bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lyssavirus Detection and Typing Using Pyrosequencing
Authors: De Benedictis Paola , De Battisti Cristian , Dacheux Laurent , Marciano Sabrina , Ormelli Silvia , Salomoni Angela , Caenazzo Silvia Tiozzo , Lepelletier Anthony , Bourhy Hervé , Capua Ilaria , Cattoli Giovanni 
Published: March 2011

ABSTRACT

Rabies is a fatal zoonosis caused by a nonsegmented negative-strand RNA virus, namely, rabies virus (RABV). Apart from RABV, at least 10 additional species are known as rabies-related lyssaviruses (RRVs), and some of them are responsible for occasional spillovers into humans. More lyssaviruses have also been detected recently in different bat ecosystems, thanks to the application of molecular diagnostic methods. Due to the variety of the members of the genus
Lyssavirus
, there is the necessity to develop a reliable molecular assay for rabies diagnosis able to detect and differentiate among the existing rabies and rabies-related viruses. In the present study, a pyrosequencing protocol targeting the 3′ terminus of the nucleoprotein (N) gene was applied for the rapid characterization of lyssaviruses. Correct identification of species was achieved for each sample tested. Results from the pyrosequencing assay were also confirmed by those obtained using the Sanger sequencing method. A pan-lyssavirus one-step reverse transcription (RT)-PCR was developed within the framework of the pyrosequencing procedure. The sensitivity (Se) of the one-step RT-PCR assay was determined by using
in vitro
-transcribed RNA and serial dilutions of titrated viruses. The assay demonstrated high analytical and relative specificity (Sp) (98.94%) and sensitivity (99.71%). To date, this is the first case in which pyrosequencing has been applied for lyssavirus identification using a cheaper diagnostic approach than the one for all the other protocols for rapid typing that we are acquainted with. Results from this study indicate that this procedure is suitable for lyssavirus detection in samples of both human and animal origin.
The rs8099917 Polymorphism, When Determined by a Suitable Genotyping Method, Is a Better Predictor for Response to Pegylated Alpha Interferon/Ribavirin Therapy in Japanese Patients than Other Single Nucleotide Polymorphisms Associated with Interleukin-28B
Authors: Ito Kiyoaki , Higami Katsuya , Masaki Naohiko , Sugiyama Masaya , Mukaide Motokazu , Saito Hiroaki , Aoki Yoshihiko , Sato Yo , Imamura Masatoshi , Murata Kazumoto , Nomura Hideyuki , Hige Shuhei , Adachi Hiroshi , Hino Keisuke , Yatsuhashi Hiroshi , Orito Etsuro , Kani Satomi , Tanaka Yasuhito , Mizokami Masashi 
Published: March 2011

ABSTRACT
We focused on determining the most accurate and convenient genotyping methods and most appropriate single nucleotide polymorphism (SNP) among four such polymorphisms associated with interleukin-28B (IL-28B) in order to design tailor-made therapy for patients with chronic hepatitis C virus (HCV) patients. First, five different methods (direct sequencing, high-resolution melting analysis [HRM], hybridization probe [HP], the InvaderPlus assay [Invader], and the TaqMan SNP genotyping assay [TaqMan]) were developed for genotyping four SNPs (rs11881222, rs8103142, rs8099917, and rs12979860) associated with IL-28B, and their accuracies were compared for 292 Japanese patients. Next, the four SNPs associated with IL-28B were genotyped by Invader for 416 additional Japanese patients, and the response to pegylated interferon/ribavirin (PEG-IFN/RBV) treatment was evaluated when the four SNPs were not in linkage disequilibrium (LD). HRM failed to genotype one of the four SNPs in five patients. In 2 of 287 patients, the results of genotyping rs8099917 by direct sequencing differed from the results of the other three methods. The HP, TaqMan, and Invader methods were accurate for determination of the SNPs associated with IL-28B. In 10 of the 708 (1.4%) patients, the four SNPs were not in LD. Eight of nine (88.9%) patients whose rs8099917 was homozygous for the major allele were virological responders, even though one or more of the other SNPs were heterozygous. The HP, TaqMan, and Invader methods were suitable to determine the SNPs associated with IL-28B. The rs8099917 polymorphism should be the best predictor for the response to the PEG-IFN/RBV treatment among Japanese chronic hepatitis C patients.
Recurrent Community-Acquired Methicillin-Resistant Staphylococcus aureus Infections in an HIV-Infected Person
Authors: Vyas Kartavya , Hospenthal Duane R. , Mende Katrin , Crum-Cianflone Nancy F. 
Published: March 2011

