Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus 1

Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicstershire LE12 5RD, United Kingdom (N.H.C., N.G., R.S., G.S., G.B.S.); Syngenta Seeds Limited, 31790 Saint Sauveur, France (J.B., L.G.); Applied Statistical Solutions, Bishops Tachbrook, Leamington Spa CV33 9RJ, United Kingdom (J.L.); School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick CV35 9EF, United Kingdom (P.G.W.); Campden BRI, Chipping Campden, Gloucestershire GL55 6LD, United Kingdom (M.P.); Institut National de la Recherche Agronomique, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 84143 Montfavet cedex, France (M.C.); Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia (G.J.K.); and Syngenta Seeds Limited, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom (C.B.)
Broadband and wideband parametric gain via intermodal four-wave mixing in optical fiber

We demonstrate a novel intermodal four-wave mixing process by dividing a pump at 1047nm between the LP<inf>0,4</inf> and LP<inf>0,5</inf> fiber modes, leading to simultaneously broadband (28nm at 1550nm) and wideband (∼1 octave) spontaneous parametric gain.
Differential effects of N-cadherin-mediated adhesion on the development of myotomal waves

Myotomal fibers form by a first wave of pioneer myoblasts from the medial epithelial somite, and by a second wave from all four lips of the dermomyotome. Then, a third wave of mitotic progenitors colonizes the myotome, initially stemming from the extreme lips and, later, from the central dermomyotome sheet. In vitro studies have suggested that N-cadherin plays a role in myogenesis, but its role in vivo remains poorly understood. We find that during the growth phase of the dermomyotome sheet, when the orientation of mitotic spindles is parallel to the mediolateral extent of the epithelium, N-cadherin protein is inherited by both daughter cells. Prior to dermomyotome dissociation into dermis and muscle progenitors, when mitoses become perpendicularly oriented, N-cadherin remains associated only with the apical cell located in apposition to the myotome, generating molecular asymmetry between basal and apical progeny. Local gene missexpression confirms that N-cadherin-mediated adhesion is sufficient to promote myotome colonization, whereas its absence drives cells towards the subectodermal domain, hence coupling the asymmetric distribution of N-cadherin to a shift in mitotic orientation and to fate segregation. Site-directed electroporation to additional, discrete somite regions, further reveals that N-cadherin-mediated adhesion is necessary for maintaining the epithelial configuration of all dermomyotome domains while promoting the onset of Myod transcription and the translocation into the myotome of myofibers and/or of Pax-positive progenitors. By contrast, N-cadherin has no effect on migration or differentiation of the first wave of myotomal pioneers. Altogether, we show for the first time that the asymmetric localization of N-cadherin during mitosis indirectly influences fate segregation by differentially driving the allocation of progenitors to muscle versus dermal primordia, that the adhesive domain of N-cadherin maintains the integrity of the dermomyotome epithelium, which is necessary for myogenic specification, and that different molecular mechanisms underlie the establishment of pioneer and later myotomal waves.
SYNDROMES AND THEMES OF PSYCHOTIC DEPRESSION: A FACTOR ANALYSIS.

This study developed from our original interest in exploring the possible existence of separate syndromes or types of depressive illness. We made the assumption that not all depressives are depressed about the same thing, and that they differ in regard to their primary values, psychodynamics, and prevailing dynamic themes. If this were so, it would then be useful to define and isolate types or subtypes of depression, and to consider what meaningful implications this classification would have for questions of prognosis, treatment, and for the understanding of the individual patient. Although many clinicians have had the impression that there are distinct types of depressives, there has been relatively little progress over the years in systematically refining the vague global concept of the abnormal state of depression. The classic psychoanalytic theory of depression expounded by Freud and Abrahams is based on consideration of ambivalence, aggressive
ORIENTAÇÃO EMPREENDEDORA COMO INDICADOR DO GRAU DE EMPREENDEDORISMO CORPORATIVO: FATORES QUE CARACTERIZAM OS INTRAEMPREENDEDORES E INFLUENCIAM SUA PERCEPÇÃO.

O presente artigo analisa a percepcao dos colaboradores em relacao ao nivel de orientacao empreendedora (OE) como um indicador apropriado para o diagnostico e mensuracao do grau de empreendedorismo corporativo. Trata-se de uma pesquisa exploratoria, quantitativa, realizada com funcionarios de uma empresa de medio porte. Os achados indicam que a percepcao dos colaboradores e significativamente influenciada pela idade e tempo de servico. Estes resultados ajudam a minimizar vieses de pesquisa e corroboram para que as empresas identifiquem com mais facilidade seus intraempreendedores e apoiem suas iniciativas inovadoras.
A new scheme for fuzzy rule-based system identification and its application to self-tuning fuzzy controllers

