bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colorimetric Nucleic Acid Testing Assay for RNA Virus Detection Based on Circle-to-Circle Amplification of Padlock Probes
Authors: Ke Rongqin , Zorzet Anna , Göransson Jenny , Lindegren Gunnel , Sharifi-Mood Batool , Chinikar Sadegh , Mardani Masoud , Mirazimi Ali , Nilsson Mats 
Published: September 2011

ABSTRACT

We developed a molecular diagnostic method for detection of RNA virus based on padlock probes and colorimetric readout. The feasibility of our approach was demonstrated by using detection of Crimean-Congo hemorrhagic fever (CCHF) virus as a model. Compared with conventional PCR-based methods, our approach does not require advanced equipment, involves easier assay design, and has a sensitivity of 10
3
viral copies/ml. By using a cocktail of padlock probes, synthetic templates representing different viral strain variants could be detected. We analyzed 34 CCHF patient samples, and all patients were correctly diagnosed when the results were compared to those of the current real-time PCR method. This is the first time that highly specific padlock probes have been applied to detection of a highly variable target sequence typical of RNA viruses.
Impact of Genomic Sequence Variability on Quantitative PCR Assays for Diagnosis of Polyomavirus BK Infection
Authors: Randhawa P. , Kant J. , Shapiro R. , Tan H. , Basu A. , Luo C. 
Published: September 2011

ABSTRACT
Knowledge of polyomavirus BK (BKV) genomic diversity has greatly expanded. The implications of BKV DNA sequence variation for the performance of molecular diagnostic assays is not well studied. We analyzed 184 publically available VP-1 sequences encompassing the BKV genomic region targeted by an in-house quantitative hydrolysis probe-based PCR assay. A perfect match with the PCR primers and probe was seen in 81 sequences. One Dun and 13 variant prototype oligonucleotides were synthesized as artificial targets to determine how they affected the performance of PCR. The sensitivity of detection of BKV in the PCR assay was a function of the viral genotype. Prototype 1 (BKV Dun) could be reliably detected at concentrations as low as 10 copies/μl. However, consistent detection of all BKV variants was possible only at concentrations of 10,000 copies/μl or higher. For BKV prototypes with 2 or more mismatches (representing genotype IV, genotype II, and genotype 1c strains), the calculated viral loads were 0.57 to 3.26% of the expected values. In conclusion, variant BKV strains lower the sensitivity of detection and may have a substantial effect on quantitation of the viral load. Physicians need to be cognizant of these effects when interpreting the results of quantitative PCR testing in transplant recipients, particularly if there is a discrepancy between the clinical impression and the measured viral load.
Dermatophyte Identification Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Theel Elitza S. , Hall Leslie , Mandrekar Jayawant , Wengenack Nancy L. 
Published: September 2011

ABSTRACT

The performance of the Bruker Biotyper matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometer (MS) for the identification of dermatophytes from clinical cultures was compared to that of dermatophyte identification using 28S rRNA gene sequencing. The MALDI Biotyper library (MBL; version 3.0) was used alone and in combination with a supplemented library containing an additional 20 dermatophyte spectra (S-MBL). Acquired spectra were interpreted using both the manufacturer-recommended scores (genus, ≥1.7; species, ≥2.0) and adjusted cutoff values established by this study (genus, ≥1.5; species, ≥1.7); identifications required a minimum 10% difference in scores between the top two different organisms to be considered correct. One hundred well-characterized, archived dermatophyte isolates and 71 fresh dermatophyte cultures were evaluated using both libraries and both sets of cutoff criteria. Collectively, the S-MBL significantly outperformed the MBL at both the genus (93% versus 37.4%;
P
< 0,0001) and species (59.6% versus 20.5%;
P
< 0.0001) levels when using the adjusted score criteria. Importantly, application of the lowered cutoff values significantly improved genus (
P
= 0.005)- and species (
P
< 0.0001)-level identification for the S-MBL, without leading to an increase in misidentifications. MALDI-TOF MS is a cost-effective and rapid alternative to traditional or molecular methods for dermatophyte identification, provided that the reference library is supplemented to sufficiently encompass clinically relevant, intraspecies strain diversity.
Identification of a Cullin5-ElonginB-ElonginC E3 Complex in Degradation of Feline Immunodeficiency Virus Vif-Mediated Feline APOBEC3 Proteins
Authors: Wang Jiawen , Zhang Wenyan , Lv Mingyu , Zuo Tao , Kong Wei , Yu Xianghui 
Published: September 2011

