Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleotide and RNA Metabolism Prime Translational Initiation in the Earliest Events of Mitochondrial Biogenesis during Arabidopsis Germination1[W][OA]

Mitochondria play a crucial role in germination and early seedling growth in Arabidopsis (Arabidopsis thaliana). Morphological observations of mitochondria revealed that mitochondrial numbers, typical size, and oval morphology were evident after 12 h of imbibition in continuous light (following 48 h of stratification). The transition from a dormant to an active metabolic state was punctuated by an early molecular switch, characterized by a transient burst in the expression of genes encoding mitochondrial proteins. Factors involved in mitochondrial transcription and RNA processing were overrepresented among these early-expressed genes. This was closely followed by an increase in the transcript abundance of genes encoding proteins involved in mitochondrial DNA replication and translation. This burst in the expression of factors implicated in mitochondrial RNA and DNA metabolism was accompanied by an increase in transcripts encoding components required for nucleotide biosynthesis in the cytosol and increases in transcript abundance of specific members of the mitochondrial carrier protein family that have previously been associated with nucleotide transport into mitochondria. Only after these genes peaked in expression and largely declined were typical mitochondrial numbers and morphology observed. Subsequently, there was an increase in transcript abundance for various bioenergetic and metabolic functions of mitochondria. The coordination of nucleus- and organelle-encoded gene expression was also examined by quantitative reverse transcription-polymerase chain reaction, specifically for components of the mitochondrial electron transport chain and the chloroplastic photosynthetic machinery. Analysis of protein abundance using western-blot analysis and mass spectrometry revealed that for many proteins, patterns of protein and transcript abundance changes displayed significant positive correlations. A model for mitochondrial biogenesis during germination is proposed, in which an early increase in the abundance of transcripts encoding biogenesis functions (RNA metabolism and import components) precedes a later cascade of gene expression encoding the bioenergetic and metabolic functions of mitochondria.
Rice RAD51 paralogs play essential roles in somatic homologous recombination for DNA repair

Synthesis-dependent strand annealing (SDSA) and single-strand annealing (SSA) are the two main homologous recombination (HR) pathways in double-strand break (DSB) repair. The involvement of rice RAD51 paralogs in HR is well known in meiosis, although the molecular mechanism in somatic HR remains obscure. Loss-of-function mutants of rad51 paralogs show increased sensitivity to the DSB-inducer bleomycin, which results in greatly compromised somatic recombination efficiencies (xrcc3 in SDSA, rad51b and xrcc2 in SSA, rad51c and rad51d in both). Using immunostaining, we found that mutations in RAD51 paralogs (XRCC3, RAD51C, or RAD51D) lead to tremendous impairment in RAD51 focus formation at DSBs. Intriguingly, the RAD51C mutation has a strong effect on the protein loading of its partners (XRCC3 and RAD51B) at DSBs, which is similar to the phenomenon observed in the case of blocking PI3K-like kinases in wild-type plant. We conclude that the rice CDX3 complex acts in SDSA recombination while the BCDX2 complex acts in SSA recombination in somatic DSB repair. Importantly, RAD51C serves as a fulcrum for the local recruitment of its partners (XRCC3 for SDSA and RAD51B for SSA) and is positively modulated by PI3K-like kinases to facilitate both the SDSA and SSA pathways in RAD51 paralog-dependent somatic HR.
Performance Effects of Exploratory and Exploitative Innovation Strategies and the Moderating Role of External Innovation Partners

In today's dynamic environment, the involvement of external partners in the innovation process is frequently assumed to be a panacea to cut costs while improving outcomes. In this study, we scrutinize how different collaboration types influence the effects of exploitative and exploratory innovation strategies on new product development (NPD) performance. For our analyses, we draw on a survey comprising a sample of 254 technology-based German firms. Our findings indicate that exploitative strategies are best pursued without comprehensive external collaborations, while the involvement of several partners in a balanced approach is most promising for exploratory strategies. Joint exploration with competitors, in particular, shows the highest effects on NPD performance. The paper discusses the findings and provides several implications for future research.
Design of IRFNN for reconfigured UPFC to power fflow control and stability improvement

