bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of a new strain of Euphorbia mosaic virus with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region
Authors: Gregorio-Jorge Josefat , Bernal-Alcocer Artemiza , Bañuelos-Hernández Bernardo , Alpuche-Solís Ángel G , Hernández-Zepeda Cecilia , Moreno-Valenzuela Oscar , Frías-Treviño Gustavo , Argüello-Astorga Gerardo R 
Published: October 2010

Abstract

Background

Euphorbia mosaic virus (EuMV) is a member of the SLCV clade, a lineage of New World begomoviruses that display distinctive features in their replication-associated protein (Rep) and virion-strand replication origin. The first entirely characterized EuMV isolate is native from Yucatan Peninsula, Mexico; subsequently, EuMV was detected in weeds and pepper plants from another region of Mexico, and partial DNA-A sequences revealed significant differences in their putative replication specificity determinants with respect to EuMV-YP. This study was aimed to investigate the replication compatibility between two EuMV isolates from the same country.

Results
A new isolate of EuMV was obtained from pepper plants collected at Jalisco, Mexico. Full-length clones of both genomic components of EuMV-Jal were biolistically inoculated into plants of three different species, which developed symptoms indistinguishable from those induced by EuMV-YP. Pseudorecombination experiments with EuMV-Jal and EuMV-YP genomic components demonstrated that these viruses do not form infectious reassortants in Nicotiana benthamiana, presumably because of Rep-iteron incompatibility. Sequence analysis of the EuMV-Jal DNA-B intergenic region (IR) led to the unexpected discovery of a 35-nt-long sequence that is identical to a segment of the rep gene in the cognate viral DNA-A. Similar short rep sequences ranging from 35- to 51-nt in length were identified in all EuMV isolates and in three distinct viruses from South America related to EuMV. These short rep sequences in the DNA-B IR are positioned downstream to a ~160-nt non-coding domain highly similar to the CP promoter of begomoviruses belonging to the SLCV clade.

Conclusions
EuMV strains are not compatible in replication, indicating that this begomovirus species probably is not a replicating lineage in nature. The genomic analysis of EuMV-Jal led to the discovery of a subgroup of SLCV clade viruses that contain in the non-coding region of their DNA-B component, short rep gene sequences located downstream to a CP-promoter-like domain. This assemblage of DNA-A-related sequences within the DNA-B IR is reminiscent of polyomavirus microRNAs and could be involved in the posttranscriptional regulation of the cognate viral rep gene, an intriguing possibility that should be experimentally explored
Characterization of human adenovirus 35 and derivation of complex vectors
Authors: McVey Duncan , Zuber Mohammed , EttyReddy Damodar , Reiter Christopher D , Brough Douglas E , Nabel Gary J , King C Richter , Gall Jason G D 
Published: October 2010

Abstract

Background
Replication-deficient recombinant adenoviral vectors based on human serotype 35 (Ad35) are desirable due to the relatively low prevalence of neutralizing antibodies in the human population. The structure of the viral genome and life cycle of Ad35 differs from the better characterized Ad5 and these differences require differences in the strategies for the generation of vectors for gene delivery.

Results
Sequences essential for E1 and E4 function were identified and removed and the effects of the deletions on viral gene transcription were determined. In addition, the non-essential E3 region was deleted from rAd35 vectors and a sequence was found that did not have an effect on viability but reduced viral fitness. The packaging capacity of rAd35 was dependent on pIX and vectors were generated with stable genome sizes of up to 104% of the wild type genome size. These data were used to make an E1-, E3-, E4-deleted rAd35 vector. This rAd35 vector with multiple gene deletions has the advantages of multiple blocks to viral replication (i.e., E1 and E4 deletions) and a transgene packaging capacity of 7.6 Kb, comparable to rAd5 vectors.

