Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of the Herpes Simplex Virus 1 Genome: Manipulation of Nicks and Gaps Can Abrogate Infectivity and Alter the Cellular DNA Damage Response

ABSTRACT The herpes simplex virus 1 (HSV-1) virion DNA contains nicks and gaps, and in this study a novel assay for estimating the size and number of gaps in virion DNA was developed. Consistent with previous reports, we estimate that there are approximately 15 gaps per genome, and we calculate the average gap length to be approximately 30 bases. Virion DNA was isolated and treated with DNA-modifying enzymes in order to fill in the gaps and modify the ends. Interestingly, filling in gaps, blunting the ends, or adding random sequences to the 3′ ends of DNA, producing 3′ flaps, did not impair the infectivity of treated DNA following transfection of Vero cells. On the other hand, the formation of 5′ flaps in the DNA following treatment resulted in a dramatic reduction (95 to 100%) in infectivity. Virion DNA stimulated DNA-PKcs activity in transfected cells, and DNA with 5′ flaps stimulated a higher level of DNA-PKcs activity than that observed in cells transfected with untreated virion DNA. The infectivity of 5′-flapped DNA was restored in cells that do not express DNA-PKcs and in cells cotransfected with the immediate early protein ICP0, which degrades DNA-PKcs. These results are consistent with previous reports that DNA-dependent protein kinase (DNA-PK) and the nonhomologous end joining (NHEJ) repair pathway are intrinsically antiviral and that ICP0 can counteract this effect. We suggest that HSV-1 DNA with 5′ flaps may induce an antiviral state due to the induction of a DNA damage response, primarily mediated by NHEJ, that renders the HSV-1 genome less efficient for lytic infection. IMPORTANCE For productive lytic infection to occur, HSV-1 must counteract a variety of cellular intrinsic antiviral mechanisms, including the DNA damage response (DDR). DDR pathways have been associated with silencing of gene expression, cell cycle arrest, and induction of apoptosis. In addition, the fate of viral genomes is likely to play a role in whether viral genomes adopt a configuration suitable for lytic DNA replication. This study demonstrates that virion DNA activates the cellular DDR kinase, DNA-PK, and that this response is inhibitory to viral infection. Furthermore, we show that HSV-1 ubiquitin ligase, ICP0, plays an important role in counteracting the negative effects of DNA-PK activation. These findings support the notion that DNA-PK is antiviral and suggest that the fate of incoming viral DNA has important consequences for the progression of lytic infection. This study underscores the complex evolutionary relationships between HSV and its host.
Analysis of the Evolution and Structure of a Complex Intrahost Viral Population in Chronic Hepatitis C Virus Mapped by Ultradeep Pyrosequencing

ABSTRACT Hepatitis C virus (HCV) causes chronic infection in up to 50% to 80% of infected individuals. Hypervariable region 1 (HVR1) variability is frequently studied to gain an insight into the mechanisms of HCV adaptation during chronic infection, but the changes to and persistence of HCV subpopulations during intrahost evolution are poorly understood. In this study, we used ultradeep pyrosequencing (UDPS) to map the viral heterogeneity of a single patient over 9.6 years of chronic HCV genotype 4a infection. Informed error correction of the raw UDPS data was performed using a temporally matched clonal data set. The resultant data set reported the detection of low-frequency recombinants throughout the study period, implying that recombination is an active mechanism through which HCV can explore novel sequence space. The data indicate that polyvirus infection of hepatocytes has occurred but that the fitness quotients of recombinant daughter virions are too low for the daughter virions to compete against the parental genomes. The subpopulations of parental genomes contributing to the recombination events highlighted a dynamic virome where subpopulations of variants are in competition. In addition, we provide direct evidence that demonstrates the growth of subdominant populations to dominance in the absence of a detectable humoral response. IMPORTANCE Analysis of ultradeep pyrosequencing data sets derived from virus amplicons frequently relies on software tools that are not optimized for amplicon analysis, assume random incorporation of sequencing errors, and are focused on achieving higher specificity at the expense of sensitivity. Such analysis is further complicated by the presence of hypervariable regions. In this study, we made use of a temporally matched reference sequence data set to inform error correction algorithms. Using this methodology, we were able to (i) detect multiple instances of hepatitis C virus intrasubtype recombination at the E1/E2 junction (a phenomenon rarely reported in the literature) and (ii) interrogate the longitudinal quasispecies complexity of the virome. Parallel to the UDPS, isolation of IgG-bound virions was found to coincide with the collapse of specific viral subpopulations.
An Interactive Method to Improve Crowdsourced Annotations

