Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing Task Migration Impact on Embedded Soft Real-Time Streaming Multimedia Applications

Multiprocessor systems on chips (MPSoCs) are envisioned as the future of embedded platforms such as game-engines, smart-phones and palmtop computers. One of the main challenge preventing the widespread diffusion of these systems is the efficient mapping of multitask multimedia applications on processing elements. Dynamic solutions based on task migration has been recently explored to perform run-time reallocation of task to maximize performance and optimize energy consumption. Even if task migration can provide high flexibility, its overhead must be carefully evaluated when applied to soft real-time applications. In fact, these applications impose deadlines that may be missed during the migration process. In this paper we first present a middleware infrastructure supporting dynamic task allocation for NUMA architectures. Then we perform an extensive characterization of its impact on multimedia soft real-time applications using a software FM Radio benchmark.
Clone-Based Encoded Neural Networks to Design Efficient Associative Memories

In this paper, we introduce a neural network (NN) model named clone-based neural network (CbNN) to design associative memories. Neurons in CbNN can be cloned statically or dynamically which allows to increase the number of data that can be stored and retrieved. Thanks to their plasticity, CbNN can handle correlated information more robustly than existing models and thus provides better memory capacity. We experiment this model in encoded neural networks also known as Gripon–Berrou NNs. Numerical simulations demonstrate that memory and recall abilities of CbNN outperform state of the art for the same memory footprint.
American Heart Association Precision Medicine Platform

Integrating the open science movement with impactful discoveries in science, velocity of technology, and raw power of cloud computing has led to an unprecedented opportunity for scientific discovery. The American Heart Association recently established the Precision Medicine Platform1 through the efforts of multiple American Heart Association volunteers and a collaboration with Amazon Web Services. The cloud-based platform, powered by Amazon Web Services and available at https://precision.heart. org, was founded on the FAIR principles (findable, accessible, interoperable, and reusable)2 and includes secure collaboration areas (workspaces) and an open sharing area. The goals of the platform are to democratize data, to make it easy to search across orthogonal data sets, to provide a secure workspace to leverage the power of cloud computing, and to provide a forum for users to share insights. Multiple learning tools are available, including video tutorials, templates using open interactive programming framework, and a forum for interaction among community members.3 When accessing large public data sets today, researchers have to find, access, download, and interpret each data set individually. Researchers must untangle and interpret the data and then expend resources to house the data. In addition, the lack of harmonization across multiple data sets obviates the ability of researchers to combine data sources and to confirm or generate cogent findings. The platform aims to address these challenges through a transparent and …
Keyword Search on RDF Graphs - A Query Graph Assembly Approach

Keyword search provides ordinary users an easy-to-use interface for querying RDF data. Given the input keywords, in this paper, we study how to assemble a query graph that is to represent user's query intention accurately and efficiently. Based on the input keywords, we first obtain the elementary query graph building blocks, such as entity/class vertices and predicate edges. Then, we formally define the query graph assembly (QGA) problem. Unfortunately, we prove theoretically that QGA is a NP-complete problem. In order to solve that, we design some heuristic lower bounds and propose a bipartite graph matching-based best-first search algorithm. The algorithm's time complexity is O(k2l . l3l), where l is the number of the keywords and k is a tunable parameter, i.e., the maximum number of candidate entity/class vertices and predicate edges allowed to match each keyword. Although QGA is intractable, both l and k are small in practice. Furthermore, the algorithm's time complexity does not depend on the RDF graph size, which guarantees the good scalability of our system in large RDF graphs. Experiments on DBpedia and Freebase confirm the superiority of our system on both effectiveness and efficiency.
Sustainable cytopathology in the precision medicine era: Exploring new sources for molecular testing in thyroid cytology specimens

