Miracle-dz/UniFAR-FTUs huggingface dataset:
Processing of Extremely-Large-Data and High Performance Computing

High performance computing implies the ability to effectively, efficiently, consistently, cohesively and coheren tly access, represent, manage, store, assess, evaluate, compute and process data, thereby enabling analysis, visualization, data mining, extraction, "knowledge generation", "learning", "intelligence", "cognition", etc. In various applications, processing is accomplished on very large heterogeneous data sets. Exceptional scalable microelectronic hardware solutions, efficient algorithms, advanced architectures, enabling organizations and other solutions were developed and effectively used. However, the nanoscale microelectronics, microelectromechanical systems, photonics and nanotechnology frequently result in diverse, incomplete, incompatible and heterogeneous extremely-large-scale data. The problems of data quality, data complexity, data consistency and data utilization have not being cohesively addressed and solved. The paper proposes coherent data complexity and data quality analyses. These solutions may enable processing of extremely-large-data, contribute to cyber security and enhance overall computing capabilities, such as robustness, reliability, throughput, etc. The macroscopic and quantum probabilistic information- and entropy-centric analyses are performed. Ability to process highly inconsistent, incomplete and heterogeneous data and information is exhibited by living organisms. Engineered systems can be designed with an attempt to typify natural systems ensuring robust, effective, low-power and cohesive processing. The data complexity and data quantity measures, as well as other relevant estimates, are derived using information theory. These measures could be applied in information assurance, information assessment, cyber security, etc. New fundamental and algorithmic solutions are reported. The results of basic, numerical and empirical studies and evaluation are presented.
Isolation and composition of milk fat globule membrane material

Summary The material surrounding the fat globules in commercial pasteurized homogenized milk was isolated by centrifugation of the freeze – thaw extract of the fat globules through a 52·5% (w/v) sucrose solution in simulated milk ultrafiltrate. The purified membrane material contained higher neutral lipid levels than fresh raw milk fat globule membrane (MFGM) material. Caseins and whey proteins, mainly β-lactoglobulin (β-lg) were found to be the major protein components of homogenized milk membrane material. Native MFGM polypeptides comprised only a small proportion of the total protein in these membranes. The total amount of membrane material isolated from homogenized milk was substantially higher than that from fresh raw milk. Analysis of homogenized milk membrane material by linear sucrose density gradient centrifugation showed a different pattern to that found with other milks, indicating the presence of new lipoprotein complexes. Commercial ultra heat treated (UHT) milks were also examined, but it was difficult to obtain isolated MFGM material free from core fat. However, fat globule fractions were isolated from these products by high speed centrifugation and these were analysed intact. Membrane material in these milks contained caseins and whey proteins (mainly β-1g). Natural MFGM polypeptides were present at extremely low levels. Phospholipid levels in UHT milk membranes were greatly reduced compared with membrane material isolated from other milks.
Teaching object-oriented programming using BETA

This paper describes the approach to teaching object-oriented programming at Aarhus University. This includes a brief discussion of the conceptual approach to teaching object-oriented programming. The BETA language is used as a basis for the teaching. The paper includes a brief description of BETA. Finally a presentation of the BETA Macintosh environment is given. This environment makes it easy for students to create object-oriented applications.
Chrom trójwartościowy (Cr III) jako pierwiastek śladowy niezbędny dla zwierząt i ludzi

Trivalent is an essential the both Animal studies confirm many beneficial effects of organic and inorganic chromium compounds on carbohydrate, protein and lipid metabolism in the body. Glucose tolerance factor (GTF) has been demonstrated to involve an active form of trivalent chromium, which sustains normal glucose metabolism. Cr(III) compounds form enzymes and ribonucleic acids, accelerate blood clotting and increase β-glucuronidase activity. Chromium also participates in antioxidant processes, in the synthesis of RNA and DNA and in the immune response, as well as affects secretion of hormones and some vitamins. It has been demonstrated that chromium improves lean body mass in animals, increases growth rate and feed conversion and improves feed intake and energy efficiency. Organic chromium reduces mortality and improves animal reproduction parameters. It also enhances immunity and strengthens response to preventive vaccination. It has been noted in many animal species that a diet low in chromium leads to deficiency symptoms, such as reduced feed intake, lower weight gains, reproductive disorders and increased lipid levels. Chromium deficiency can also result from stress. Moderate chromium deficiency is a risk factor of ischemic heart disease with myocardial infarction. Such a condition may pose a great risk of coronary artery disease. Dietary chromium requirement of an animal body is probably 300 μg Cr/kg d.w. of feed, which is usually satisfied by the ration provided. The highest concentration of chromium is found in the hair, skin and teeth, followed by the liver, kidneys, spleen, and slightly lower in the heart, muscles, pancreas, lungs, bones and brain. Chromium absorption rates in the human intestine range between 0.5 and 2% of the daily intake of inorganic Cr forms, and from 25 to 30% of the element ingested as organic complexes. Clinical studies show that the kinetics of chromium excretion from the system are complex and can be described by a multi-range model, the half-life ranging from 13 min to 192 days. Dietary chromium nanocomposite supplementation (CrNano) used in pigs nutrition has significantly increased Cr content in the blood, longissimus muscle, heart, liver, kidneys, jejunum and ileum. Chromium nanocomposite supplementation acts more effectively on the tissues and, as a consequence, increases the accumulation of the element.
Distinct neuronal activity patterns induce different gene expression programs

