Miracle-dz/UniFAR-FTUs huggingface dataset:
Norovirus Regulation of the Innate Immune Response and Apoptosis Occurs via the Product of the Alternative Open Reading Frame 4

Small RNA viruses have evolved many mechanisms to increase the capacity of their short genomes. Here we describe the identification and characterization of a novel open reading frame (ORF4) encoded by the murine norovirus (MNV) subgenomic RNA, in an alternative reading frame overlapping the VP1 coding region. ORF4 is translated during virus infection and the resultant protein localizes predominantly to the mitochondria. Using reverse genetics we demonstrated that expression of ORF4 is not required for virus replication in tissue culture but its loss results in a fitness cost since viruses lacking the ability to express ORF4 restore expression upon repeated passage in tissue culture. Functional analysis indicated that the protein produced from ORF4 antagonizes the innate immune response to infection by delaying the upregulation of a number of cellular genes activated by the innate pathway, including IFN-Beta. Apoptosis in the RAW264.7 macrophage cell line was also increased during virus infection in the absence of ORF4 expression. In vivo analysis of the WT and mutant virus lacking the ability to express ORF4 demonstrated an important role for ORF4 expression in infection and virulence. STAT1-/- mice infected with a virus lacking the ability to express ORF4 showed a delay in the onset of clinical signs when compared to mice infected with WT virus. Quantitative PCR and histopathological analysis of samples from these infected mice demonstrated that infection with a virus not expressing ORF4 results in a delayed infection in this system. In light of these findings we propose the name virulence factor 1, VF1 for this protein. The identification of VF1 represents the first characterization of an alternative open reading frame protein for the calicivirus family. The immune regulatory function of the MNV VF1 protein provide important perspectives for future research into norovirus biology and pathogenesis.
Column-Matching BIST Exploiting Test Don ' t-Cares

We propose a new test-per-clock BIST method for com binational or full-scan circuits. Our aim is to des ign a combinational block transforming the LFSR code word s into deterministic test patterns pre-computed by some ATPG tool. The proposed algorithm is an enhancement of a colum n matching method, in which the maximum of the outp ut variables of the decoder is tried to be implemented as mere wire s, thus without any logic. The enhancement consists in extending the use of the method for a test set containing don’t c ares. These don’t cares allow us to reach a higher number of column matches, which significantly reduces the BIST logic .
Sleep Loss and Cytokines Levels in an Experimental Model of Psoriasis

Up to 80% of people develop a cutaneous condition closely connected to their exposure to stressful life events. Psoriasis is a chronic recurrent inflammatory skin disorder with multifactorial etiology, including genetic background, environmental factors, and immune system disturbances with a strong cytokine component. Moreover, psoriasis is variably associated with sleep disturbance and sleep deprivation. This study evaluated the influence of sleep loss in the context of an animal model of psoriasis by measuring cytokine and stress-related hormone levels. Male adult Balb/C mice with or without psoriasis were subjected to 48 h of selective paradoxical sleep deprivation (PSD). Sleep deprivation potentiated the activities of kallikrein-5 and kallikrein-7 in the skin of psoriatic groups. Also, mice with psoriasis had significant increases in specific pro-inflammatory cytokines (IL-1β, IL-6 and IL-12) and decreases in the anti-inflammatory cytokine (IL-10) after PSD, which were normalized after 48 h of sleep rebound. Linear regression showed that IL-2, IL-6 and IL-12 levels predicted 66% of corticosterone levels, which were selectively increased in psoriasis mice subject to PSD. Kallikrein-5 was also correlated with pro-inflammatory cytokines, explaining 58% of IL-6 and IL-12 variability. These data suggest that sleep deprivation plays an important role in the exacerbation of psoriasis through modulation of the immune system in the epidermal barrier. Thus, sleep loss should be considered a risk factor for the development of psoriasis.
Fundamental Differences between Fracture Behavior of Thin Sheets under Plane Strain Bending and Tension