ABSTRACT
Various feline APOBEC3 (fA3) proteins exhibit broad antiviral activities against a wide range of viruses, such as feline immunodeficiency virus (FIV), feline foamy virus (FFV), and feline leukemia virus (FeLV), as well as those of other species. This activity can be counteracted by the FIV Vif protein, but the mechanism by which FIV Vif suppresses fA3s is unknown. In the present study, we demonstrated that FIV Vif could act via a proteasome-dependent pathway to overcome fA3s. FIV Vif interacted with feline cellular proteins Cullin5 (Cul5), ElonginB, and ElonginC to form an E3 complex to induce degradation of fA3s. Both the dominant-negative Cul5 mutant and a C-terminal hydrophilic replacement ElonginC mutant potently disrupted the FIV Vif activity against fA3s. Furthermore, we identified a BC-box motif in FIV Vif that was essential for the recruitment of E3 ubiquitin ligase and also required for FIV Vif-mediated degradation of fA3s. Moreover, despite the lack of either a Cul5-box or a HCCH zinc-binding motif, FIV Vif specifically selected Cul5. Therefore, FIV Vif may interact with Cul5 via a novel mechanism. These finding imply that SOCS proteins may possess distinct mechanisms to bind Cul5 during formation of the Elongin-Cullin-SOCS box complex.
RNA-Based Immunity Terminates Viral Infection in Adult Drosophila in the Absence of Viral Suppression of RNA Interference: Characterization of Viral Small Interfering RNA Populations in Wild-Type and Mutant Flies
Authors: Han Yan-Hong , Luo Ying-Jun , Wu Qingfa , Jovel Juan , Wang Xiao-Hong , Aliyari Roghiyh , Han Chenggui , Li Wan-Xiang , Ding Shou-Wei 
Published: September 2011

ABSTRACT

Replication of viral RNA genomes in fruit flies and mosquitoes induces the production of virus-derived small interfering RNAs (siRNAs) to specifically reduce virus accumulation by RNA interference (RNAi). However, it is unknown whether the RNA-based antiviral immunity (RVI) is sufficiently potent to terminate infection in adult insects as occurs in cell culture. We show here that, in contrast to robust infection by Flock house virus (FHV), infection with an FHV mutant (FHVΔB2) unable to express its RNAi suppressor protein B2 was rapidly terminated in adult flies. FHVΔB2 replicated to high levels and induced high mortality rates in
dicer-2
and
argonaute-2
mutant flies that are RNAi defective, demonstrating that successful infection of adult
Drosophila
requires a virus-encoded activity to suppress RVI.
Drosophila
RVI may depend on the RNAi activity of viral siRNAs since efficient FHVΔB2 infection occurred in
argonaute-2
and
r2d2
mutant flies despite massive production of viral siRNAs. However, RVI appears to be insensitive to the relative abundance of viral siRNAs since FHVΔB2 infection was terminated in flies carrying a partial loss-of-function mutation in
loquacious
required for viral siRNA biogenesis. Deep sequencing revealed a low-abundance population of Dicer-2-dependent viral siRNAs accompanying FHVΔB2 infection arrest in RVI-competent flies that included an approximately equal ratio of positive and negative strands. Surprisingly, viral small RNAs became strongly biased for positive strands at later stages of infection in RVI-compromised flies due to genetic or viral suppression of RNAi. We propose that degradation of the asymmetrically produced viral positive-strand RNAs associated with abundant virus accumulation contributes to the positive-strand bias of viral small RNAs.
Adenovirus with Hexon Tat-Protein Transduction Domain Modification Exhibits Increased Therapeutic Effect in Experimental Neuroblastoma and Neuroendocrine Tumors
Authors: Yu Di , Jin Chuan , Leja Justyna , Majdalani Nadim , Nilsson Berith , Eriksson Fredrik , Essand Magnus 
Published: September 2011

