Miracle-dz/UniFAR-FTUs huggingface dataset:
A Survey on Parallel Architectures and Programming Models

In addition to large-scale computers, multicore processors have taken a significant part in all kinds of devices, from personal computers to cell phones. Although programming techniques for parallel systems exist for a while, the development of applications that can appropriately utilize multicores is still challenging in many aspects, especially for full exploitation of the computational resources. Additionally, another challenge is the efficient and easy programming of heterogeneous systems for the complete exploitation of silicon resources. Solutions to making parallel programming more developer-friendly are various programming models that abstract parallelism and concurrency. Implementations of those models need to extend even to lower layers of software parallelism and hardware parallelism as well.This paper gives an overview of parallel architectures and trending programming models for such processing units and systems. It also presents challenges to scalability and portability in parallel systems and presents up to date trends in heterogeneous systems that heavily exploit parallelism.
Heterozygous deletions of noncoding parts of the PRPF31 gene cause retinitis pigmentosa via reduced gene expression

Purpose Heterozygous mutations in the gene PRPF31, encoding a pre-mRNA splicing factor, cause autosomal dominant retinitis pigmentosa (adRP) with reduced penetrance. At the molecular level, pathogenicity results from haploinsufficiency, as the largest majority of such mutations trigger nonsense-mediated mRNA decay or involve large deletions of coding exons. We investigated genetically two families with a history of adRP, one of whom showed incomplete penetrance. Methods All patients underwent thorough ophthalmological examination, including electroretinography (ERG) and Goldmann perimetry. Array-based comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) were used to map heterozygous deletions, while real-time PCR on genomic DNA and long-range PCR allowed resolving the mutations at the base-pair level. PRPF31 transcripts were quantified with real-time PCR on patient-derived lymphoblastoid cell lines. Results We identified two independent deletions affecting the promoter and the 5′ untranslated region (UTR) of PRPF31 but leaving its coding sequence completely unaltered. Analysis of PRPF31 mRNA from lymphoblastoid cell lines from one of these families showed reduced levels of expression in patients versus controls, probably due to the heterozygous ablation of its promoter sequences. Conclusions In addition to reporting the identification of two novel noncoding deletions in PRPF31, this study provides strong additional evidence that mRNA-mediated haploinsufficiency is the primary cause of pathogenesis for PRPF31-linked adRP.
Correlation between Class Size and Pupils’ Acquisition of Early Mathematics Competencies: A Case of Kericho County, Kenya

Mathematics is one of the core subjects in the Basic Education Curriculum in Kenya. It means that all pupils are required to have a strong grounding in the subject which depends on the level of their early mathematics competencies. The purpose of the study was therefore to establish the level of pupils’ acquisition of early mathematics competencies. The study was also to determine how class size was related to pupils’ acquisition of early mathematics competencies. The study was guided by Social Development Theory by Lev Vygotsky. The study adopted a correlation research design and a mixed research method approach. The dependent variable was pupils’ acquisition of early mathematics competencies while the independent variable was class size. The results from data analysis revealed that majority of the pupils had acquired early mathematics competencies and there was a difference in pupils’ acquisition of early mathematics competencies between grade three pupils in public and those in private primary schools. The relationship between class size and pupils’ acquisition of early mathematics competencies was significant at p<0.05 level of significance. Keywords: Class Size; Pupils; Acquisition of Early Mathematics Competencies; Kericho County; Kenya DOI : 10.7176/JEP/11-21-23 Publication date :July 31st 2020
Optimal Discretization Approach to the Enhanced Single-Particle Model for Li-Ion Batteries

Enhanced single-particle models (eSPMs) have been extensively studied in the development of advanced battery management systems for their accuracy and capability of tracking physical quantities, as well as for the reduced computational load. This article proposes an optimal discretization approach to model reduction for the eSPM using a particle swarm optimization algorithm. The battery diffusion dynamics were solved using different finite difference approaches, that is, an even discretization approach (baseline model) and an uneven discretization approach (optimized model). Because of the structure of the eSPM, internal nodes locations of the solid phase and the electrolyte phase are separately optimized. For the solid phase, a weighted multiobjective cost function is considered for achieving accurate surface and bulk concentration, aiming for accurate terminal-voltage and state-of-charge prediction. For the electrolyte phase, the optimization aims for accurate concentration prediction at the boundary of the electrolyte. The optimally reduced uneven discretization model can predict the battery dynamics accurately and with an improved computational cost: 1) the maximum voltage and SOC prediction errors demonstrated under dynamic current profiles are less than 2.73 mV and 0.37%, respectively, and 2) the number of states reduces by at least 11 times, leading to about a 64% reduction in the computation time.
Development of sustainable fisheries management and monitoring for sensitive soft-bottom habitats and species in the Kattegat