A numerical investigation of thin sheets under plane strain tension and bending is presented. Bending simulations are based on a VDA plane-strain bending test while tensile simulations depict a notched plane-strain tensile coupon. A comparative analysis of the stress and strain distributions inside the localized zone of deformation is performed for two investigated modes of behavior. The analyses suggests significant stress state differences in bending and tension driven primarily by the through-thickness response. The results offer insight into fundamental differences in tensile and bending fracture behaviors of thin sheets, as evidenced by discrepancies in strain at fracture experimentally measured using notched tensile coupons comparing to VDA bend tests. The consequences of these differences for material characterization and model calibration for large-scale crash simulations are also briefly discussed.
Insulin secretion rates estimated by two mathematical methods in pancreas-kidney transplant recipients

ERIK CHRISTIANSEN,1 LISE L. KJEMS,3 AAGE VØLUND,2 ANNIKA TIBELL,4 CHRISTIAN BINDER,1 AND STEN MADSBAD3 1Steno Diabetes Center, 2820 Gentofte; 2Novo Nordisk Research Institute, 2880 Bagsvaerd; and 3Department of Endocrinology, Hvidovre Hospital, University of Copenhagen, 2750 N Copenhagen, Denmark; and 4Department of Transplantation Surgery, Huddinge Hospital, Karolinska Institute, S-105 21 Stockholm, Sweden
In Silico Identification, Phylogenetic and Bioinformatic Analysis of Argonaute Genes in Plants

Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Argonaute proteins were highly conserved across plant kingdom. Phylogenic analysis divided plant Argonautes into three classes. Argonaute proteins have three conserved domains PAZ, MID and PIWI. In addition to three conserved domains namely, PAZ, MID, and PIWI, we identified few more domains in AGO of some plant species. Expression profile analysis of Argonaute proteins showed that expression of these genes varies in most of tissues, which means that these proteins are involved in regulation of most pathways of the plant system. Numbers of alternative transcripts of Argonaute genes were highly variable among the plants. A thorough analysis of large number of putative Argonaute genes revealed several interesting aspects associated with this protein and brought novel information with promising usefulness for both basic and biotechnological applications.
Process modelling of weld repair in aeroengine components

Weld repair is a specific application of fusion welding processes adopted to correct defects which arise during the manufacturing process of aeroengine components and, also, to repair damage in order to extend the operative life, if safe and correctly performed. The operation is carried out by removing the anomaly and re-filling the slot with a fusion welding process. The thermal cycles induced by fusion welding processes produce undesirable residual stresses, which significantly affect the fatigue life of the component and, in some cases, they may give a larger contribution to the total stress field than the stresses caused by the service loads themselves. Based on the sequentially coupled thermo-mechanical analysis, two numerical methodologies have been implemented to simulate the residual stress field induced by weld repair operations. Differently from models presented in the literature, the modelling approaches allow taking into account the pre-existing stress in the component subjected to the weld repair. The experimental work to validate the numerical models involved a full thermal characterization of the welding apparatus used to produce the welds. Residual stress predictions were validated by means of neutron diffraction measurements using the most advanced diffractometer, ENGIN-X, available at ISIS neutron source at the Rutherford Appleton Laboratory. The model can be used a priori, in the attempt of mitigating the effects of the repair operations on the final residual stress field. It can also be used a posteriori, with the aim of determining the stress state in the component, producing the input for the analysis of the fatigue life. In order to prove the applicability of the numerical methodology in the case of aeroengine components, the model was used to study a weld repair in a demonstrative case study. The effects of number and direction of passes were investigated in the weld repair of a laser beam weld in a stainless steel pipe. It was concluded that the interaction between the pre-existing stress in a component and the stress induced by weld repair operations cannot be generalized and established a priori. Numerical models that simulate the process by neglecting the history of the components, ignore the contribution of the pre-existing stress to the final residual stress distribution. Predictions from such models approximate the global stress distribution in the component. The entire characterization of the residual stress field in a component that undergoes a weld repair operation can only be achieved by using models which take into account the pre-existing stress.
Quaking Regulates Hnrnpa1 Expression through Its 3′ UTR in Oligodendrocyte Precursor Cells

