bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Epstein‐Barr virus infection with oral squamous cell carcinoma in a case–control study
Authors: Acharya Sulav , Ekalaksananan Tipaya , Vatanasapt Patravoot , Loyha Kulchaya , Phusingha Pensiri , Promthet Supannee , Kongyingyoes Bunkerd , Pientong Chamsai 
Published: August 2014

BackgroundBesides the well‐known risk factors, Epstein‐Barr virus (EBV) might play a significant role in oral squamous cell carcinoma (OSCC). To explore the role of EBV in OSCC, the prevalence of EBV infection in oral exfoliated cells of OSCC cases and controls in northeastern Thailand was investigated, and the association of EBV in tumor lesion cells was further confirmed.MethodsOral exfoliated cells were collected from OSCC cases and non‐cancer controls. Cells from tumor lesions were taken from OSCC patients for further strong confirmation of the association of EBV with OSCC. EBV DNA was detected by polymerase chain reaction (PCR) using primers specific for EBV DNA polymerase. The EBV DNA positive samples were confirmed further by nested PCR.ResultsEpstein‐Barr virus was detected in the oral exfoliated cells of 45.05% of OSCC patients and 18.08% of the non‐cancer control (P < 0.001). Similarly, EBV was detected in 32.5% of the tumor lesions. Betel quid chewing was statistically significantly associated with EBV prevalence (OR = 2.08), whereas no association with tobacco smoking and alcohol consumption. Alcohol consumption and betel quid chewing were significantly associated with OSCC (OR = 3.05 and OR = 5.05, respectively), but tobacco smoking was not associated. Interestingly, EBV was significantly associated with OSCC (OR = 3.76).ConclusionsEpstein‐Barr virus prevalence is associated with OSCC and seems to be enhanced by betel quid chewing, suggesting that EBV may, together with betel quid chewing, act as an important etiological risk factor of OSCC.
Molecular characterization of immortalized normal and dysplastic oral cell lines
Authors: Dickman Christopher T. D. , Towle Rebecca , Saini Rajan , Garnis Cathie 
Published: August 2014

BackgroundCell lines have been developed for modeling cancer and cancer progression. The molecular background of these cell lines is often unknown to those using them to model disease behaviors. As molecular alterations are the ultimate drivers of cell phenotypes, having an understanding of the molecular make‐up of these systems is critical for understanding the disease biology modeled.MethodsSix immortalized normal, one immortalized dysplasia, one self‐immortalized dysplasia, and two primary normal cell lines derived from oral tissues were analyzed for DNA copy number changes and changes in both mRNA and miRNA expression using SMRT‐v.2 genome‐wide tiling comparative genomic hybridization arrays, Agilent Whole Genome 4x44k expression arrays, and Exiqon V2.M‐RT‐PCR microRNA Human panels.ResultsDNA copy number alterations were detected in both normal and dysplastic immortalized cell lines—as well as in the single non‐immortalized dysplastic cell line. These lines were found to have changes in expression of genes related to cell cycle control as well as alterations in miRNAs that are deregulated in clinical oral squamous cell carcinoma tissues. Immortal lines—whether normal or dysplastic—had increased disruption in expression relative to primary lines. All data are available as a public resource.ConclusionsMolecular profiling experiments have identified DNA, mRNA, and miRNA alterations for a panel of normal and dysplastic oral tissue cell lines. These data are a valuable resource to those modeling diseases of the oral mucosa, and give insight into the selection of model cell lines and the interpretation of data from those lines.
Elevated CO2 concentration impacts cell wall polysaccharide composition of green microalgae of the genus Chlorella
Authors: Cheng Y.-S. , Labavitch J.M. , VanderGheynst J.S. 
Published: August 2014

Abstract
The effect of CO2 concentration on the relative content of starch, lipid and cell wall carbohydrates in microalgal biomass was investigated for the four following Chlorella strains: C. vulgaris (UTEX 259), C. sorokiniana (UTEX 2805), C. minutissima (UTEX 2341) and C. variabilis (NC64A). Each strain had a different response to CO2 concentration. The starch content was higher in UTEX259 and NC64A cultured with 2% CO2 in the air supply than in cells cultured with ca. 0·04% CO2 (ambient air), while starch content was not affected for UTEX 2805 and UTEX 2341. The lipid content was higher in Chlorella minutissima UTEX 2341 cultured in 2% CO2 than in cells cultured in ambient air, but was unchanged for the other three strains. All four Chlorella strains tended to have a higher percentage of uronic acids and lower percentage of neutral sugars in their cell wall polysaccharide complement when grown with 2% CO2 supply. Although the percentage of neutral sugars in the cell walls varied with CO2 concentration, the relative proportions of different neutral sugar constituents remained constant for both CO2 conditions. The results demonstrate the importance of considering the effects of CO2 on the cell wall carbohydrate composition of microalgae.

