bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence of hepatitis A in Iranian adolescents: is it time to introduce a vaccine?
Authors: HOSEINI S. G. , KELISHADI R. , ATAEI B. , YARAN M. , MOTLAGH M. E. , ARDALAN G. , TAJADINI M. H. , MOSTAFAVI S. N. 
Published: June 2015

SUMMARYUniversal vaccination of children for hepatitis A virus (HAV) has emerged as a cost-effective strategy to prevent this infection in regions with high incidence of symptomatic disease. Age-specific seroprevalence surveys are practical and reliable methods to estimate the rate of susceptibility in populations, and to help the implementation of vaccination policies. We surveyed the age-specific HAV seroprevalence in a nationally representative sample of Iranian adolescent students aged 10–18 years. Serum samples (n = 2494) were tested by enzyme immunoassay for total anti-HAV antibody. The overall rate of HAV seropositivity was 64% [95% confidence interval (CI), 62–66), which increased sharply from 14·8% (95% CI 7–23) at age 10 years to 72·9% (95% CI 68–78) at age 13 years, without a significant increase up to age 18 years. No significant difference in HAV seroprevalence was observed between males and females (63% vs. 65·1%), or urban and rural areas (63·4% vs. 65·2%); the seropositivity rate was similar in four different socioeconomic regions of Iran. We conclude that the seroconversion rate of HAV is high in Iranian adolescents and therefore mass vaccination of children may be necessary and should be considered by national health authorities.
Detection of GB virus C genomic sequence in the cerebrospinal fluid of a HIV-infected patient in China: a case report and literature review
Authors: LIU Z. , ZHANG Y. , WEI F. , XU M. , MOU D. , ZHANG T. , LI W. , CHEN D. , WU H. 
Published: June 2015

SUMMARYHepatitis G virus or GB virus C (GBV-C) is a human virus of the Flaviviridae family that is structurally and epidemiologically closest to hepatitis C virus, but replicates primarily in lymphocytes. Co-infection with GBV-C has been reported to confer beneficial outcomes in some HIV-positive patients. Up to now, however, studies on GBV-C infection in the central nervous system (CNS) of HIV-infected patient have rarely been reported. Herein, we report on a 32-year-old HIV-1-infected patient with cerebral toxoplasmosis and fungal encephalitis. GBV-C viral loads were detected in CSF by quantitative real-time reverse transcription polymerase chain reaction (RT–PCR), and the results showed that GBV-C viral load was 6·5 log copies/ml. We amplified and sequenced the E2 and 5′-untranslated regions from the purified viral RNA from CSF by RT–PCR. Both sequences belong to genotype 3 and there were some minor nucleotide divergence among the E2 sequences from the CSF of the patient. These data suggest that GBV-C may be able to penetrate the blood–brain barrier and colonize the CNS of HIV-infected patients. However, the exact mechanisms and potential effect of the infected GBV-C in CNS on HIV-associated neuropathy needs to be further explored.
Amburana cearensis leaf extract maintains survival and promotes in vitro development of ovine secondary follicles
Authors: Barberino R.S. , Barros V.R.P. , Menezes V.G. , Santos L.P. , Araújo V.R. , Queiroz M.A.A. , Almeida J.R.G.S. , Palheta R.C. , Matos M.H.T. 
Published: June 2015

