Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenylacetic Acid Is ISR Determinant Produced by Bacillus fortis IAGS162, Which Involves Extensive Re-modulation in Metabolomics of Tomato to Protect against Fusarium Wilt

Bacillus fortis IAGS162 has been previously shown to induce systemic resistance in tomato plants against Fusarium wilt disease. In the first phase of current study, the ISR determinant was isolated from extracellular metabolites of this bacterium. ISR bioassays combined with solvent extraction, column chromatography and GC/MS analysis proved that phenylacetic acid (PAA) was the potential ISR determinant that significantly ameliorated Fusarium wilt disease of tomato at concentrations of 0.1 and 1 mM. In the second phase, the biochemical basis of the induced systemic resistance (ISR) under influence of PAA was elucidated by performing non-targeted whole metabolomics through GC/MS analysis. Tomato plants were treated with PAA and fungal pathogen in various combinations. Exposure to PAA and subsequent pathogen challenge extensively re-modulated tomato metabolic networks along with defense related pathways. In addition, various phenylpropanoid precursors were significantly up-regulated in treatments receiving PAA. This work suggests that ISR elicitor released from B. fortis IAGS162 contributes to resistance against fungal pathogens through dynamic reprogramming of plant pathways that are functionally correlated with defense responses.
Integrative MicroRNA and Proteomic Approaches Identify Novel Osteoarthritis Genes and Their Collaborative Metabolic and Inflammatory Networks

Background Osteoarthritis is a multifactorial disease characterized by destruction of the articular cartilage due to genetic, mechanical and environmental components affecting more than 100 million individuals all over the world. Despite the high prevalence of the disease, the absence of large-scale molecular studies limits our ability to understand the molecular pathobiology of osteoathritis and identify targets for drug development. Methodology/Principal Findings In this study we integrated genetic, bioinformatic and proteomic approaches in order to identify new genes and their collaborative networks involved in osteoarthritis pathogenesis. MicroRNA profiling of patient-derived osteoarthritic cartilage in comparison to normal cartilage, revealed a 16 microRNA osteoarthritis gene signature. Using reverse-phase protein arrays in the same tissues we detected 76 differentially expressed proteins between osteoarthritic and normal chondrocytes. Proteins such as SOX11, FGF23, KLF6, WWOX and GDF15 not implicated previously in the genesis of osteoarthritis were identified. Integration of microRNA and proteomic data with microRNA gene-target prediction algorithms, generated a potential “interactome” network consisting of 11 microRNAs and 58 proteins linked by 414 potential functional associations. Comparison of the molecular and clinical data, revealed specific microRNAs (miR-22, miR-103) and proteins (PPARA, BMP7, IL1B) to be highly correlated with Body Mass Index (BMI). Experimental validation revealed that miR-22 regulated PPARA and BMP7 expression and its inhibition blocked inflammatory and catabolic changes in osteoarthritic chondrocytes. Conclusions/Significance Our findings indicate that obesity and inflammation are related to osteoarthritis, a metabolic disease affected by microRNA deregulation. Gene network approaches provide new insights for elucidating the complexity of diseases such as osteoarthritis. The integration of microRNA, proteomic and clinical data provides a detailed picture of how a network state is correlated with disease and furthermore leads to the development of new treatments. This strategy will help to improve the understanding of the pathogenesis of multifactorial diseases such as osteoarthritis and provide possible novel therapeutic targets.
Collective Innovation in Open Source Hardware

A growing community that shares digital 3D designs has created an opportunity to study, encourage and stimulate innovation. This remix community allows people not only to prototype at a minimal cost but also to work on projects they are genuinely interested in (Acosta 2009; Dougherty 2012). Participants free of the limitations typically imposed by formal organizations develop products driven by their own interest.
CHALLENGES AND RESEARCH ISSUES FOR PRODUCT AND PROCESS DESIGN OPTIMIZATION

Optimization as an enabling technology has been one of the big success stories in process systems engineering. In this paper we present first a general review of optimization and its applications to a variety of problems in process systems engineering. Next, we provide an overview of two key areas: nonlinear programming and logic-based discrete/continuous optimization. In particular, recent advances are presented in the modeling and solution of nonlinear programming, dynamic optimization, mixed-integer and generalized disjunctive programming, global optimization and constraint programming. The impact of these techniques is illustrated with several example problems.
HER2 Dimerization Inhibitor Pertuzumab - Mode of Action and Clinical Data in Breast Cancer