Ancillary molecular tests for thyroid fine-needle aspiration (FNA) specimens help to refine cancer risk estimates for cytologically indeterminate nodules based on their genetic and/or gene expression profiles. Primarily intended for nodules classified in the atypia of undetermined significance or follicular lesion of undetermined significance (AUS/FLUS) and follicular neoplasm or suspicious for follicular neoplasm (FN/SFN) categories of The Bethesda System for Reporting Thyroid Cytopathology, these tests aim to distinguish nodules that are safe to follow using clinical observation from those that require surgical resection for diagnostic or therapeutic purposes. Commercially available molecular tests for indeterminate thyroid FNA specimens such as the Afirma Gene Sequencing Classifier (Veracyte Inc, South San Francisco, California) and ThyroSeq v3 (University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, and CBLPath Inc, Rye Brook, New York) have relied largely on cellular material collected in a vial of nucleic acid preservative as the source for molecular testing. Although this approach may be optimal for nucleic acid yield and preservation, drawbacks include: 1) the potential for sampling error (ie, because the FNA pass for microscopic evaluation is different from that for molecular analysis); 2) the need for extra FNA passes specifically to collect cells for molecular testing; and 3) the need to re-aspirate a nodule if a sample for molecular testing was not collected at the time of the initial FNA. These challenges, coupled with the increasing breadth of ancillary tests that sometimes are requested on limited cellular material, have inspired laboratories to seek alternative FNA-derived sample types on which molecular analysis can be performed. For example, cells on routinely prepared cytology smears have proven to be a practical source of nucleic acid for analysis and mitigate many of the sampling issues noted above. The RosettaGX Reveal Thyroid miRNA Classifier was an early adopter of using direct smears for molecular testing, and the ThyGeNEXT/ThyraMIR tests (Interpace Diagnostics Group, Parsippany, New Jersey) have extended this practice to the current day. Cellular material remaining in cytology fixative after preparation of a liquid-based cytology slide also has been adapted for ancillary molecular testing in thyroid as well as other tumor types, akin to how reflexive human papillomavirus testing is performed on liquid-based Papanicolaou tests. Finally, thyroid FNA needle rinsing specimens (containing cells that remain in the needle after expulsion of the majority of the aspirated material onto slides for direct smears) also have been used for nucleic acid extraction and analysis by targeted nextgeneration sequencing (NGS) platforms. Of the sample types listed above, FNA needle rinsing specimens offer additional dimensions for ancillary testing. Needle rinsing specimens routinely are centrifuged to prepare
A Rare Case of Acquired Thoracic Aortic Coarctation Treated Medically.

A 51-year-old woman originating from Africa presented to our institution with newly intermittent claudication, headache, and dyspnea associated with a 4-month history of weight loss and tiredness. Clinical examination showed hypertension and a marked pressure gradient between the upper and lower limbs (140/80 versus 80/50 mm Hg). There was no sign of digestive claudication or renal insufficiency. Computed tomography angiography demonstrated an 80% segmental stenosis of the descending thoracic aorta associated with aortic wall thickening >95 mm in length (Figure A), together with pulmonary infiltrates and cervicomediastinal lymphadenopathies. Combined positron emission tomography-computed tomography showed a hypermetabolism of the aortic thickening (Figure B) and cervicomediastinal lymphadenopathies. The surgical biopsy of a cervical lymphadenopathy showed the presence of granuloma consistent with a tuberculosis infection. Figure. A , PET scan showing hypermetabolism of aortic thickening. B …
U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene Regulation.

SUMMARYRecent observations showed that nascent RNA polymerase II transcripts, pre-mRNAs, and noncoding RNAs are highly susceptible to premature 3'-end cleavage and polyadenylation (PCPA) from numerous intronic cryptic polyadenylation signals (PASs). The importance of this in gene regulation was not previously appreciated as PASs, despite their prevalence, were thought to be active in terminal exons at gene ends. Unexpectedly, antisense oligonucleotide interference with U1 snRNA base-pairing to 5' splice sites, which is necessary for U1 snRNP's (U1) function in splicing, caused widespread PCPA in metazoans. This uncovered U1's PCPA suppression activity, termed telescripting, as crucial for full-length transcription in thousands of vertebrate genes, providing a general role in transcription elongation control. Progressive intron-size expansion in metazoan evolution greatly increased PCPA vulnerability and dependence on U1 telescripting. We describe how these observations unfolded and discuss U1 telescripting's role in shaping the transcriptome.
SEED CAROTENOID DEFICIENT Functions in Isoprenoid Biosynthesis via the Plastid MEP Pathway1

