bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable contribution of protein kinases to the generation of the human phosphoproteome: a global weblogo analysis
Authors: Salvi Mauro , Cesaro Luca , Pinna Lorenzo A. 
Published: June 2010

AbstractIn an attempt to evaluate the contribution of individual protein kinases to the generation of the human phosphoproteome, we performed a global weblogo analysis exploiting a database of 45641 phosphosites (80% pSer, 11% pTyr, 9% pThr). The outcome of this analysis was then interpreted by comparison with similar logos constructed from bona fide phospoacceptor sites of individual pleiotropic kinases. The main conclusions that were drawn are as follows: (i) the hallmarks surrounding phosphorylated Ser/Thr residues are more pronounced than and sharply different from those found around phosphorylated Tyr, which is consistent with the view that local consensus sequences are particularly important for substrate recognition by Ser/Thr protein kinases. (ii) Only six residues are positively selected around phosphorylated Ser/Thr residues, notably Pro (particularly at n+1), Glu, and to a lesser extent Asp, at various positions with special reference to n+3, Arg (and to a much lesser extent Lys), particularly at n-3 and n-5, and Ser, at various positions, particularly n+4 and n-4. (iii) This composite signature reflects the contribution of kinases whose bona fide substrates exhibit logos partially overlapping that of the whole phosphoproteome. These are Pro-directed kinases belonging to the CMGC group, some basophilic kinases belonging to the ACG and CAMK groups, phosphate-directed kinases such as GSK3 and members of the CK1 group and the individual highly acidophilic CK2. Collectively taken our data support the concept that a relatively small number of highly pleiotropic kinases contribute to the generation of the great majority of the human Ser/Thr phosphoproteome.
Errors in transfusion: causes and measures to avoid them
Authors: Franchini Massimo 
Published: June 2010

AbstractAdverse events related to medical errors are common worldwide and largely unreported. However, they represent a serious problem within the health care community, resulting in avoidable loss of life and/or extremely high costs. Likewise, errors in transfusion medicine, which most frequently involve misidentification of the patient, not rarely may have life-threatening consequences. In this review, the errors related to blood transfusion are briefly summarized along with new technologies developed for improving blood safety.Clin Chem Lab Med 2010;48:1075–7.
Development and evaluation of an automated hepatitis C virus NS5B sequence-based subtyping assay
Authors: Koletzki Diana , Dumont Stéphanie , Vermeiren Hans , Fevery Bart , De Smet Pieter , Stuyver Lieven J. 
Published: June 2010

Abstract

Background: Hepatitis C virus (HCV) genotyping and accurate subtype determination is becoming increasingly important to better understand viral evolution, the development of resistance to STAT-C, and possibly even for the treatment and management of chronic HCV-infected patients.

Methods: A subtyping assay based on a 329-bp sequence of the NS5B region, together with an automated subtype interpretation tool was developed. Clinical samples of the six major genotypes were used to assess assay performance characteristics.

Results: The NS5B BLAST-based subtyping assay showed clinical sensitivity for amplification of 89% (n=603 random samples). Assessment of analytical sensitivity of amplification for genotypes 1, 2, 3 and 4 revealed a suitable performance for high viral load samples and decreased only with low viral loads. The results were 100% and 99% accurate at the genotype and subtype level, respectively. A concordance of 97% on genotype level and 62% on subtype level was observed by comparison with subtype results from 5′ non-coding-based assays with a panel of 276 isolates.

Conclusions: The HCV NS5B subtyping assay has been validated for research use. Based on its performance, it is the method of choice in cases where subtype rather than genotype information is needed.
Clin Chem Lab Med 2010;48:1095–102.
Coeliac disease – a diagnostic and therapeutic challenge
Authors: Kaukinen Katri , Lindfors Katri , Collin Pekka , Koskinen Outi , Mäki Markku 
Published: June 2010