ABSTRACTHIV-infected persons are at heightened risk for recurrent community-acquired methicillin-resistantStaphylococcus aureus(CA-MRSA) infections, but there are limited data regarding the molecular characterization of these events. We describe an HIV-infected patient with 24 soft tissue infections and multiple colonization events. Molecular genotyping from 33 nonduplicate isolates showed all strains were USA300, Panton-Valentine leukocidin (PVL) and arginine catabolic mobile element (ACME) positive, and genetically related.
Ribosome Binding to a 5′ Translational Enhancer Is Altered in the Presence of the 3′ Untranslated Region in Cap-Independent Translation of Turnip Crinkle Virus
Authors: Stupina Vera A. , Yuan Xuefeng , Meskauskas Arturas , Dinman Jonathan D. , Simon Anne E. 
Published: March 2011

ABSTRACT

Plus-strand RNA viruses without 5′ caps require noncanonical mechanisms for ribosome recruitment. A translational enhancer in the 3′ untranslated region (UTR) of
Turnip crinkle virus
(TCV) contains an internal T-shaped structure (TSS) that binds to 60S ribosomal subunits. We now report that the 63-nucleotide (nt) 5′ UTR of TCV contains a 19-nt pyrimidine-rich element near the initiation codon that supports translation of an internal open reading frame (ORF) independent of upstream 5′ UTR sequences. Addition of 80S ribosomes to the 5′ UTR reduced the flexibility of the polypyrimidine residues and generated a toeprint consistent with binding to this region. Binding of salt-washed 40S ribosomal subunits was reduced 6-fold when the pyrimidine-rich sequence was mutated. 40S subunit binding generated the same toeprint as 80S ribosomes but also additional ones near the 5′ end. Generation of out-of-frame AUGs upstream of the polypyrimidine region reduced translation, which suggests that 5′-terminal entry of 40S subunits is followed by scanning and that the polypyrimidine region is needed for an alternative function that requires ribosome binding. No evidence for RNA-RNA interactions between 5′ and 3′ sequences was found, suggesting that TCV utilizes an alternative means for circularizing its genome. Combining 5′ and 3′ UTR fragments
in vitro
had no discernible effect on the structures of the RNAs. In contrast, when 80S ribosomes were added to both fragments, structural changes were found in the 5′ UTR polypyrimidine tract that were not evident when ribosomes interacted with the individual fragments. This suggests that ribosomes can promote an interaction between the 5′ and 3′ UTRs of TCV.
U
L
31 of Herpes Simplex Virus 1 Is Necessary for Optimal NF-κB Activation and Expression of Viral Gene Products
Authors: Roberts Kari L. , Baines Joel D. 
Published: March 2011

ABSTRACT

Previous results suggested that the U
L
31 gene of herpes simplex virus 1 (HSV-1) is required for envelopment of nucleocapsids at the inner nuclear membrane and optimal viral DNA synthesis and DNA packaging. In the current study, viral gene expression and NF-κB and c-Jun N-terminal kinase (JNK) activation of a herpes simplex virus mutant lacking the U
L
31 gene, designated ΔU
L
31, and its genetic repair construct, designated ΔU
L
31-R, were studied in various cell lines. In Hep2 and Vero cells infected with ΔU
L
31, expression of the immediate-early protein ICP4, early protein ICP8, and late protein glycoprotein C (gC) were delayed significantly. In Hep2 cells, expression of these proteins failed to reach levels seen in cells infected with ΔU
L
31-R or wild-type HSV-1(F) even after 18 h. The defect in protein accumulation correlated with poor or no activation of NF-κB and JNK upon infection with ΔU
L
31 compared to wild-type virus infection. The protein expression defects of the U
L
31 deletion mutant were not explainable by a failure to enter nonpermissive cells and were not complemented in an ICP27-expressing cell line. These data suggest that pU
L
31 facilitates initiation of infection and/or accelerates the onset of viral gene expression in a manner that correlates with NF-κB activation and is independent of the transactivator ICP27. The effects on very early events in expression are surprising in light of the fact that U
L
31 is designated a late gene and pU
L
31 is not a virion component. We show herein that while most pUL31 is expressed late in infection, low levels of pU
L
31 are detectable as early as 2 h postinfection, consistent with an early role in HSV-1 infection.
Metamorphic evolution of the Tethyan Himalayan flysch in SE Tibet
Authors: Dunkl I. , AntolÍn B. , Wemmer K. , Rantitsch G. , Kienast M. , Montomoli C. , Ding L. , Carosi R. , Appel E. , El Bay R. , Xu Q. , Von Eynatten H. 
Published: March 2011