Bottom trawling alters the abundance, diversity, size-composition, and function of benthic communities. However, the ability to detect these impacts over large spatial scales can be obscured by various complicating factors, such as community adaptation to disturbance and co-varying environmental conditions. An ecosystem-based approach to fisheries management therefore requires ecological indicators which can ‘disentangle’ trawling effects from other natural and human drivers, and respond effectively to shifts in ecological quality. We collected benthic macrofaunal samples at 21 sites across a Norway lobster Nephrops norvegicus fishing ground in the Kattegat, and separated the benthic community into small (1-4mm) and large (>4mm) size fractions. Four taxonomic indicators (total density, species density, Shannon diversity, and biomass) and four functional indicators (functional diversity, functional richness, functional evenness, and functional dispersion) were calculated based on each size fraction, and the two fractions combined (pooled community). Here, we compare the ability of these indicators to detect trawling impacts across size categories. We show that indicators derived from large macrofauna were highly effective in this regard, and were less influenced by other environmental drivers, such as depth, sediment grain size, bottom current velocity, salinity, and temperature. This suggests that the taxonomic and functional characteristics of benthic communities display a size-dependent sensitivity to trawling disturbance, and therefore community metrics based on large benthic macrofauna may provide useful indicators. By contrast, indicators derived from the small fraction performed poorly, and those based on the pooled community demonstrated a varied ability to detect trawling. Small macrofauna are typically characterised by high density, diversity, and population growth rates, and their relative resilience to trawling may mask the response of the more sensitive macrofauna. This highlights an underlying issue with calculating indicators based on the whole benthic community. The approach outline here is easily applied, improves indicator performance, and has the potential to reduce laboratory workloads due to the fewer taxa and individuals required for analyses.
Intra-Seasonal and Brood-Size Dependent Variation in the Diet of Black Stork (Ciconia nigra) Nestlings

Abstract. Nestling diet and parental provisioning rate are important determinants of reproductive success and future offspring performance in birds. The diet of Black Stork (Ciconia nigra) nestlings was characterized and tested for intra-seasonal and brood-size dependent variation in the type and mass of prey provisioned to the brood. Data were collected on 576 prey items from 45 Black Stork broods in central Poland during 2005–2016. Black Stork nestlings were provisioned almost exclusively with fish and amphibians; the proportion of invertebrates in their diet was marginal. Fish were a dominant component of nestling diet, comprising up to 65% of prey items and over 85% of total prey mass. Common spadefoot tadpoles (Pelobates fuscus), weatherfish (Misgurnus fossilis) and Prussian carp (Carassius gibelio) were among the most abundant prey. Black Storks foraged on relatively small prey, with an average length of 101.4 ± 1.5 mm (n = 576) and an average mass of 13.8 ± 1.0 g (n = 550). Larger broods were significantly more often fed with amphibians and with lighter prey. As the season progressed, the probability of preying on amphibians increased. This study provides evidence for Black Stork provisioning effort optimization mediated by selection of smaller, but easier to catch and handle prey, such as common spadefoot tadpoles.
Gametic specialization of centromeric histone paralogs in Drosophila virilis

Somatic and germline centromeric functions could differ because of different chromatin environments in male and female gametes versus somatic cells. We show that two different centromeric histone paralogs are alternately retained in male versus female gametes in many Drosophila species. In most eukaryotes, centromeric histone (CenH3) proteins mediate mitosis and meiosis and ensure epigenetic inheritance of centromere identity. We hypothesized that disparate chromatin environments in soma versus germline might impose divergent functional requirements on single CenH3 genes, which could be ameliorated by gene duplications and subsequent specialization. Here, we analyzed the cytological localization of two recently identified CenH3 paralogs, Cid1 and Cid5, in Drosophila virilis using specific antibodies and epitope-tagged transgenic strains. We find that only ancestral Cid1 is present in somatic cells, whereas both Cid1 and Cid5 are expressed in testes and ovaries. However, Cid1 is lost in male meiosis but retained throughout oogenesis, whereas Cid5 is lost during female meiosis but retained in mature sperm. Following fertilization, only Cid1 is detectable in the early embryo, suggesting that maternally deposited Cid1 is rapidly loaded onto paternal centromeres during the protamine-to-histone transition. Our studies reveal mutually exclusive gametic specialization of divergent CenH3 paralogs. Duplication and divergence might allow essential centromeric genes to resolve an intralocus conflict between maternal and paternal centromeric requirements in many animal species.
Remuneration of Distribution Grids for Enhanced Regenerative Electricity Deployment—An Analysis and Model for the Analysis of Grid Structures in Southern Germany Using Linear Programming