Significance and Impact of the Study
Microalgae have the potential to produce products that will reduce society's reliance on fossil fuels and address challenges related to food and feed production. An overlooked yet industrially relevant component of microalgae are their cell walls. Cell wall composition affects cell flocculation and the recovery of intracellular products. In this study, we show that increasing CO2 level results in greater cell wall polysaccharide and uronic acid content in the cell walls of three strains of microalgae. The results have implications on the management of systems for the capture of CO2 and production of fuels, chemicals and food from microalgae.
The genetics of a putative social trait in natural populations of yeast
Authors: Bozdag G. O. , Greig D. 
Published: August 2014

AbstractThe sharing of secreted invertase by yeast cells is a well‐established laboratory model for cooperation, but the only evidence that such cooperation occurs in nature is that the SUC loci, which encode invertase, vary in number and functionality. Genotypes that do not produce invertase can act as ‘cheats’ in laboratory experiments, growing on the glucose that is released when invertase producers, or ‘cooperators’, digest sucrose. However, genetic variation for invertase production might instead be explained by adaptation of different populations to different local availabilities of sucrose, the substrate for invertase. Here we find that 110 wild yeast strains isolated from natural habitats, and all contained a single SUC locus and produced invertase; none were ‘cheats’. The only genetic variants we found were three strains isolated instead from sucrose‐rich nectar, which produced higher levels of invertase from three additional SUC loci at their subtelomeres. We argue that the pattern of SUC gene variation is better explained by local adaptation than by social conflict.
Brain metastasis is predetermined in early stages of cutaneous melanoma by CD44v6 expression through epigenetic regulation of the spliceosome
Authors: Marzese Diego M. , Liu Michelle , Huynh Jamie L. , Hirose Hajime , Donovan Nicholas C. , Huynh Kelly T. , Kiyohara Eiji , Chong Kelly , Cheng David , Tanaka Ryo , Wang Jinhua , Morton Donald L. , Barkhoudarian Garni , Kelly Daniel F. , Hoon Dave S. B. 
Published: August 2014

SummaryMelanoma brain metastasis (MBM) is frequent and has a very poor prognosis with no current predictive factors or therapeutic molecular targets. Our study unravels the molecular alterations of cell‐surface glycoprotein CD44 variants during melanoma progression to MBM. High expression of CD44 splicing variant 6 (CD44v6) in primary melanoma (PRM) and regional lymph node metastases from AJCC Stage IIIC patients significantly predicts MBM development. The expression of CD44v6 also enhances the migration of MBM cells by hyaluronic acid and hepatocyte growth factor exposure. Additionally, CD44v6‐positive MBM migration is reduced by blocking with a CD44v6‐specific monoclonal antibody or knocking down CD44v6 by siRNA. ESRP1 and ESRP2 splicing factors correlate with CD44v6 expression in PRM, and ESRP1 knockdown significantly decreases CD44v6 expression. However, an epigenetic silencing of ESRP1 is observed in metastatic melanoma, specifically in MBM. In advanced melanomas, CD44v6 expression correlates with PTBP1 and U2AF2 splicing factors, and PTBP1 knockdown significantly decreases CD44v6 expression. Overall, these findings open a new avenue for understanding the high affinity of melanoma to progress to MBM, suggesting CD44v6 as a potential MBM‐specific factor with theranostic utility for stratifying patients.
Differential effect of body mass index on pediatric heart transplant outcomes based on diagnosis
Authors: Godown Justin , Donohue Janet E. , Yu Sunkyung , Friedland‐Little Joshua M. , Gajarski Robert J. , Schumacher Kurt R. 
Published: August 2014