Abstract

The metamorphic conditions and the age of thermal overprint were determined in metapelites, metaarenites and metabasites of the Tethyan Himalayan Sequence (THS) in SE Tibet using Kübler Index and vitrinite reflectance data and applying thermobarometrical (Thermocalc and PERPLEX) and geochronological methods (illite/muscovite K–Ar and zircon and apatite (U–Th)/He chronology). The multiple folded thrust pile experienced a thermal overprint reaching locally peak conditions between the diagenetic stage (
c
. 170 °C) and the amphibolite facies (
c
. 600 °C at 10 kbar). Burial diagenesis and heating due to Early Cretaceous dyke emplacement triggered the growth of illite in the metapelites. Eocene collision-related peak metamorphic conditions have been reached at
c
. 44 Ma. During collision the different tectonic blocks of the THS were tectonically buried to different structural levels so that they experienced maximum greenschist to amphibolite facies metamorphism. Later, during Oligocene to Miocene times the entire THS underwent anchi- to epizonal metamorphic conditions, probably associated to continuous deformation in the flysch fold-thrust-system. This period terminated at
c
. 24–22 Ma. Adjacent to the north Himalayan metamorphic domes, the base of the THS was metamorphosed during Miocene times (
c
. 13 Ma). Post-metamorphic cooling below
c
. 180 °C lasted until Late Miocene and took place at different times.
Physicians' Colorectal Cancer Screening Discussion and Recommendation Patterns
Authors: Zapka Jane M. , Klabunde Carrie N. , Arora Neeraj K. , Yuan Gigi , Smith Judith Lee , Kobrin Sarah C. 
Published: March 2011

Abstract
Background: Primary care physician (PCP) actions are pivotal to colorectal cancer (CRC) screening performance, and guidelines recommend discussion with patients about test options and potential benefits and harms. This article profiles patterns of discussion about and recommendations for screening and explores potential associations with multilevel factors (patient, clinician, practice, and environment).
Methods: In 2009, we analyzed data from 1,266 physicians responding to the 2006–2007 National Survey of Primary Care Physicians' Recommendations and Practices for Breast, Cervical, Colorectal, and Lung Cancer Screening (absolute response rate = 69.3%; cooperation rate = 75.0%). Descriptive statistics examined physicians' reports of discussion and recommendations. Multivariate analyses assessed the associations of these practices with multilevel factors.
Results: Although few respondents reported discussion of all options, 46% usually discuss more than one option; the vast majority of these respondents discuss fecal occult blood testing (FOBT) and colonoscopy (49%) or FOBT, sigmoidoscopy, and colonoscopy (32%). Of physicians who discuss more than one option, a majority reported usually recommending one or more test options, most commonly colonoscopy alone (43%) and FOBT and colonoscopy (43%). Several personal characteristics (specialty), perceived patient characteristics (prefer physician to decide), practice characteristics (geographic location), and community barriers (specialist availability) were independently associated with discussion and/or recommendation patterns.
Conclusions: PCPs do not discuss the full menu of test options, but many report selecting one or two options for discussion and recommendation. To ensure that patients' perspectives and concerns are elicited and considered, patient decision-making approaches should be considered.
Impact: Attention to informed decision making in CRC screening will be important for enhancing patient-centered quality care. Cancer Epidemiol Biomarkers Prev; 20(3); 509–21. ©2011 AACR.
Disclosing Individual CDKN2A Research Results to Melanoma Survivors: Interest, Impact, and Demands on Researchers
Authors: Christensen Kurt D. , Roberts J. Scott , Shalowitz David I. , Everett Jessica N. , Kim Scott Y.H. , Raskin Leon , Gruber Stephen B. 
Published: March 2011

AbstractBackground: Whether to return individual research results from cancer genetics studies is widely debated, but little is known about how participants respond to results disclosure or about its time and cost burdens on investigators.Methods: We recontacted participants at one site of a multicenter genetic epidemiologic study regarding their CDKN2A gene test results and implications for melanoma risk. Interested participants were disclosed their results by telephone and followed for 3 months.Results: Among 39 patients approached, 27 were successfully contacted, and 19 (70% uptake) sought results, including three with mutations. Prior to disclosure, participants endorsed numerous benefits of receiving results (mean = 7.7 of 9 posed), including gaining information relevant to their children's disease risk. Mean psychological well-being scores did not change from baseline, and no decreases to melanoma prevention behaviors were noted. Fifty-nine percent of participants reported that disclosure made participation in future research more likely. Preparation for disclosure required 40 minutes and $611 per recontact attempt. An additional 78 minutes and $68 was needed to disclose results.Conclusion: Cancer epidemiology research participants who received their individual genetic research results showed no evidence of psychological harm or false reassurance from disclosure and expressed strong trust in the accuracy of results. Burdens to our investigators were high, but protocols may differ in their demands and disclosure may increase participants' willingness to enroll in future studies.Impact: Providing individual study results to cancer genetics research participants poses potential challenges for investigators, but many participants desire and respond positively to this information. Cancer Epidemiol Biomarkers Prev; 20(3); 522–9. ©2011 AACR.
Menopausal Hormone Therapy Does Not Influence Lung Cancer Risk: Results from the California Teachers Study
Authors: Clague Jessica , Reynolds Peggy , Sullivan-Halley Jane , Ma Huiyan , Lacey James V. , Henderson Katherine D. , Ursin Giske , West Dee , Chang Shine , Delclos George L. , Du Xianglin L. , Forman Michele R. , Bernstein Leslie 
Published: March 2011