This paper proposed the reconfigured unified power flow controller (RUPFC) design with the cascaded H-bridge converter to realize the transferability between the converter branches of shunt and series. An improved recurrent fuzzy neural network (IRFNN) was used to improve the interaction performance of real and reactive power. The flow control for the RUPFC is formed for the series converter. The fast and stable response of dc link voltage and bus voltage of RUPFC control are expected. The proposed control schemes can improve the shortcoming of the conventional power flow controllers, such as small disturbance linearizing methods. Finally, the effectiveness of the proposed scheme is provided to demonstrate in simulation results.
Development and Evaluation of a Model-Driven System to Support Mobile Learning in Field Trips

While field trips promote the scientific spirit of students by increasing their ability of observation and discovery in various areas of knowledge, the introduction of ubiquitous technologies, such as sensors and actuators, during the field trips, improves students' motivation and learning. However, the development of systems for this purpose implies to deal with the seamless treatment of the devices heterogeneity, absence of fixed communication infrastructure, dynamics of the computational elements of the environment, and support for user mobility. This paper presents then the development and evaluation of a system, called Ubiquitous Field Classes Inventor (UFC-Inventor), which aims to promote the use of mobile and ubiquitous technologies in field trips. The UFC-Inventor evaluation is performed in two stages: first, with five teachers of natural sciences; and later, during a field trip with seventeen students. Two of the teachers were from higher education (Geology and Animal Science) and three of them from high school (two in Geography and one in Biology). The seventeen students who participated in the case study were undergraduate students in the third year of their Geology course. The results suggest a good acceptance of UFC-Inventor and indicate that its execution occurred correctly.
Affine Variance Swap Curve Models

This paper provides a brief overview of the stochastic modeling of variance swap curves. Focus is on affine factor models. We propose a novel drift parametrization which assures that the components of the state process can be matched with any pre-specified points on the variance swap curve. This should facilitate the empirical estimation for such stochastic models. Moreover, sufficient and yet flexible conditions that guarantee positivity of the rates are readily available. We finally discuss the relation and differences to affine yield-factor models introduced by Duffie and Kan [8]. It turns out that, in contrast to variance swap models, their yield factor representation requires imposing constraints on systems of nonlinear equations that are often not solvable in closed form.
eDisco: Discovering Edge Nodes Along the Path

Edge computing is seen as an enabler for upcoming applications requiring low latency offloading, such as augmented reality, and as a key building block for Internet of Things. Edge computing extends the centralized cloud computing model by distributing servers also close to the users, at the edge of the network. A key challenge for the clients remains on how to discover the nearby edge servers and how to access them. In this paper, we present eDisco, DNS-based edge discovery, that leverages existing protocols and requires no modifications to deployed infrastructure. eDisco enables service providers and clients to discover edge servers, and determine the optimal edge deployment configuration.
Strategic implications of manufacturing performance comparisons for newly industrialising countries

The manufacturing strategies and practices in a number of newly industrialising countries (NICs) are studied. The IMSS data for four Latin American industrialising countries, referred to as Group 1, are analysed, comparing these with two benchmarks, which represent more advanced manufacturing situations in well established industrialised countries. Comparing results indicated similarities for Group 1 with the two benchmarks, on simultaneously aiming at all their competitive goals. The study also proved a mismatch in their emphasis on the goals and the level of the objectives achieved in this regard. Links for this mismatch were searched for in various areas including human resource and technological aspects. Results also highlighted serious shortcomings for Group 1 in process technology criteria as compared with the two benchmarks. Comparison results with regard to human resources as well as planning and control aspects are also discussed in the paper. Based on this study, it has been concluded that environmental features have to be thoroughly analysed before any manufacturing strategy is developed for the firms in NICs. Further, continual interactions between manufacturing strategies for these firms with their environmental features have to be included in their strategy formulation process.
ALA induced photodynamic effects on Gram positive and negative bacteria