There are many important issues that need to be resolved for identification of a fuzzy rule-based system using clustering. We address three such important issues: 1) deciding on the proper domain(s) of clustering; 2) deciding on the number of rules; and 3) getting an initial estimate of parameters of the fuzzy systems. We justify that one should start with separate clustering of X (input) and Y (output). We propose a scheme to establish correspondence between the clusters obtained in X and Y. The correspondence dictates whether further splitting/merging of clusters is needed or not. If X and Y do not exhibit strong cluster substructures, then again clustering of X* (input data augmented by the output data) exploiting the results of separate clustering of X and Y, and of the correspondence scheme is recommended. We justify that usual cluster validity indices are not suitable for finding the number of rules, and the proposed scheme does not use any cluster validity index. Three methods are suggested to get the initial estimate of membership functions (MFs). The proposed scheme is used to identify the rule base needed to realize a self-tuning fuzzy PI-type controller and its performance is found to be quite satisfactory.
Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold

Transferases and hydrolases catalyze different chemical reactions and express different dynamic responses upon ligand binding. To insulate the ligand molecule from the surrounding water, transferases bury it inside the protein by closing the cleft, while hydrolases undergo a small conformational change and leave the ligand molecule exposed to the solvent. Despite these distinct ligand‐binding modes, some transferases and hydrolases are homologous. To clarify how such different catalytic modes are possible with the same scaffold, we examined the solvent accessibility of ligand molecules for 15 SCOP superfamilies, each containing both transferase and hydrolase catalytic domains. In contrast to hydrolases, we found that nine superfamilies of transferases use two major strategies, oligomerization and domain fusion, to insulate the ligand molecules. The subunits and domains that were recruited by the transferases often act as a cover for the ligand molecule. The other strategies adopted by transferases to insulate the ligand molecule are the relocation of catalytic sites, the rearrangement of secondary structure elements, and the insertion of peripheral regions. These findings provide insights into how proteins have evolved and acquired distinct functions with a limited number of scaffolds.
Silicon X-Ray Detector With Integrated Thin-Film Transistor for Biomedical Applications

A novel silicon X-ray detector with an integrated thin-film-transistor (TFT) readout circuit is presented. The device consists of a bulk-silicon photodiode and a TFT atop the photodiode. X-ray photons are absorbed and converted to electronic charges by the bulk-silicon photodiode and then read out via the modulation of the TFT drain-source current through an internal gate. Such a device is promising for low-energy X-ray or gamma-ray applications including protein crystallography and X-ray spectroscopy.
Determining the effectiveness of ALMP on youth in Serbia

The focus of research in this paper is on analysing the effective-ness of the active labour market policies in one of the largest vulnerable groups in Serbian labour market - youth population. By means the nearest neighbour matched pair design applied on the youth population cohort at the labour market, the aim was to determine what policies bring about the most gains in comparison to their absence. Moreover by using PSM methodology there was performed a micro-evaluation of several different types of ALMP used in Serbia with a goal of obtaining precise information on the difference in effects among such policies. Main results show that labour market policies for youth population are at least as effective as for general population, leading to around 28% higher chance of a person participating in the treatment to remain employed 6 months later as compared to non-participants. Employment and start-up incentives and apprenticeship training show best results, but surpris-ingly public works have shown nearly no effects, with an expected net loss in a long term.
Conformal coating of poly(glycidyl methacrylate) as a lithographic polymer by initiated chemical vapor deposition

This study reports on the investigation of the conformability and photo and electron beam (EB) patternability of a poly-glycidyl methacrylate (PGMA) film formed by initiated chemical vapor deposition (i-CVD). It is demonstrated that the PGMA film can be conformally deposited on a Si trench structure via i-CVD. In addition, the pattern definition of the film is also successfully demonstrated by deep ultraviolet and EB lithography. These achievements indicate that i-CVD has the potential to become a powerful method to achieve the conformal coating of a lithographic resist.
Impact of Macrolophus caliginosus Presence on Damage Production by Dicyphus tamaninii (Heteroptera: Miridae) on Tomato Fruits

Abstract In northeast Spain, the most common predators found in tomato fields and greenhouses are the mirids Macrolophus caliginosus Wagner and Dicyphus tamaninii Wagner. Natural colonization occurs during the growing season and both species prey on whiteflies. Because D. tamaninii can damage tomato fruits during periods of prey scarcity, a semifield experiment was carried out to evaluate whether the presence of M. caliginosus affects damage produced by D. tamaninii. In a tomato greenhouse, 60 plants were individually caged and distinct predator treatments were introduced: D. tamaninii, D. tamaninii + eggs of Ephestia kuehniella Zeller, D. tamaninii + M. caliginosus, M. caliginosus alone, and a control without any insect. Damage to tomato fruits was recorded (>25% of the fruit) in all the treatments with D. tamaninii, whereas no significant damage was detected with M. caliginosus alone. Finally, no intraguild predation was detected between both mirid species.
A probabilistic model of chronological errors in layer-counted climate proxies: applications to annually banded coral archives