In mice, Quaking (Qk) is required for myelin formation; in humans, it has been associated with psychiatric disease. QK regulates the stability, subcellular localization, and alternative splicing of several myelin-related transcripts, yet little is known about how QK governs these activities. Here, we show that QK enhances Hnrnpa1 mRNA stability by binding a conserved 3′ UTR sequence with high affinity and specificity. A single nucleotide mutation in the binding site eliminates QK-dependent regulation, as does reduction of QK by RNAi. Analysis of exon expression across the transcriptome reveals that QK and hnRNP A1 regulate an overlapping subset of transcripts. Thus, a simple interpretation is that QK regulates a large set of oligodendrocyte precursor genes indirectly by increasing the intracellular concentration of hnRNP A1. Together, the data show that hnRNP A1 is an important QK target that contributes to its control of myelin gene expression.
Estimation of energy conversion processes in an electromechanical complex with the use of instantaneous power method

The instantaneous power component analysis of energy conversion processes in all the elements of electromechanical complex power channel has been performed. It has been established that effective power is a quality measure for power processes in the system. An index of electromechanical complex power channel capacity has been offered. It has been proved that instantaneous power component, reflecting energy exchange processes in the system, causes decrease of the object power channel capacity.
Hay fever and hypertension in the US adult population

Abstract Purpose: Hypertension is associated with inflammation. Whether the inflammation caused by allergic diseases such as allergic rhinitis can predispose to hypertension is controversial. Therefore, we studied the association between hay fever and hypertension in the United States National Health and Nutrition Examination Survey (NHANES). Methods: We analyzed data on 1883 men and 2029 women in NHANES 2005–2006. We included participants aged 20 years or older who had valid data on hay fever and hypertension. Results: 13.5% of the participants had a previous diagnosis of hay fever and 36.2% of them had hypertension. There were ethnic differences in the prevalence of previous hay fever diagnosis (p < 0.001) and hypertension (p < 0.001). There was no significant association between previous hay fever diagnosis and hypertension in men in any age group. The association between previous hay fever diagnosis and hypertension in women was significant in those aged 20–39 years (OR = 2.59, 95%CI = 1.26–5.30, p = 0.013). The association between previous hay fever diagnosis and hypertension in women aged form 20 to 39 years remained significant after adjustment for age, race and body mass index (OR = 2.74, 95%CI = 1.48–5.06, p = 0.003). After further adjustment for physical activity, alcohol consumption and smoking, the association was not attenuated (OR = 2.68, 95%CI = 1.38–5.18, p = 0.006). Further adjustment for liver enzymes, C-reactive protein and immunoglobulin E level attenuated the association slightly (OR = 2.72, 95%CI = 1.19–6.22, p = 0.021). Conclusions: In this nationally representative population-based survey, previous hay fever diagnosis is not significantly associated with hypertension in adults overall. There is an association in subgroup of young women aged 20–39. Further work is needed to confirm that this is a true association.
Effects of Structural Ageing on Blast Analyses of a Naval Vessel: A Technical Review

As vessels are being asked to perform over longer service lives and under more intensive operational tempos, it is becoming more pertinent that the effects of structural aging be accounted for. Fatigue is an important aspect of structural aging of a vessel. Currently, fatigue analyses are conducted in order to determine the point at which fatigue failure might occur. However, fatigue can induce changes to the material properties long before full fatigue failure has occurred. These changes in material properties can affect the outcomes of other forms of structural failure. One such form which is of particular importance for naval vessels is failure due to blast loading. Blast modelling utilising coupled CFD/FEA simulations are conducted when investigating the effects of an internal blast, requiring the use of a constitutive model to account for the material properties. Fatigue damage can result in a reduction of modulus of toughness of some steels, especially so under high strain rate loading conditions. However, these changes in material properties are not currently considered in constitutive models. This paper reviews experimental investigations conducted into the effects of fatigue on high strain rate loading. It is shown that the effects can be significant, and that further work is required before the allowance of the effects can be introduced to blast analyses.
Anatomy of the retroperitoneum: observations of the distribution of pathologic fluid collections.

