Miracle-dz/UniFAR-FTUs huggingface dataset:
IP Core Steganography Using Switch Based Key-Driven Hash-Chaining and Encoding for Securing DSP Kernels Used in CE Systems

Intellectual property (IP) core of digital signal processing (DSP) kernels act as hardware accelerators in consumer electronics (CE) systems. However due to rising threats of cloning and counterfeiting to an IP core, security remains an important subject of research for these hardware accelerators. This paper presents a novel key-driven hash-chaining based hardware steganography for securing such IP cores used in CE systems. The proposed approach is capable to implant secret invisible stego-marks in design using hash-chaining process that incorporates switches, strong large stego-keys, multiple encoding algorithms and hash blocks. The methodology proposed provides massive security against IP cloning and counterfeiting while incurring nominal design overhead (<0.3 %). The results of the proposed approach on comparison with state of the art indicated significantly stronger digital evidence (lower probability of co-incidence), stronger key size (in bits) and lower design cost using proposed stego-marks. Further, from an attacker’s perspective, the proposed steganography increases an attacker’s effort manifold during decoding the valid stego-key value (for generating/extracting original secret stego-mark), compared to existing approaches.
Hierarchical Hybrid MPC for Management of Distributed Phase Change Thermal Energy Storage*

A rapid increase in the electrical power on board vehicles has presented significant challenges to their thermal management. One proposed solution for large vehicles is the use of thermal energy storage (TES) modules containing phase change material (PCM) to quickly absorb large thermal loads, buffering fast thermal transients to reduce peak cooling requirements. However, the inherent nonlinearity and multi-timescale nature of vehicles with phase change energy storage must be addressed in control design. This paper presents a hierarchical hybrid model predictive control (MPC) framework to meet this need. A hierarchical control framework coordinates between the relatively slow phase change dynamics of the TES and relatively fast temperature dynamics elsewhere, excited by highly transient loading. Switched linear models are used to approximate nonlinearities across a wide range of operating conditions, resulting in hybrid MPC formulations that balance model accuracy and computational burden. The proposed approach is demonstrated in simulation on a candidate thermal management system with multiple TES modules.
Clinico-biochemical and Electrocardiographic Changes in Cattle Naturally Infected with Lumpy Skin Disease

Lumpy skin disease (LSD) is an economically important viral disease of cattle caused by Capripox virus. The disease is characterized clinically by fever, nodules on the skin, mucous membranes and internal organs, emaciation, enlarged lymph nodes, edema of the skin and deaths in some cases. The aim of this study is to investigate the clinico-biochemical picture of LSD infected cattle with special reference to the cardiac abnormalities. This study was carried out on LSD infected cattle showing typical clinical signs of the disease in Kaliobia governorate (𝑛 = 50; and aged between 2 to 5 years old). Clinical and electrocardiographic examination (ECG) were performed firstly, then skin nodules were aseptically collected from infected cattle for molecular detection of LSDV using PCR, on the other hand, serum samples were collected for biochemical analysis. The results of the current study revealed that, all examined tissue samples showed successful amplification of the viral attachment protein gene of LSDV with presence of positive bands at the target size (192 bp). Furthermore, troponin I (cTnI), urea, creatinine ALT, AST, ALP and potassium were significantly increased in LSD infected cattle compared to the control ones. In contrast, serum calcium, iron and sodium concentrations were significantly decreased. The ECG of LSD infected cattle showed abnormal P waves, shortening of P and T-waves amplitudes and decrease in RT interval compared to healthy cattle. The cardiac alterations in case of LSD infection could be related to the elevation of cTnI because of direct effect of the virus on the heart beside electrolyte imbalance, acidosis and hypocalcaemia.
Cross-species analysis of enhancer logic using deep learning