SummaryThe antioxidant properties of Amburana cearensis extract may be a useful substitute for standard cell culture medium. Thus, the aim of this study was to evaluate the effect of this extract, with or without supplementation, on in vitro survival and development of sheep isolated secondary follicles. After collection of the ovaries, secondary follicles were isolated and cultured for 18 days in α-MEM+ supplemented with bovine serum albumin, insulin, transferrin, selenium, glutamine, hypoxanthine and ascorbic acid (control medium) or into medium composed of different concentrations of A. cearensis extract without supplements (Amb 0.1; 0.2 or 0.4 mg/ml) or A. cearensis extract supplemented with the same substances described above for α-MEM+ supplementation. The A. cearensis supplemented medium was named Amb 0.1+; 0.2+ or 0.4+ mg/ml. There were more morphologically normal follicles in Amb 0.1 or Amb 0.4 mg/ml than in the control medium (α-MEM+) after 18 days of culture. Moreover, the percentage of antrum formation was significantly higher in Amb 0.1 or Amb 0.2 mg/ml than in α-MEM+ and Amb 0.1+ mg/ml, and similar to the other treatments. All A. cearensis extract media induced a progressive and significant increase in follicular diameter throughout the culture period. In conclusion, this study showed that 0.1 mg/ml of this extract, without supplementation, maintains follicular survival and promotes the development of ovine isolated secondary follicles in vitro. This extract can be an alternative culture medium for preantral follicle development.
Unmet needs of caregivers of severely affected multiple sclerosis patients: A qualitative study
Authors: Golla Heidrun , Mammeas Stephanie , Galushko Maren , Pfaff Holger , Voltz Raymond 
Published: June 2015

ABSTRACTObjective:Multiple sclerosis (MS) patients' caregivers are sometimes considered as “hidden patients.” How much more this might be true for caregivers of severely affected MS patients has so far been scarcely studied. Palliative care also addressing relatives' needs might therefore be very relevant for these caregivers. However, we do not yet know which unmet needs they have and how these could be met. Our aim was to gain an insight into the subjectively unmet needs of caregivers of severely affected MS patients in Germany.Method:The study employed a qualitative cross-sectional approach for assessing unmet needs. Twelve caregivers of severely affected MS patients were recruited using a convenience sampling approach. Face-to-face interviews were conducted, audiotaped, and transcribed verbatim, followed by qualitative content analysis.Results:Unmet needs were sorted into the following categories: “relationship to physician,” “individual support by the healthcare system,” “relationship to the individual severely affected by MS,” “end-of-life issues,” “self-care,” and “higher awareness of MS.” Caregivers tended to group the unmet needs of their care recipients with their own and rarely focused on their own wishes and restrictions.Significance of Results:A close patient–caregiver dyad makes it difficult to differentiate unmet caregiver needs. However, the palliative care approach might help caregivers of severely affected MS patients by answering questions on disease progress and end-of-life issues, as well as by offering respite care, support for self-care, and help in preserving one's identity, and also anticipating the time to come after the death.
Analyzing Food-Related Life Satisfaction and other Predictors of Life Satisfaction in Central Chile
Authors: Schnettler Berta , Lobos Germán , Orellana Ligia , Grunert Klaus , Sepúlveda José , Mora Marcos , Denegri Marianela , Miranda Horacio 
Published: June 2015

AbstractThis study aimed to assess the effect of satisfaction with food-related life on life satisfaction among inhabitants of the main municipalities of central Chile. A survey was applied to a sample of 1,277 people, distributed proportionally by municipality. The questionnaire included the following scales: SWLS (Satisfaction with Life Scale), SWFL (Satisfaction with Food-related Life) and the Health-Related Quality of Life Index (HRQOL). Questions were asked regarding eating habits inside and outside the home, time available for meals at home, the assessment of five sources of happiness and the demographic characteristics of those surveyed. An ordered logit model was proposed, in which the dependent variable was satisfaction with life. Satisfaction with life was significantly related to the respondent’s socioeconomic status, self-perception of health, degree of satisfaction with food-related life, monthly food expenditure, time available for supper with the family (p < .01); gender, self-reported number of days affected by mental health problems, frequency of supper with the family, the degree of agreement with respect to family being an important source of happiness (p < .05); and family size and frequency of food consumption in fast food outlets (p < .10). Satisfaction with life in the study sample is related to aspects associated with health, family and eating, and the family interaction associated with eating may play an important role in overall satisfaction with life.
Enhanced Mechanical Stability of Gold Nanotips through Carbon Nanocone Encapsulation
Authors: Cano-Marquez Abraham G. , Schmidt Wesller G. , Ribeiro-Soares Jenaina , Gustavo Cançado Luiz , Rodrigues Wagner N. , Santos Adelina P. , Furtado Clascidia A. , Autreto Pedro A.S. , Paupitz Ricardo , Galvão Douglas S. , Jorio Ado 
Published: June 2015

