Miracle-dz/UniFAR-FTUs huggingface dataset:
Ripening of pepper (Capsicum annuum) fruit is characterized by an enhancement of protein tyrosine nitration.

BACKGROUND AND AIMS Pepper (Capsicum annuum, Solanaceae) fruits are consumed worldwide and are of great economic importance. In most species ripening is characterized by important visual and metabolic changes, the latter including emission of volatile organic compounds associated with respiration, destruction of chlorophylls, synthesis of new pigments (red/yellow carotenoids plus xanthophylls and anthocyanins), formation of pectins and protein synthesis. The involvement of nitric oxide (NO) in fruit ripening has been established, but more work is needed to detail the metabolic networks involving NO and other reactive nitrogen species (RNS) in the process. It has been reported that RNS can mediate post-translational modifications of proteins, which can modulate physiological processes through mechanisms of cellular signalling. This study therefore examined the potential role of NO in nitration of tyrosine during the ripening of California sweet pepper. METHODS The NO content of green and red pepper fruit was determined spectrofluorometrically. Fruits at the breaking point between green and red coloration were incubated in the presence of NO for 1 h and then left to ripen for 3 d. Profiles of nitrated proteins were determined using an antibody against nitro-tyrosine (NO2-Tyr), and profiles of nitrosothiols were determined by confocal laser scanning microscopy. Nitrated proteins were identified by 2-D electrophoresis and MALDI-TOF/TOF analysis. KEY RESULTS Treatment with NO delayed the ripening of fruit. An enhancement of nitrosothiols and nitroproteins was observed in fruit during ripening, and this was reversed by the addition of exogenous NO gas. Six nitrated proteins were identified and were characterized as being involved in redox, protein, carbohydrate and oxidative metabolism, and in glutamate biosynthesis. Catalase was the most abundant nitrated protein found in both green and red fruit. CONCLUSIONS The RNS profile reported here indicates that ripening of pepper fruit is characterized by an enhancement of S-nitrosothiols and protein tyrosine nitration. The nitrated proteins identified have important functions in photosynthesis, generation of NADPH, proteolysis, amino acid biosynthesis and oxidative metabolism. The decrease of catalase in red fruit implies a lower capacity to scavenge H2O2, which would promote lipid peroxidation, as has already been reported in ripe pepper fruit.
An upper bound for the lower central series quotients of a free associative algebra

Feigin and Shoikhet conjectured in math/0610410 that successive quotients $B_m(A_n)$ of the lower central series filtration of a free associative algebra $A_n$ have polynomial growth. In this paper we give a proof of this conjecture, using the structure of $W_n$-representation on $B_m(A_n)$ which was defined in math/0610410 . We also prove that the number of squares in a Young diagram $D$ corresponding to an irreducible $W_n$-module in the Jordan-Holder series of $B_m(A_n)$ is bounded above by the integer $(m-1)^2+2[(n-2)/2](m-1)$. This bound combined with MAGMA computations by Rains in math/0610410 allows us to confirm the $W_n$-module structure of $B_3(A_3)$ conjectured in math/0610410 .
The Potential of Non-Formal Laboratory Environments for Innovating the Chemistry Curriculum and Promoting Secondary School Level Students Education for Sustainability

Developing skills and attitudes among students in terms of Education for Sustainable Development (ESD) requires that educators address issues of sustainability in both formal and non-formal education. However, up to now, ESD seems to have been insufficiently implemented in secondary science education in many countries in general, and in high school chemistry learning in particular. A lack of suitable experiments, coupled with missing teaching and learning materials and insufficient teacher professional development have been identified as the reasons for this gap. This paper describes a project of innovation and research in the field of ESD for secondary school chemistry education. Within the project, both half- and full-day learning environments have been developed for non-formal, laboratory-based learning of secondary level students at the university. The research-based development focuses on teaching-learning modules which link formal and non-formal learning. The pedagogy employed is both learner-centered and inquiry-based. All the modules focus on sustainability issues in chemistry-related contexts. Data was collected by questionnaires from teachers and students both prior to and after the visit of the non-formal learning environment. Likert-items were analyzed statistically and the evaluation of the open-ended questions was done by Qualitative Content Analysis. An overview of the project, a case from the non-formal laboratory setting, and findings from accompanying research and evaluation are discussed in this paper. Potential impacts on teacher professional development and curriculum innovation are also outlined.
Evolution of infrared luminosity functions of galaxies in the AKARI NEP-deep field - Revealing the cosmic star formation history hidden by dust