ABSTRACT
Adenovirus serotype 5 (Ad5) is widely used as an oncolytic agent for cancer therapy. However, its infectivity is highly dependent on the expression level of coxsackievirus-adenovirus receptor (CAR) on the surfaces of tumor cells. Furthermore, infected cells overproduce adenovirus fiber proteins, which are released prior to cell lysis. The released fibers block CAR on noninfected neighboring cells, thereby preventing progeny virus entry. Our aim was to add a CAR-independent infection route to Ad5 to increase the infectivity of tumor cells with low CAR expression and prevent the fiber-masking problem. We constructed Ad5 viruses that encode the protein transduction domain (PTD) of the HIV-1 Tat protein (Tat-PTD) in hypervariable region 5 (HVR5) of the hexon protein. Tat-PTD functions as a cell-penetrating peptide, and Tat-PTD-modified Ad5 showed a dramatic increased transduction of CAR-negative cell lines compared to unmodified vector. Moreover, while tumor cell infectivity was severely reduced for Ad5 in the presence of fiber proteins, it was only marginally reduced for Tat-PTD-modified Ad5. Furthermore, because of the sequence alteration in the hexon HVR, coagulation factor X-mediated virus uptake was significantly reduced. Mice harboring human neuroblastoma and neuroendocrine tumors show suppressed tumor growths and prolonged survival when treated with Tat-PTD-modified oncolytic viruses. Our data suggest that modification of Ad5 with Tat-PTD in HVR5 expands its utility as an oncolytic agent.
Inhibitory Effects of Bile Acids and Synthetic Farnesoid X Receptor Agonists on Rotavirus Replication
Authors: Kim Yunjeong , Chang Kyeong-Ok 
Published: September 2011

ABSTRACTRotaviruses (group A rotaviruses) are the most important cause of severe gastroenteritis in infants and children worldwide. Currently, an antiviral drug is not available and information on therapeutic targets for antiviral development is limited for rotavirus infection. Previously, it was shown that lipid homeostasis is important in rotavirus replication. Since farnesoid X receptor (FXR) and its natural ligands bile acids (such as chenodeoxycholic acid [CDCA]) play major roles in cholesterol and lipid homeostasis, we examined the effects of bile acids and synthetic FXR agonists on rotavirus replication in association with cellular lipid levels. In a mouse model of rotavirus infection, effects of oral administration of CDCA on fecal rotavirus shedding were investigated. The results demonstrate the following. First, the intracellular contents of triglycerides were significantly increased by rotavirus infection. Second, CDCA, deoxycholic acid (DCA), and other synthetic FXR agonists, such as GW4064, significantly reduced rotavirus replication in cell culture in a dose-dependent manner. The reduction of virus replication correlated positively with activation of the FXR pathway and reduction of cellular triglyceride contents (r2= 0.95). Third, oral administration of CDCA significantly reduced fecal virus shedding in mice (P< 0.05). We conclude that bile acids and FXR agonists play important roles in the suppression of rotavirus replication. The inhibition mechanism is proposed to be the downregulation of lipid synthesis induced by rotavirus infection.
Kaposi's Sarcoma-Associated Herpesvirus Noncoding Polyadenylated Nuclear RNA Interacts with Virus- and Host Cell-Encoded Proteins and Suppresses Expression of Genes Involved in Immune Modulation
Authors: Rossetto Cyprian C. , Pari Gregory S. 
Published: September 2011

ABSTRACT

During lytic infection, Kaposi's sarcoma-associated herpesvirus (KSHV) expresses a polyadenylated nuclear RNA (PAN RNA). This noncoding RNA (ncRNA) is localized to the nucleus and is the most abundant viral RNA during lytic infection; however, to date, the role of PAN RNA in the virus life cycle is unknown. Many examples exist where ncRNAs have a defined key regulatory function controlling gene expression by various mechanisms. Our goal for this study was to identify putative binding partners for PAN RNA in an effort to elucidate a possible function for the transcript in KSHV infection. We employed an
in vitro
affinity protocol where PAN RNA was used as bait for factors present in BCBL-1 cell nuclear extract to show that PAN RNA interacts with several virus- and host cell-encoded factors, including histones H1 and H2A, mitochondrial and cellular single-stranded binding proteins (SSBPs), and interferon regulatory factor 4 (IRF4). RNA chromatin immunoprecipitation (ChIP) assays confirmed that PAN RNA interacted with these factors in the infected cell environment. A luciferase reporter assay showed that PAN RNA expression interfered with the ability of IRF4/PU.1 to activate the interleukin-4 (IL-4) promoter, strongly suggesting a role for PAN RNA in immune modulation. Since the proteomic screen and functional data suggested a role in immune responses, we investigated if constitutive PAN RNA expression could affect other genes involved in immune responses. PAN RNA expression decreased expression of gamma interferon, interleukin-18, alpha interferon 16, and RNase L. These data strongly suggest that PAN RNA interacts with viral and cellular proteins and can function as an immune modulator.
Autophagy Required for Hepatitis B Virus Replication in Transgenic Mice
Authors: Tian Yongjun , Sir Donna , Kuo Cheng-fu , Ann David K. , Ou Jing-hsiung James 
Published: September 2011