Ecological concerns on the climatic effects of the emissions from electricity production stipulate the remuneration of electricity grids to accept growing amounts of intermittent regenerative electricity feed-in from wind and solar power. Germany’s eager political target to double regenerative electricity production by 2030 puts pressure on grid operators to adapt and restructure their transmission and distribution grids. The ability of local distribution grids to operate autonomous of transmission grid supply is essential to stabilize electricity supply at the level of German federal states. Although congestion management and collaboration at the distribution system operator (DSO) level are promising approaches, relatively few studies address this issue. This study presents a methodology to assess the electric energy balance for the low-voltage grids in the German federal state of Baden-Württemberg, assuming the typical load curves and the interchange potential among local distribution grids by means of linear programming of the supply function and for typical seasonal electricity demands. The model can make a statement about the performance and development requirements for grid architecture for scenarios in 2035 and 2050 when regenerative energies will—according to present legislation—account for more than half of Germany’s electricity supply. The study details the amendment to Baden-Württemberg’s electricity grid required to fit the system to the requirements of regenerative electricity production. The suggested model for grid analysis can be used in further German regions and internationally to systematically remunerate electricity grids for the acceptance of larger amounts of regenerative electricity inflows. This empirical study closes the research gap of assessing the interchange potential among DSO and considers usual power loads and simultaneously usual electricity inflows.
Vertical Specialization and Wage Inequality: A Simple Model of Monopolistic Competition

We analyze the relationship between vertical specialization and skilled unskilled wage inequality by using a monopolistic competition model in which firms can disintegrate their production activities between countries. We develop a new diagrammatic exposition to show that vertical specialization arises, i.e., a country produces final goods by using domestic labor with imported inputs and exports final goods abroad. We show that a country with a larger share of vertical specialization has greater wage inequality.
Academic inventors and patent rights: structure of collaboration in academic patents and university patents in Brazil

Many countries have adopted measures to protect the results of academic research through the use of patents and to promote the transfer of knowledge from the public to the private sector. In parallel, studies have focused on discussing the importance of networks of university researchers for the transfer of university specialization in economically viable applications. This paper uses the dynamics of academic patent ownership to analyze the collaborative networks university-industry in Brazil. The database was built from the patents published by PCT with Brazilian priority for the period 2001-2015. Academic patents can be described as “university academic patents” under the ownership of the university; and “academic non-university patents” are those that have at least one professor bonded to the University and listed as an inventor in the patent application. It was verified that the collaboration of Brazilian universities with the productive sector is still small, only 11,8%. However, the lack of university-industry interactions is more significant when the patent is under the ownership of the university compared to “academic nonuniversity patents”. 68.2% of university patents do not collaborate with other institutions. If we add to the public research organizations, the percentage is 73.5%. Of the total non-university patents, 49.7% owned to companies, followed by 30.6% of patents attributed to individuals. Ownership of the patent may be an indicator of the commercial interest of the invention, but the evidence in this paper indicates that higher university ownership is not correlated with higher quality academic patents. Our discussion reinforces that recent innovation policies in Brazil have encouraged the hype of university patenting. Another factor is also in the ability of companies to absorb knowledge. The results achieved are pioneering in what regards Brazil. It would be interesting to analyze the potential and economic value of the licensing of the university and non-university academic patents.
Re-oligotrophication trajectories of macrophyte assemblages in Mediterranean coastal lagoons based on 17-year time-series

: Since the mid-20th century, Mediterranean lagoons have been affected by eutrophication, leading to significant changes in primary producers. In the early 2000s, management actions have been implemented to reduce nutrient inputs with the aim to achieve a good ecological status as requested by the EU water framework directive. As a result of these actions, a sharp decline in nutrient loads has been recorded in several lagoons leading to an oligotrophication of the water column. The analyses of a long-term data set (1998−2015) of 21 polyhaline and euhaline lagoons with contrasting trophic status allowed us to infer a general scheme for the changes in macrophyte assemblages during the oligotrophication process. Placing hypertrophic and oligotrophic conditions end to end, we inferred that the general pattern for the re-oligotrophication trajectory in Mediterranean coastal lagoons is described by the following sequence, with regime shifts between each state: (1) bare non-vegetated sediments, phytoplankton-dominated state; (2) opportunistic macroalgae; (3) seagrass and perennial macroalgae dominated state. However, we did not observe the latter regime shift for the most eutrophicated lagoons, which, so far, remained stuck in the opportunistic macroalgae state. So far, the shift from dominance of opportunistic macroalgae to a system dominated by seagrasses was only observed in a single lagoon where seagrasses had never completely disappeared, which possibly relates to resilience. More generally, the conditions favoring regime shifts from opportunistic macroalgae to seagrasses are still poorly understood. In conclusion, we describe a generic pattern for re-oligotrophication of Mediterranean coastal lagoons, although a full recovery from highly eutrophied to oligotrophic conditions may require more than a decade and may include conditions that remain so far poorly recognized. … partial recovery prevails, degradation and recovery typically follow different pathways as buffers act to maintain the degraded state, and recovery trajectories can depend on the nature of the pressure as well as the connectivity of ecosystems and can differ among ecosystems components and among ecosystems …
Quantitative study of the somitogenetic wavefront in zebrafish