In order to effectively infer correct labels from noisy crowdsourced annotations, learning-from-crowds models have introduced expert validation. However, little research has been done on facilitating the validation procedure. In this paper, we propose an interactive method to assist experts in verifying uncertain instance labels and unreliable workers. Given the instance labels and worker reliability inferred from a learning-from-crowds model, candidate instances and workers are selected for expert validation. The influence of verified results is propagated to relevant instances and workers through the learning-from-crowds model. To facilitate the validation of annotations, we have developed a confusion visualization to indicate the confusing classes for further exploration, a constrained projection method to show the uncertain labels in context, and a scatter-plot-based visualization to illustrate worker reliability. The three visualizations are tightly integrated with the learning-from-crowds model to provide an iterative and progressive environment for data validation. Two case studies were conducted that demonstrate our approach offers an efficient method for validating and improving crowdsourced annotations.
Characterization of Cross-Reactive CD8+ T-Cell Recognition of HLA-A2-Restricted HIV-Gag (SLYNTVATL) and HCV-NS5b (ALYDVVSKL) Epitopes in Individuals Infected with Human Immunodeficiency and Hepatitis C Viruses

ABSTRACT The immunologic mechanisms underlying the faster progression of hepatitis C virus (HCV) disease in the presence of human immunodeficiency virus (HIV) coinfection are not clearly understood. T-cell cross-reactivity between HCV and influenza virus-specific epitopes has been associated with rapid progression of HCV disease (S. Urbani, B. Amadei, P. Fisicaro, M. Pilli, G. Missale, A. Bertoletti, and C. Ferrari, J. Exp. Med. 201:675-680, 2005). We asked whether T-cell cross-reactivity between HCV and HIV could exist during HCV/HIV coinfection and affect pathogenesis. Our search for amino acid sequence homology between the HCV and HIV proteomes revealed two similar HLA-A2-restricted epitopes, HIV-Gag (SLYNTVATL [HIV-SL9]) and HCV-NS5b (ALYDVVSKL [HCV-AL9]). We found that 4 out of 20 HLA-A2-positive (HLA-A2+) HIV-infected individuals had CD8+ T cells that recognized both the HIV-SL9 and HCV-AL9 epitopes. However, the AL9 epitope was generally shown to be a weak agonist. Although HCV-monoinfected individuals in our study did not show AL9-specific responses, we found that about half of HCV/HIV-coinfected individuals had dual responses to both epitopes. High dual T-cell recognition among coinfected subjects was usually due to separate T-cell populations targeting each epitope, as determined by pentamer staining. The one individual demonstrating cross-reactive T cells to both epitopes showed the most advanced degree of liver disease. In coinfected individuals, we observed a positive correlation between the magnitudes of T-cell responses to both the SL9 and the AL9 epitopes, which was also positively associated with the clinical parameter of liver damage. Thus, we find that HIV infection induces T cells that can cross-react to heterologous viruses or prime for T cells that are closely related in sequence. However, the induction of cross-reactive T cells may not be associated with control of disease caused by the heterologous virus. This demonstrates that degeneracy of HIV-specific T cells may play a role in the immunopathology of HCV/HIV coinfection.
Relative timing [asynchronous design]

Relative timing (RT) is introduced as a method for asynchronous design. Timing requirements of a circuit are made explicit using relative timing. Timing can be directly added, removed, and optimized using this style. RT synthesis and verification are demonstrated on three example circuits, facilitating transformations from speed-independent circuits to burst-mode and pulse-mode circuits. Relative timing enables improved performance, area, power, and functional testability of up to a factor of 3/spl times/ in all three cases. This method is the foundation of optimized timed circuit designs used in an industrial test chip, and may be formalized and automated.
Multiresolution transmission of video using an EZW coder with GA generated motion vectors

