bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural Occurrence and Characterization of Two Internal Ribosome Entry Site Elements in a Novel Virus, Canine Picodicistrovirus, in the Picornavirus-Like Superfamily
Authors: Woo Patrick C. Y. , Lau Susanna K. P. , Choi Garnet K. Y. , Huang Yi , Teng Jade L. L. , Tsoi Hoi-Wah , Tse Herman , Yeung Man Lung , Chan Kwok-Hung , Jin Dong-Yan , Yuen Kwok-Yung 
Published: December 2011

ABSTRACT

Dicistroviridae
and
Picornaviridae
are two phylogenetically related families of positive-sense single-stranded RNA viruses in the picornavirus-like superfamily with similar gene contents but different genome organizations and hosts. In a surveillance study involving 1,472 samples from 368 dogs over a 22-month period, we identified a novel picornavirus-like virus from 47 fecal and urine samples by the use of reverse transcription-PCR (RT-PCR). Sequencing and phylogenetic analysis of three complete genomes revealed that, although it seemed that the virus was most closely related to other picornaviruses, P1, P2, and P3 of the virus possessed very low amino acid identities of <30% to those of all other known picornaviruses and that the amino acid identities between the 3D
pol
and 2C of the virus and the RNA-dependent RNA polymerases and helicases of all other picornaviruses were <35%. Distinct from other picornaviruses, the genomes of the virus contain two putative internal ribosome entry sites (IRESs) and two open reading frames, encoding two polyprotein precursors (844 and 1,406 amino acids), separated by an intergenic region (IGR) of 588 bases. A dual-luciferase activity assay using DNA and RNA transfection revealed that both IRESs were functional. Quantitative RT-PCR showed that numbers of viral RNAs ranged from 7.55 × 10
6
to 1.26 × 10
9
copies/ml of urine and 1.82 × 10
6
to 4.97 × 10
10
copies/ml of fecal sample. This is the first report of the natural occurrence of two functional IRESs in nondicistroviruses. Based on our results, we have proposed a novel species, canine picodicistrovirus (CPDV), to describe this novel member of the picornavirus-like superfamily, which could represent a novel family of viruses.
Targeting HIV-1 Envelope Glycoprotein Trimers to B Cells by Using APRIL Improves Antibody Responses
Authors: Melchers Mark , Bontjer Ilja , Tong Tommy , Chung Nancy P. Y. , Klasse Per Johan , Eggink Dirk , Montefiori David C. , Gentile Maurizio , Cerutti Andrea , Olson William C. , Berkhout Ben , Binley James M. , Moore John P. , Sanders Rogier W. 
Published: December 2011

ABSTRACTAn HIV-1 vaccine remains elusive, in part because various factors limit the quantity and quality of the antibodies raised against the viral envelope glycoprotein complex (Env). We hypothesized that targeting Env vaccines directly to B cells, by fusing them to molecules that bind and activate these cells, would improve Env-specific antibody responses. Therefore, we fused trimeric Env gp140 to A PRoliferation-Inducing Ligand (APRIL), B-cell Activating Factor (BAFF), and CD40 Ligand (CD40L). The Env-APRIL, Env-BAFF, and Env-CD40L gp140 trimers all enhanced the expression of activation-induced cytidine deaminase (AID), the enzyme responsible for inducing somatic hypermutation, antibody affinity maturation, and antibody class switching. They also triggered IgM, IgG, and IgA secretion from human B cellsin vitro. The Env-APRIL trimers induced higher anti-Env antibody responses in rabbits, including neutralizing antibodies against tier 1 viruses. The enhanced Env-specific responses were not associated with a general increase in total plasma antibody concentrations, indicating that the effect of APRIL was specific for Env. All the rabbit sera raised against gp140 trimers, irrespective of the presence of CD40L, BAFF, or APRIL, recognized trimeric Env efficiently, whereas sera raised against gp120 monomers did not. The levels of trimer-binding and virus-neutralizing antibodies were strongly correlated, suggesting that gp140 trimers are superior to gp120 monomers as immunogens. Targeting and activating B cells with a trimeric HIV-1 Env-APRIL fusion protein may therefore improve the induction of humoral immunity against HIV-1.
Equine Herpesvirus Type 1-Mediated Oncolysis of Human Glioblastoma Multiforme Cells
Authors: Courchesne Michael J. , White Maria C. , Stanfield Brent A. , Frampton Arthur R. 
Published: December 2011