PURPOSE To correlate anatomic dissections with clinical observations regarding anatomic distribution of retroperitoneal fluid, and to document the existence of planes that lie between classically described retroperitoneal spaces. MATERIALS AND METHODS Latex was injected in varying amounts into the pancreatic tail in three fresh cadavers to simulate peripancreatic fluid collections. Spiral computed tomography (CT) was performed of the abdomen and pelvis after each latex injection. Two cadavers were subsequently frozen and sectioned in axial planes; limited dissections were performed on these specimens. One was embalmed and underwent extensive anatomic dissection. Five embalmed, unprepared cadavers were also dissected to confirm observations made in the three prepared cadavers. RESULTS Latex injected into the tail of the pancreas entered a retromesenteric plane that was posterior to the anterior pararenal space and anterior to the anterior renal fascia. The plane continued superiorly, extending to the diaphragm near the esophageal hiatus; inferiorly, extending to the pelvis along the anterolateral surface of the psoas muscle; and laterally, posterior to the descending colon and its mesentery. The plane also communicated with a retrorenal plane lying between the posterior renal fascia and the posterior pararenal space. CONCLUSION Embryologic development of the dorsal mesenteries suggests the existence of retromesenteric planes, and clinical observations further support their existence. These findings may explain the observed distribution of retroperitoneal fluid collections from diaphragm to pelvis.
Curing Regular Expressions Matching Algorithms from Insomnia , Amnesia , and Acalulia Complete

The importance of network security has grown tremendously and a collection of devices have been introduced, which can improve the security of a network. Network intrusion detection systems (NIDS) are among the most widely deployed such system; popular NIDS use a collection of signatures of known security threats and viruses, which are used to scan each packet's payload. Today, signatures are often specified as regular expressions; thus the core of the NIDS comprises of a regular expressions parser, such parsers are traditionally implemented as finite automata. Deterministic Finite Automata (DFA) are fast, therefore they are often desirable at high network link rates. DFA for the signatures, which are used in the current security devices, however require prohibitive amounts of memory, which limits their practical use. In this paper, we argue that the traditional DFA based NIDS has three main limitations: first they fail to exploit the fact that normal data streams rarely match any virus signature; second, DFAs are extremely inefficient in following multiple partially matching signatures and explodes in size, and third finite automaton are incapable of efficiently keeping track of counts. We propose mechanisms to solve each of these drawbacks and demonstrate that our solutions can implement a NIDS much more securely and economically, and at the same time substantially improve the packet throughput. Type of Report: Other Department of Computer Science & Engineering Washington University in St. Louis Campus Box 1045 St. Louis, MO 63130 ph: (314) 935-6160 Curing Regular Expressions Matching Algorithms from Insomnia, Amnesia, and Acalulia Sailesh Kumar, Balakrishnan Chandrasekaran, Jonathan Turner Washington University in St. Louis {sailesh, balakrishnan, jst}@arl.wustl. edu George Varghese University of California, San Diego varghese@cs.ucsd. edu
Spatial distribution of seropositivity to the causative agent of granulocytic ehrlichiosis in dogs in California.