Deciphering the genomic regulatory code of enhancers is a key challenge in biology because this code underlies cellular identity. A better understanding of how enhancers work will improve the interpretation of noncoding genome variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable enhancer models. We apply this strategy to decipher the enhancer code in melanoma, a relevant case study owing to the presence of distinct melanoma cell states. We trained and validated a deep learning model, called DeepMEL, using chromatin accessibility data of 26 melanoma samples across six different species. We show the accuracy of DeepMEL predictions on the CAGI5 challenge, where it significantly outperforms existing models on the melanoma enhancer of IRF4. Next, we exploit DeepMEL to analyze enhancer architectures and identify accurate transcription factor binding sites for the core regulatory complexes in the two different melanoma states, with distinct roles for each transcription factor, in terms of nucleosome displacement or enhancer activation. Finally, DeepMEL identifies orthologous enhancers across distantly related species, where sequence alignment fails, and the model highlights specific nucleotide substitutions that underlie enhancer turnover. DeepMEL can be used from the Kipoi database to predict and optimize candidate enhancers and to prioritize enhancer mutations. In addition, our computational strategy can be applied to other cancer or normal cell types.
Mortality in COVID-19 patients with acute respiratory distress syndrome and corticosteroids use: a systematic review and meta-analysis

ABSTRACT Objectives The acute respiratory distress syndrome (ARDS) secondary to viral pneumonitis is one of the main causes of high mortality in patients with COVID-19 (novel coronavirus disease 2019). We systematically reviewed mortality in COVID-19 patients with ARDS and the potential role of systemic corticosteroids in COVID-19 patients. Methods Electronic databases and country-specific healthcare databases were searched to identify relevant studies/reports. The quality assessment of individual studies was conducted using the Newcastle–Ottawa Scale. Country-specific proportion of individuals with COVID-19 who developed ARDS and reported death were combined in a random-effect meta-analysis to give a pooled mortality estimate of ARDS. Results The overall pooled mortality estimate among 10,815 ARDS cases in COVID-19 patients was 39% (95% CI: 23–56%). The pooled mortality estimate for China was 69% (95% CI: 67–72%). In Europe, the highest mortality estimate among COVID-19 patients with ARDS was reported in Poland (73%; 95% CI: 58–86%) while Germany had the lowest mortality estimate (13%; 95% CI: 2–29%) among COVID-19 patients with ARDS. The median crude mortality rate of COVID-19 patients with reported corticosteroid use was 28.0% (lower quartile: 13.9%; upper quartile: 53.6%). Conclusions The high mortality in COVID-19 associated ARDS necessitates a prompt and aggressive treatment strategy which includes corticosteroids. Most of the studies included no information on the dosing regimen of corticosteroid therapy, however, low-dose corticosteroid therapy or pulse corticosteroid therapy appears to have a beneficial role in the management of severely ill COVID-19 patients.
Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations

Given the enormous social and health impact of the pandemic triggered by severe acute respiratory syndrome 2 (SARS-CoV-2), the scientific community made a huge effort to provide an immediate response to the challenges posed by Coronavirus disease 2019 (COVID-19). One of the most important proteins of the virus is an enzyme, called 3CLpro or main protease, already identified as an important pharmacological target also in SARS and Middle East respiratory syndrome virus (MERS) viruses. This protein triggers the production of a whole series of enzymes necessary for the virus to carry out its replicating and infectious activities. Therefore, it is crucial to gain a deeper understanding of 3CLpro structure and function in order to effectively target this enzyme. All-atoms molecular dynamics (MD) simulations were performed to examine the different conformational behaviors of the monomeric and dimeric form of SARS-CoV-2 3CLpro apo structure, as revealed by microsecond time scale MD simulations. Our results also shed light on the conformational dynamics of the loop regions at the entry of the catalytic site. Studying, at atomic level, the characteristics of the active site and obtaining information on how the protein can interact with its substrates will allow the design of molecules able to block the enzymatic function crucial for the virus.
Body Representations in Children with Cerebral Palsy