Brief and sustained neuronal activity patterns can have opposite effects on synaptic strength that both require activity-regulated gene (ARG) expression. However, whether distinct patterns of activity induce different sets of ARGs is unknown. In genome-scale experiments, we reveal that a neuron’s activity-pattern history can be predicted from the ARGs it expresses. Surprisingly, brief activity selectively induces a small subset of the ARG program that that corresponds precisely to the first of three temporal waves of genes induced by sustained activity. These first-wave genes are distinguished by an open chromatin state, proximity to rapidly activated enhancers, and a requirement for MAPK/ERK signaling for their induction. MAPK/ERK mediates rapid RNA polymerase recruitment to promoters, as well as enhancer RNA induction but not histone acetylation at enhancers. Thus, the same mechanisms that establish the multi-wave temporal structure of ARG induction also enable different sets of genes to be induced by distinct activity patterns.
Nueva reacción en cadena de la polimerasa múltiple para el diagnóstico específico de especies implicadas en la candidiasis humana

Introduccion. Las candidiasis son un grupo de infecciones oportunistas causadas por levaduras del genero Candida . Candida albicans es la especie de mayor prevalencia en las infecciones superficiales y profundas. Sin embargo, en la ultima decada, la frecuencia de especies diferentes a C. albicans ha aumentado y, por ende, su relevancia clinica, lo cual exige la utilizacion de tecnicas diagnosticas que permitan su deteccion y el tratamiento adecuado de los pacientes afectados. Objetivo. Disenar y optimizar una tecnica de reaccion en cadena de la polimerasa multiple (PCR multiple) considerando parametros termodinamicos para la deteccion simultanea de cinco especies de Candida relevantes en la etiologia de la candidiasis humana. Materiales y metodos. Para el diseno de los cebadores se consideraron restricciones fisicas y termodinamicas que afectan la PCR multiple, usando el programa Gene Runner y la herramienta Mult-PSOS. Como plantillas se utilizaron la region transcrita interna 2 (ITS2) (AJ249486.1) para C. albicans y la topoisomerasa II (TOPII) para C. parasilopsis (AB049144.1), C. krusei (AB049139.1), C. tropicalis (AB049141.1) y C. guillermondii (AB049145.1), y como moldes, extractos de ADN total obtenidos de cepas ATCC y de aislamientos clinicos de las especies de Candida . Resultados. Se disenaron diez cebadores para la amplificacion simultanea de las especies de Candida . Se obtuvo el siguiente patron de bandas: C. albicans (206 pb), C. guillermondii (244 pb), C. tropicalis (474 pb), C. parasilopsis (558 pb) y C. krusei (419 pb). Conclusion. El ensayo disenado de PCR multiple permitio la amplificacion simultanea y eficiente de todos los amplicones correspondientes a las especies estudiadas de Candida , asi como su adecuada resolucion en gel de agarosa al 1,3 %.
Proceedings of the International Workshop "What can FCA do for Artificial Intelligence?" (FCA4AI 2014)

This is the third edition of the FCA4AI workshop, whose first edition was organized at ECAI 2012 Conference (Montpellier, August 2012) and second edition was organized at IJCAI 2013 Conference (Beijing, August 2013, see http://www.fca4ai.hse.ru/). Formal Concept Analysis (FCA) is a mathematically well-founded theory aimed at data analysis and classification that can be used for many purposes, especially for Artificial Intelligence (AI) needs. The objective of the workshop is to investigate two main main issues: how can FCA support various AI activities (knowledge discovery, knowledge representation and reasoning, learning, data mining, NLP, information retrieval), and how can FCA be extended in order to help AI researchers to solve new and complex problems in their domain.
Novel chromosome organization pattern in actinomycetales–overlapping replication cycles combined with diploidy

Bacteria regulate chromosome replication and segregation tightly with cell division to ensure faithful segregation of DNA to daughter generations. The underlying mechanisms have been addressed in several model species. It became apparent that bacteria have evolved quite different strategies to regulate DNA segregation and chromosomal organization. We have investigated here how the actinobacterium Corynebacterium glutamicum organizes chromosome segregation and DNA replication. Unexpectedly, we find that C. glutamicum cells are at least diploid under all conditions tested and that these organisms have overlapping C-periods during replication with both origins initiating replication simultaneously. Based on experimentally obtained data we propose growth rate dependent cell cycle models for C. glutamicum.
Bdellovibrio et organismes apparentés : Des prédateurs bactériens hors du commun !