Conclusions
The results reported here allow the generation of larger capacity rAd35 vectors and will guide the derivation of adenovirus vectors from other serotypes.
Acute exposure of mice to high-dose ultrafine carbon black decreases susceptibility to pneumococcal pneumonia
Authors: Tellabati Ananth , Fernandes Vitor E , Teichert Friederike , Singh Rajinder , Rylance Jamie , Gordon Stephen , Andrew Peter W , Grigg Jonathan 
Published: October 2010

Abstract

Background
Epidemiological studies suggest that inhalation of carbonaceous particulate matter from biomass combustion increases susceptibility to bacterial pneumonia. In vitro studies report that phagocytosis of carbon black by alveolar macrophages (AM) impairs killing of Streptococcus pneumoniae. We have previously reported high levels of black carbon in AM from biomass smoke-exposed children and adults. We therefore aimed to use a mouse model to test the hypothesis that high levels of carbon loading of AM in vivo increases susceptibility to pneumococcal pneumonia.

Methods
Female outbred mice were treated with either intranasal phosphate buffered saline (PBS) or ultrafine carbon black (UF-CB in PBS; 500 μg on day 1 and day 4), and then infected with S. pneumoniae strain D39 on day 5. Survival was assessed over 72 h. The effect of UF-CB on AM carbon loading, airway inflammation, and a urinary marker of pulmonary oxidative stress was assessed in uninfected animals.

Results
Instillation of UF-CB in mice resulted a pattern of AM carbon loading similar to that of biomass-smoke exposed humans. In uninfected animals, UF-CB treated animals had increased urinary 8-oxodG (P = 0.055), and an increased airway neutrophil differential count (P < 0.01). All PBS-treated mice died within 72 h after infection with S. pneumoniae, whereas morbidity and mortality after infection was reduced in UF-CB treated animals (median survival 48 h vs. 30 h, P < 0.001). At 24 hr post-infection, UF-CB treated mice had lower lung and the blood S. pneumoniae colony forming unit counts, and lower airway levels of keratinocyte-derived chemokine/growth-related oncogene (KC/GRO), and interferon gamma.

Conclusion
Acute high level loading of AM with ultrafine carbon black particles per se does not increase the susceptibility of mice to pneumococcal infection in vivo.
Biological changes in auditory function following training in children with autism spectrum disorders
Authors: Russo Nicole M , Hornickel Jane , Nicol Trent , Zecker Steven , Kraus Nina 
Published: October 2010

Abstract

Background
Children with pervasive developmental disorders (PDD), such as children with autism spectrum disorders (ASD), often show auditory processing deficits related to their overarching language impairment. Auditory training programs such as Fast ForWord Language may potentially alleviate these deficits through training-induced improvements in auditory processing.

Methods
To assess the impact of auditory training on auditory function in children with ASD, brainstem and cortical responses to speech sounds presented in quiet and noise were collected from five children with ASD who completed Fast ForWord training.

Results
Relative to six control children with ASD who did not complete Fast ForWord, training-related changes were found in brainstem response timing (three children) and pitch-tracking (one child), and cortical response timing (all five children) after Fast ForWord use.

Conclusions
These results provide an objective indication of the benefit of training on auditory function for some children with ASD.
Protective effect of extract of Cordyceps sinensis in middle cerebral artery occlusion-induced focal cerebral ischemia in rats
Authors: Liu Zhenquan , Li Pengtao , Zhao Dan , Tang Huiling , Guo Jianyou 
Published: October 2010

AbstractBackgroundIschemic hypoxic brain injury often causes irreversible brain damage. The lack of effective and widely applicable pharmacological treatments for ischemic stroke patients may explain a growing interest in traditional medicines. From the point of view of "self-medication" or "preventive medicine,"Cordyceps sinensiswas used in the prevention of cerebral ischemia in this paper.MethodsThe right middle cerebral artery occlusion model was used in the study. The effects ofCordyceps sinensis(Caterpillar fungus) extract on mortality rate, neurobehavior, grip strength, lactate dehydrogenase, glutathione content, Lipid Peroxidation, glutathione peroxidase activity, glutathione reductase activity, catalase activity, Na+K+ATPase activity and glutathione S transferase activity in a rat model were studied respectively.ResultsCordyceps sinensisextract significantly improved the outcome in rats after cerebral ischemia and reperfusion in terms of neurobehavioral function. At the same time, supplementation ofCordyceps sinensisextract significantly boosted the defense mechanism against cerebral ischemia by increasing antioxidants activity related to lesion pathogenesis. Restoration of the antioxidant homeostasis in the brain after reperfusion may have helped the brain recover from ischemic injury.ConclusionsThese experimental results suggest that complementCordyceps sinensisextract is protective after cerebral ischemia in specific way. The administration ofCordyceps sinensisextract significantly reduced focal cerebral ischemic/reperfusion injury. The defense mechanism against cerebral ischemia was by increasing antioxidants activity related to lesion pathogenesis.
A simple, rapid method to isolate salt glands for three-dimensional visualization, fluorescence imaging and cytological studies
Authors: Tan Wee-Kee , Lim Tit-Meng , Loh Chiang-Shiong 
Published: October 2010