Aims. Dust-obscured star-formation increases with increasing intensity and increasing redshift. We aim to reveal the cosmic starformation history obscured by dust using deep infrared observation with AKARI. Methods. We constructed restframe 8 μm, 12 μm, and total infrared (TIR) luminosity functions (LFs) at 0.15 < z < 2.2 using 4128 infrared sources in the AKARI NEP-deep field. A continuous filter coverage in the mid-IR wavelength (2.4, 3.2, 4.1, 7, 9, 11, 15, 18, and 24 μm) by the AKARI satellite allowed us to estimate restframe 8 μm and 12 μm luminosities without using a large extrapolation based on an SED fit, which was the largest uncertainty in previous work. Results. We find that all 8 μm (0.38 < z < 2.2), 12 μm (0.15 < z < 1.16), and TIR LFs (0.2 < z < 1.6) show continuous and strong evolution toward higher redshift. Our direct estimate of 8 μm LFs is useful since previous work often had to use a large extrapolation from the Spitzer 24 μm to 8 μm, where SED modeling is more difficult because of the PAH emissions. In terms of cosmic infrared luminosity density (Ω_(IR)), which was obtained by integrating analytic fits to the LFs, we find good agreement with previous work at z < 1.2. We find the ΩIR evolves as ∝(1 + z)^(4.4±1.0). When we separate contributions to Ω_(IR) by LIRGs and ULIRGs, we found more IR luminous sources are increasingly more important at higher redshift. We find that the ULIRG (LIRG) contribution increases by a factor of 10 (1.8) from z = 0.35 to z = 1.4.
TMBMODEL : Automatic modeling of transmembrane β barrel proteins based and topology predictions , idealized models and Z-coordinage predictions .

Motivation: Two types of transmembrane proteins exist, α-helical membrane proteins and transmembrane β-barrels. The later type exists in the outer membrane of gram-negative bacteria and in chloroplast and mitochondria where they play a major role in the translocation machinery. Here, we aim to build three-dimensional models for transmembrane β-barrels based on a large set of predicted topologies used to generate alternative three-dimensional models. Thereafter, the predicted Z-coordinate, i.e. the distance of a residue from the membrane center, is used to identify the best model. Results: We present TMBMODEL; a method for generating threedimensional models based on predicted topologies. TMBMODEL employs theoretic principles from known structures to construct a model for a barrel of a given transmembrane β-barrel sequence. Firstly, different topologies are obtained from running the BOCTOPUS topology predictor and then three-dimensional models are constructed for different shear numbers. The best model is then selected based on a novel Z-coordinate predictor. Based on a leaveone-out cross-validation, the Z-coordinate predictor predicts 74% residues within 2 Å on a non-redundant dataset of 36 transmembrane β-barrels. The average error and correctly identified membrane residues is 1.61 Å and 71%, respectively. TMBMODEL chose the correct topology for 75% proteins in the data set, which is a slight improvement over BOCTOPUS. More importantly TMBMODEL provides a Cα template for more detailed structural analysis. The average RMSD for this template is 7.24 Å. Availability: TMBMODEL is freely available as a web-server at: http://tmbmodel.cbr. su.se/. The data sets used for training and evaluations are also available from this site. Contact: arne@bioinfo.se Abbreviations: TMB, transmembrane β-barrel protein; HMM, Hidden Markov Model; SVM, support vector machine.
Psychological Skill Development in Children and Adolescents

Psychological skills and methods that can be applied to working with children and adolescents in sport are examined from a theory-to-practice as well as a practice-to-theory approach. In addition to an emphasis on the reciprocal nature of theory and practice, the philosophy adopted in this paper includes a focus on personal development rather than performance, and a multidisciplinary or integrated sport science approach to understanding children’s experiences in the physical domain. The types of psychological skills discussed are self-perceptions, motivation, positive attitude, coping with stress, and moral development. Psychological methods include environmental influences such as physical practice methods, coach and parent education, communication styles, and modeling; and individual control strategies in the form of goal setting, relaxation, and mental imagery. Numerous anecdotal stories based on the author’s experiences working with children and adolescents are used to support the major philosophical .
PFEAST: A High Performance Sparse Eigenvalue Solver Using Distributed-Memory Linear Solvers