The humanized monoclonal antibody pertuzumab prevents the dimerization of HER2 with other HER receptors, in particular the pairing of the most potent signaling heterodimer HER2/HER3, thus providing a potent strategy for dual HER2 inhibition. It binds to the extracellular domain of HER2 at a different epitope than trastuzumab. Pertuzumab and trastuzumab act in a complementary fashion and provide a more complete blockade of HER2-mediated signal transduction than either agent alone. Phase II studies demonstrated that pertuzumab was generally well tolerated as a single agent or in combination with trastuzumab and/or cytotoxic agents, and implied an improved clinical efficacy of the combination of pertuzumab and trastuzumab in early and advanced HER2-positive breast cancer. Results of the pivotal phase III study CLEOPATRA in patients with HER2-positive metastatic breast cancer demonstrated that the addition of pertuzumab to first-line combination therapy with docetaxel and trastuzumab significantly prolonged progression-free and overall survival without increasing cardiac toxicity. Currently, the combination of both antibodies is being explored in the palliative setting as well as in the treatment of early HER2-positive breast cancer. Dual HER2 inhibition with the HER2 dimerization inhibitor pertuzumab and trastuzumab may change clinical practice in HER2-positive first-line metastatic breast cancer treatment.
Hydrothermal Synthesis of Various Hierarchical ZnO Nanostructures and Their Methane Sensing Properties

Hierarchical flower-like ZnO nanorods, net-like ZnO nanofibers and ZnO nanobulks have been successfully synthesized via a surfactant assisted hydrothemal method. The synthesized products were characterized by X-ray powder diffraction and field emission scanning electron microscopy, respectively. A possible growth mechanism of the various hierarchical ZnO nanostructures is discussed in detail. Gas sensors based on the as-prepared ZnO nanostructures were fabricated by screen-printing on a flat ceramic substrate. Furthermore, their gas sensing characteristics towards methane were systematically investigated. Methane is an important characteristic hydrocarbon contaminant found dissolved in power transformer oil as a result of faults. We find that the hierarchical flower-like ZnO nanorods and net-like ZnO nanofibers samples show higher gas response and lower operating temperature with rapid response-recovery time compared to those of sensors based on ZnO nanobulks. These results present a feasible way of exploring high performance sensing materials for on-site detection of characteristic fault gases dissolved in transformer oil.
Seeing Is Not the Same as Thinking: Commentary on ''Making Sense of Infant Categorization''

Abstract Madole and Oakes claim that there is only one kind of categorization and that what changes with development is that infants become increasingly attentive to abstract features of objects and so their categorization becomes more abstract. In my commentary, I show why both of these hypotheses are incorrect. First, conceptual development frequently goes from the abstract to the concrete, and second, an extensive literature shows that there is more than one kind of categorization. I discuss some of the ways in which perceptual and conceptual categorization differ.
The Fluctuation Theorem

The question of how reversible microscopic equations of motion can lead to irreversible macroscopic behaviour has been one of the central issues in statistical mechanics for more than a century. The basic issues were known to Gibbs. Boltzmann conducted a very public debate with Loschmidt and others without a satisfactory resolution. In recent decades there has been no real change in the situation. In 1993 we discovered a relation, subsequently known as the Fluctuation Theorem (FT), which gives an analytical expression for the probability of observing Second Law violating dynamical fluctuations in thermostatted dissipative non-equilibrium systems. The relation was derived heuristically and applied to the special case of dissipative non-equilibrium systems subject to constant energy 'thermostatting'. These restrictions meant that the full importance of the Theorem was not immediately apparent. Within a few years, derivations of the Theorem were improved but it has only been in the last few of years that the generality of the Theorem has been appreciated. We now know that the Second Law of Thermodynamics can be derived assuming ergodicity at equilibrium, and causality. We take the assumption of causality to be axiomatic. It is causality which ultimately is responsible for breaking time reversal symmetry and which leads to the possibility of irreversible macroscopic behaviour. The Fluctuation Theorem does much more than merely prove that in large systems observed for long periods of time, the Second Law is overwhelmingly likely to be valid. The Fluctuation Theorem quantifies the probability of observing Second Law violations in small systems observed for a short time. Unlike the Boltzmann equation, the FT is completely consistent with Loschmidt's observation that for time reversible dynamics, every dynamical phase space trajectory and its conjugate time reversed 'anti-trajectory', are both solutions of the underlying equations of motion. Indeed the standard proofs of the FT explicitly consider conjugate pairs of phase space trajectories. Quantitative predictions made by the Fluctuation Theorem regarding the probability of Second Law violations have been confirmed experimentally, both using molecular dynamics computer simulation and very recently in laboratory experiments.
[Baby massage].