In the present study we examined the production of high amounts of porphyrins upon induction by d-aminolevulinic acid (ALA) in 9 bacterial strains. This was performed by solely inducing the porphyrin biosynthesis pathway. Four of the strains were Gram positive bacteria and five were Gram negative strains. All strains, except Streptococcus faecalis , produced porphyrins when incubated in PBS with 0.38 mM ALA for 4 h. Excess porphyrin production was excreted to the medium. Gram positive bacteria exhibited fluorescent emission peaks at 622 nm for the endogenous and 617 nm for the excreted porphyrins. Gram negative bacteria exhibited a 630 nm emission peak for the endogenous and a 615 nm emission peak for the excreted extracellular porphyrins. Upon illumination of the ALA induced Staphylococcal strains with 407–420 nm blue light, a decrease of five orders of magnitude was demonstrated with a light dose of 50 J cm^-2. Total eradication of the Staphylococcal strains could be achieved with a 100 J cm^-2 dose, which resulted in a decrease in viability of seven orders of magnitude. The viability of all the induced Gram negative strains and B. cereus decreased by one or two orders of magnitude upon illumination with 50 and 100 J cm^-2, respectively. This difference in the photoinactivation rate was found to be due to the distribution and amounts of the various porphyrins in the bacterial strains. The predominant porphyrin in the Staphylococcal strains was coproporphyrin (68.3–74.6%). In the Gram negative strains there was no predominant porphyrin and the porphyrins found were mostly 5-carboxyporphyrin, uroporphyrin, 7- carboxyporphyrin, coproporphyrin and protoporphyrin. In the B. cereus (Gram positive) strain the predominant porphyrin was uroporphyrin (75.8%). Although the total production of porphyrins in the Gram negative bacteria was higher than in the Staphylococcal strains, the amount of coproporphyrin produced by the latter was twice to three times higher than in the Gram negative strains. The extracellular excreted porphyrins did not contribute to the photoinactivation in any of the tested strains. Significant decreases in the Na^+ and K^+ content were detected in induced S. aureus after illumination while only small changes were observed in E. coli B. The green fluorescent protein within the cytoplasm of induced E. coli strains was only partially disrupted (by 60% only). These results indicate a partial yield of the effects generated by ^1O_2 radicals resulting from the photoinactivation of Gram negative bacteria and a successful generation of the same effects in the Staphylococcal strains.
Optimal secondary control for DC microgrids

In this paper, DC microgrids are modeled as parallel interconnection DC/DC converters. Classical control of such a topology uniformly distributes the total current over branches. This paper demonstrates that such a strategy does not minimize the overall losses when heterogeneous converters are considered. Consequently, a novel control scheme is proposed. It minimizes total losses as well as correcting voltage deviation. Depending on the operating point, current distribution is controlled to maintain optimality.
A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.
The Europeanization of National Planning: Explaining the Causes and the Potentials of Change

Abstract This article proposes a methodological framework for analyzing the Europeanization of national planning, that is, EU influence on domestic planning systems and policies. It seeks in particular to examine whether, where, and how Europeanization of national planning occurs and under which analytic frameworks it may be explained. To this end, the article proposes a three-step research approach. First, it highlights the main patterns of Europeanization in the area of national planning in relation to different modes of EU governance and ideal types of Europeanization. Second, it suggests a typology for the examination of the potential effects of the Europeanization of planning at the domestic level. Finally, it develops some hypotheses on how different institutional, socio-economic and cultural contexts may accommodate or restrain the Europeanization of national planning.
Structure-Based Identification, Characterization, and Disruption of Human Securin-Binding SH3 Domains in Lung Cancer

ABSTRACT The human securin is an oncogenic transcription factor that has been found to promote migration and invasion of lung cancer and many other tumors. The protein contains a PxxP motif that can be recognized and bound by diverse cellular partners via Src homology (SH3) domain to regulate biological and pathological events. The motif is covered by a decapeptide segment 161LGPPSPVKMP170 (SecPeptide) as the potential binding site of SH3 domains. Here, we attempted to systemically identify the SH3 binding partners of human securin in lung cancer and to characterize the intermolecular interaction between SecPeptide and the identified SH3 domains. A bioinformatics protocol that integrated literature curation, complex structural modeling, and binding affinity analysis was described to perform systematic search against an array of SH3-containing proteins involved in lung cancer signaling pathway and, consequently, three putative domains, namely GRB2, CRK, and RasGAP, were identified that have high potential to recognize and bind SecPeptide. The molecular mechanism and biological implication underlying the intermolecular interaction between these domains and SecPetide were investigated at structural and energetic level. Surface plasmon resonance assay revealed a high or moderate affinity of SecPeptide and its two mutants binding to CRK-SH3 domain with dissociation constants Kd = 79.8, 24.2, and 64.6 µM, respectively.
Comparative amino acid sequence analysis of hemolysins produced by Vibrio hollisae and Vibrio parahaemolyticus