ABSTRACT

Recent studies indicate that hepatitis B virus (HBV) may induce autophagy to enhance its replication in cell cultures. To understand whether autophagy can indeed enhance HBV replication
in vivo
, we generated HBV transgenic mice with liver-specific knockout of the Atg5 gene, a gene critical for the initiation of autophagy. Immunoblot analyses confirmed the inhibition of autophagy in the livers of Atg5 knockout mice. This inhibition of autophagy slightly reduced HBV gene expression and affected nuclear localization of the HBV core protein. It also reduced the HBV DNA level in sera by more than 90% and the level of the HBV DNA replicative intermediate in the mouse liver to an almost undetectable level. Our results thus demonstrate that autophagy is important for HBV replication
in vivo
and raise the possibility of targeting this pathway to treat HBV patients.
Communicating the risk of injury in schoolboy rugby: using Poisson probability as an alternative presentation of the epidemiology
Authors: Parekh Nikesh , Hodges Stewart D , Pollock Allyson M , Kirkwood Graham 
Published: September 2011

BackgroundThe communication of injury risk in rugby and other sports is underdeveloped and parents, children and coaches need to be better informed about risk.MethodA Poisson distribution was used to transform population based incidence of injury into average probabilities of injury to individual players.ResultsThe incidence of injury in schoolboy rugby matches range from 7 to 129.8 injuries per 1000 player-hours; these rates translate to average probabilities of injury to a player of between 12% and 90% over a season.ConclusionIncidence of injury and average probabilities of injury over a season should be published together in all future epidemiological studies on school rugby and other sports. More research is required on informing and communicating injury risks to parents, staff and children and how it affects monitoring, decision making and prevention strategies.
Opportunities for the Primary Prevention of Colorectal Cancer in the United States
Authors: Joshu Corinne E. , Parmigiani Giovanni , Colditz Graham A. , Platz Elizabeth A. 
Published: September 2011

Abstract
Several studies indicate that screening in combination with lifestyle modification may produce a greater reduction in colorectal cancer rates than screening alone. To identify national opportunities for the primary prevention of colorectal cancer, we assessed the prevalence of modifiable lifestyle risk factors in the United States. We used nationally representative, cross-sectional data from 5 NHANES cycles (1999–2000, n = 2,753; 2001–2002, n = 3,169; 2003–2004, n = 2,872; 2005–2006, n = 2,993; 2007–2008, n = 3,438). We evaluated the 5 colorectal cancer risk factors deemed “convincing” by the World Cancer Research Fund (obesity, physical inactivity, intake of red meat, processed meat, alcohol), and cigarette smoking, a “suggestive” risk factor in the Surgeon General's report. We estimated the prevalence of each risk factor separately and jointly, and report it overall, and by sex, race/ethnicity, age, and year. In 2007 to 2008, 81% percent of U.S. adults, aged 20 to 69 years, had at least one modifiable risk factor for colorectal cancer. More than 15% of those younger than 50 years had 3 or more risk factors. There was no change in the prevalence of risk factors between 1999 and 2008. The most common risk factors were risk factors for other chronic diseases. Our findings provide additional support for the prioritization of preventive services in health care reform. Increasing awareness, especially among young adults, that lifestyle factors influence colorectal cancer risk, and other chronic diseases, may encourage lifestyle changes and adherence to screening guidelines. Complementary approaches of screening and lifestyle modification will likely provide the greatest reduction of colorectal cancer. Cancer Prev Res; 5(1); 138–45. ©2011 AACR.
Mode of Action and Effects of Standardized Collaborative Disease Management on Mortality and Morbidity in Patients With Systolic Heart Failure
Authors: Angermann Christiane E. , Störk Stefan , Gelbrich Götz , Faller Hermann , Jahns Roland , Frantz Stefan , Loeffler Markus , Ertl Georg 
Published: September 2011

Background—
Trials investigating efficacy of disease management programs (DMP) in heart failure reported contradictory results. Features rendering specific interventions successful are often ill defined. We evaluated the mode of action and effects of a nurse-coordinated DMP (HeartNetCare-HF, HNC).