A quantitative description of the molecular networks that sustain morphogenesis is one of the challenges of developmental biology. Specifically, a molecular understanding of the segmentation of the antero-posterior axis in vertebrates has yet to be achieved. This process known as somitogenesis is believed to result from the interactions between a genetic oscillator and a posterior-moving determination wavefront. Here we quantitatively study and perturb the network in zebrafish that sustains this wavefront and compare our observations to a model whereby the wavefront is due to a switch between stable states resulting from reciprocal negative feedbacks of Retinoic Acid (RA) on the activation of ERK and of ERK on RA synthesis. This model quantitatively accounts for the near linear shortening of the post-somitic mesoderm (PSM) in response to the observed exponential decrease during somitogenesis of the mRNA concentration of a morphogen (Fgf8). It also accounts for the observed dynamics of the PSM when the molecular components of the network are perturbed. The generality of our model and its robustness allows for its test in other model organisms.
Impact of energy restriction during late gestation on muscle and blood transcriptome of beef calves

Maternal nutrition during gestation has long-term effects on skeletal muscle development of the offspring. In this thesis, we studied the effect of energy restriction during late gestation on gene expression in the blood and muscle tissues of preconditioned beef calves. The first chapter corresponds to a literature review in which we describe aspects related to this research, such as muscle and immune system development, gene expression, and the use of RNA-seq data to answer complex biological questions. The second chapter describes a research project in which, multiparous cows were divided into two groups: cows fed 70% and 100% of their energy requirements during the last third of gestation. Blood and muscle samples were collected from the offspring, and total RNA was extracted and sequenced (RNA-seq). Finally, statistical analyses were performed to identify differentially expressed genes as an effect of maternal energy restriction, overrepresentation of related biological functions, and to construct gene-gene networks. A total of 160, 164, and 346 DEG (q-value < 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in the muscle metabolism. On muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 6 genes associated with muscle metabolism and development, SLCO3A1, ATP6V0D1, SLC2A1, GPC4, RASD2, and SLC2A1. On blood, among the top 10 DEG, we found genes related to response to stress overexpressed in the REST after weaning, such as SOD3 and INO80D, and to immune response down-regulated in the REST after vaccination, such as OASL,
Bacterial Diversity Greatly Affects Ammonia and Overall Nitrogen Levels inAquabioponics Bioflocs Systems, Based on 16S rRNA Gene AmpliconMetagenomics

AquaBioPonics Bioflocs system, that synergistically combines aquaculture with bioflocs technology, algae cultivation, hydroponics and rainwater harvesting, is an efficient aquaculture biotechnology to produce fish, shrimp and organic vegetables. By adding a commercial probiotic to our systems, we observed an improved productivity and significantly lower ammonia concentrations. We provide initial insight into the overall microbiome and the presence of nitrogen metabolizing bacteria present in these high-yield aquaculture systems.
Spatiotemporal analysis for detection of pre-symptomatic shape changes in neurodegenerative diseases: applied to GENFI study

Brain atrophy as measured from structural MR images, is one of the primary imaging biomarkers used to track neurodegenerative disease progression. In diseases such as frontotemporal dementia or Alzheimer’s disease, atrophy can be observed in key brain structures years before any clinical symptoms are present. Atrophy is most commonly captured as volume change of key structures and the shape changes of these structures are typically not analysed despite being potentially more sensitive than summary volume statistics over the entire structure. In this paper we propose a spatiotemporal analysis pipeline based Large Diffeomorphic Deformation Metric Mapping (LDDMM) to detect shape changes from volumetric MRI scans. We applied our framework to a cohort of individuals with genetic variants of frontotemporal dementia and healthy controls from the Genetic FTD Initiative (GENFI) study. Our method, take full advantage of the LDDMM framework, and relies on the creation of a population specific average spatiotemporal trajectory of a relevant brain structure of interest, the thalamus in our case. The residuals from each patient data to the average spatiotemporal trajectory are then clustered and studied to assess when presymptomatic mutation carriers differ from healthy control subjects. We found statistical differences in shape in the anterior region of the thalamus at least five years before the mutation carrier subjects develop any clinical symptoms. This region of the thalamus has been shown to be predominantly connected to the frontal lobe, consistent with the pattern of cortical atrophy seen in the disease.