We constantly process top-down and bottom-up inputs concerning our own body that interact to form body representations (BR). Even if some evidence showed BR deficits in children with cerebral palsy, a systematic study that evaluates different kinds of BR in these children, taking into account the possible presence of a general deficit affecting non-body mental representations, is currently lacking. Here we aimed at investigating BR (i.e., Body Semantics, Body Structural Representation and Body Schema) in children with cerebral palsy (CP) taking into account performance in tasks involving body stimuli and performance in tasks involving non-body stimuli. Thirty-three CP (age range: 5–12 years) were compared with a group of 103 typically-developing children (TDC), matched for age and sex. 63.64% of children with CP showed a very poor performance in body representation processing. Present data also show alterations in different body representations in CP in specific developmental stages. In particular, CP and TDC performances did not differ between 5 to 7 years old, whereas CP between 8 and 12 years old showed deficits in the Body Structural Representation and Body Schema but not in Body Semantics. These findings revealed the importance of taking into account the overall development of cognitive domains when investigating specific stimuli processing in children who do not present a typical development and were discussed in terms of their clinical implications.
The Barley stripe mosaic virus γb protein promotes viral cell-to-cell movement by enhancing ATPase-mediated assembly of ribonucleoprotein movement complexes

Nine genera of viruses in five different families use triple gene block (TGB) proteins for virus movement. The TGB modules fall into two classes: hordei-like and potex-like. Although TGB-mediated viral movement has been extensively studied, determination of the constituents of the viral ribonucleoprotein (vRNP) movement complexes and the mechanisms underlying their involvement in vRNP-mediated movement are far from complete. In the current study, immunoprecipitation of TGB1 protein complexes formed during Barley stripe mosaic virus (BSMV) infection revealed the presence of the γb protein in the products. Further experiments demonstrated that TGB1 interacts with γb in vitro and in vivo, and that γb-TGB1 localizes at the periphery of chloroplasts and plasmodesmata (PD). Subcellular localization analyses of the γb protein in Nicotiana benthamiana epidermal cells indicated that in addition to chloroplast localization, γb also targets the ER, actin filaments and PD at different stages of viral infection. By tracking γb localization during BSMV infection, we demonstrated that γb is required for efficient cell-to-cell movement. The N-terminus of γb interacts with the TGB1 ATPase/helicase domain and enhances ATPase activity of the domain. Inactivation of the TGB1 ATPase activity also significantly impaired PD targeting. In vitro translation together with co-immunoprecipitation (co-IP) analyses revealed that TGB1-TGB3-TGB2 complex formation is enhanced by ATP hydrolysis. The γb protein positively regulates complex formation in the presence of ATP, suggesting that γb has a novel role in BSMV cell-to-cell movement by directly promoting TGB1 ATPase-mediated vRNP movement complex assembly. We further demonstrated that elimination of ATPase activity abrogates PD and actin targeting of Potato virus X (PVX) and Beet necrotic yellow vein virus (BNYVV) TGB1 proteins. These results expand our understanding of the multifunctional roles of γb and provide new insight into the functions of TGB1 ATPase domains in the movement of TGB-encoding viruses.
Fetal Lymphoid Organ Immune Responses to Transient and Persistent Infection with Bovine Viral Diarrhea Virus