Obligate predatory bacteria, i.e. bacteria requiring a Gram negative prey cell in order to complete their cell cycle, belong to the polyphyletic group referred to as the Bdellovibrio And Like Organisms (BALO). Predatory interactions between bacteria are complex, yet their dynamics and impact on bacterial communities in the environment are becoming better understood. BALO have unique life cycles: they grow epibiotically with the predator remaining attached to the prey's envelope, dividing in a binary manner or periplasmically, i.e. by penetrating the prey's periplasm to generate a number of progeny cells. The periplasmic life cycle includes unique gene and protein patterns and unique signaling features. These ecological and cellular features, along with applications of the BALO in the medical, agricultural and environmental fields are surveyed.
The rodent hippocampus as a bilateral structure: A review of hemispheric lateralization

The left and right rodent hippocampi exhibit striking lateralization in some of the very neural substrates considered to be critical for hippocampal cognitive function. Despite this, there is an overwhelming lack of consideration for hemispheric differences in studies of the rodent hippocampus. Asymmetries identified so far suggest that a bilateral model of the hippocampus will be essential for an understanding of this brain region, and perhaps of the brain more widely. Although hypotheses have been proposed to explain how the left and right hippocampi contribute to behavior and cognition, these hypotheses have either been refuted by more recent studies or have been limited in the scope of data they explain. Here, I will first review data on human and rodent hippocampal lateralization. The implications of these data suggest that considering the hippocampus as a bilateral structure with functional lateralization will be critical moving forward in understanding the function and mechanisms of this brain region. In exploring these implications, I will then propose a hypothesis of the hippocampus as a bilateral structure. This discrete-continuous (DC) hypothesis proposes that the left and right hippocampi contribute to spatial memory and navigation in a complementary manner. Specifically, the left hemisphere stores spatial information as discrete, salient locations and that the right hemisphere represents space continuously, contributing to route computation and flexible spatial navigation. Consideration of hippocampal lateralization in designing future studies may provide insight into the function of the hippocampus and resolve debates concerning its function.
Investigations on the Optimal Support Vector Machine Classifiers for Predicting Design Feasibility in Analog Circuit Optimization

In simulation-based circuit optimization, many simulation runs may be wasted while evaluating infeasible designs, i.e. the designs that do not meet the constraints. To avoid such a waste, this paper investigates the use of support vector machine (SVM) classifiers in predicting the design's feasibility prior to simulation and the optimal selection of the SVM parameters, namely, the Gaussian kernel shape parameter γ and the misclassification penalty parameter C. These parameters affect the complexity as well as the accuracy of the model that SVM represents. For instance, the higher γ is good for detailed modeling and the higher C is good for rejecting noise in the training set. However, our empirical study shows that a low γ value is preferable due to the high spatial correlation among the circuit design candidates while C has negligible impacts due to the smooth and clean constraint boundaries of most circuit designs. The experimental results with an LC-tank oscillator example show that an optimal selection of these parameters can improve the prediction accuracy from 80 to 98% and model complexity by 10×.
Braided pneumatic actuator control of a multi-jointed manipulator

Problems with control and compliance of pneumatic systems have prevented their widespread use in advanced robotics. However, their compactness, power/weight ration and safety are factors that could potentially be exploited in sophisticated dexterous manipulator designs. This paper reports on the design of a dexterous manipulation with three fingers and an opposal thumb powered by 18 new compact braided pneumatic muscle actuators (PMA). These muscles (which are variants on the McKibben Muscle design) have considerable power output potential, combined with controllable motion and inherent compliance to prevent damage to handled objects. When arranged as antagonistic pairs the joints of the gripper can be driven independently. Using experimental data a system model can be developed and control of these muscles can be explored showing that accurate regulated performance is feasible. <<ETX>>
Post-mortem T2*- weighted MRI imaging of cortical iron reflects severity of Alzheimer’s Disease