AbstractBackgroundSome plants inhabiting saline environment remove salts via the salt glands embedded in the epidermal tissues. Cytological studies of salt glands will provide valuable information to our understanding of the secretory process. Previous studies on salt gland histology relied mainly on two-dimensional microscopic observations of microtome sections. Optical sectioning properties of confocal laser scanning microscope offer alternative approach for obtaining three-dimensional structural information of salt glands. Difficulty in light penetration through intact leaves and interference from neighbouring leaf cells, however, impede the acquiring of good optical salt gland sections and limit its applications in salt gland imaging. Freeing the glands from adjacent leaf tissues will allow better manipulations for three-dimensional imaging through confocal laser scanning microscopy.ResultsHere, we present a simple and fast method for the isolation of individual salt glands released from the interference of neighbouring cells. About 100-200 salt glands could be isolated from just one cm2ofAvicenniaofficinalisleaf within hours and microscopic visualization of isolated salt glands was made possible within a day. Using these isolated glands, confocal laser scanning microscopic techniques could be applied and better resolution salt gland images could be achieved. By making use of their intrinsic fluorescent properties, optical sections of the gland cells could be acquired without the use of fluorescent probes and the corresponding three-dimensional images constructed. Useful cytological information of the salt gland cells could also be obtained through the applications of fluorescent dyes (e.g., LysoTracker®Red, FM®4-64, Texas Red®).ConclusionsThe study of salt glands directly at the glandular level are made possible with the successful isolation of these specialized structures. Preparation of materials for subsequent microscopic observations of salt glands could be achieved within a day. Potential applications of confocal fluorescence microscopic techniques could also be performed using these isolated glands. Experiments designed and targeted directly at the salt glands were explored and cytological information obtained herein could be further incorporated towards the understanding of the mechanism underlying secretion in plant salt glands.
Radiation induced apoptosis and initial DNA damage are inversely related in locally advanced breast cancer patients
Authors: Pinar Beatriz , Henríquez-Hernández Luis Alberto , Lara Pedro C , Bordon Elisa , Rodriguez-Gallego Carlos , Lloret Marta , Nuñez Maria Isabel , De Almodovar Mariano Ruiz 
Published: October 2010

Abstract

Background
DNA-damage assays, quantifying the initial number of DNA double-strand breaks induced by radiation, have been proposed as a predictive test for radiation-induced toxicity. Determination of radiation-induced apoptosis in peripheral blood lymphocytes by flow cytometry analysis has also been proposed as an approach for predicting normal tissue responses following radiotherapy. The aim of the present study was to explore the association between initial DNA damage, estimated by the number of double-strand breaks induced by a given radiation dose, and the radio-induced apoptosis rates observed.

Methods
Peripheral blood lymphocytes were taken from 26 consecutive patients with locally advanced breast carcinoma. Radiosensitivity of lymphocytes was quantified as the initial number of DNA double-strand breaks induced per Gy and per DNA unit (200 Mbp). Radio-induced apoptosis at 1, 2 and 8 Gy was measured by flow cytometry using annexin V/propidium iodide.

Results
Radiation-induced apoptosis increased in order to radiation dose and data fitted to a semi logarithmic mathematical model. A positive correlation was found among radio-induced apoptosis values at different radiation doses: 1, 2 and 8 Gy (p < 0.0001 in all cases). Mean DSB/Gy/DNA unit obtained was 1.70 ± 0.83 (range 0.63-4.08; median, 1.46). A statistically significant inverse correlation was found between initial damage to DNA and radio-induced apoptosis at 1 Gy (p = 0.034). A trend toward 2 Gy (p = 0.057) and 8 Gy (p = 0.067) was observed after 24 hours of incubation.