AbstractDuring the past 20 years the diagnosis of coeliac disease has improved significantly. However, at the same time the true prevalence of the condition has doubled, involving more than 2% of the population in some countries. Due to mild or atypical symptoms, the diagnosis remains a challenge for the health care system. Highly sensitive and specific serum endomysial and transglutaminase-2 antibody tests are helpful in identifying patients for diagnostic endoscopy and small-bowel biopsy. The diagnosis of the disease is still based on the demonstration of gluten-induced small-bowel mucosal villous atrophy with crypt hyperplasia. However, coeliac disease may manifest itself before the development of the overt small-intestinal lesion. Positive endomysial and transglutaminase antibodies in patients with normal small-bowel mucosal villous architecture may indicate early stage coeliac disease. Currently, the only effective treatment for the condition is a life-long strict gluten-free diet. Long-term regular follow-up of patients is recommended in order to maintain good adherence to the diet.Clin Chem Lab Med 2010;48:1205–16.
Serum soluble tumour necrosis factor receptor type I concentrations independently predict prognosis in patients with breast cancer
Authors: Fuksiewicz Malgorzata , Kowalska Maria , Kotowicz Beata , Rubach Maryna , Chechlinska Magdalena , Pienkowski Tadeusz , Kaminska Janina 
Published: June 2010

Abstract

Background: The aim of this study was to exploit the potential clinical use of circulating cytokine assessment in patients with breast cancer.

Methods: The following circulating cytokines were measured in 210 histopathologically confirmed, untreated breast cancer patients: interleukin 6 (IL-6), tumour necrosis factor-α (TNFα), interleukin 8 (IL-8), soluble tumour necrosis factor receptor type I (sTNF RI), sTNF RII, interleukin 1 receptor antagonist (IL-1ra), interleukin 10 (IL-10), macrophage colony-stimulating factor, vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF). The patients have been followed-up for 10 years.

Results: bFGF and VEGF showed the highest diagnostic sensitivity. Only IL-6 concentrations were related to the clinical stage. A high percentage of patients in clinical stage I showed increased serum sTNF RII, VEGF and bFGF concentrations, of which only sTNF RII was found to be increased in a smaller percentage of patients with more advanced disease compared with patients with early stage disease. Patients aged 50 years and more presented with significantly higher concentrations of sTNF RI, IL-10, IL-6 and VEGF compared with younger patients. In multivariate analysis, a significant value of pretreatment serum sTNF RI concentrations, next to stage and oestrogen receptors status, was its utility as an independent prognostic factor of the overall survival in patients with breast cancer.

Conclusions: Serum sTNF RI may be considered an additional, independent and clinically useful factor of poor prognosis in patients with breast cancer.
Clin Chem Lab Med 2010;48:1481–6.
High resolution melting for the identification of mutations in the iron responsive element of the ferritin light chain gene
Authors: Castiglioni Emanuela , Soriani Nadia , Girelli Domenico , Camaschella Clara , Spiga Ivana , Della Porta Matteo G. , Ferrari Maurizio , Cremonesi Laura 
Published: June 2010

Abstract

Background: Among the causes of hyperferritinemia, hereditary hyperferritinemia cataract syndrome (HHCS) is an autosomal dominant disease characterized by distinctive cataracts and high serum ferritin. It is caused by mutations in the iron responsive element (IRE) of the ferritin light chain gene (FTL).

Methods: To speed up and simplify mutational scanning in this genomic region, we developed a protocol based on high-resolution melting (HRM) analysis.

Results: Validation was carried out using 18 wild-type and 14 DNA samples carrying different mutations, each analyzed in replicates of 20. The method allowed for correct identification and genotyping of all mutant samples, and each variant generated a specific profile distinguishable from the wild type. A 5.5% proportion of false positive results were obtained. In addition, in two patients with HHCS, two new mutations were identified by HRM based on an altered melting profile. These mutations were subsequently characterized by direct sequencing (7C>G+40A>G and 49A>C).