AbstractGold is a noble metal that, in comparison with silver and copper, has the advantage of corrosion resistance. Despite its high conductivity, chemical stability and biocompatibility, gold exhibits high plasticity, which limits its applications in some nanodevices. Here, we report an experimental and theoretical study on how to attain enhanced mechanical stability of gold nanotips. The gold tips were fabricated by chemical etching and further encapsulated with carbon nanocones via nanomanipulation. Atomic force microscopy experiments were carried out to test their mechanical stability. Molecular dynamics simulations show that the encapsulated nanocone changes the strain release mechanisms at the nanoscale by blocking gold atomic sliding, redistributing the strain along the whole nanostructure. The carbon nanocones are conducting and can induce magnetism, thus opening new avenues on the exploitation of transport, mechanical and magnetic properties of gold covered by sp2 carbon at the nanoscale.
Enhanced light collection in fluorescence microscopy using self-assembled micro-reflectors
Authors: Göröcs Zoltán , McLeod Euan , Ozcan Aydogan 
Published: June 2015

AbstractIn fluorescence microscopy, the signal-to-noise ratio (SNR) of the optical system is directly linked to the numerical aperture (NA) of the microscope objective, which creates detection challenges for low-NA, wide-field and high-throughput imaging systems. Here we demonstrate a method to increase the light collection efficiency from micron-scale fluorescent objects using self-assembled vapor-condensed polyethylene glycol droplets, which act as micro-reflectors for fluorescent light. Around each fluorescent particle, a liquid meniscus is formed that increases the excitation efficiency and redirects part of the laterally-emitted fluorescent light towards the detector due to internal reflections at the liquid-air interface of the meniscus. The three-dimensional shape of this micro-reflector can be tuned as a function of time, vapor temperature and substrate contact angle, providing us optimized SNR performance for fluorescent detection. Based on these self-assembled micro-reflectors, we experimentally demonstrate ~2.5-3 fold enhancement of the fluorescent signal from 2-10 μm sized particles. A theoretical explanation of the formation rate and shapes of these micro-reflectors is presented, along with a ray tracing model of their optical performance. This method can be used as a sample preparation technique for consumer electronics-based microscopy and sensing tools, thus increasing the sensitivity of low-NA systems that image fluorescent micro-objects.
Improving access to endogenous DNA in ancient bones and teeth
Authors: Damgaard Peter B. , Margaryan Ashot , Schroeder Hannes , Orlando Ludovic , Willerslev Eske , Allentoft Morten E. 
Published: June 2015

AbstractPoor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bone samples from temperate and tropical environments, we show that an EDTA-based enzymatic ‘pre-digestion’ of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we observe an asymptotic increase in endogenous DNA content, with a 2.7-fold average increase reached at 1 hour. We repeat the experiment using a brief pre-digestion (15 or 30 mins) on 21 ancient bones and teeth from a variety of archaeological contexts and observe an improvement in 16 of these. We here advocate the implementation of a brief pre-digestion step as a standard procedure in ancient DNA extractions. Finally, we demonstrate on 14 ancient teeth that by targeting the outer layer of the roots we obtain up to 14 times more endogenous DNA than when using the inner dentine. Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization.
Multiscale Prediction of Whirling Disease Risk in the Blackfoot River Basin, Montana: a Useful Consideration for Restoration Prioritization?
Authors: Eby L. A. , Pierce R. , Sparks M. , Carim K. , Podner C. 
Published: June 2015