Conclusions
An inverse association was observed for the first time between these variables, both considered as predictive factors to radiation toxicity.
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
Authors: Sigurdsson Martin I , Jamshidi Neema , Steingrimsson Eirikur , Thiele Ines , Palsson Bernhard Ø 
Published: October 2010

Abstract

Background
Well-curated and validated network reconstructions are extremely valuable tools in systems biology. Detailed metabolic reconstructions of mammals have recently emerged, including human reconstructions. They raise the question if the various successful applications of microbial reconstructions can be replicated in complex organisms.

Results
We mapped the published, detailed reconstruction of human metabolism (Recon 1) to other mammals. By searching for genes homologous to Recon 1 genes within mammalian genomes, we were able to create draft metabolic reconstructions of five mammals, including the mouse. Each draft reconstruction was created in compartmentalized and non-compartmentalized version via two different approaches. Using gap-filling algorithms, we were able to produce all cellular components with three out of four versions of the mouse metabolic reconstruction. We finalized a functional model by iterative testing until it passed a predefined set of 260 validation tests. The reconstruction is the largest, most comprehensive mouse reconstruction to-date, accounting for 1,415 genes coding for 2,212 gene-associated reactions and 1,514 non-gene-associated reactions.
We tested the mouse model for phenotype prediction capabilities. The majority of predicted essential genes were also essential in vivo. However, our non-tissue specific model was unable to predict gene essentiality for many of the metabolic genes shown to be essential in vivo. Our knockout simulation of the lipoprotein lipase gene correlated well with experimental results, suggesting that softer phenotypes can also be simulated.

Conclusions
We have created a high-quality mouse genome-scale metabolic reconstruction, iMM1415 (Mus Musculus, 1415 genes). We demonstrate that the mouse model can be used to perform phenotype simulations, similar to models of microbe metabolism. Since the mouse is an important experimental organism, this model should become an essential tool for studying metabolic phenotypes in mice, including outcomes from drug screening.
Successful management of refractory pleural effusion due to systemic immunoglobulin light chain amyloidosis by vincristine adriamycin dexamethasone chemotherapy: a case report
Authors: Araoka Toshikazu , Takeoka Hiroya , Nishioka Keisuke , Ikeda Masaki , Kondo Makiko , Hoshina Azusa , Kishi Seiji , Araki Makoto , Mimura Rokuro , Murakami Taichi , Mima Akira , Nagai Kojiro , Abe Hideharu , Doi Toshio 
Published: October 2010

Abstract

Introduction
Refractory pleural effusion in systemic immunoglobulin light chain amyloidosis without cardiac decompensation is rarely reported and has a poor prognosis in general (a median survival of 1.6 months). Moreover, the optimum treatment for this condition is still undecided. This is the first report on the successful use of vincristine, adriamycin and dexamethasone chemotherapy for refractory pleural effusion due to systemic immunoglobulin light chain amyloidosis without cardiac decompensation.

Case presentation
We report the case of a 68-year old Japanese male with systemic immunoglobulin light chain amyloidosis presenting with bilateral pleural effusion (more severe on the right side) in the absence of cardiac decompensation that was refractory to diuretic therapy. The patient was admitted for fatigue, exertional dyspnea, and bilateral lower extremity edema. He had been receiving intermittent melphalan and prednisone chemotherapy for seven years. One month before admission, his dyspnea had got worse, and his chest radiograph showed bilateral pleural effusion; the pleural effusion was ascertained to be a transudate. The conventionally used therapeutic measures, including diuretics and thoracocentesis, failed to control pleural effusion. Administration of vincristine, adriamycin, and dexamethasone chemotherapy led to successful resolution of the effusion.