OBJECTIVE To assess spatial and temporal patterns of seroprevalence among dogs in California to the causative agent of granulocytic ehrlichiosis (GE). SAMPLE POPULATION Sera of 1,082 clinically normal dogs from 54 of 59 counties in California in 1997 to 1998. PROCEDURES Serum-specific IgG reactivity to Ehrlichia equi was assessed by use of an immunofluorescent antibody assay, using E. equi-infected horse neutrophils as substrate. Data were analyzed, using a geographic information system. Spatial analysis of seroprevalence included first order Bayesian analysis of seroprevalence and second order analysis of clustering by K-function and Cuzick-Edwards tests. Monthly seroprevalence among dogs was examined by use of regression on monthly densities of Ixodes pacificus adults and nymphs. RESULTS Seroprevalence among dogs to E. equi was 8.68%. Data were seasonally bimodal with highest prevalence in winter (when adult ticks were abundant) and a secondary peak in late spring (corresponding to nymphal ticks). Humboldt County had the highest seroprevalence (47.3%), and other northern coast range counties had seroprevalence from 15 to 30%. CONCLUSIONS AND CLINICAL RELEVANCE The patchy distribution of exposure to Ehrlichia organisms is a subset of the distribution of the tick vector. This may reflect enzootic cycles or climatic or historical factors that limited the range of the disease. Dogs, horses, and humans from north coast range counties in California are at increased risk of GE. These data provide a background for assessing risk of infection in horses and dogs, depending on geographic location. Dogs may be sentinels for assessing risk of GE in humans.
Characteristics of a PVDF Membrane Hydrophone for Use in the Range 1-100 MHz

Abstrocr-The experimental determination of the frequency response, directionality, and electrical characteristics of membrane hydrophones are reported. These characteristics are interpreted in terms of theoretical models, based mainly on published values for the properties of polyvinylidene fluoride (pvdf). The frequency response was determined using both linear and nonlinear acoustic fields. The directionality is affected by the angular variation of piezoelectric sensitivity and also, for large angles of incidence, by Lamb wave propagation in the membrane. The hydrophones are shown to be useful experimental devices both for studying acoustic waves in the frequency range 1-100 MHz and for investigating the properties of pvdf. They are well-suited to the study of nonlinear ultrasonic fields, and those used in medicine and nondestructive testing.
Phase detection of multi-channel SSVEPs via complex sparse spatial weighting

A brain-computer interface (BCI) based on steady-state visual evoked potentials (SSVEP) is one of the most practical BCI, because of high recognition accuracies and short time training. Phase of SSVEPs can be potentially applicable for generating device commands. However, the effective method of estimating the phase of SSVEPs has not yet been established, especially, in the case of using multi-channel electroencephalogram (EEG). In this paper, we propose a novel method for estimating the phase of SSVEPs from multi-channel EEG, which uses complex sparse spatial weighting. We conducted experiments with the phase-coded SSVEPs based BCI for evaluating performance of our proposed method. As a result, our proposed method showed higher recognition accuracies than conventional methods in all six subjects.
Chemotherapy-Induced Cardiotoxicity: Overview of the Roles of Oxidative Stress

Chemotherapy-induced cardiotoxicity is a serious complication that poses a serious threat to life and limits the clinical use of various chemotherapeutic agents, particularly the anthracyclines. Understanding molecular mechanisms of chemotherapy-induced cardiotoxicity is a key to effective preventive strategies and improved chemotherapy regimen. Although no reliable and effective preventive treatment has become available, numerous evidence demonstrates that chemotherapy-induced cardiotoxicity involves the generation of reactive oxygen species (ROS). This review provides an overview of the roles of oxidative stress in chemotherapy-induced cardiotoxicity using doxorubicin, which is one of the most effective chemotherapeutic agents against a wide range of cancers, as an example. Current understanding in the molecular mechanisms of ROS-mediated cardiotoxicity will be explored and discussed, with emphasis on cardiomyocyte apoptosis leading to cardiomyopathy. The review will conclude with perspectives on model development needed to facilitate further progress and understanding on chemotherapy-induced cardiotoxicity.