Abstract. The ability to precisely date climate proxies is central to the reconstruction of past climate variations. To a degree, all climate proxies are affected by age uncertainties, which are seldom quantified. This article proposes a probabilistic age model for proxies based on layer-counted chronologies, and explores its use for annually banded coral archives. The model considers both missing and doubly counted growth increments (represented as independent processes), accommodates various assumptions about error rates, and allows one to quantify the impact of chronological uncertainties on different diagnostics of variability. In the case of a single coral record, we find that time uncertainties primarily affect high-frequency signals but also significantly bias the estimate of decadal signals. We further explore tuning to an independent, tree-ring-based chronology as a way to identify an optimal age model. A synthetic pseudocoral network is used as testing ground to quantify uncertainties in the estimation of spatiotemporal patterns of variability. Even for small error rates, the amplitude of multidecadal variability is systematically overestimated at the expense of interannual variability (El Nino–Southern Oscillation, or ENSO, in this case), artificially flattening its spectrum at periods longer than 10 years. An optimization approach to correct chronological errors in coherent multivariate records is presented and validated in idealized cases, though it is found difficult to apply in practice due to the large number of solutions. We close with a discussion of possible extensions of this model and connections to existing strategies for modeling age uncertainties.
Legal Compliance by Design (LCbD) and through Design (LCtD): Preliminary Survey

The purpose of this paper is twofold: (i) carrying out a preliminary survey of the literature and research projects on Compliance by Design (CbD); and (ii) clarifying the double process of (a) extending business managing techniques to other regulatory fields, and (b) converging trends in legal theory, legal technology and Artificial Intelligence. The paper highlights the connections and differences we found across different domains and proposals. We distinguish three different policy-driven types of CbD: (i) business, (ii) regulatory, (iii) and legal. The recent deployment of ethical views, and the implementation of general principles of privacy and data protection lead to the conclusion that, in order to appropriately define legal compliance, Compliance through Design (CtD) should be differentiated from CbD.
Deconvolution of bolus-tracking data: a comparison of discretization methods

Model-free measurement of perfusion from bolus-tracking data requires a discretization of the tracer kinetic model. In this study a classification is provided of existing approaches to discretization, and the accuracy of these methods is compared. Two methods are included which are delay invariant (circulant and time shift) and three methods which are not (volterra, singular and hybrid). Simulations of magnetic resonance imaging (MRI) in the brain are performed for two tissue types (plug flow and compartment) with variable delay and dispersion times, temporal resolution and signal to noise. Simulations were compared to measurements in a patient data set. Both delay-invariant methods are equally accurate, but the circulant method is sensitive to data truncation. Overall volterra produces highest estimates of perfusion, followed by hybrid, singular and delay-invariant methods. Volterra is most accurate except in plug-flow without delay or dispersion, which represents an unrealistic tissue type. Differences between methods vanish when delay or dispersion times increase above the temporal resolution. It is concluded that when negative delays cannot be avoided or when an accurate estimate of left–right perfusion ratios is required, the time shift is the method of choice. When delays are certain to be positive and absolute accuracy is the objective, the volterra method is to be preferred.
Characterising Emotion Signalling and Affected Group Behaviour in Virtual Mammals

This paper investigates how emotions, in this case fear, affect behaviour. We consider deer and sheep as exemplary flocking mammals. The paper also describes and applies a mechanism to measure different types of flocking, using singular values and entropy to compute complexity. Results show that emotion can be used to regulate two competing and vital behaviours inherent in herding animals: the group behaviour (herding) and the individual behaviour (grazing), thus demonstrating that emotion is a functional organiser of group behaviour.
Designing an AHP methodology to prioritize critical elements for product innovation: an intellectual capital perspective

Intellectual capital has for the past decades been evidenced as an important source of competitive advantages and differentiation at the firm level. At the same time, innovation has become a critical factor for companies to ensure their sustainability and even their survival in a globalized business landscape. Having in mind these two crucial concepts for business success, this study intends to build on the relationships between intellectual capital and product innovation at the firm level. Specifically, we will design and test a model based on the Analytic Hierarchy Process, whose aim is to allow the prioritization of intellectual capital elements according to their relative importance for product innovation performance at the firm level. The main goal of this research is to build a diagnosis and action tool that helps business managers incorporate an intellectual capital perspective into their product innovation initiatives. This framework will help managers to better understand which intellectual capital elements are more critical to their product innovation efforts, and thereby systematize actions and clarify resource allocation priorities to improve their product innovation capabilities. In order to validate the practicability of this proposal, the methodology was empirically applied to a Portuguese innovative company.
Modulation of the Unfolded Protein Response by the Severe Acute Respiratory Syndrome Coronavirus Spike Protein