This paper proposes a novel method to combine an embedded zerotree wavelet (EZW) coder with an object based genetic algorithm motion vector generator. This type of approach is able to handle the translation, rotation, scaling, and overlapping due to movement of video objects within a specific search field unlike the more conventional block based motion estimation schemes. It is also capable of transmitting a single bitstream of video objects and corrective frames which can be decoded at different bit rates due to the EZW based algorithm. The combination of these properties creates a powerful approach to video sequence coding for multiple decoding environments. Effectiveness of the proposed method is shown by simulations using synthetic objects.
Viperin, MTAP44, and Protein Kinase R Contribute to the Interferon-Induced Inhibition of Bunyamwera Orthobunyavirus Replication

ABSTRACT The first line of defense against viral infection is the interferon (IFN) response, which culminates in the expression of hundreds of proteins with presumed antiviral activity, and must be overcome by a virus for successful replication. The nonstructural NSs protein is the primary IFN antagonist encoded by Bunyamwera virus (BUNV), the prototype of the Orthobunyavirus genus and the family Bunyaviridae. The NSs protein interferes with RNA polymerase II-mediated transcription, thereby inhibiting cellular mRNA production, including IFN mRNAs. A recombinant virus, rBUNdelNSs, that is unable to express the NSs protein does not inhibit cellular transcription and is a strong IFN inducer. We report here that cells stimulated into the antiviral state by IFN-β treatment were protected against wild-type BUNV and rBUNdelNSs infection but addition of IFN-β after infection had little effect on the replication cycle of either virus. By screening a panel of cell lines that overexpressed individual IFN-stimulated genes, we found that protein kinase R (PKR), MTAP44, and particularly viperin appreciably restricted BUNV replication. The enzymatic activities of PKR and viperin were required for their inhibitory activities. Taken together, our data show that the restriction of BUNV replication mediated by IFN is an accumulated effect of at least three IFN-stimulated genes that probably act on different stages of the viral replication cycle.
Complete Genome Sequence of a Street Rabies Virus Isolated from a Rabid Dog in China

ABSTRACT A rabies virus (RABV) was isolated from a dog in Anhui Province, China, in 2008. The virus was designated DRV-AH08. Its entire genome was sequenced and found to be closely related to RABV recently isolated in China and other Asian countries (homology of 87 to 98%) but distantly related to RABV in the “cosmopolitan” group (homology of 84 to 85%) in the clade I of RABV.
Simultaneous V/sub t/ selection and assignment for leakage optimization

This paper presents a novel approach for leakage optimization through simultaneous V/sub t/ selection and assignment. V/sub t/ selection implies deciding the right value for V/sub t/ and assignment implies deciding which gates should be assigned a particular threshold voltage. We also include the effect of variability in threshold voltage on delay and leakage due to fabrication process variations in our formulations and present a scheme that lets the designer control the leakage and delay variability in his design. The proposed algorithm is a general mathematical formulation that has been shown to trivially extend to multiple threshold voltages.
Embedding CSII therapy in the routine management of diabetes in children: a clinical audit of this service in Leeds

The aim of this study was to document the clinical and secondary care cost benefit of continuous subcutaneous insulin infusion (CSII) over a five-year period in the Leeds Paediatric Diabetes Service. Patients with type 1 diabetes treated using CSII therapy since 2002 who attended the paediatric diabetes clinics in Leeds, UK, were eligible for inclusion. Information on glycaemic control (HbA1c) and frequency/type of hospital admission was collected during the 12-month period before CSII was initiated and compared prospectively after the transition to pump therapy. Multi-level regression modelling was used to assess the change in HbA1c levels and the effect of patient characteristics. Data were included on 84 individuals ranging in age from 0 to 18 years, 54% of whom were female. Mean (SD) HbA1c levels improved from a baseline of 9.4 ± 1.7% to 8.9 ± 1.5%, with a significant overall reduction of 0.53% within the first year (95% CI 0.29-0.78%). The improvement in HbA1c levels was sustained for up to five years after CSII therapy commenced. Regression modelling showed that age, sex and duration of diabetes were not significantly associated with change in HbA1c levels. Hospital admission rates fell for severe hypoglycaemia from 8.9 to 2.4 per 100 patient years although hyperglycaemia admissions remained largely the same (7.6 vs 7.3 on CSII per 100 patient years). We concluded that patients treated using CSII appear to exhibit both improved glycaemic control, which is sustained over the short/medium term, and lower hospital admission rates for hypoglycaemia. Copyright © 2009 John Wiley & Sons.
Attenuation of Vesicular Stomatitis Virus Encephalitis through MicroRNA Targeting