Vibrio hollisae produces a hemolysin (Vh-rTDH) that is related to the thermostable direct hemolysin of Vibrio parahaemolyticus (Vp-TDH). Although both hemolysins are essentially similar biologically and immunologically, they differ markedly in heat stability; Vp-TDH is heat stable, whereas Vh-rTDH is heat labile. To elucidate the relationships between their characteristics and molecular structures, we analyzed the amino acid sequence of Vh-rTDH and compared it with that of Vp-TDH. Vh-rTDH consisted of 165 residues, of which 23 residues, spread over the peptide chain, differed from those of Vp-TDH.
Atrioventricular Node Dysfunction and Ion Channel Transcriptome in Pulmonary Hypertension

Background—Heart block is associated with pulmonary hypertension, and the aim of the study was to test the hypothesis that the heart block is the result of a change in the ion channel transcriptome of the atrioventricular (AV) node. Methods and Results—The most commonly used animal model of pulmonary hypertension, the monocrotaline-injected rat, was used. The functional consequences of monocrotaline injection were determined by echocardiography, ECG recording, and electrophysiological experiments on the Langendorff-perfused heart and isolated AV node. The ion channel transcriptome was measured by quantitative PCR, and biophysically detailed computer modeling was used to explore the changes observed. After monocrotaline injection, echocardiography revealed the pattern of pulmonary artery blood flow characteristic of pulmonary hypertension and right-sided hypertrophy and failure; the Langendorff-perfused heart and isolated AV node revealed dysfunction of the AV node (eg, 50% incidence of heart block in isolated AV node); and quantitative PCR revealed a widespread downregulation of ion channel and related genes in the AV node (eg, >50% downregulation of Cav1.2/3 and HCN1/2/4 channels). Computer modeling predicted that the changes in the transcriptome if translated into protein and function would result in heart block. Conclusions—Pulmonary hypertension results in a derangement of the ion channel transcriptome in the AV node, and this is the likely cause of AV node dysfunction in this disease.
Generating Music Medleys via Playing Music Puzzle Games

Generating music medleys is about finding an optimal permutation of a given set of music clips. Toward this goal, we propose a self-supervised learning task, called the music puzzle game, to train neural network models to learn the sequential patterns in music. In essence, such a game requires machines to correctly sort a few multisecond music fragments. In the training stage, we learn the model by sampling multiple non-overlapping fragment pairs from the same songs and seeking to predict whether a given pair is consecutive and is in the correct chronological order. For testing, we design a number of puzzle games with different difficulty levels, the most difficult one being music medley, which requiring sorting fragments from different songs. On the basis of state-of-the-art Siamese convolutional network, we propose an improved architecture that learns to embed frame-level similarity scores computed from the input fragment pairs to a common space, where fragment pairs in the correct order can be more easily identified. Our result shows that the resulting model, dubbed as the similarity embedding network (SEN), performs better than competing models across different games, including music jigsaw puzzle, music sequencing, and music medley. Example results can be found at our project website, https://remyhuang.github. io/DJnet.
Strain Imaging of the Breast by Compression Microwave Imaging

A method that uses microwave pulses to achieve strain imaging of the breast is presented. In the proposed method, the breast is inserted in an enclosure that defines the boundary conditions for the breast deformation under the influence of external pressure. The upper plate of the enclosure, which also includes an antenna array, is attached to a compression tool, whereas the lower and the front plates are fixed. The breast is allowed to extend in the lateral direction when pressed by the top plate. Each of the antennas at the top plate is used to send an ultrawideband pulse to penetrate the breast and measure the backscattered pulse. Two sets of measurements are taken: one pre- and another post-compression of the breast. A sliding window of cross correlation is then performed on the two sets of data to establish the time delay of each segment of the scattered pulse due to compression. That time delay is then employed to get a three-dimensional strain image of the breast. As lesion tissue is typically much stiffer than normal breast tissue, then regions of low or zero strain indicate areas in need of further diagnostic checks. Full-wave simulations are used to validate the presented imaging method.