SEED CAROTENOID DEFICIENT functions in the methylerythritol phosphate pathway in maize and affects the accumulation of downstream isoprenoids. Plastid isoprenoids, a diverse group of compounds that includes carotenoids, chlorophylls, tocopherols, and multiple hormones, are essential for plant growth and development. Here, we identified and characterized SEED CAROTENOID DEFICIENT (SCD), which encodes an enzyme that functions in the biosynthesis of plastid isoprenoids in maize (Zea mays). SCD converts 2C-methyl-d-erytrithol 2,4-cyclodiphosphate to 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the penultimate step of the methylerythritol phosphate (MEP) pathway. In scd mutants, plant growth and development are impaired and the levels of MEP-derived isoprenoids, such as carotenoids, chlorophylls, and tocopherols, as well as abscisic and gibberellic acids, are reduced in leaves and seeds. This scd metabolic alteration varies among plant tissues and under different light conditions. RNA-sequencing of the scd mutant and wild type identified a limited number of differentially expressed genes in the MEP pathway, although isoprenoid levels were significantly reduced in scd seeds and dark-grown leaves. Furthermore, SCD-overexpressing transgenic lines showed little or no differences in isoprenoid levels, indicating that SCD may be subject to posttranslational regulation or not represent a rate-limiting step in the MEP pathway. These results enhance our understanding of the transcriptomic and metabolic regulatory roles of enzymes in the MEP pathway and of their effects on downstream isoprenoid pathways in various plant tissues and under different light conditions.
Liver‐specific Sirtuin6 ablation impairs liver regeneration after 2/3 partial hepatectomy

Sirtuin 6 (Sirt6) is an NAD+‐dependent deacetylase that regulates central metabolic functions such as glucose homeostasis, fat metabolism, and cell apoptosis. However, the tissue‐specific function of Sirt6 in liver regeneration remains unknown. Here, we show that liver‐specific Sirt6 knockout (Sirt6LKO) impaired liver reconstitution after 2/3 partial hepatectomy, which was attributed to an alteration of cell cycle progression. Sirt6 LKO delayed hepatocyte transition into S phase during liver regeneration, as shown by the analysis of cell cycle‐related proteins and the immuno staining of Ki‐67 and 5‐bromo‐2‐deoxyuridine (BrdU). The delayed cell cycle in Sirt6 LKO mice was attributed to the disruption of m‐TOR and Akt activity, which is an important pro‐proliferation pathway in liver regeneration. Sirt6 LKO also reduced carbon tetrachloride (CCl4)‐induced liver damage. Our results suggest that Sirt6 LKO impaired liver regeneration via delayed cell cycle and impaired m‐TOR and Akt activity.
Critical role of post-transcriptional regulation for IFN-γ in tumor-infiltrating T cells

Protective T cell responses against tumors require the production of Interferon gamma (IFN-γ). However, tumor-infiltrating T cells (TILs) gradually lose their capacity to produce IFN-γ and therefore fail to clear malignant cells. Dissecting the underlying mechanisms that block cytokine production is thus key for improving T cell products. Here we show that although TILs express substantial levels of Ifng mRNA, post-transcriptional mechanisms impede the production of IFN-γ protein due to loss of mRNA stability. CD28 triggering, but not PD1 blocking antibodies, effectively restores the stability of Ifng mRNA. Intriguingly, TILs devoid of AU-rich elements within the 3’untranslated region maintain stabilized Ifng mRNA and produce more IFN-γ protein than wild-type TILs. This sustained IFN-γ production translates into effective suppression of tumor outgrowth, which is almost exclusively mediated by direct effects on the tumor cells. We therefore conclude that post-transcriptional mechanisms could be modulated to potentiate effective T cell therapies in cancer.
The usefulness of visual rating of posterior atrophy in predicting rapid cognitive decline in Alzheimer disease: A preliminary study