ABSTRACT
The cytolytic animal virus equine herpesvirus type 1 (EHV-1) was evaluated for its oncolytic potential against five human glioblastoma cell lines. EHV-1 productively infected four of these cell lines, and the degree of infection was positively correlated with glioma cell death. No human major histocompatibility complex class 1 (MHC-I) was detected in the resistant glioma line, while infection of the susceptible glioma cell lines, which expressed human MHC-I, were blocked with antibody to MHC-I, indicating that human MHC-I acts as an EHV-1 entry receptor on glioma cells.
Differential Transmission of HIV Traversing Fetal Oral/Intestinal Epithelia and Adult Oral Epithelia
Authors: Tugizov Sharof M. , Herrera Rossana , Veluppillai Piri , Greenspan Deborah , Soros Vanessa , Greene Warner C. , Levy Jay A. , Palefsky Joel M. 
Published: December 2011

ABSTRACT

While human immunodeficiency virus (HIV) transmission through the adult oral route is rare, mother-to-child transmission (MTCT) through the neonatal/infant oral and/or gastrointestinal route is common. To study the mechanisms of cell-free and cell-associated HIV transmission across adult oral and neonatal/infant oral/intestinal epithelia, we established
ex vivo
organ tissue model systems of adult and fetal origin. Given the similarity of neonatal and fetal oral epithelia with respect to epithelial stratification and density of HIV-susceptible immune cells, we used fetal oral the epithelium as a model for neonatal/infant oral epithelium. We found that cell-free HIV traversed fetal oral and intestinal epithelia and infected HIV-susceptible CD4
+
T lymphocytes, Langerhans/dendritic cells, and macrophages. To study the penetration of cell-associated virus into fetal oral and intestinal epithelia, HIV-infected macrophages and lymphocytes were added to the surfaces of fetal oral and intestinal epithelia. HIV-infected macrophages, but not lymphocytes, transmigrated across fetal oral epithelia. HIV-infected macrophages and, to a lesser extent, lymphocytes transmigrated across fetal intestinal epithelia. In contrast to the fetal oral/intestinal epithelia, cell-free HIV transmigration through adult oral epithelia was inefficient and virions did not infect intraepithelial and subepithelial HIV-susceptible cells. In addition, HIV-infected macrophages and lymphocytes did not transmigrate through intact adult oral epithelia. Transmigration of cell-free and cell-associated HIV across the fetal oral/intestinal mucosal epithelium may serve as an initial mechanism for HIV MTCT.
The ABC of handover: impact on shift handover in the emergency department
Authors: Farhan Maisse , Brown Ruth , Vincent Charles , Woloshynowych Maria 
Published: December 2011

IntroductionA study was undertaken to test the impact of a new tool for shift handover, ‘The ABC of Handover’, in the emergency department (ED). The impact on shift handover following implementation of this structured tool, the effect on clinical and organisational aspects of the subsequent shift and the opinions of users of this new tool are reported.MethodsA prospective observational before and after study was performed to explore the effect of implementing ‘The ABC of Handover’ on clinical and organisational practice using a questionnaire.Results41 handovers were observed before implementation of ‘The ABC of Handover’ and 42 were observed after. The new tool was successfully implemented and resulted in a change of practice which led to a significant increase in the operational issues mentioned at handover from a mean of 34% to a mean of 86% of essential items with the ABC method. Over the study period, middle-grade staff demonstrated improved situational awareness as they adopted proactive management of operational issues such as staffing or equipment shortages. All participants reported that ‘The ABC of Handover’ improved handover regardless of the seniority of the doctor giving it, and found the ABC method easy to learn.ConclusionsSuccessful implementation of ‘The ABC of Handover’ led to a change of practice in the ED. Improving handover resulted in better organisation of the shift and heightened awareness of potential patient safety issues. The ABC method provides a framework for organising the shift and preparing for events in the subsequent shift.
Better never than late
Authors: Wilson Christo , Ballani Hitesh , Karagiannis Thomas , Rowtron Ant 
Published: December 2011

