix whose elements indicate how changes in conductances influence model outputs. We show here that if the number of linearly-independent outputs equals the number of inputs, the regression matrix can be inverted. This is significant, because it implies that the inverted matrix can specify the ionic conductances that are required to generate a particular combination of model outputs. Applying this idea to the myocyte model tested, we found that most ionic conductances could be specified with precision (R2 > 0.77 for 12 out of 16 parameters). We also applied this method to a test case of changes in electrophysiology caused by heart failure and found that changes in most parameters could be well predicted. We complemented our findings using a Bayesian approach to demonstrate that model parameters cannot be specified using limited outputs, but they can be successfully constrained if multiple outputs are considered. Our results place on a solid mathematical footing the intuition-based procedure simultaneously matching a model's output to several data sets. More generally, this method shows promise as a tool to define model parameters, in electrophysiology and in other biological fields.
Real time corrosion monitoring in atmosphere using automated battery driven corrosion loggers

Abstract A logger enabling continuous measurement of corrosion rate of selected metals in indoor and outdoor atmospheres has been developed. Principle of the measurement method is based on the increasing electrical resistance of a measuring element made of the material concerned as its cross-sectional area diminishes due to corrosion. Zinc, iron, copper and nickel sensors at several thicknesses are available. Sensitivity of the corrosion measurement varies from 1 to 10 nm depending on the type and thickness of the sensor. Changes in the air corrosivity can be thus detected within hours or even tens of minutes. The logger lifetime in medium corrosive environments is designed to be 2 years with full autonomy. Data on the sensor corrosion rate are available any time through GPRS connection or by a non-contact inductive reading without the need of retracting the logger from the exposure site.