ABSTRACT Perturbation of the function of endoplasmic reticulum (ER) causes stress leading to the activation of cell signaling pathways known as the unfolded protein response (UPR). Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) uses ER as a site for synthesis and processing of viral proteins. In this report, we demonstrate that infection with SARS-CoV induces the UPR in cultured cells. A comparison with M, E, and NSP6 proteins indicates that SARS-CoV spike (S) protein sufficiently induces transcriptional activation of several UPR effectors, including glucose-regulated protein 78 (GRP78), GRP94, and C/EBP homologous protein. A substantial amount of S protein accumulates in the ER. The expression of S protein exerts different effects on the three major signaling pathways of the UPR. Particularly, it induces GRP78/94 through PKR-like ER kinase but has no influence on activating transcription factor 6 or X box-binding protein 1. Taken together, our findings suggest that SARS-CoV S protein specifically modulates the UPR to facilitate viral replication.
Biomarkers in Connective Tissue Disease-Associated Interstitial Lung Disease

Abstract This article reviews major biomarkers in serum and bronchoalveolar lavage fluid (BALF) with respect to their diagnostic and prognostic value in connective tissue disease–associated interstitial lung disease (CTD-ILD). In some CTD such as systemic sclerosis (SSc), the incidence of ILD is up to two-third of patients, and currently ILD represents the leading cause of death in SSc. Because of the extremely variable incidence and outcome of ILD in CTD, progress in the discovery and validation of biomarkers for diagnosis, prognosis, patients' subtyping, response to treatment, or as surrogate endpoints in clinical trials is extremely important. In contrast to idiopathic interstitial pneumonias, autoantibodies play a crucial role as biomarkers in CTD-ILD because their presence is strictly linked to the pathogenesis and tissue damage. Patterns of autoantibodies, for instance, anticitrullinated peptide antibodies in rheumatoid arthritis or aminoacyl-tRNA synthetases (ARS) in polymyositis/dermatomyositis, have been found to correlate with the presence and occasionally with the course of ILD in CTD. Besides autoantibodies, an increase in serum or BALF of a biomarker of pulmonary origin may be able to predict or reflect the development of fibrosis, the impairment of lung function, and ideally also the prognosis. Promising biomarkers are lung epithelium-derived proteins such as KL-6 (Krebs von den Lungen-6), SP-D (surfactant protein-D), SP-A (surfactant protein-A), YKL-40 (chitinase-3-like protein 1 [CHI3L1] or cytokines such as CCL18 [chemokine (C-C) motif ligand 18]). In the future, genetic/epigenetic markers, such as human leukocyte antigen (HLA) haplotypes, single nucleotide polymorphisms, and micro-RNA, may help to identify subtypes of patients with different needs of management and treatment strategies.
Impact of Recombination on the Base Composition of Bacteriaand Archaea

The mutational process in bacteria is biased toward A and T, and most species are GC-rich relative to the mutational input to their genome. It has been proposed that the shift in base composition is an adaptive process-that natural selection operates to increase GC-contents-and there is experimental evidence that bacterial strains with GC-rich versions of genes have higher growth rates than those strains with AT-rich versions expressing identical proteins. Alternatively, a nonadaptive process, GC-biased gene conversion (gBGC), could also increase the GC-content of DNA due to the mechanistic bias of gene conversion events during recombination. To determine what role recombination plays in the base composition of bacterial genomes, we compared the spectrum of nucleotide polymorphisms introduced by recombination in all microbial species represented by large numbers of sequenced strains. We found that recombinant alleles are consistently biased toward A and T, and that the magnitude of AT-bias introduced by recombination is similar to that of mutations. These results indicate that recombination alone, without the intervention of selection, is unlikely to counteract the AT-enrichment of bacterial genomes.
Characterization of bacteriocinogenic strains of lactic acid bacteria from traditional Slovenian cheese 'Tolminc'

Summary The purpose of this research was to examine traditional Slovenian ‘Tolminc’ cheese for the presence of lactic acid bacteria that produce several bacteriocins. The presence of gene determinants for different bacteriocins in this type of cheese and in the cultivable population of ‘Tolminc’ microbiota, have already been demonstrated, as well as its antimicrobial activity. Due to the difficulties in connecting the presence of gene determinants for bacteriocins with the observed antimicrobial activity it was decided to examine in this study the same features on the level of individual bacteriocinogenic strains. Like in previous results, enterococci and their bacteriocins prevailed in cheese microbial consortia. None of isolated strains inhibited growth of Staphylococcus aureus, while the other indicator strains were inhibited in a strain specific manner. Most of isolated strains carried gene determinants for cytolysin. On the basis of gene determinants for bacteriocins, antimicrobial activity, phenotyping by PhP (PhenePlate TM ) system and PCR identification, some similarities found were among Enterococcus isolates.