AbstractThe impact of nutritional status on HTx waitlist mortality in children is unknown, and there are conflicting data regarding the role of nutrition in post‐HTx survival. This study examined the influence of nutrition on waitlist and post‐HTx outcomes in children. Children 2–18 yr listed for HTx from 1997 to 2011 were identified from the OPTN database and stratified by BMI percentile. Multivariable logistic regression evaluated the influence of BMI on waitlist mortality. Cox proportional hazard regression assessed the impact of BMI on post‐HTx mortality. When all 2712 patients were analyzed, BMI did not impact waitlist, one‐, or five‐yr mortality. However, when stratified by diagnosis, BMI > 95% (AOR 1.96; 95% CI 1.24, 3.09) and BMI < 1% (AOR 2.17; 95% CI 1.28, 3.68) were independent risk factors for waitlist mortality in patients with CM. BMI did not impact waitlist mortality in CHD and did not impact post‐HTx outcomes, regardless of diagnosis. BMI > 95% and BMI < 1% are independent risk factors for waitlist mortality in patients with CM, but not CHD. This suggests differing risk factors based on disease etiology, and an individualized approach to risk assessment based on diagnosis may be warranted.
Increasing first‐time blood donation of newly registered donors using implementation intentions and explicit commitment techniques
Authors: Wevers A. , Wigboldus D. H. J. , van den Hurk K. , van Baaren R. , Veldhuizen I. J. T. 
Published: August 2014

Background and ObjectivesMost blood donors stop donating blood at the beginning of their donor career. This intervention study aims to increase first‐time return behaviour of newly registered donors using implementation intentions and explicit commitment techniques.Materials and MethodsNewly registered donors (N = 937) received an extra information sheet during their medical check‐up wherein implementation intentions and explicit commitment techniques were tested. Donors were randomly assigned to either the control condition, information sheet only condition, information sheet with implementation intentions condition, information sheet with explicit commitment condition, or information sheet with both implementation intentions and explicit commitment condition. Logistic regression analyses examined actual first‐time return behaviour after an appeal to donate blood.ResultsDonors in the information sheet with both implementation intentions and explicit commitment condition had an 11·5% higher return rate than donors in the control condition. Logistic regression analyses revealed that the information sheet with both implementation intentions and explicit commitment condition significantly increased the odds on return behaviour compared with the control condition (OR = 1·65, 95%CI = 1·08–2·50).ConclusionThis study successfully increased actual first‐time return behaviour of newly registered donors by using both implementation intentions and explicit commitment techniques.
Automated identification of retinal vessels using a multiscale directional contrast quantification (MDCQ) strategy
Authors: Zhen Yi , Gu Suicheng , Meng Xin , Zhang Xinyuan , Zheng Bin , Wang Ningli , Pu Jiantao 
Published: August 2014

Purpose:A novel algorithm is presented to automatically identify the retinal vessels depicted in color fundus photographs.Methods:The proposed algorithm quantifies the contrast of each pixel in retinal images at multiple scales and fuses the resulting consequent contrast images in a progressive manner by leveraging their spatial difference and continuity. The multiscale strategy is to deal with the variety of retinal vessels in width, intensity, resolution, and orientation; and the progressive fusion is to combine consequent images and meanwhile avoid a sudden fusion of image noise and/or artifacts in space. To quantitatively assess the performance of the algorithm, we tested it on three publicly available databases, namely, DRIVE, STARE, and HRF. The agreement between the computer results and the manual delineation in these databases were quantified by computing their overlapping in both area and length (centerline). The measures include sensitivity, specificity, and accuracy.Results:For the DRIVE database, the sensitivities in identifying vessels in area and length were around 90% and 70%, respectively, the accuracy in pixel classification was around 99%, and the precisions in terms of both area and length were around 94%. For the STARE database, the sensitivities in identifying vessels were around 90% in area and 70% in length, and the accuracy in pixel classification was around 97%. For the HRF database, the sensitivities in identifying vessels were around 92% in area and 83% in length for the healthy subgroup, around 92% in area and 75% in length for the glaucomatous subgroup, around 91% in area and 73% in length for the diabetic retinopathy subgroup. For all three subgroups, the accuracy was around 98%.Conclusions:The experimental results demonstrate that the developed algorithm is capable of identifying retinal vessels depicted in color fundus photographs in a relatively reliable manner.
Role of Cytomegalovirus (CMV) IgG Avidity Testing in Diagnosing Primary CMV Infection during Pregnancy
Authors: Prince Harry E. , Lapé-Nixon Mary 
Published: August 2014