Conclusion
Treatment with vincristine, adriamycin, and dexamethasone chemotherapy was effective for the refractory pleural effusion in systemic immunoglobulin light chain amyloidosis without cardiac decompensation and appears to be associated with improvement in our patient's prognosis.
Granulomatous pyoderma preceding chronic recurrent multifocal osteomyelitis triggered by vaccinations in a two-year-old boy: a case report
Authors: Karaca Neslihan , Aksu Guzide , Ozturk Can , Gulez Nesrin , Kutukculer Necil 
Published: October 2010

Abstract

Introduction
Chronic recurrent multifocal osteomyelitis is a rare, systemic, aseptic, inflammatory disorder that involves different sites. Pathogenesis of chronic recurrent multifocal osteomyelitis is currently unknown.

Case presentation
A two-year-old Caucasian boy, diagnosed with chronic recurrent multifocal osteomyelitis with granulomatous pyoderma following routine vaccinations is presented for the first time in the literature.

Conclusion
We conclude that antigen exposures might have provoked this inflammatory condition for our case. Skin and/or bone lesions following vaccinations should raise suspicion of an inflammatory response such as chronic recurrent multifocal osteomyelitis only after thorough evaluation for chronic infection, autoimmune, immunodeficiency or vasculitic diseases.
Change in condom and other barrier method use during and after an HIV prevention trial in Zimbabwe
Authors: van der Straten Ariane , Cheng Helen , Minnis Alexandra M 
Published: October 2010

BackgroundWe examined the use of male condoms and the diaphragm following completion of a clinical trial of the diaphragm's HIV prevention effectiveness. In the trial, called Methods for Improving Reproductive Health in Africa (MIRA), women were randomized to a diaphragm group (diaphragm, gel and condoms) or a condom‐only control group. At trial exit, all women were offered the diaphragm and condoms.MethodsOur sample consisted of 801 Zimbabwean MIRA participants who completed one post‐trial visit (median lapse: nine months; range two to 20 months). We assessed condom, diaphragm and any barrier method use at last sex act at enrolment, final MIRA and post‐trial visits. We used multivariable random effects logistic regression to examine changes in method use between these three time points.Results and discussionIn the condom group, condom use decreased from 86% at the final trial visit to 67% post trial (AOR = 0.20; 95% CI: 0.12 to 0.33). In the diaphragm group, condom use was 61% at the final trial visit, and did not decrease significantly post trial (AOR = 0.77; 95% CI: 0.55 to 1.09), while diaphragm use decreased from 79% to 50% post trial (AOR = 0.18; 95% CI: 0.12 to 0.28). Condom use significantly decreased between the enrolment and post‐trial visits in both groups. Use of any barrier method was similar in both groups: it significantly decreased between the final trial and the post‐trial visits, but did not change between enrolment and the post‐trial visits.ConclusionsHigh condom use levels achieved during the trial were not sustained post trial in the condom group. Post‐trial diaphragm use remained relatively high in the diaphragm group (given its unknown effectiveness), but was very low in the condom group. Introducing “new” methods for HIV prevention may require time and user skills before they get adopted. Our findings underscore the potential benefit of providing a mix of methods to women as it may encourage more protected acts.
Malignant head and neck paragangliomas: Is there an optimal treatment strategy?
Authors: Moskovic Daniel J , Smolarz Joseph R , Stanley Douglas , Jimenez Camilo , Williams Michelle D , Hanna Ehab Y , Kupferman Michael E 
Published: October 2010

Abstract

Background
Little is known about management and prognosis for malignant head & neck paragangliomas. We reviewed records of these patients to determine optimal treatment strategies.

Methods
We reviewed 113 cases of head & neck paragangliomas treated at our institution from 1970 to 2005. Nineteen patients were included in the study. All had primary surgical treatment at another institution. Metastatic disease was treated with radiation, chemotherapy, or both. Survival and complications were evaluated. P values were determined by Fischer's exact test.

Results
All patients treated with chemotherapy and radiation age ≥ 40 years had disease progression. Of the patients < 40, two had stable disease; one had regression of disease with treatment. Patients without disease progression had better prognosis and were alive at last follow-up.

Conclusions
Clinical benefit was derived from aggressive treatment. However, careful consideration of the risks of observation versus intensive therapy should be undertaken when managing these patients.