The soft real-time nature of large scale web applications in today's datacenters, combined with their distributed workflow, leads to deadlines being associated with the datacenter application traffic. A network flow is useful, and contributes to application throughput and operator revenue if, and only if, it completes within its deadline. Today's transport pro- tocols (TCP included), given their Internet origins, are agnostic to such flow deadlines. Instead, they strive to share network resources fairly. We show that this can hurt application performance.
Motivated by these observations, and other (previously known) deficiencies of TCP in the datacenter environment, this paper presents the design and implementation of D3, a deadline-aware control protocol that is customized for the datacenter environment. D3 uses explicit rate control to apportion bandwidth according to flow deadlines. Evaluation from a 19-node, two-tier datacenter testbed shows that D3, even without any deadline information, easily outper- forms TCP in terms of short flow latency and burst tolerance. Further, by utilizing deadline information, D3 effectively doubles the peak load that the datacenter network cansupport.
Clearing the RF smog
Authors: Gollakota Shyamnath , Adib Fadel , Katabi Dina , Seshan Srinivasan 
Published: December 2011

Recent studies show that high-power cross-technology interference is becoming a major problem in today's 802.11 networks. Devices like baby monitors and cordless phones can cause a wireless LAN to lose connectivity. The existing approach for dealing with such high-power interferers makes the 802.11 network switch to a different channel; yet the ISM band is becoming increasingly crowded with diverse technologies, and hence many 802.11 access points may not find an interference-free channel.
This paper presents TIMO, a MIMO design that enables 802.11n to communicate in the presence of high-power cross-technology interference. Unlike existing MIMO designs, however, which require all concurrent transmissions to belong to the same technology, TIMO can exploit MIMO capabilities to decode in the presence of a signal from a different technology, hence enabling diverse technologies to share the same frequency band. We implement a prototype of TIMO in GNURadio-USRP2 and show that it enables 802.11n to communicate in the presence of interference from baby monitors, cordless phones, and microwave ovens, transforming scenarios with a complete loss of connectivity to operational networks.
Understanding CS1 students; defective software
Authors: Guzdial Mark , Meyer Bertrand 
Published: December 2011

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM
http://cacm.acm.org/blogs/blog-cacm
ark Guzdial writes about why teachers must grasp introductory CS students' theories about computing. Bertrand Meyer argues for the necessity of analyzing large-scale software disasters and publishing a detailed technical study.
Peroxisome Proliferator–Activated Receptors Modulate Proliferation and Angiogenesis in Human Endometrial Carcinoma
Authors: Nickkho-Amiry Mahshid , McVey Rhona , Holland Cathrine 
Published: December 2011

AbstractPeroxisome proliferator-activated receptors (PPAR) and retinoid X receptors (RXR) are implicated in the development of several obesity-related cancers. Little is known of either the expression or function of PPARs and RXRs in endometrial cancer although this increasingly common disease is highly associated with both obesity and insulin resistance. We investigated the expression of PPAR and RXR subtypes in human endometrial cancers and normal endometrium with immunoblotting and immunohistochemistry and subsequently showed PPAR/RXR binding preferences by coimmunoprecipitation. To determine the functions of PPARs within the endometrium, we investigated proliferation, apoptosis, PTEN expression, and secretion of vascular endothelial growth factor (VEGF) in endometrial cell lines after reducing the expression of PPARα and PPARγ with antisense RNA. The functional effects of PPAR ligands were also investigated in vitro. We identified differential expression of PPAR and RXR subtypes in endometrial cancers and discovered that PPARγ expression correlated with expression of PTEN. PPARα activation influences endometrial cell growth and VEGF secretion. PPARγ activation reduces proliferation of endometrial cells via regulation of PTEN and appears to reduce VEGF secretion. We conclude that the PPAR/RXR pathway contribute to endometrial carcinogenesis by control of PTEN expression and modulation of VEGF secretion. We propose that PPAR ligands should be considered for clinical investigation in early phase studies of women with endometrial cancer. Mol Cancer Res; 10(3); 441–53. ©2011 AACR.
Greek Alchemists at Work: 'Alchemical Laboratory' in the Greco-Roman Egypt
Authors: Martelli Matteo 
Published: December 2011