ABSTRACT Vesicular stomatitis virus (VSV) has long been regarded as a promising recombinant vaccine platform and oncolytic agent but has not yet been tested in humans because it causes encephalomyelitis in rodents and primates. Recent studies have shown that specific tropisms of several viruses could be eliminated by engineering microRNA target sequences into their genomes, thereby inhibiting spread in tissues expressing cognate microRNAs. We therefore sought to determine whether microRNA targets could be engineered into VSV to ameliorate its neuropathogenicity. Using a panel of recombinant VSVs incorporating microRNA target sequences corresponding to neuron-specific or control microRNAs (in forward and reverse orientations), we tested viral replication kinetics in cell lines treated with microRNA mimics, neurotoxicity after direct intracerebral inoculation in mice, and antitumor efficacy. Compared to picornaviruses and adenoviruses, the engineered VSVs were relatively resistant to microRNA-mediated inhibition, but neurotoxicity could nevertheless be ameliorated significantly using this approach, without compromise to antitumor efficacy. Neurotoxicity was most profoundly reduced in a virus carrying four tandem copies of a neuronal mir125 target sequence inserted in the 3′-untranslated region of the viral polymerase (L) gene.
miR-181b-5p Modulates Cell Migratory Proteins, Tissue Inhibitor of Metalloproteinase 3, and Annexin A2 During In Vitro Decidualization in a Human Endometrial Stromal Cell Line

Decidualization is essential for successful embryo implantation and is regulated by concerted actions of growth factors and hormones. More recently, microRNAs, small RNA molecules that regulate posttranscriptional gene expression, have been implicated to play a role in the decidualization process. Of these microRNAs, miR-181b-5p has been associated with decidualization but its precise role and targets are not well established. To address this gap in our knowledge, we assessed the expression of miR-181b-5p, and its target tissue inhibitor of metalloproteinase 3 (TIMP-3), during in vitro decidualization using the well-characterized human endometrial stromal cell line, t-HESC. miR-181b-5p expression was highest prior to decidualization and significantly decreased in response to decidualization stimulus. In contrast, TIMP-3 expression was absent prior to in vitro decidualization and increased during decidualization. Regulation of TIMP-3 expression by miR-181b-5p was confirmed in vitro by quantitative reverse transcription polymerase chain reaction (qRT-PCR), Western blot analysis, and 3′ untranslated region reporter constructs. To identify unforeseen targets of miR-181b-5p during in vitro decidualization, t-HESC cells were transfected with pre-miR-181b-5p, and protein profiles were determined by 2-dimensional differential in-gel electrophoresis followed by matrix-assisted laser desorption-ionization time-of-flight/time-of-flight (MALDI TOF/TOF) tandem mass spectrometry. Of these proteins, several downregulated proteins associated with cell migration were identified including annexin A2, which we subsequently confirmed by qRT-PCR and Western blot analysis to be regulated by miR-181b-5p. In conclusion, miR-181b-5p is downregulated during the process of in vitro decidualization and may regulate the expression of proteins associated with cell migration including TIMP-3 and annexin A2.
Predictors of Family Involvement in Residential Long-Term Care

Abstract While much of the gerontological literature emphasizes the institutionalization of an older adult as an endpoint of family care, research has emerged illustrating the continued involvement of family members in the lives of residents. The purpose of the present study was to determine how resident setting, family context, resident background, staff background, and resident function influence the provision of family involvement in three long-term care environments: nursing homes, assisted living facilities, and family care homes. Five nursing homes, five assisted living facilities, and 16 family care homes and residents (N= 112) in the state of Kentucky were randomly selected. Results showed that type of facility was less important in accounting for different dimensions of family involvement than family context, family orientation of facilities, or resident need. The findings demonstrate the complex process of family involvement across the long-term care landscape, and have several research and practice implications for the facilitation of family integration in residential long-term care.
Preferências por alimentos doces e cárie dentária em pré-escolares

