bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Freeze-Dried Kefir Coculture as Starter in Feta-Type Cheese Production
Authors: Kourkoutas Y. , Kandylis P. , Panas P. , Dooley J. S. G. , Nigam P. , Koutinas A. A. 
Published: September 2006

ABSTRACT

The use of freeze-dried kefir coculture as a starter in the production of feta-type cheese was investigated. Maturation of the produced cheese at 4°C was monitored for up to 70 days, and the effects of the starter culture, the salting method, and the ripening process on quality characteristics were studied. The use of kefir coculture as a starter led to increased lactic acid concentrations and decreased pH values in the final product associated with significantly higher conversion rates compared to salted rennet cheese. Determination of bacterial diversity at the end of the ripening process in salted kefir and rennet cheeses by denaturing gradient gel electrophoresis technology, based on both DNA and RNA analyses, suggested a potential species-specific inhibition of members of the genera
Staphylococcus
and
Psychrobacter
by kefir coculture. The main active microbial associations in salted kefir cheese appeared to be members of the genera
Pseudomonas
and
Lactococcus
, while in salted rennet cheese,
Oxalobacteraceae
,
Janthinobacterium
,
Psychrobacter
, and
Pseudomonas
species were noted. The effect of the starter culture on the production of aroma-related compounds responsible for cheese flavor was also studied by the solid-phase microextraction-gas chromatography-mass spectrometry technique. Kefir coculture also appeared to extend the shelf life of unsalted cheese. Spoilage of kefir cheese was observed on the 9th and 20th days of preservation at 10 and 5°C, respectively, while spoilage in the corresponding rennet cheese was detected on the 7th and 16th days. Microbial counts during preservation of both types of unsalted cheese increased steadily and reached similar levels, with the exception of staphylococci, which were significantly lower in unsalted kefir cheese. All types of cheese produced with kefir as a starter were approved and accepted by the panel during the preliminary sensory evaluation compared to commercial feta-type cheese.
Evidence that the JAK2 G1849T (V617F) mutation occurs in a lymphomyeloid progenitor in polycythemia vera and idiopathic myelofibrosis
Authors: Delhommeau François , Dupont Sabrina , Tonetti Carole , Massé Aline , Godin Isabelle , Couedic Jean-Pierre Le , Debili Najet , Saulnier Patrick , Casadevall Nicole , Vainchenker William , Giraudier Stéphane 
Published: September 2006

AbstractThe JAK2 V617F mutation has recently been described as an essential oncogenic event associated with polycythemia vera (PV), idiopathic myelofibrosis (IMF), and essential thrombocythemia. This mutation has been detected in all myeloid lineages but has not yet been detected in lymphoid cells. This raises the question whether this molecular event occurs in a true lymphomyeloid progenitor cell. In this work, we studied the presence of the mutation in peripheral blood cells and sorted B, T, and natural killer (NK) cells from PV and IMF. We detected the JAK2 V617F mutation in B and NK cells in approximately half the patients with IMF and a minority of those with PV. Moreover, in a few cases patients with IMF had mutated peripheral T cells. The mutation (homozygous or heterozygous) could be subsequently detected in B/NK/myeloid progenitors from PV and IMF, with a much higher frequency in clones derived from IMF. Using the fetal thymus organ culture (FTOC) assay, the mutation was also detected in all T-cell fractions derived from IMF and PV CD34+ cells. These results demonstrate that myeloproliferative disorders take their origin in a true myeloid/lymphoid progenitor cell but that their phenotype is related to a downstream selective proliferative advantage of the myeloid lineages.
RDMAS: a web server for RNA deleterious mutation analysis
Authors: Shu Wenjie , Bo Xiaochen , Liu Rujia , Zhao Dongsheng , Zheng Zhiqiang , Wang Shengqi 
Published: September 2006

Abstract

Background
The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious. RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness.

Results
The RDMAS web server we describe here is an online tool for evaluating structural deleteriousness of single nucleotide mutation in RNA genes. Several structure comparison methods have been integrated; sub-optimal structures predicted can be optionally involved to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate quick analysis.