Approximately 10% to 30% of Alzheimer disease (AD) patients progress rapidly in severity and become more dependent on caregivers. Although several studies have investigated whether imaging biomarkers such as medial temporal atrophy (MTA) and posterior atrophy (PA) are useful for predicting the rapid progression of AD, their results have been inconsistent.
C2H2-Type Zinc Finger Proteins: Evolutionarily Old and New Partners of the Nuclear Hormone Receptors

Nuclear hormone receptors (NRs) are evolutionarily conserved ligand-dependent transcription factors. They are essential for human life, mediating the actions of lipophilic molecules, such as steroid hormones and metabolites of fatty acid, cholesterol, and external toxic compounds. The C2H2-type zinc finger proteins (ZNFs) form the largest family of the transcription factors in humans and are characterized by multiple, tandemly arranged zinc fingers. Many of the C2H2-type ZNFs are conserved throughout evolution, suggesting their involvement in preserved biological activities, such as general transcriptional regulation and development/differentiation of organs/tissues observed in the early embryonic phase. However, some C2H2-type ZNFs, such as those with the Krüppel-associated box (KRAB) domain, appeared relatively late in evolution and have significantly increased family members in mammals including humans, possibly modulating their complicated transcriptional network and/or supporting the morphological development/functions specific to them. Such evolutional characteristics of the C2H2-type ZNFs indicate that these molecules influence the NR functions conserved through evolution, whereas some also adjust them to meet with specific needs of higher organisms. We review the interaction between NRs and C2H2-type ZNFs by focusing on some of the latter molecules.
Enhancing production of microalgal biopigments through metabolic and genetic engineering

Abstract The versatile use of biopigments in food, feed, cosmetic, pharmaceutical and analytical industries emphasized to find different and renewable sources of biopigments. Microalgae, including cyanobacteria, are becoming a potential candidate for pigment production as these have fast-growing ability, high pigment content, highly variable and also have “Generally recognized as safe” status. These algal groups are known to produce different metabolites that include hormones, vitamins, biopolythene and biochemicals. We discuss here the potential use of microalgal biopigments in our daily life as well as in food and cosmetic industries. Pigment like carotenoids has many health benefits such as antioxidant, anti-inflammatory properties and also provide photo-protection against UV radiation. This review details the effect of various abiotic and biotic factors such as temperature, light, nutrition on maximizing the pigment content in the microalgal cell. This review also highlights the potential of microalgae, whether in present native or engineered strain including the many metabolic strategies which are used or can be used to produce a higher amount of these valuable biopigments. Additionally, future challenges in the context of pigment production have also been discussed.
Chromosome Translocations, Inversions and Telomere Length for Retrospective Biodosimetry on Exposed U.S. Atomic Veterans

It has now been over 60 years since U.S. nuclear testing was conducted in the Pacific islands and Nevada, exposing military personnel to varying levels of ionizing radiation. Actual doses are not well-established, as film badges in the 1950s had many limitations. We sought a means of independently assessing dose for comparison with historical film badge records and dose reconstruction conducted in parallel. For the purpose of quantitative retrospective biodosimetry, peripheral blood samples from 12 exposed veterans and 12 age-matched (>80 years) veteran controls were collected and evaluated for radiation-induced chromosome damage utilizing directional genomic hybridization (dGH), a cytogenomics-based methodology that facilitates simultaneous detection of translocations and inversions. Standard calibration curves were constructed from six male volunteers in their mid-20s to reflect the age range of the veterans at time of exposure. Doses were estimated for each veteran using translocation and inversion rates independently; however, combining them by a weighted-average generally improved the accuracy of dose estimations. Various confounding factors were also evaluated for potential effects on chromosome aberration frequencies. Perhaps not surprisingly, smoking and age-associated increases in background frequencies of inversions were observed. Telomere length was also measured, and inverse relationships with both age and combined weighted dose estimates were observed. Interestingly, smokers in the non-exposed control veteran cohort displayed similar telomere lengths as those in the never-smoker exposed veteran group, suggesting that chronic smoking had as much effect on telomere length as a single exposure to radioactive fallout. Taken together, we find that our approach of combined chromosome aberration-based retrospective biodosimetry provided reliable dose estimation capability, particularly on a group average basis, for exposures above statistical detection limits.
Mammalian Long-Chain Acyl-CoA Synthetases