OBJETIVO: Avaliar as preferencias pelo sabor doce e sua associacao com as condicoes socioeconomicas e a prevalencia de carie dentaria em pre-escolares. METODOS: A amostra foi composta por 572 criancas de 4 a 6 anos, matriculadas em pre-escolas, dividida em estratos socioeconomicos segundo a procedencia (um bairro central, um periferico e Programa de Desfavelamento). Estudo transversal, foi desenvolvido em duas etapas. A preferencia pelo sabor doce foi avaliada atraves do Sweet Preference Inventory modificado. A concentracao das solucoes variou de 0 a 400 g/litro (0 a 1,17 molar). Foi utilizado o indice ceos para verificar a prevalencia de carie. RESULTADOS: Foram encontradas diferencas estatisticamente significantes entre as criancas do Programa de Desfavelamento e dos demais grupos na preferencia pelo sabor doce e no consumo de acucar, bem como associacao entre a procedencia e o percentual de criancas livres de carie, sendo o grupo do Desfavelamento o menos favorecido (p<0,05). CONCLUSAO: Os achados sustentam a hipotese de que o nivel socioeconomico influencia a preferencia por acucar e esta, por sua vez, esta associada a prevalencia de carie dentaria na denticao decidua.
Methods of traffic flow measurement using spatio-temporal image

Traffic flow measurement sensors, which measure vehicle velocity and detect traffic accidents, traffic congestion and so on using image processing, have been installed. For the sensors we utilized spatio-temporal images, which are used to process sequential images; as a recognition method for vehicles, we developed Directional-Temporal plane Transform (DTT) which transforms spatio-temporal image to 2-D data onto a directional-temporal plane. The rear-end-collision prevention system using this method decreased accidents to 1/3 as compared to the last few years before installation at a place on a national highway where many rear-end collisions had occurred. However, in the case where cameras are set up at low positions such as in tunnels, it is difficult to measure vehicle velocity in heavy traffic conditions because one vehicle often blocks the view of another in the images. To overcome this drawback, we propose a method for measurement of velocity for a group of vehicles by way of measuring moving time of the group by matching patterns, of DTT data at several points. We describe DTT-including its application-and the method for measurement of velocity for a group of vehicles, and then show the experimental results using road images.
Cardiovascular Autonomic Responses in the VCD Rat Model of Menopause: Effects of Short- and Long-Term Ovarian Failure

After menopause, hypertension elevates the risk of cardiac diseases, one of the major causes of women’s morbidity. The gradual depletion of ovarian follicles in rats, induced by 4-vinylcyclohexene diepoxide (VCD), is a model for studying the physiology of menopause. 4-Vinylcyclohexene diepoxide treatment leads to early ovarian failure (OF) and a hormonal profile comparable to menopause in humans. We have hypothesized that OF can compromise the balance between sympathetic and parasympathetic tones of the cardiovascular system, shifting toward dominance of the former. We aimed to study the autonomic modulation of heart and blood vessels and the cardiovascular reflexes in rats presenting short-term (80 days) or long-term (180 days) OF induced by VCD. Twenty-eight-day-old Wistar rats were submitted to VCD treatment (160 mg/kg, intraperitoneally) or vehicle (control) for 15 consecutive days and experiments were conducted at 80 or 180 days after the onset of treatment. Long-term OF led to an increase in the sympathetic activity to blood vessels and an impairment in the baroreflex control of the heart, evoked by physiological changes in arterial pressure. Despite that, long-term OF did not cause hypertension during the 180 days of exposure. Short-term OF did not cause any deleterious effect on the cardiovascular parameters analyzed. These data indicate that long-term OF does not disrupt the maintenance of arterial pressure homeostasis in rats but worsens the autonomic cardiovascular control. In turn, this can lead to cardiovascular complications, especially when associated with the aging process seen during human menopause.