Methods and Results—

Patients hospitalized for systolic heart failure were randomly assigned to HNC or usual care (UC). Besides telephone-based monitoring and education, HNC addressed individual problems raised by patients, pursued networking of health care providers and provided training for caregivers. End points were time to death or rehospitalization (combined primary), heart failure symptoms, and quality of life (SF-36). Of 1007 consecutive patients, 715 were randomly assigned (HNC: n=352; UC: n=363; age, 69±12 years; 29% female; 40% New York Heart Association class III-IV). Within 180 days, 130 HNC and 137 UC patients reached the primary end point (hazard ratio, 1.02; 95% confidence interval, 0.81–1.30;
P
=0.89), since more HNC patients were readmitted. Overall, 32 HNC and 52 UC patients died (1 UC patient and 4 HNC patients after dropout); thus, uncensored hazard ratio was 0.62 (0.40–0.96;
P
=0.03). HNC patients improved more regarding New York Heart Association class (
P
=0.05), physical functioning (
P
=0.03), and physical health component (
P
=0.03). Except for HNC, health care utilization was comparable between groups. However, HNC patients requested counseling for noncardiac problems even more frequently than for cardiovascular or heart-failure–related issues.

Conclusions—
The primary end point of this study was neutral. However, mortality risk and surrogates of well-being improved significantly. Quantitative assessment of patient requirements suggested that besides (tele)monitoring individualized care considering also noncardiac problems should be integrated in efforts to achieve more sustainable improvement in heart failure outcomes.

Clinical Trial Registration—

URL:
http://www.controlled-trials.com
. Unique identifier: ISRCTN23325295.
Independent Distractor Frequency and Age-of-Acquisition Effects in Picture–Word Interference: fMRI Evidence for Post-lexical and Lexical Accounts according to Distractor Type
Authors: de Zubicaray Greig I. , Miozzo Michele , Johnson Kori , Schiller Niels O. , McMahon Katie L. 
Published: September 2011

Abstract
In two fMRI experiments, participants named pictures with superimposed distractors that were high or low in frequency or varied in terms of age of acquisition. Pictures superimposed with low-frequency words were named more slowly than those superimposed with high-frequency words, and late-acquired words interfered with picture naming to a greater extent than early-acquired words. The distractor frequency effect (Experiment 1) was associated with increased activity in left premotor and posterior superior temporal cortices, consistent with the operation of an articulatory response buffer and verbal self-monitoring system. Conversely, the distractor age-of-acquisition effect (Experiment 2) was associated with increased activity in the left middle and posterior middle temporal cortex, consistent with the operation of lexical level processes such as lemma and phonological word form retrieval. The spatially dissociated patterns of activity across the two experiments indicate that distractor effects in picture–word interference may occur at lexical or postlexical levels of processing in speech production.
Thermodynamic Consistency of a Pseudoincompressible Approximation for General Equations of State
Authors: Klein Rupert , Pauluis Olivier 
Published: September 2011

Abstract
In soundproof model equations for geophysical fluid dynamics, the momentum and mechanical energy budgets decouple from the thermodynamics for adiabatic flows. In applying such models to nonadiabatic flows of fluids with general equations of state, thermodynamic consistency of the soundproof approximations needs to be ensured. Specifically, a physically meaningful total energy conservation law should arise as an integral of adiabatic dynamics, while for diabatic flows the effective energy source terms should be related through thermodynamic relationships to the rates of change of entropy and other pertinent internal degrees of freedom. Complementing earlier work by one of the authors on the Lipps and Hemler-type anelastic approximation, this paper discusses the thermodynamic consistency of an extension of Durran’s pseudoincompressible model to moist atmospheric motions allowing for a general equation of state.