Conclusion
RDMAS can be used to explore the structure alterations which cause mutations pathogenic, and to predict deleterious mutations which may help to determine the functionally critical regions. RDMAS is freely accessed via http://biosrv1.bmi.ac.cn/rdmas.
Indications that "codon boundaries" are physico-chemically defined and that protein-folding information is contained in the redundant exon bases
Authors: Biro Jan Charles 
Published: September 2006

Abstract

Background
All the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, but this is not represented by the known genetic code.

Results
Nucleic acid subsequences comprising the 1st and/or 3rd codon residues in mRNAs express significantly higher free folding energy (FFE) than the subsequence containing only the 2nd residues (p < 0.0001, n = 81). This periodic FFE difference is not present in introns. It is therefore a specific physico-chemical characteristic of coding sequences and might contribute to unambiguous definition of codon boundaries during translation. The FFEs of the 1st and 3rd residues are additive, which suggests that these residues contain a significant number of complementary bases and that may contribute to selection for local RNA secondary structures in coding regions. This periodic, codon-related structure-formation of mRNAs indicates a connection between the structures of exons and the corresponding (translated) proteins. The folding energy dot plots of RNAs and the residue contact maps of the coded proteins are indeed similar. Residue contact statistics using 81 different protein structures confirmed that amino acids that are coded by partially reverse and complementary codons (Watson-Crick (WC) base pairs at the 1st and 3rd codon positions and translated in reverse orientation) are preferentially co-located in protein structures.

Conclusion
Exons are distinguished from introns, and codon boundaries are physico-chemically defined, by periodically distributed FFE differences between codon positions. There is a selection for local RNA secondary structures in coding regions and this nucleic acid structure resembles the folding profiles of the coded proteins. The preferentially (specifically) interacting amino acids are coded by partially complementary codons, which strongly supports the connection between mRNA and the corresponding protein structures and indicates that there is protein folding information in nucleic acids that is not present in the genetic code. This might suggest an additional explanation of codon redundancy.
Green fluorescent protein as a reporter of prion protein folding
Authors: Vasiljevic Snezana , Ren Junyuan , Yao YongXiu , Dalton Kevin , Adamson Catherine S , Jones Ian M 
Published: September 2006

Abstract

Background
The amino terminal half of the cellular prion protein PrPc is implicated in both the binding of copper ions and the conformational changes that lead to disease but has no defined structure. However, as some structure is likely to exist we have investigated the use of an established protein refolding technology, fusion to green fluorescence protein (GFP), as a method to examine the refolding of the amino terminal domain of mouse prion protein.

Results
Fusion proteins of PrPc and GFP were expressed at high level in E.coli and could be purified to near homogeneity as insoluble inclusion bodies. Following denaturation, proteins were diluted into a refolding buffer whereupon GFP fluorescence recovered with time. Using several truncations of PrPc the rate of refolding was shown to depend on the prion sequence expressed. In a variation of the format, direct observation in E.coli, mutations introduced randomly in the PrPc protein sequence that affected folding could be selected directly by recovery of GFP fluorescence.

Conclusion
Use of GFP as a measure of refolding of PrPc fusion proteins in vitro and in vivo proved informative. Refolding in vitro suggested a local structure within the amino terminal domain while direct selection via fluorescence showed that as little as one amino acid change could significantly alter folding. These assay formats, not previously used to study PrP folding, may be generally useful for investigating PrPc structure and PrPc-ligand interaction.
Refuting phylogenetic relationships
Authors: Bucknam James , Boucher Yan , Bapteste Eric 
Published: September 2006

AbstractBackgroundPhylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny.ResultsWe discuss some of the limits of a methodology restricted to verificationism, the philosophy on which gene concatenation practices generally rely. As an alternative, we describe a software which identifies and focuses on impossible or refuted relationships, through a simple analysis of bootstrap bipartitions, followed by multivariate statistical analyses. We show how refuting phylogenetic relationships could in principle facilitate systematics. We also apply our method to the study of two complex phylogenies: the phylogeny of the archaea and the phylogeny of the core of genes shared by all life forms. While many groups are rejected, our results left open a possible proximity ofN. equitansand the Methanopyrales, of the Archaea and the Cyanobacteria, and as well the possible grouping of the Methanobacteriales/Methanoccocales and Thermosplasmatales, of the Spirochaetes and the Actinobacteria and of the Proteobacteria and firmicutes.ConclusionIt is sometimes easier (and preferable) to decide which species do not group together than which ones do. When possible topologies are limited, identifying local relationships that are rejected may be a useful alternative to classical concatenation approaches aiming to find a globally resolved tree on the basis of weak phylogenetic markers.ReviewersThis article was reviewed by Mark Ragan, Eugene V Koonin and J Peter Gogarten.
Substance abuse prevention infrastructure: a survey-based study of the organizational structure and function of the D.A.R.E. program
Authors: Merrill Jeffrey C , Pinsky Ilana , Killeya-Jones Ley A , Sloboda Zili , Dilascio Tracey 
Published: September 2006

Abstract

Background
The only national drug abuse prevention delivery system that supports the rapid diffusion of new prevention strategies and includes uniform training and credentialing of instructors who are monitored for quality implementation of prevention programming is the Drug Abuse Resistance Education network (D.A.R.E.) linking community law enforcement to schools. Analysis of the organizational structure and function of D.A.R.E. provides an understanding of the essential parameters of this successful delivery system that can be used in the development of other types of national infrastructures for community-based prevention services. Information regarding organizational structure and function around funding issues, training, quality control and community relationships was gathered through telephone surveys with 50 state D.A.R.E. coordinators (including two major cities), focus groups with local D.A.R.E. officers and mentors, and interviews with national D.A.R.E. office staff.

Results
The surveys helped identify several strengths inherent in the D.A.R.E. program necessary for building a prevention infrastructure, including a well-defined organizational focus (D.A.R.E. America), uniform training and means for rapid dissemination (through its organized training structure), continuing education mechanisms (through the state and national conference and website), mechanisms for program monitoring and fidelity of implementation (formal and informal), branding and, for several states, predictable and consistent financing. Weaknesses of the program as currently structured include unstable funding and the failure to incorporate components for the continual upgrading of curricula reflecting research evidence and "principles of prevention".

Conclusion
The D.A.R.E. organization and service delivery network provides a framework for the rapid dissemination of evidence-based prevention strategies. The major strength of D.A.R.E. is its natural affiliation to local law enforcement agencies through state coordinators. Through these affiliations, it has been possible for D.A.R.E. to become established nationally within a few years and internationally within a decade. Understanding how this structure developed and currently functions provides insights into how other such delivery systems could be developed.
Correlations Between O6-Methylguanine DNA Methyltransferase Promoter Methylation Status, 1p and 19q Deletions, and Response to Temozolomide in Anaplastic and Recurrent Oligodendroglioma: A Prospective GICNO Study
Authors: Brandes Alba A. , Tosoni Alicia , Cavallo Giovanna , Reni Michele , Franceschi Enrico , Bonaldi Laura , Bertorelle Roberta , Gardiman Marina , Ghimenton Claudio , Iuzzolino Paolo , Pession Annalisa , Blatt Valeria , Ermani Mario 
Published: September 2006