Bovine Viral Diarrhea Virus (BVDV) fetal infections occur in two forms; persistent infection (PI) or transient infection (TI), depending on what stage of gestation the fetus is infected. Examination of lymphoid organs from both PI and TI fetuses reveals drastically different fetal responses, dependent upon the developmental stage of the fetal immune system. Total RNA was extracted from the thymuses and spleens of uninfected control, PI, and TI fetuses collected on day 190 of gestation to test the hypothesis that BVDV infection impairs the innate and adaptive immune response in the fetal thymus and spleen of both infection types. Transcripts of genes representing the innate immune response and adaptive immune response genes were assayed by Reverse Transcription quatitative PCR (RT-qPCR) (2−ΔΔCq; fold change). Genes of the innate immune response, interferon (IFN) inducible genes, antigen presentation to lymphocytes, and activation of B cells were downregulated in day 190 fetal PI thymuses compared to controls. In contrast, innate immune response genes were upregulated in TI fetal thymuses compared to controls and tended to be upregulated in TI fetal spleens. Genes associated with the innate immune system were not different in PI fetal spleens; however, adaptive immune system genes were downregulated, indicating that PI fetal BVDV infection has profound inhibitory effects on the expression of genes involved in the innate and adaptive immune response. The downregulation of these genes in lymphocytes and antigen-presenting cells in the developing thymus and spleen may explain the incomplete clearance of BVDV and the persistence of the virus in PI animals while the upregulation of the TI innate immune response indicates a more mature immune system, able to clear the virus.
Visible Implant Elastomer Color Determination, Tag Visibility, and Tag Loss: Potential Sources of Error for Mark–Recapture Studies

Abstract Errors in visible implant elastomer (VIE) color determination may exert stronger influences on mark–recapture data quality than poor tag visibility and tag loss. I applied individual VIE tags to 567 wild long-snouted seahorses Hippocampus guttulatus using four fluorescent colors (red, orange, green, and yellow). Given VIE tag data were compared with tag data recorded by observers as they released recently tagged individuals back to initial capture locations. During releases, 13.3% of VIE tags were incorrectly read, primarily because of confusions between orange and red markings and between green and yellow markings. Tags were partially invisible in 5% of released individuals; yellow and green markings were the least visible. Whole or partial tag loss was 2.3% within 14 months of tagging. The ability to correctly determine VIE tag colors or detect markings varied among observers and according to the VIE tag color employed, skin color, and shade of the skin color (e.g., light versus dark green). Ob.
Development of New Water Temperature Criteria to Protect Colorado's Fisheries

Abstract Water temperature fundamentally influences aquatic diversity and ecosystem health. In Colorado, temperature water quality criteria were revised in January 2007 based on a rigorous evaluation of the thermal requirements of fish species resident in Colorado. This article presents an account of how this process was conducted, and details the resultant criteria. The purpose of developing these criteria was to protect coldwater and warmwater fishes, especially native species such as cutthroat trout (Oncorhynchus clarki), from thermal stress. As such, lethal temperatures and optimal temperature conditions were determined from a literature review for species of the state, and these data were compiled into the Colorado Temperature Database. Acute and chronic thermal thresholds were then calculated for individual fish species. Finally, assemblages of fish were grouped into thermal tiers and temperature criteria were developed based on biological criteria for each assemblage. A case study is presented deta.
Comparison of 4-Mercaptobenzoic Acid Surface-Enhanced Raman Spectroscopy-Based Methods for pH Determination in Cells

Measurements of cellular pH are used to infer information such as stage of cell cycle, presence of cancer and other diseases, as well as delivery or effect of a therapeutic drug. Surface-enhanced Raman spectroscopy (SERS) of nanoparticle-based pH probes have been used to interrogate intracellular pH, with the significant advantage of avoiding photobleaching compared to fluorescent indicators. 4-Mercaptobenzoic acid (MBA) is a commonly used pH-sensitive reporter molecule. Intracellular pH sensing by SERS requires analysis of the observed MBA spectrum and spectral interference can affect the pH determination. Background from common cell containers, imaging too few particles, signal-to-noise ratios, and degradation of reporter molecules are among the factors that may alter appropriate SERS-based pH determination in cells. Here, we have compared common methods of spectral analysis to see how different factors alter the calculated pH in Raman maps of MBA functionalized Au nanostars in SW620 cancer cells. The methods included in our comparison use the relative intensity of the ν(COO–) stretch, chemometric analysis of the ν8a mode, and analyzing the frequency shift of the ν8a mode. These methods show different sensitivity to some of these sources of error in live cell experiments. pH determination based on Raman frequency shift appears to give a more reliable pH determination, though in high signal-to-noise environments, intensity ratios may provide better sensitivity to small changes in pH for cellular imaging.
Nutritional Quality of Vegetarian and Non-Vegetarian Dishes at School: Are Nutrient Profiling Systems Sufficiently Informative?