The FEAST algorithm and eigensolver for interior eigenvalue problems naturally possesses three distinct levels of parallelism. The solver is then suited to exploit modern computer architectures containing many interconnected processors. This paper highlights a recent development within the software package that allows the dominant computational task, solving a set of complex linear systems, to be performed with a distributed memory solver. The software, written with a reverse-communication-interface, can now be interfaced with any generic MPI linear-system solver using a customized data distribution for the eigenvector solutions. This work utilizes two common “black-box” distributed memory linear-systems solvers (Cluster-MKL-Pardiso and MUMPS), as well as our own application-specific domain-decomposition MPI solver, for a collection of 3-dimensional finite-element systems. We discuss and analyze how parallel resources can be placed at all three levels simultaneously in order to achieve good scalability and optimal use of the computing platform.
North Pacific decadal variability in the Community Climate System Model version 2

Abstract North Pacific decadal oceanic and atmospheric variability is examined from a 650-yr control integration of the Community Climate System Model version 2. The dominant pattern of winter sea surface temperature (SST) variability is similar to the observed “Pacific decadal oscillation,” with maximum amplitude along the Kuroshio Extension. SST anomalies in this region exhibit significant spectral peaks at approximately 16 and 40 yr. Lateral geostrophic heat flux divergence, caused by a meridional shift of the Kuroshio Extension forced by basin-scale wind stress curl anomalies 3–5 yr earlier, is responsible for the decadal SST variability; local surface heat flux and Ekman heat flux divergence act as a damping and positive feedback, respectively. A simple linear Rossby wave model is invoked to explicitly demonstrate the link between the wind stress curl forcing and decadal variability in the Kuroshio Extension. The Rossby wave model not only successfully reproduces the two decadal spectral peaks, but a.
A Theory of Antenna Electromagnetic Near Field—Part I

We present in this paper a comprehensive theory of antenna near fields in two parts, highlighting in particular the engineering perspective. Part I starts by providing a general conceptual framework for the more detailed spectral theory to be developed in Part II. This paper proceeds by proposing a general spatial description for the electromagnetic field in the antenna exterior region based on an asymptotic interpretation of the Wilcox expansion. This description is then extended by constructing the fields in the entire exterior domain by a direct computation starting from the far-field radiation pattern. This we achieve by deriving the Wilcox expansion from the multipole expansion, which allows us to analyze the energy exchange processes between various regions in the antenna surrounding domain, spelling out the effect and contribution of each mode in an analytical fashion. The results are used subsequently to evaluate the reactive energy of arbitrary antennas in a complete form written in terms of the TE and TM modes. Finally, the concept of reactive energy is reexamined in depth to illustrate the inherent ambiguity of the circuit total electric and magnetic reactive energies. We conclude that the traditional reactive field concept is inadequate to the characterization of the antenna near field in general.
Notes on Hierarchical Splines, DCLNs and i-theory

We define an extension of classical additive splines for multivariate function approximation that we call hierarchical splines. We show that the case of hierarchical, additive, piece-wise linear splines includes present-day Deep Convolutional Learning Networks (DCLNs) with linear rectifers and pooling (sum or max). We discuss how these observations together with i-theory may provide a framework for a general theory of deep networks.
Extensive Regulation of Metabolism and Growth during the Cell Division Cycle