Purpose To date, no data are available on the relationship between 1p/19q deletions and the response to temozolomide (TMZ) in primary anaplastic oligodendroglioma (AO) and anaplastic oligoastrocytoma (AOA) recurrent after surgery and standard radiotherapy. The aim of this study was to evaluate correlations between 1p/19q deletions, O6-methylguanine DNA methyltransferase (MGMT) promoter methylation, and response rate to TMZ in this setting. Patients and Methods From June 2000 to February 2005, 67 patients were enrolled; 39 patients (58%) had AO and 28 patients (42%) had AOA. All patients received 150 to 200 mg/m2 of TMZ every 28 days. Chromosome 1p and 19q deletions were detected by fluorescence in situ hybridization and MGMT promoter methylation was analyzed using methylation specific polymerase chain reaction. Results The overall response rate was 46.3% (17 complete responses and 14 partial responses). The response rate was higher in patients with AO than in those with AOA (61.5% v 25%, P = .003). Combined 1p/19q allelic loss was found in 32 patients (47.8%), while MGMT methylation occurred in 37 (68.5%) of 54 assessable patients. 1p/19q loss was significantly correlated with response rate (P = .04), time-to-progression (P = .003), and overall survival (P = .0001). Despite the significant concordance found between MGMT promoter methylation and 1p/19q deletions (P = .02), MGMT promoter methylation showed only a borderline correlation with overall survival (P = .09). Conclusion TMZ is active in anaplastic oligodendroglial tumors treated at first recurrence. In this setting, 1p/19q allelic loss is an important predictive and prognostic factor. Further studies on MGMT promoter methylation should be performed in randomized trials to test its correlation with survival.
Acute In Vivo Regulation of 11β-Hydroxysteroid Dehydrogenase Type 1 Activity by Insulin and Intralipid Infusions in Humans
Authors: Wake Deborah J. , Homer Natalie Z. M. , Andrew Ruth , Walker Brian R. 
Published: September 2006

Abstract
Context: Extraadrenal regeneration of cortisol by 11β-hydroxysteroid dehydrogenase type 1 (11HSD1) is increased after a mixed meal. It is unknown which tissue is responsible and whether this reflects the complex transcriptional control of 11HSD1 or posttranscriptional control exerted by supply of reduced nicotinamide adenine dinucleotide phosphate from hexose-6-phosphate dehydrogenase.
Objective: The objective of this study was to test whether hyperinsulinemia and/or increased serum free fatty acids increase whole-body and intraadipose 11HSD1, and whether adipose 11HSD1 switches from dehydrogenase to reductase activity.
Methods: In nine healthy men, we measured whole-body cortisol regeneration (by iv infusion of 9,11,12,12-[2H]4-cortisol) and intra-adipose interconversion of cortisol and cortisone (by sc microdialysis infusion of [3H]4-cortisol and [3H]2-cortisone in separate cannulae) during: 1) a hyperinsulinemic euglycemic clamp; 2) iv lipid infusion (Intralipid 20% fat emulsion); and 3) saline infusion, each for 3.5 h.
Results: Hyperinsulinemia increased rate of appearance of 9,12,12-[2H]3-cortisol (19.3 ± 0.8 vs. 16.7 ± 1.1 nmol/min with saline, P &lt; 0.001), indicating increased whole-body 11HSD1. Within adipose, the predominant reaction was reductase conversion of cortisone to cortisol (after 3.5 h of saline infusion, reaching 11.0 ± 2.7% per hour reductase vs. 5.2 ± 1.3 dehydrogenase, P &lt; 0.02); insulin increased reductase (reaching 15.8 ± 3.0, P &lt; 0.05) and tended to increase dehydrogenase activity. Intralipid infusion had no effects on whole-body deuterated cortisol metabolism, but increased both dehydrogenase and reductase (reaching 16.7 ± 1.8, P &lt; 0.01) activities in adipose.
Conclusions: Hyperinsulinemia and increased free fatty acids induce acute increases in 11HSD1 activity in adipose tissue that are not attributable to a switch from dehydrogenase to reductase. Hyperinsulinemia also increases systemic cortisol regeneration. These effects may enhance intracellular cortisol concentrations after a meal.
Heat Shock Treatment of Tumor Lysate-Pulsed Dendritic Cells Enhances Their Capacity to Elicit Antitumor T Cell Responses against Medullary Thyroid Carcinoma
Authors: Bachleitner-Hofmann Thomas , Strohschneider Michaela , Krieger Peter , Sachet Monika , Dubsky Peter , Hayden Hubert , Schoppmann Sebastian F. , Pfragner Roswitha , Gnant Michael , Friedl Josef , Stift Anton 
Published: September 2006