In France, school canteens must offer a vegetarian meal at least once per week. The objective was to evaluate the nutritional quality of school main dishes. A database of main dishes served in primary schools was first split into non-vegetarian (n = 669) and vegetarian (n = 315) categories. The latter has been divided into three sub-categories: vegetarian dishes containing cheese, vegetarian dishes containing eggs and/or dairy products but no cheese and vegetarian dishes without any eggs, cheese or other dairy products (vegan). Categories and sub-categories were compared based on nutrient adequacy ratios for “protective” nutrients (proteins, fibres, vitamins, minerals, essential fatty acids), the contents of nutrients to be limited (saturated fatty acids (SFA), sodium, free sugars) and on two nutrient profiling systems (SAIN,LIM and Nutri-Score). The vegetarian category and the non-vegetarian category displayed “adequate” levels (≥5% adequacy for 100 kcal) on average for almost all “protective” nutrients. The three sub-categories of vegetarian dishes displayed good SAIN,LIM and Nutri-Score profiles on average, although key nutrients were lacking (vitamin B12, vitamin D and DHA) or were present in insufficient amounts (vitamin B2 and calcium) in the vegan sub-category. The sub-category containing eggs and/or dairy products other than cheese was a good compromise, as it provided protective nutrients associated with eggs and fresh dairy products, while the sub-category containing cheese provided higher levels of SFA. Nutrient profile algorithms are insufficiently informative to assess the nutritional quality of school dishes.
Visualization of Multidimensional Data with Applications in Molecular Biology

Visualization is important when analyzing multidimensional datasets, since it can help humans discover and understand complex relationships in data. Whereas analyzing large individual datasets is both important and difficult, many problems can only be solved when considering multiple datasets simultaneously. This dissertation introduces novel visualization techniques that can be employed for both, visualizing individual datasets and visualizing relationships among multiple datasets alike. The concept is based on stratifying (dividing) datasets into homogeneous subsets, which can then be visualized individually. The relationships lost due to the division are re-introduced by drawing visual links between the subsets. Conceptually it is irrelevant whether the subsets are from one or from multiple datasets, which makes a seamless integration of multiple, cross-referenced datasets possible. The subsets can be visualized in multiple forms. Multiform visualization gives users the freedom to choose the visualization technique most suitable for the data type, the degree of homogeneity, the level of detail, and the current task – for each of the subsets individually. The division of datasets also makes focus and context, as well as drill-down techniques straightforward to realize. A set of interaction techniques enable seamless transition from a global overview down to details on individual data items. While the visualization techniques introduced in this thesis are generally applicable, they are designed to support researchers working in molecular biology. Specifically, we support collaborators in two different scenarios: in uncovering the genetic causes of steatohepatitis, a precursory disease to cirrhosis of the liver, and in analyzing cancer subtypes. We evaluated our methods with cases studies and report on how investigators reproduced known findings and discovered new insights with the introduced visualization techniques. In addition to discussing the analysis of multidimensional datasets, we also describe an integrative approach to analyze general heterogeneous datasets. We show how modeling of the analysis setup can be employed to support users. Finally, we introduce crossapplication and context-preserving visual links, which can be used for highlighting in heterogeneous datasets.
Afternoon Depression In Photosynthesis in Grapevine Leaves—Evidence for a High Light Stress Effect

Recherche des causes de la diminution des echanges gazeux l'apres-midi chez la vigne. Apres avoir verifie que cette diminution de l'activite photosynthetique avait bien lieu dans les feuilles de plantes correctement arrosees et en absence de stress dus a la temperature ou a l'humidite de l'air; les caracteristiques photosynthetiques des feuilles exposees a des densites de flux de photons fortes et moderees ont ete comparees afin de comprendre le role d'une exposition prolongee a une forte luminosite