One day, you will discover a new adventure and knowledge by spending more money. But when? Do you think that you need to obtain those all requirements when having much money? Why don't you try to get something simple at first? That's something that will lead you to know more about the world, adventure, some places, history, entertainment, and more? It is your own time to continue reading habit. One of the books you can enjoy now is baby massage here.
The antigen receptors on mature and immature T lymphocytes are coupled to phosphatidylcholine‐specific phospholipase D activation

Phosphatidylcholine–phospholipase D has been proposed to play a key role in the transduction of the proliferative responses of a wide range of mitogens and growth factors. We now report that the antigen receptors on T lymphocytes derived from human tonsillar or murine splenic preparations are coupled to phosphatidylcholine (PtdCho)–phospholipase D (PLD) activation following stimulation of these T cells with anti‐CD3 antibodies. However, since we also demonstrate that the antigen receptors on murine thymocytes are coupled to PtdCho–PLD activation, we propose that it is unlikely that this PLD pathway plays a central role in the transduction of T‐cell proliferative responses, but rather, may be involved in either driving cells into cycle or maintaining cell cycle progression, processes required both for proliferation and activation‐induced cell death. Whilst the molecular mechanisms underlying T‐cell receptor (TCR)‐coupling to PtdCho–PLD activation in these cells have not been fully defined, kinetics studies and experiments using pharmacological inhibitors of protein tyrosine phosphatases (PTPases) and reconstituting CD3‐coupled PtdCho–PLD activity in streptolysin‐O permeabilized cells, suggest that the TCR/CD3 complex, under optimal conditions of activation, may be predominantly coupled to PtdCho–PLD activation downstream of tyrosine phosphorylation of phospholipase C‐γ (PLC‐γ), phosphatidylinositol (PtdIns)P2hydrolysis, calcium mobilization and protein kinase C (PKC) activation.
Et århundrede efter Spearmans g

Hartman, P. (2004). A Century after Spearmans g. Nordisk Psykologi, 56 (1) 3–18. 100 years ago Spearman discovered that all cognitive ability tests had one common factor that could account for the majority of the common variance among all these cognitive ability tests. He labelled this general factor the g factor. The g factor is found across sex, age, nationality and culture which points to the robustness of g as a statistical construct. The g factor can be measured and estimated adequately through the use of several cognitive ability tests followed by a factor analysis. The g factor is more than advanced statistics it is also a biological phenomenon. The heritability of g factor scores amount to 40–80% depending on the age of the subjects. Furthermore, several correlations between g factor scores and physiological processes have been found, all pointing to the fact that the g factor is rooted in biology. The g factor also has major implications for social life, which is seen by the fact that g factor scores correlate with a host of social behaviour like obtained education, learning ability and job performance. This is not to say that a persons g factor score controls the destiny of that person. Other factors like personality, luck and such, also influence the social behaviour of that person. In conclusion, although the g factor is not the only relevant factor in regards to the understanding of cognitive abilities and it's structure, it is certainly the most important one.
The phenotype in vitro and in infected cells of herpes simplex virus 1 alpha trans-inducing factor (VP16) carrying temperature-sensitive mutations introduced by substitution of cysteines

alpha trans-inducing factor (alpha TIF, VP16, Vmw65) is an essential structural protein of herpes simplex virus, being required for virion assembly. The protein also forms complexes with host proteins and a response element and transactivates the alpha genes which carry this element. The protein contains an acidic carboxyl terminus required for transactivation and a much larger amino-terminal domain required for promoter recognition. We report the first set of temperature-sensitive (ts) mutations deliberately introduced into the protein by substitution of the cysteine codons with those specifying glycine at positions 78, 102, and 176, either singly or in combinations. We report the following results. (i) All mutated proteins synthesized in vitro formed complexes with the DNA response element at room temperature. However, the mutant with the triple substitution and two mutants with substitutions in two of the three cysteines exhibited a ts phenotype at 33 and 37 degrees C, and one exhibited a ts phenotype only at 37 degrees C. (ii) Replacement of wild-type alpha TIF with genes carrying substitutions in any two cysteines conferred a ts phenotype for replication at 39.5 degrees C. Shift-down experiments indicated that the 10(4)- to 10(5)-fold reduction in virus yield at the nonpermissive temperature was due to the disfunction of alpha TIF late in infection, presumably in virion maturation. (iii) The alpha TIF expressed in cells infected with mutant viruses exhibited the same ts phenotype in protein-DNA complex formation as those expressed in vitro from mutated plasmids. Although the virus carrying the alpha TIF substitutions at Cys-102 and Cys-176 failed to induce a reporter gene linked to the alpha 4 promoter at 39.5 degrees C, it replicated as well as the parent virus in cells maintained for the first 10 h of infection at 39.5 degrees C. We conclude the following. (i) Formation of DNA-protein complexes containing alpha TIF is a poor prognosticator of alpha TIF function. (ii) The data presented here and in the literature strongly support the hypothesis that the secondary structure of the alpha TIF is very sensitive to deletions or insertions which probably affect the interaction of alpha TIF with both viral proteins in the virion and cellular proteins during infection. As a consequence, deletion-insertion mutagenesis may not shed useful information on the role of transactivating function of alpha TIF in infection. (iii) Since cysteines may play a role in stabilizing the secondary structure of proteins, substitutions of cysteines may be a powerful technique for site-specific construction of ts mutants in essential viral proteins.
Improved depth map estimation in stereo vision