The value of iron-based MRI changes for the diagnosis and staging of Alzheimer’s disease (AD) depends on an association between cortical iron accumulation and AD pathology. Therefore, this study determined the cortical distribution pattern of MRI contrast changes in cortical regions selected based on the known distribution pattern of tau pathology and investigated whether MRI contrast changes reflect the underlying AD pathology in the different lobes. -weighted MRI was performed on post-mortem cortical tissue of controls, late-onset AD, and early-onset AD followed by histology and correlation analyses. Combining ex-vivo high-resolution MRI and histopathology revealed that: LOAD and EOAD have a different distribution pattern of AD pathological hallmarks and MRI contrast changes over the cortex, with EOAD showing more severe MRI changes; (2) per lobe, severity of AD pathological hallmarks correlates with iron accumulation, and hence with MRI. Therefore, iron-sensitive MRI sequences allow detection of the cortical distribution pattern of AD pathology ex-vivo. Abbreviations AD Alzheimer’s disease EOAD early-onset AD GM gray matter IRP iron regulating proteins LOAD late-onset AD MCI mild cognitive impairment PBS phosphate buffered saline QSM quantitative susceptibility mapping WM white matter
Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars

Background Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale. Results Here, we provide a comparative sequence analysis of the ~700-megabase chromosome 2D between two bread wheat genotypes – the old landrace Chinese Spring and the elite Swiss spring wheat line ‘CH Campala Lr22a’. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of >100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of ~8 Mb, ~9 Mb and ~48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Conclusions This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.
Control of nonlinear robotic manipulators

This paper develops an innovative design procedure using the Lyapunov stability theory. In particular, nonlinear control laws are synthesized for rigid robotic manipulators. The technique deals explicitly with nonlinear robot models, and develops the controller for nonlinear manipulators. An example illustrates the design for two-degree-of-freedom planar robot.
TELOS, a Service-Oriented Framework to Support Learning and Knowledge Management

This chapter presents the basic orientations, the main use cases and the conceptual framework of a TeleLearning Operating System. TELOS is a system under development within the LORNET research network (www.lornet.org) aiming to integrate components and services, and research results, produced by the different LORNET teams. TELOS research is at the convergence of three main trends: learning object repositories that facilitate the access to knowledge resources; learning and knowledge management support systems that use these referentials as building blocks; and the integration of these referentials and these systems in the context of the Semantic Web.
A selective filter to smooth ultrasound images

Ultrasound images are usually strongly affected by speckle noise, making hard the tasks of visual and computational analysis of the objects presented. Computational techniques to overcome the interference induced by this type of noise have been widely proposed [1, 2, 3, 4, 5, 6]. The speckle noise is more difficult to be smoothed than the additive noise, then some researchers have been adapting methods proposed for additive noise smoothing to process images affected by speckle noise, as Jin and Yang in [7] that proposed a variational model based on the work proposed by Rudin and collaborators [8] for additive noise smoothing. These methods use specific parameters that are usually defined for specific applications. The smoothing of ultrasound images is an area where these methods should be improved for denoising the original images without affecting the quality of information further extracted. In order to overcome the problem of smoothing ultrasound images of the female pelvic cavity, we propose a selective smoothing method for such images with the objective to perform a soft smoothing in the image regions representing the interesting borders. The pixels to be strongly or weakly smoothed are selected based in their radiation intensity [9]. The level of smoothing is controlled changing the convolution window size used for the average filtering calculation. From the tests that have been performed, we can conclude that if a pixel receives a positive radiance, the probability of this pixel belongs to an inner object region is high, so this pixel should be processed using an average filter with a bigger window. Several tests were performed using bladder ultrasound videos, and the results obtained revealed that the method is able to smooth successfully the input images, as can be seen in Fig. 1. In this figure, two image frames from two distinct ultrasound videos are shown together with the respective images filtered using the proposed method. The regions indicated by the white rectangles were manually chosen, taking into account their visually homogeneousity and the suitability to calculate the associated Equivalent Numbers of Looks (ENL) [10]. It should be noted that, a high ENL value indicates a good
The affinity of the S9.6 antibody for double-stranded RNAs impacts the mapping of R-loops in fission yeast

R-loops, which result from the formation of stable DNA:RNA hybrids, can both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loops in fission yeast, we used the S9.6 antibody-based DRIPc-seq method to sequence the RNA strand of R-loops and obtain strand-specific R-loop maps at near nucleotide resolution. Surprisingly, preliminary DRIPc-seq experiments identified mostly RNase H-resistant but exosome-sensitive RNAs that mapped to both DNA strands and resembled RNA:RNA hybrids (dsRNAs), suggesting that dsRNAs form widely in fission yeast. We confirmed in vitro that S9.6 can immuno-precipitate dsRNAs and provide evidence that dsRNAs can interfere with its binding to R-loops. dsRNA elimination by RNase III treatment prior to DRIPc-seq allowed the genome-wide and strand-specific identification of genuine R-loops that responded in vivo to RNase H levels and displayed classical features associated with R-loop formation. We also found that most transcripts whose levels were altered by in vivo manipulation of RNase H levels did not form detectable R-loops, suggesting that prolonged manipulation of R-loop levels could indirectly alter the transcriptome. We discuss the implications of our work in the design of experimental strategies to probe R-loop functions.