Yeast cells grown in culture can spontaneously synchronize their respiration, metabolism, gene expression and cell division. Such metabolic oscillations in synchronized cultures reflect single-cell oscillations, but the relationship between the oscillations in single cells and synchronized cultures is poorly understood. To understand this relationship and the coordination between metabolism and cell division, we collected and analyzed DNA-content, gene-expression and physiological data, at hundreds of time-points, from cultures metabolically-synchronized at different growth rates, carbon sources and biomass densities. The data enabled us to extend and generalize our mechanistic model, based on ensemble average over phases (EAP), connecting the population-average geneexpression of asynchronous cultures to the gene-expression dynamics in the single-cells comprising the cultures. The extended model explains the carbon-source specific growth-rate responses of hundreds of genes. Our physiological data demonstrate that the frequency of metabolic cycling in synchronized cultures increases with the biomass density, suggesting that this cycling is an emergent behavior, resulting from the entraining of the single-cell metabolic cycle by a quorum-sensing mechanism, and thus underscoring the difference between metabolic cycling in single cells and in synchronized cultures. Measurements of constant levels of residual glucose across metabolically synchronized cultures indicate that storage carbohydrates are required to fuel not only the G1/S transition of the division cycle but also the metabolic cycle. Despite the large variation in profiled conditions and in the scale of their dynamics, most genes preserve invariant dynamics of coordination with each other and with the rate of oxygen consumption. Similarly, the G1/S transition always occurs at the beginning, middle or end of the high oxygen consumption phases, analogous to observations in human and drosophila cells. These results highlight evolutionary conserved coordination among metabolism, cell growth and division.
Scavenger receptor class B, type I (Scarb1) deficiency promotes osteoblastogenesis but stunts terminal osteocyte differentiation

Scavenger receptor class B type I (SR‐BI), the Scarb1 gene product, is a high‐density lipoprotein (HDL) receptor which was shown to influence bone metabolism. Its absence in mice is associated with alterations of the glucocorticoid/adrenocorticotropic hormone axis, and translated in high bone mass and enhanced bone formation. Since the cellular alterations underlying the enhanced bone formation remain unknown, we investigated Scarb1‐deficient marrow stromal cells (MSC) behavior in vitro. No difference in HDL3, cholesteryl ester (CE) or estradiol (E) association/binding was measured between Scarb1‐null and wild‐type (WT) cells. Scarb1 genic expression was down‐regulated twofold following osteogenic treatment. Neither WT nor null cell proliferation was influenced by HDL3 exposure whereas this condition decreased genic expression of osteoblastic marker osterix (Sp7), and osteocyte markers sclerostin (Sost) and dentin matrix protein 1 (Dmp1) independently of genotype. Sost and Dmp1 basal expression in null cells was 40% and 50% that of WT cells; accordingly, osteocyte density was 20% lower in vertebrae from Scarb1‐null mice. Genic expression of co‐receptors for Wnt signaling, namely LDL‐related protein (Lrp) 5 and Lrp8, was increased, respectively, by two‐ and threefold, and of transcription target‐genes axis inhibition protein 2 (Axin2) and lymphoid enhancer‐binding factor 1 (Lef1) over threefold. Gene expression of Wnt signaling agonist Wnt5a and of the antagonist dickkopfs‐related protein 1 (Dkk1) were found to be increased 10‐ to 20‐fold in null MSC. These data suggest alterations of Wnt pathways in Scarb1‐deficient MSC potentially explaining their enhanced function, hence contributing to the high bone mass observed in these mice.
Euclidean geometry : cognitive gender differences

The standardized system in most South African secondary schools coupled with a uniform core curriculum for mathematics lends itself to an advantageous environment for empirical studies in mathematics performance. Performance in Euclidian geometry was evaluated for possible gender differences by means of multiple choice and open ended question. No statistically significant gender difference in mean performance was found. Further analysis at item level was undertaken for the multiple choice component of the test items were identified as producing differential gender performance. The performance was in favour of most males for each of these items. In all four cases females of higher ability surpassed males of a corresponding ability level
ORIENTATION AND WAYFINDING: A REVIEW

Spatial orientation can take place in three separate scales: scenes within an individual's visual field, surrounds including information to the front, side, and rear, and neighborhoods, that contain points not visible from the current location. When asked to orient in a surround people are especially sensitive to information to their fronts and backs. However if the surround has been experienced by viewing a map time to access information about a point increases with the angle between the forward direction and the queried point. As people become familiar with neighborhoods they first notice landmarks, then paths between landmarks, and finally develop configurational knowledge of the key locations. The last stage is not always reached, even after years of experience. On the average, people can orient themselves toward an unseen point in a neighborhood with an accuracy of about twenty degrees. However there are very large individual differences in orienting ability. People can acquire orienting information from viewing a map, listening to a description, or experience in a computer-generated virtual environment. The characteristics of the representation may depend upon the medium through which the information is presented. Orientation and Wayfinding 3 ORIENTATION AND WAYFINDING: A REVIEW
Kinematics and hydrodynamics analysis of swimming anurans reveals striking inter-specific differences in the mechanism for producing thrust