In this paper, we present a new approach for dense stereo matching which is mainly oriented towards the recovery of depth map of an observed scene. The extraction of depth information from the disparity map is well understood, while the correspondence problem is still subject to errors. In our approach, we propose optimizing correlation based technique by detecting and rejecting mismatched points that occur in the commonly challenging image regions such as textureless areas, occluded portions and discontinuities. The missing values are completed by incorporating edges detection to avoid that a window contains more than one object. It is an efficient method for selecting a variable window size with adaptive shape in order to get accurate results at depth discontinuities and in homogeneous areas while keeping a low complexity of the whole system. Experimental results using the Middlebury datasets demonstrate the validity of our presented approach. The main domain of applications for this study is the design of new functionalities within the context of mobile devices.
Accessible Texts for Autism: An Eye-Tracking Study

People with Autism Spectrum Disorder (ASD) are known to experience difficulties in reading comprehension, as well as to have unusual attention patterns, which makes the development of user-centred tools for this population a challenging task. This paper presents the first study to use eye-tracking technology with ASD participants in order to evaluate text documents. Its aim is two-fold. First, it evaluates the use of images in texts and provides evidence of a significant difference in the attention patterns of participants with and without autism. Sets of two types of images, photographs and symbols, are compared to establish which ones are more useful to include in simple documents. Second, the study evaluates human-produced easy-read documents, as a gold standard for accessible documents, on 20 adults with autism. The results provide an understanding of the perceived level of difficulty of easy-read documents according to this population, as well as the preferences of autistic individuals in text presentation. The results are synthesized as set of guidelines for creating accessible text for autism.
Human-centric visual access control for clinical data management

This paper introduces a novel human-centric, visual, and context-aware access control (AC) system for distributed clinical data management and health information systems. Human-centricity in this context means that medical staff should be able to configure AC rules, both in a timesaving and reliable manner. Since medical data often include meta information about a patient, it is essential that an AC system only grants access requests that meet the patient's intent. Hence, it is desirable that a patient be included in the AC process. To cater for the strong security needs in the medical domain, both the AC policy creation by medical staff as well as the patient-interaction feature need to be supervised by governing policies. While traditional AC systems such as role-based access control offer sufficient security in theory, they lack in comfort and flexibility. This property does not fulfil the requirements of flexible and distributed environments. Distributed medical institutions could enormously benefit from the opportunity of dynamic AC configuration at an end-user level while adhering to legal, ethical or other privacy requirements. Hence, this paper presents a human-centric visual AC model for medical data, addressing usability, information security and patient interaction. To demonstrate our approach, an integration with the DCM4CHE open source system is presented.
Identification of a Magnesium-dependent NAD(P)(H)-binding Domain in the Nicotinoprotein Methanol Dehydrogenase from Bacillus methanolicus *

The Bacillus methanolicusmethanol dehydrogenase (MDH) is a decameric nicotinoprotein alcohol dehydrogenase (family III) with one Zn2+ion, one or two Mg2+ ions, and a tightly bound cofactor NAD(H) per subunit. The Mg2+ ions are essential for binding of cofactor NAD(H) in MDH. A B. methanolicus activator protein strongly stimulates the relatively low coenzyme NAD+-dependent MDH activity, involving hydrolytic removal of the NMN(H) moiety of cofactor NAD(H) (Kloosterman, H., Vrijbloed, J. W., and Dijkhuizen, L. (2002)J. Biol. Chem. 277, 34785–34792). Members of family III of NAD(P)-dependent alcohol dehydrogenases contain three unique, conserved sequence motifs (domains A, B, and C). Domain C is thought to be involved in metal binding, whereas the functions of domains A and B are still unknown. This paper provides evidence that domain A constitutes (part of) a new magnesium-dependent NAD(P)(H)-binding domain. Site-directed mutants D100N and K103R lacked (most of the) bound cofactor NAD(H) and had lost all coenzyme NAD+-dependent MDH activity. Also mutants G95A and S97G were both impaired in cofactor NAD(H) binding but retained coenzyme NAD+-dependent MDH activity. Mutant G95A displayed a rather low MDH activity, whereas mutant S97G was insensitive to activator protein but displayed “fully activated” MDH reaction rates. The various roles of these amino acid residues in coenzyme and/or cofactor NAD(H) binding in MDH are discussed.