AbstractThe paper focuses on the alchemical laboratory of ancient Greco-Egyptian alchemists, by taking into account especially the earliest alchemical texts (both in the Greek and in the Syriac tradition), ascribed to Pseudo-Democritus, Maria the Jewish and Zosimus. The first part analyzes the possible relationships between the workshops of Egyptian craftsmen (first of all, dyers, metals workers and glass workers) and the activity of the alchemists. The second part gives a general overview on the alchemical instruments described in the Corpus alchemicum.
Evaluation of Radar Precipitation Estimates from the National Mosaic and Multisensor Quantitative Precipitation Estimation System and the WSR-88D Precipitation Processing System over the Conterminous United States
Authors: Wu Wanru , Kitzmiller David , Wu Shaorong 
Published: December 2011

Abstract
This study evaluated 24-, 6-, and 1-h radar precipitation estimated from the National Mosaic and Multisensor Quantitative Precipitation Estimation System (NMQ) and the Weather Surveillance Radar-1988 Doppler (WSR-88D) Precipitation Processing System (PPS) over the conterminous United States (CONUS) for the warm season April–September 2009 and the cool season October 2009–March 2010. Precipitation gauge observations from the Automated Surface Observing System (ASOS) were used as the ground truth. Gridded StageIV multisensor precipitation estimates were applied for supplementary verification. The comparison of the two systems consisted of a series of analyses including the linear correlation coefficient (CC) and the root-mean-square error (RMSE) between the radar precipitation estimates and the gauge observations, large precipitation amount detection categorical scores, and the reliability of precipitation amount distribution. Data stratified for the 12 CONUS River Forecast Centers (RFCs) and for the cold rains events with bright-band effects were analyzed additionally. Major results are 1) the linear CC of NMQ versus ASOS are generally higher than that of PPS versus ASOS over CONUS, while the spatial variations stratified by the RFCs may switch with seasons; 2) compared to the precipitation distribution of ASOS, NMQ shows less deviation than PPS; 3) for the cold rains verified against ASOS, NMQ has higher CC and PPS has lower RMSE for 6-h and higher RMSE for 1-h cold rains; and 4) for the precipitation detection categorical scores, either NMQ or PPS can be superior, depending on the time interval and season. The verification against StageIV gridded precipitation estimates showed that NMQ consistently had higher correlations and lower biases than did PPS.
Clear Cell Sarcoma of the Ileum
Authors: D’Amico Francesco E. , Ruffolo Cesare , Romeo Salvatore , Massani Marco , Dei Tos Angelo P. , Bassi Nicolò 
Published: December 2011

Introduction. Clear cell sarcoma of the gastrointestinal tract (CCS-GI) is an extremely rare and aggressive tumor, which often mimics other neoplastic processes. Because of this feature, its real incidence may have been underestimated, especially in the past when genetic tests were less available than nowadays. To date, less then 30 cases have been described in the literature on the GI tract. Case presentation. We report the case of a 69-year-old woman who presented with active rectal bleeding. After a negative colonoscopy, the patient underwent a video-capsule endoscopy. The latter detected an ileal mass that was surgically resected. The microscopic appearance was consistent with a malignant mesenchymal neoplasm; immunohistochemistry was positive for S100 protein, CD56, and INI1. Fluorescence in situ hybridization showed a translocation involving the EWSR1 (Ewing sarcoma 1) gene region. All these findings were consistent with a CCS-GI. Conclusion. Herein we present a case of CCS-GI, discuss its clinical and pathological features, and review the literature on the subject.
A nationwide survey of the prevalence of multiple sclerosis in immigrant populations of Sweden
Authors: Ahlgren Cecilia , Odén Anders , Lycke Jan 
Published: December 2011