SUMMARY This study aimed to compare the swimming kinematics and hydrodynamics within and among aquatic and semi-aquatic/terrestrial frogs. High-speed video was used to obtain kinematics of the leg joints and feet as animals swam freely across their natural range of speeds. Blade element analysis was then used to model the hydrodynamic thrust as a function of foot kinematics. Two purely aquatic frogs, Xenopus laevis and Hymenochirus boettgeri, were compared with two semi-aquatic/terrestrial frogs, Rana pipiens and Bufo americanus. The four species performed similarly. Among swimming strokes, peak stroke velocity ranged from 3.3±1.1 to 20.9±2.5, from 6.8±2.1 to 28.6±3.7 and from 4.9±0.5 to 20.9±4.1 body lengths per second (BL s−1) in X. laevis, H. boettgeri and R. pipiens, respectively (means ± s.d.; N=4 frogs for each). B. americanus swam much more slowly at 3.1±0.3 to 7.0±2.0 BL s−1 (N=3 frogs). Time-varying joint kinematics patterns were superficially similar among species. Because foot kinematics result from the cumulative motion of joints proximal to the feet, small differences in time-varying joint kinematics among species resulted in species-specific foot kinematics (therefore hydrodynamics) patterns. To obtain a simple measure of the hydrodynamically useful motion of the foot, this study uses ‘effective foot velocity’ (EFV): a measure of the component of foot velocity along the axis of swimming. Resolving EFV into translational and rotational components allows predictions of species-specific propulsion strategies. Additionally, a novel kinematic analysis is presented here that enables the partitioning of translational and rotational foot velocity into velocity components contributed by extension at each individual limb joint. Data from the kinematics analysis show that R. pipiens and B. americanus translated their feet faster than their body moved forward, resulting in positive net translational EFV. Conversely, translational EFV was slower than the body velocity in H. boettgeri and X. laevis, resulting in negative net translational EFV. Consequently, the translational component of thrust (caused mostly by hip, knee and ankle extension) was twofold higher than rotational thrust in Rana pipiens. Likewise, rotational components of thrust were nearly twofold higher than translational components in H. boettgeri. X. laevis, however, was the most skewed species observed, generating nearly 100% of total thrust by foot rotation generated by hip, ankle and tmt extension. Thus, this study presents a simple kinematics analysis that is predictive of hydrodynamic differences among species. Such differences in kinematics reveal a continuum of different propulsive strategies ranging from mostly rotation-powered (X. laevis) to mostly translation-powered (R. pipiens) swimming.
Structure and function of the N‐terminal domain of the human mitochondrial calcium uniporter

The mitochondrial calcium uniporter (MCU) is responsible for mitochondrial calcium uptake and homeostasis. It is also a target for the regulation of cellular anti‐/pro‐apoptosis and necrosis by several oncogenes and tumour suppressors. Herein, we report the crystal structure of the MCU N‐terminal domain (NTD) at a resolution of 1.50 Å in a novel fold and the S92A MCU mutant at 2.75 Å resolution; the residue S92 is a predicted CaMKII phosphorylation site. The assembly of the mitochondrial calcium uniporter complex (uniplex) and the interaction with the MCU regulators such as the mitochondrial calcium uptake‐1 and mitochondrial calcium uptake‐2 proteins (MICU1 and MICU2) are not affected by the deletion of MCU NTD. However, the expression of the S92A mutant or a NTD deletion mutant failed to restore mitochondrial Ca2+ uptake in a stable MCU knockdown HeLa cell line and exerted dominant‐negative effects in the wild‐type MCU‐expressing cell line. These results suggest that the NTD of MCU is essential for the modulation of MCU function, although it does not affect the uniplex formation.