Abstract
Background: Results from studies examining the association between hormone therapy (HT) and lung cancer risk disagree.
Methods: We examined the associations between HT use and lung cancer risk among 60,592 postmenopausal women enrolled in the prospective California Teachers Study cohort. Between 1995 and 2007, a total of 727 women had a diagnosis of lung cancer. Multivariable Cox proportional hazards regression models were fit using age as the time metric.
Results: No measure of HT use was associated with lung cancer risk (all Ptrend values ≥0.4). In addition, no variations in risk by smoking status (never, ever, former, current), type of HT [estrogen (E)-alone, E + progestin (P) use], type of menopause, or lung cancer histology were observed.
Conclusions: Our findings do not support an association between HT and lung cancer.
Impact: This large-scale, prospective study, which capitalizes on the detailed hormone use, smoking history, and type of menopause information available within this unique cohort, was unable to find any association between intake of HT and lung cancer risk. Cancer Epidemiol Biomarkers Prev; 20(3); 560–4. ©2011 AACR.
Obesity and Thyroid Cancer Risk among U.S. Men and Women: A Pooled Analysis of Five Prospective Studies
Authors: Kitahara Cari M. , Platz Elizabeth A. , Freeman Laura E. Beane , Hsing Ann W. , Linet Martha S. , Park Yikyung , Schairer Catherine , Schatzkin Arthur , Shikany James M. , Berrington de González Amy 
Published: March 2011

AbstractBackground: Thyroid cancer incidence has risen dramatically in the United States since the early 1980s. Although the prevalence of obesity has doubled during this time period, the relationship between obesity and thyroid cancer is uncertain.Methods: We examined the association between body mass index (BMI) and thyroid cancer risk in a pooled analysis of five prospective U.S. studies, including 413,979 women and 434,953 men. Proportional hazards models with attained age as the time metric were adjusted for education, race, marital status, smoking, alcohol intake, and (where appropriate) cohort and sex.Results: Over follow-up (mean = 10.3 years), 768 women and 388 men were diagnosed with thyroid cancer. The risk of thyroid cancer was greater with increasing BMI [per 5 kg/m2: HR in women, 1.16 (95% CI, 1.08–1.24); HR in men, 1.21 (95% CI, 0.97–1.49)]. There was no significant heterogeneity between studies (both P &gt; 0.05). For women and men combined, the HRs for overweight (25.0–29.9 kg/m2) and obesity (≥30 kg/m2) compared with normal-weight (18.5–24.9 kg/m2) were 1.20 (95% CI, 1.04–1.38) and 1.53 (95% CI, 1.31–1.79), respectively. We found no significant effect modification by other factors, and the results did not differ significantly by histologic type. A significant positive association for BMI in young adulthood (ages 18–20) with thyroid cancer risk was also observed [per 5-kg/m2 increase: HR, 1.18 (95% CI, 1.03–1.35)].Conclusion: BMI was positively associated with thyroid cancer risk in both men and women.Impact: Our study provides strong evidence that obesity is an independent risk factor for thyroid cancer. Cancer Epidemiol Biomarkers Prev; 20(3); 464–72. ©2011 AACR.
The Analysis of Depression and Subsequent Cancer Risk in Taiwan
Authors: Liang Ji-An , Sun Li-Min , Muo Chih-Hsin , Sung Fung-Chang , Chang Shih-Ni , Kao Chia-Hung 
Published: March 2011