Abstract
Background: In vitro and in vivo studies have shown that dendritic cells (DCs) can stimulate antitumor T cell responses against medullary thyroid carcinoma (MTC). However, despite promising results in selected cases, the clinical efficacy of DC immunotherapy in patients with MTC has been limited. Recently, it has been demonstrated in mice that heat shock enhances the capacity of bone-marrow-derived DCs to stimulate antigen-specific T cells. The aim of our investigations was to evaluate whether heat shock also increases the capacity of human monocyte-derived DCs to stimulate antitumor T cell responses against MTC tumor cells.
Methods: DCs from six patients with metastatic MTC were pulsed with tumor lysate derived from allogeneic MTC tumor cells and were heat shocked for 12 h at 40 C or kept at 37 C. Thereafter, the DCs were matured and cocultured with T cells. Finally, the cytotoxic activity of T cells against MTC tumor cells was measured in vitro.
Results: In all patient samples, cytotoxic T cell responses against MTC tumor cells could be induced. Notably, heat-shocked DCs were more potent stimulators of cytotoxic T cell responses than control DCs, with T cells stimulated with heat-shocked DCs displaying a significantly increased cytotoxic activity against MTC tumor cells as compared with T cells stimulated with control DCs. In none of the experiments was a cytotoxic T cell response against unrelated pancreatic tumor cells (PANC-1) observed, using both control and heat-shocked DCs.
Conclusions: Our study shows that heat-shocking DCs may be a valuable strategy to increase the immunostimulatory capacity of DCs used for immunotherapy of MTC.
Cryosurgery in chronic rhinitis
Authors: Ozenberger James M. 
Published: September 2006

AbstractCryotherapy, a tool of dermatologists for many years, has received increasing attention among otolaryngologists since being “reintroduced” as a surgical technique by Cooper in 1961.1 Miller2 and others have studied extensively its value in treatment of tumors of the head and neck. In non‐neoplastic diseases, freezing has been used by House3 and others for Ménière's syndrome, and by Hill4,5 for tonsils, nasal polyps, and for epistaxis. The response of tissues to freezing have been summarized by Hanckel.6
Basal cell nevus syndrome: A case report with associated carcinoma of the maxilla
Authors: Shapiro Myron J. 
Published: September 2006

AbstractBasal cell nevus syndrome is a rare hereditary multiple‐system progressive disorder which was first reported as such by Binkley and Johnson in 1951.1 Since then, retrospectively and de novo, over 150 cases have been reported. Reviews2,3,4 have tried to define the clinical features which constitute the syndrome, but so many anomalies have been described that for the sake of clarity, I have eliminated all but the more salient features.
The bifid uvula
Authors: Taylor G. Dekle 
Published: September 2006

AbstractSeemingly minor anatomical variants may herald more serious and complicated anatomical or physiological abnormalities. A white forelock is present in 20 percent of cases with Waardenburg's syndrome. Blue sclera suggests the diagnosis of otosclerosis or osteogenesis imperfecta. A subtle variation of the ear lobe may suggest a congenital defect of the ossicular chain in the patient with conductive deafness and normal appearing tympanic membranes. I believe the bifid uvula to be a sentinel, manifesting a disturbance of the normal embryological development of the palate and related structures. Otologic sequelae and velo‐pharyngeal incompetency seen with the more familiar cleft palate may also occur in patients with a bifid uvula. An increased awareness for this seemingly benign variant may aid the otolaryngologist in his quest for ways to prevent conductive deafness and the adverse anatomical changes accompanying tubal inefficiency.
Nasopharyngeal malignancies in children
Authors: Straka John A. , Bluestone Charles D. 
Published: September 2006

AbstractNasopharyngeal malignancies are thought to be uncommon in children. A review of the literature reveals 166 documented cases of nasopharyngeal malignancy in childhood. This appears to be a deceptively small number due to a lack of specificity in the reporting of oral and pharyngeal neoplasms. This report adds six more cases, making a total of 172.Children with this disease are more likely to present with neurological signs and symptoms than adults. Neurological involvement carries a poor prognosis.Patients with nasopharyngeal malignancy are often misdiagnosed and subjected to needless surgical procedures. The fact that the early symptoms of nasopharyngeal malignancy are common in childhood from benign causes and the false security that a malignancy in this area is rare in childhood, undoubtedly contribute to the diagnostic delay.