Acyl-CoA synthetase enzymes are essential for de novo lipid synthesis, fatty acid catabolism, and remodeling of membranes. Activation of fatty acids requires a two-step reaction catalyzed by these enzymes. In the first step, an acyl-AMP intermediate is formed from ATP. AMP is then exchanged with CoA to produce the activated acyl-CoA. The release of AMP in this reaction defines the superfamily of AMP-forming enzymes. The length of the carbon chain of the fatty acid species defines the substrate specificity for the different acyl-CoA synthetases (ACS). On this basis, five sub-families of ACS have been characterized. The purpose of this review is to report on the large family of mammalian long-chain acyl-CoA synthetases (ACSL), which activate fatty acids with chain lengths of 12 to 20 carbon atoms. Five genes and several isoforms generated by alternative splicing have been identified and limited information is available on their localization. The structure of these membrane proteins has not been solved for the mammalian ACSLs but homology to a bacterial form, whose structure has been determined, points at specific structural features that are important for these enzymes across species. The bacterial form acts as a dimer and has a conserved short motif, called the fatty acid Gate domain, that seems to determine substrate specificity. We will discuss the characterization and identification of the different spliced isoforms, draw attention to the inconsistencies and errors in their annotations, and their cellular localizations. These membrane proteins act on membrane-bound substrates probably as homo- and as heterodimer complexes but have often been expressed as single recombinant isoforms, apparently purified as monomers and tested in Triton X-100 micelles. We will argue that such studies have failed to provide an accurate assessment of the activity and of the distinct function of these enzymes in mammalian cells.
Fracture Resistance of Titanium, Zirconia, and Ceramic-Reinforced Polyetheretherketone Implant Abutments Supporting CAD/CAM Monolithic Lithium Disilicate Ceramic Crowns After Aging.

PURPOSE The purpose of this study was to compare the fracture resistances and the fracture types of titanium, zirconia, and ceramic-reinforced polyetheretherketone (PEEK) implant abutments supporting CAD/CAM monolithic lithium disilicate ceramic crowns after in vitro dynamic loading and thermocycling aging. MATERIALS AND METHODS Three implant abutment (SKY Implant) groups-titanium (group Ti, control); zirconia with titanium base (group Zr); and ceramic-reinforced PEEK (BioHPP) with titanium base (group RPEEK); n = 12 each-were used. Thirty-six CAD/CAM monolithic lithium disilicate crowns (IPS e.max CAD) in the form of a maxillary central incisor were cemented with Panavia V5 on the abutments. The specimens were subjected to dynamic loading and thermocycling. Fracture resistances of the restorations were tested with a universal testing machine (0.5 mm/min), and their fracture patterns were analyzed. One-way ANOVA and Tukey post-hoc test were used for statistical analyses (α = .05). RESULTS All samples survived after aging. The fracture strength values (mean ± standard deviation) of the groups were as follows: group Ti, 787.8 ± 120.9 N; group Zr, 623.9 ± 97.4 N; and group RPEEK, 602.9 ± 121 N. The fracture strengths were significantly higher in group Ti compared to groups Zr and RPEEK (P = .001). No significant difference was observed between groups Zr and RPEEK. Failures generally occurred due to fracture of the screw in group Ti, abutment and crown in group Zr, and crown in group RPEEK. CONCLUSION Ceramic-reinforced PEEK abutments may be an alternative to zirconia abutments with a titanium base for single-implant restorations in the anterior region. However, there is need for further in vitro and clinical studies to evaluate the long-term performance of ceramic-reinforced PEEK abutments.