AbstractHabitat restoration for inland trout (family Salmonidae) is common across western North America, but planners rarely consider disease risk when prioritizing restoration sites. Whirling disease is a parasitic infection caused by the invasive myxosporean parasite Myxobolus cerebralis and has been implicated in declines of wild trout populations across western North America. For planners to consider disease, disease risk needs to be predictable across the landscape and influence restoration outcomes. We collated the history of whirling disease infection severity scores on the MacConnell–Baldwin scale from sentinel cage studies for hatchery Rainbow Trout Oncorhynchus mykiss in the Blackfoot River basin from 1998 to 2009. At these same sites, we performed reach‐scale geomorphic assessments, derived landscape variables from GIS data layers, and assembled fish composition data. We examined relationships between the severity of infection and several landscape‐scale and reach‐scale variables for 13 basin‐fed streams in the Blackfoot River basin of west‐central Montana using classification and regression tree analyses. In our data set, valley slope and forest cover were the best predictors of fine sediment. Both spring creeks and gently sloping alluvial basin‐fed tributaries to the Blackfoot River basin with higher proportions of fine sediment (particle size < 0.85 mm) were associated with a high severity (≥ grade 3) of infection. Additionally, we explored differences in trout species composition (i.e., susceptible versus resistant species) before and after the whirling disease enzootic using seven basin‐fed streams and two spring creeks. We did not detect trout community shifts from susceptible to disease‐resistant salmonids in basin‐fed disease‐positive streams. However, spring creeks showed a negative trend in disease‐susceptible salmonids after the whirling disease enzootic. Disease risk appears to be predictable across the landscape and may limit possible restoration outcomes by influencing species composition in spring creeks.
Using Next‐Generation Sequencing to Assist a Conservation Hatchery: a Single‐Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt
Authors: Lew Ryan M. , Finger Amanda J. , Baerwald Melinda R. , Goodbla Alisha , May Bernie , Meek Mariah H. 
Published: June 2015

AbstractThe Delta Smelt Hypomesus transpacificus, listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single‐nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site‐associated DNA sequencing (RAD‐seq). We then created a linkage map by genotyping three single‐pair crosses at 2,317 newly discovered loci with RAD‐seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species.
Characterization of vacuolar amino acid transporter from Fusarium oxysporum in Saccharomyces cerevisiae
Authors: Lunprom Siriporn , Pongcharoen Pongsanat , Sekito Takayuki , Kawano-Kawada Miyuki , Kakinuma Yoshimi , Akiyama Koichi 
Published: June 2015

Abstract
Fusarium oxysporum causes wilt disease in many plant families, and many genes are involved in its development or growth in host plants. A recent study revealed that vacuolar amino acid transporters play an important role in spore formation in Schizosaccharomyces pombe and Saccharomyces cerevisiae. To investigate the role of vacuolar amino acid transporters of this phytopathogenic fungus, the FOXG_11334 (FoAVT3) gene from F. oxysporum was isolated and its function was characterized. Transcription of FoAVT3 was upregulated after rapamycin treatment. A green fluorescent protein fusion of FoAvt3p was localized to vacuolar membranes in both S. cerevisiae and F. oxysporum. Analysis of the amino acid content of the vacuolar fraction and amino acid transport activities using vacuolar membrane vesicles from S. cerevisiae cells heterologously expressing FoAVT3 revealed that FoAvt3p functions as a vacuolar amino acid transporter, exporting neutral amino acids. We conclude that the FoAVT3 gene encodes a vacuolar neutral amino acid transporter.
Value functions and Dubrovin valuation rings on simple algebras
Authors: Ferreira Mauricio , Wadsworth Adrian 
Published: June 2015

In this paper we prove relationships between two generalizations of commutative valuation theory for noncommutative central simple algebras: (1) Dubrovin valuation rings; and (2) the value functions called gauges introduced by Tignol and Wadsworth. We show that if

v
v

is a valuation on a field

F
F

with associated valuation ring

V
V

and

v
v

is defectless in a central simple

F
F

-algebra

A
A

, and

C
C

is a subring of

A
A

, then the following are equivalent: (a)