Background: In 2008, immigrants constituted 14% of the population of Sweden, a high-risk area for multiple sclerosis (MS). We investigated the largest Swedish immigrant populations for the prevalence of MS. Method: Data on foreign-born MS patients were retrieved from Swedish national health and population registers. We calculated observed versus expected numbers of MS patients and gender- and age-specific prevalence ratios (PR) between immigrant populations and the general population of Sweden and, where possible, of the countries of birth. Results: The 19 largest immigrant populations included 1327 MS patients. The global variation in MS prevalence was reflected in Sweden. The prevalence in immigrant populations who had moved to Sweden from countries with a lower MS risk was however higher than in their countries of birth. Notably, the MS prevalence in the population born in Iran was at least as high as in the general population of Sweden (men: PR = 1.10, 95% CI 0.81–1.46, p = 0.537, women: PR = 1.18, 95% CI 0.97–1.44, p = 0.855) and more than twice as high as in Isfahan, Iran (men: PR = 3.06 (95% CI 2.26–4.06), p <0.001, women: PR = 2.21 (95% CI 1.81–2.68), p <0.001). Conclusions: The MS prevalence increased in migrants who moved to Sweden from countries with a lower MS risk. In the Iranian immigrant population the prevalence exceeded that in the general population of Sweden. This indicates that Iranians carry genetic factors that contribute to a higher MS risk when environmental–lifestyle MS risk factors change.
Employee-Led, Employee Engagement in the Federal Government
Authors: Rivera Aurelio “PJ” , Flinck Jacob 
Published: December 2011

The Problem. Estimates show that in recent employee engagement studies, employees who are disengaged cost organizations approximately 35% of their payrolls. Disengagement is purported to cost organizations US$343 billion annually, including US$65 billion of taxpayer dollars of lost employee productivity for the federal government alone. The Solution. In 2008, the U.S. Department of Health and Human Services’ (HHS) Substance Abuse and Mental Health Services Administration (SAMHSA) undertook a substantive employee-led, employee engagement initiative, resulting in improved employee satisfaction and sense of ownership in creating a positive place to work. Using a case review method, the authors share personal stories of insight and challenge that detail specific steps taken to increase levels of engagement in the federal government. The Stakeholders. Researchers and HRD practitioners interested in designing, implementing and evaluating employee-led employee engagement initiatives for public service workers, will find this case study offers insights into the many facets of a successful intervention.
Both variant and IGHV4-34–expressing hairy cell leukemia lack the BRAF V600E mutation
Authors: Xi Liqiang , Arons Evgeny , Navarro Winnifred , Calvo Katherine R. , Stetler-Stevenson Maryalice , Raffeld Mark , Kreitman Robert J. 
Published: December 2011

Abstract
Recently, the BRAF V600E mutation was reported in all cases of hairy cell leukemia (HCL) but not in other peripheral B-cell neoplasms. We wished to confirm these results and assess BRAF status in well-characterized cases of HCL associated with poor prognosis, including the immunophenotypically defined HCL variant (HCLv) and HCL expressing the IGHV4-34 immunoglobulin rearrangement. Fifty-three classic HCL (HCLc) and 16 HCLv cases were analyzed for BRAF, including 5 HCLc and 8 HCLv expressing IGHV4-34. BRAF was mutated in 42 (79%) HCLc, but wild-type in 11 (21%) HCLc and 16 (100%) HCLv. All 13 IGHV4-34+ HCLs were wild-type. IGHV gene usage in the 11 HCLc BRAF wild-type cases included 5 IGHV4-34, 5 other, and 1 unknown. Our results suggest that HCLv and IGHV4-34+ HCLs have a different pathogenesis than HCLc and that a significant minority of other HCLc are also wild-type for BRAF V600.
Expression divergence measured by transcriptome sequencing of four yeast species
Authors: Busby Michele A , Gray Jesse M , Costa Allen M , Stewart Chip , Stromberg Michael P , Barnett Derek , Chuang Jeffrey H , Springer Michael , Marth Gabor T 
Published: December 2011

Abstract

Background
The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial.

Results
We quantified gene expression with whole-transcriptome sequencing in four diploid, prototrophic strains of Saccharomyces species grown under the same condition to investigate the evolution of gene expression. We found that variation in expression is gene-dependent with large variations in each gene's expression between replicates of the same species. This confounds the identification of genes differentially expressed across species. To address this, we developed a statistical approach to establish significance bounds for inter-species differential expression in RNA-Seq data based on the variance measured across biological replicates. This metric estimates the combined effects of technical and environmental variance, as well as Poisson sampling noise by isolating each component. Despite a paucity of large expression changes, we found a strong correlation between the variance of gene expression change and species divergence (R2 = 0.90).

Conclusion
We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects.
GEO Accession Number: GSE32679