ABSTRACT
The risk of intrauterine transmission of cytomegalovirus (CMV) during pregnancy is much greater for women who contract primary CMV infection after conception than for women with evidence of infection (circulating CMV antibodies) before conception. Thus, laboratory tests that aid in the identification of recent primary CMV infection are important tools for managing the care of pregnant women suspected of having been exposed to CMV. CMV IgM detection is a sensitive marker of primary CMV infection, but its specificity is poor because CMV IgM is also produced during viral reactivation and persists following primary infection in some individuals. Studies conducted over the last 20 years convincingly demonstrate that measurement of CMV IgG avidity is both a sensitive and a specific method for identifying pregnant women with recent primary CMV infection and thus at increased risk for vertical CMV transmission. IgG avidity is defined as the strength with which IgG binds to antigenic epitopes expressed by a given protein; it matures gradually during the 6 months following primary infection. Low CMV IgG avidity is an accurate indicator of primary infection within the preceding 3 to 4 months, whereas high avidity excludes primary infection within the preceding 3 months. In this minireview, we summarize published data demonstrating the clinical utility of CMV IgG avidity results for estimating time since primary infection in pregnant women, describe commercially available CMV IgG avidity assays, and discuss some of the issues and controversies surrounding CMV IgG avidity testing during pregnancy.
An International, Prospective, Multicenter Evaluation of the Combination of AdvanDx Staphylococcus
Quick
FISH BC with
mecA Xpress
FISH for Detection of Methicillin-Resistant Staphylococcus aureus Isolates from Positive Blood Cultures
Authors: Salimnia H. , Fairfax M. R. , Lephart P. , Morgan M. , Gilbreath J. J. , Butler-Wu S. M. , Templeton K. E. , Hamilton F. J. , Wu F. , Buckner R. , Fuller D. , Davis T. E. , Abdelhamed A. M. , Jacobs M. R. , Miller A. , Pfrommer B. , Carroll K. C. 
Published: August 2014

ABSTRACT

Sepsis caused by
Staphylococcus aureus
is a major health problem worldwide. Better outcomes are achieved when rapid diagnosis and determination of methicillin susceptibility enable early optimization of antimicrobial therapy. Eight large clinical laboratories, seven from the United States and one from Scotland, evaluated the combination of the
Staphylococcus
Quick
FISH BC and the new
mecA Xpress
FISH assay (both AdvanDx, Woburn, MA, USA) for the detection of methicillin-resistant
S. aureus
in positive blood cultures. Blood cultures flagged as positive by automated blood culture instruments and demonstrating only Gram-positive cocci in clusters on Gram stain were tested by
Quick
FISH, a 20-min assay. If only
S. aureus
was detected,
mecA Xpress
FISH testing followed. The recovered
S. aureus
isolates were tested by cefoxitin disk diffusion as the reference method. The
Quick
FISH assay results were concordant with the routine phenotypic testing methods of the testing laboratories in 1,211/1,221 (99.1%) samples and detected 488/491
S. aureus
organisms (sensitivity, 99.4%; specificity, 99.6%). Approximately 60% of the samples (730) contained coagulase-negative staphylococci or nonstaphylococci as assessed by the
Quick
FISH assay and were not tested further. The 458 compliant samples positive exclusively for
S. aureus
by the
Quick
FISH assay were tested by the
mecA Xpress
FISH assay, which detected 209 of 211 methicillin-resistant
S. aureus
organisms (sensitivity, 99.1%; specificity, 99.6%). The
mecA Xpress
FISH assay also showed high reproducibility, with 534/540 tests performed by 6 operators over 5 days achieving reproducible results (98.9% agreement). The combination of the
Staphylococcus
Quick
FISH BC and
mecA Xpress
FISH assays is sensitive, specific, and reproducible for the detection of methicillin-resistant
S. aureus
and yields complete results in 2 h after the blood culture turns positive.
Evaluation of Anatomically Designed Flocked Rectal Swabs for Molecular Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis in Botswana
Authors: Goldfarb David M. , Steenhoff Andrew P. , Pernica Jeffrey M. , Chong Sylvia , Luinstra Kathy , Mokomane Margaret , Mazhani Loeto , Quaye Isaac , Goercke Irene , Mahony James , Smieja Marek 
Published: August 2014