C
C

is the gauge ring of some minimal

v
v

-gauge on

A
A

, i.e., a gauge with the minimal number of simple components of

C

/

J
(
C
)

C/J(C)

; (b)

C
C

is integral over

V
V

with

C
=

B
1

∩
…
∩

B
ξ

C = B_1 \cap \ldots \cap B_\xi

where each

B
i

B_i

is a Dubrovin valuation ring of

A
A

with center

V
V

, and the

B
i

B_i

satisfy Gräter’s Intersection Property. Along the way we prove the existence of minimal gauges whenever possible and we show how gauges on simple algebras are built from gauges on central simple algebras.
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins
Authors: Savojardo Castrense , Martelli Pier Luigi , Fariselli Piero , Casadio Rita 
Published: June 2015

Abstract
Motivation: Molecular recognition of N-terminal targeting peptides is the most common mechanism controlling the import of nuclear-encoded proteins into mitochondria and chloroplasts. When experimental information is lacking, computational methods can annotate targeting peptides, and determine their cleavage sites for characterizing protein localization, function, and mature protein sequences. The problem of discriminating mitochondrial from chloroplastic propeptides is particularly relevant when annotating proteomes of photosynthetic Eukaryotes, endowed with both types of sequences.
Results: Here, we introduce TPpred3, a computational method that given any Eukaryotic protein sequence performs three different tasks: (i) the detection of targeting peptides; (ii) their classification as mitochondrial or chloroplastic and (iii) the precise localization of the cleavage sites in an organelle-specific framework. Our implementation is based on our TPpred previously introduced. Here, we integrate a new N-to-1 Extreme Learning Machine specifically designed for the classification task (ii). For the last task, we introduce an organelle-specific Support Vector Machine that exploits sequence motifs retrieved with an extensive motif-discovery analysis of a large set of mitochondrial and chloroplastic proteins. We show that TPpred3 outperforms the state-of-the-art methods in all the three tasks.
Availability and implementation: The method server and datasets are available at http://tppred3.biocomp.unibo.it.
Contact: gigi@biocomp.unibo.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Definitive Radiation Therapy for Stage I-II Endometrial Cancer
Authors: Yoo Stella , Hegarty Sarah E. , Mishra Mark V. , Patel Nirav , Cantrell Leigh A. , Showalter Timothy N. 
Published: June 2015

Objective:
There is limited evidence to inform the management of patients with endometrial cancer who are not candidates for hysterectomy, and treatment alternatives have not been compared directly in randomized trials. We analyzed the prognostic factors and outcomes for patients with stage I or II endometrial adenocarcinoma in the National Cancer Institute’s Surveillance, Epidemiology, and End Results public database.

Methods:
We identified a cohort of patients with stage I-II endometrial adenocarcinoma who were managed without hysterectomy and who were diagnosed during 1989 to 2010. Patients with prior primary tumors were excluded. Statistical analyses were performed to test associations between patient characteristics, radiotherapy modality, and overall and endometrial cancer-specific survival. Multivariable analyses were performed to evaluate the impact of radiation therapy (RT) type on survival outcomes after adjusting for other factors.

Results:
Among the 997 women included in the analyses, 605 received no RT (60.7%), 207 (20.8%) received external-beam radiation therapy (EBRT) alone, and 185 (18.6%) received brachytherapy, either alone or in combination with EBRT. After adjusting for other tumor and demographic factors, RT type was not associated with overall or endometrial cancer-specific survival. Significant predictors of survival included: tumor stage and grade, age at diagnosis, and marital status.

Conclusions:
For patients in this population-based cohort with early-stage endometrial cancer managed without hysterectomy, the delivery of brachytherapy was not associated with improved survival, compared with EBRT alone. It seems worthwhile to pursue future clinical trials to evaluate definitive EBRT-alone strategies, omitting brachytherapy, for selected patients with medically inoperable endometrial cancer.