Abstract
Background: Patients with depression are suggestive of having a tendency toward a marginally significant association with the subsequent cancer risk. The aim of this study was to evaluate the possible relationship between depression and cancer risk in Taiwan.
Methods: We used the data of the National Health Insurance system of Taiwan to assess this issue. The Cox proportional hazard regression analysis was conducted to estimate the effects of depression on the cancer risk.
Results: In patients with depression, there was no significant change in the risk of developing overall cancer or for the site-specific cancer and all showed the same direction (positive) except for colorectal cancer, which had a negative direction.
Conclusions: This population-based study did not find Taiwanese patients with depression to have a higher risk to develop overall cancer or site-specific cancer.
Impact: Depression does not increase cancer risk. Cancer Epidemiol Biomarkers Prev; 20(3); 473–5. ©2011 AACR.
Chemoprevention of Intestinal Polyps in ApcMin/+ Mice Fed with Western or Balanced Diets by Drinking Annurca Apple Polyphenol Extract
Authors: Fini Lucia , Piazzi Giulia , Daoud Yahya , Selgrad Michael , Maegawa Shinji , Garcia Melissa , Fogliano Vincenzo , Romano Marco , Graziani Giulia , Vitaglione Paola , Carmack Susanne W. , Gasbarrini Antonio , Genta Robert M. , Issa Jean-Pierre , Boland C. Richard , Ricciardiello Luigi 
Published: March 2011

Abstract
The Western diet (WD) is associated with a higher incidence of colorectal cancer (CRC) than the Mediterranean diet. Polyphenols extracted from Annurca apple showed chemopreventive properties in CRC cells. A multifactorial, four-arm study by using wild-type (wt) and ApcMin/+ mice was carried out to evaluate the effect on polyp number and growth of APE treatment (60 μmol/L) ad libitum in drinking water combined with a WD or a balanced diet (BD) for 12 weeks. Compared with APE treatment, we found a significant drop in body weight (P &lt; 0.0001), severe rectal bleeding (P = 0.0076), presence of extraintestinal tumors, and poorer activity status (P = 0.0034) in water-drinking ApcMin/+ mice, more remarkably in the WD arm. In the BD and WD groups, APE reduced polyp number (35% and 42%, respectively, P &lt; 0.001) and growth (60% and 52%, respectively, P &lt; 0.0001) in both colon and small intestine. Increased antioxidant activity was found in wt animals fed both diets and in ApcMin/+ mice fed WD and drinking APE. Reduced lipid peroxidation was found in ApcMin/+ mice drinking APE fed both diets and in wt mice fed WD. In normal mucosa, mice drinking water had lower global levels of DNA methylation than mice drinking APE. APE treatment is highly effective in reducing polyps in ApcMin/+ mice and supports the concept that a mixture of phytochemicals, as they are naturally present in foods, represent a plausible chemopreventive agent for CRC, particularly in populations at high risk for colorectal neoplasia. Cancer Prev Res; 4(6); 907–15. ©2011 AACR.
S100A9 Differentially Modifies Phenotypic States of Neutrophils, Macrophages, and Dendritic Cells
Authors: Averill Michelle M. , Barnhart Shelley , Becker Lev , Li Xin , Heinecke Jay W. , LeBoeuf Renee C. , Hamerman Jessica A. , Sorg Clemens , Kerkhoff Claus , Bornfeldt Karin E. 
Published: March 2011

Background—
S100A9 is constitutively expressed in neutrophils, dendritic cells, and monocytes; is associated with acute and chronic inflammatory conditions; and is implicated in obesity and cardiovascular disease in humans. Most of the constitutively secreted S100A9 is derived from myeloid cells. A recent report demonstrated that mice deficient in S100A9 exhibit reduced atherosclerosis compared with controls and suggested that this effect was due in large part to loss of S100A9 in bone marrow–derived cells.

Methods and Results—
To directly investigate the role of bone marrow–derived S100A9 in atherosclerosis and insulin resistance in mice, low-density lipoprotein receptor–deficient, S100A9-deficient bone marrow chimeras were generated. Neither atherosclerosis nor insulin resistance was reduced in S100A9-deficient chimeras fed a diet rich in fat and carbohydrates. To investigate the reason for this lack of effect, myeloid cells were isolated from the peritoneal cavity or bone marrow. S100A9-deficient neutrophils exhibited a reduced secretion of cytokines in response to toll-like receptor-4 stimulation. In striking contrast, S100A9-deficient dendritic cells showed an exacerbated release of cytokines after toll-like receptor stimulation. Macrophages rapidly lost S100A9 expression during maturation; hence, S100A9 deficiency did not affect the inflammatory status of macrophages.

Conclusions—
S100A9 differentially modifies phenotypic states of neutrophils, macrophages, and dendritic cells. The effect of S100A9 deficiency on atherosclerosis and other inflammatory diseases is therefore predicted to depend on the relative contribution of these cell types at different stages of disease progression. Furthermore, S100A9 expression in nonmyeloid cells is likely to contribute to atherosclerosis.