ABSTRACT

Two-hundred eighty matched bulk stool and anatomically designed flocked rectal swab samples were collected from children admitted to the hospital with acute diarrhea in Botswana. Their parents were asked about the acceptability of the swab collection method compared with bulk stool sampling. All samples underwent identical testing with a validated 15-target (9 bacterial, 3 viral, and 3 parasite) commercial multiplex PCR assay. The flocked swabs had a 12% higher yield for bacterial pathogen targets (241 versus 212;
P
= 0.003) compared with that of stool samples, as well as similar yields for viral targets (110 versus 113;
P
= 0.701) and parasite targets (59 versus 65;
P
= 0.345). One hundred sixty-four of the flocked swab-stool pairs were also tested with separate laboratory-developed bacterial and viral multiplex assays, and the flocked rectal swabs had a performance that was similar to that seen with commercial assay testing. Almost all parents/guardians found the swabs acceptable. Flocked rectal swabs significantly facilitate the molecular diagnosis of diarrheal disease in children.
Acceleration of Antimicrobial Susceptibility Testing of Positive Blood Cultures by Inoculation of Vitek 2 Cards with Briefly Incubated Solid Medium Cultures
Authors: Idelevich Evgeny A. , Schüle Isabel , Grünastel Barbara , Wüllenweber Jörg , Peters Georg , Becker Karsten 
Published: August 2014

ABSTRACTBriefly incubated agar cultures from positive blood cultures were used for antimicrobial susceptibility testing (AST) by Vitek 2. The cultivation time until inoculation was 3.8 h for Gram-positive cocci and 2.4 h for Gram-negative rods. The error rates were low, providing early and reliable AST without additional time or cost expenditure.
HIV Control Is Mediated in Part by CD8
+
T-Cell Targeting of Specific Epitopes
Authors: Pereyra Florencia , Heckerman David , Carlson Jonathan M. , Kadie Carl , Soghoian Damien Z. , Karel Daniel , Goldenthal Ariel , Davis Oliver B. , DeZiel Charles E. , Lin Tienho , Peng Jian , Piechocka Alicja , Carrington Mary , Walker Bruce D. 
Published: August 2014

ABSTRACT

We investigated the hypothesis that the correlation between the class I HLA types of an individual and whether that individual spontaneously controls HIV-1 is mediated by the targeting of specific epitopes by CD8
+
T cells. By measuring gamma interferon enzyme-linked immunosorbent spot (ELISPOT) assay responses to a panel of 257 optimally defined epitopes in 341 untreated HIV-infected persons, including persons who spontaneously control viremia, we found that the correlation between HLA types and control is mediated by the targeting of specific epitopes. Moreover, we performed a graphical model-based analysis that suggested that the targeting of specific epitopes is a cause of such control—that is, some epitopes are protective rather than merely associated with control—and identified eight epitopes that are significantly protective. In addition, we use an
in silico
analysis to identify protein regions where mutations are likely to affect the stability of a protein, and we found that the protective epitopes identified by the ELISPOT analysis correspond almost perfectly to such regions. This
in silico
analysis thus suggests a possible mechanism for control and could be used to identify protective epitopes that are not often targeted in natural infection but that may be potentially useful in a vaccine. Our analyses thus argue for the inclusion (and exclusion) of specific epitopes in an HIV vaccine.

IMPORTANCE
Some individuals naturally control HIV replication in the absence of antiretroviral therapy, and this ability to control is strongly correlated with the HLA class I alleles that they express. Here, in a large-scale experimental study, we provide evidence that this correlation is mediated largely by the targeting of specific CD8
+
T-cell epitopes, and we identify eight epitopes that are likely to cause control. In addition, we provide an
in silico
analysis indicating that control occurs because mutations within these epitopes change the stability of the protein structures. This
in silico
analysis also identified additional epitopes that are not typically targeted in natural infection but may lead to control when included in a vaccine, provided that other epitopes that would otherwise distract the immune system from targeting them are excluded from the vaccine.