Conclusions: The high reliability of HRM in detecting known and new DNA variations indicate that this could be an effective and sensitive method for molecular scanning of mutations in the IRE of the FTL gene in patients presenting with either HHCS or unexplained hyperferritinemia.
Clin Chem Lab Med 2010;48:1415–8.
Generalized Ramanujan conjecture over general imaginary quadratic fields
Authors: Nakasuji Maki 
Published: June 2010

Abstract.
The new bound toward the generalized Ramanujan conjecture for

G

L
n

(

𝐀
𝐐

)

$\textup {GL}_n({\bf A}_{\bf Q})$
is given by Kim–Sarnak [4].
We generalize it to that for

G

L
n

(

𝐀
F

)

$\textup {GL}_n({\bf A}_{F})$
with

F

$F$
being an imaginary quadratic field.
Applying the obtained bound to the automorphic representation of

G

L
5

$\textup {GL}_5$

gives the following estimate for the first positive eigenvalue of the Laplacian on

L
2

(

3

)

$L^2(\Gamma \backslash {\mathbb {H}}^3)$
, where

$\Gamma $
is any congruence subgroups of

S

L
2

(

F

)

$\textup {SL}_2({\mathcal {O}}_F)$

with

F

${\mathcal {O}}_F$
the ring of integers of

F

$F$
:

1

(

)

0
.
952

$\lambda _1(\Gamma ) \ge 0.952\cdots $
.
Crown-free highly arc-transitive digraphs
Authors: Amato Daniela , Truss John K. 
Published: June 2010

Abstract.
We construct a family of infinite, non-locally finite highly arc-transitive digraphs which do
not have universal reachability relation and which omit special digraphs called `crowns'. Moreover, there
is no homomorphism from any of our digraphs onto

Z

$Z$
. The methods are adapted from [6] and [7].
Quantifying the Economic Effects of Hypoxia on a Fishery for Brown Shrimp Farfantepenaeus aztecus
Authors: Huang Ling , Smith Martin D. , Craig J. Kevin 
Published: June 2010

Abstract
Although hypoxia is a threat to coastal ecosystems, policy makers have limited information about its economic impacts on fisheries. Studies using spatially and temporally aggregated data generally fail to detect statistically significant effects of hypoxia on fisheries. Limited recent work using disaggregated fishing data (microdata) has revealed modest effects of hypoxia on the catches of recreationally harvested species. These studies did not account for important spatial and temporal aspects of the system, however. For example, the effects of hypoxia on catch may not materialize instantaneously but involve a lagged process reflecting cumulative past exposure. This paper develops a differenced bioeconomic model to account for the lagged effects of hypoxia on the North Carolina fishery for brown shrimp Farfantepenaeus aztecus. The model integrates high-resolution oxygen monitoring data with fishery-dependent microdata from North Carolina's trip ticket program to investigate the detailed spatial and temporal relationships of hypoxia to commercial fishery harvests. The main finding is that hypoxia may have resulted in a 12.9% annual decrease in the brown shrimp harvest during the period 1999–2005. The paper also develops two alternative models—a nondifferenced model and a polynomial distributed lag model—whose results are consistent with those of the main model.
Autogenous Periosteal Barrier Membranes and Bone Grafts in the Treatment of Periodontal Intrabony Defects of Single‐Rooted Teeth: A 12‐Month Reentry Randomized Controlled Clinical Trial
Authors: Paolantonio Michele , Femminella Beatrice , Coppolino Evelina , Sammartino Gilberto , D'Arcangelo Camillo , Perfetti Giorgio , Perinetti Giuseppe 
Published: June 2010

Background: This randomized clinical trial compares the outcomes of combination treatment by autogenous periosteal membranes and bone graft versus guided tissue regeneration (GTR) with collagen membranes or open‐flap debridement (OFD) only in the treatment of intraosseous defects.Methods: Forty‐two patients affected by moderate to severe chronic periodontitis were enrolled. Each patient had one deep intrabony defect (≥6 mm). They were randomly assigned into three groups: patients treated with 1) an OFD procedure alone (OFD group); 2) a GTR procedure with collagen membranes (GTR group); and 3) a combined treatment procedure by autogenous periosteal membranes and autogenous bone chips (aCPRT group). Clinical and intrasurgical examinations including probing depth (PD), clinical attachment level (CAL), gingival recession (GR), and defect bone level (DBL) were performed at baseline and after 1 year.Results: After 1 year, all of the evaluated clinical parameters showed statistically significant changes from baseline within each group (P <0.01). The GTR and aCPRT groups had significantly greater PD reductions (5.2 and 4.4 mm, respectively) and CAL (3.2 and 3.9 mm) and DBL gains (2.4 and 3.1 mm) compared to the OFD group (PD, 2.9 mm; CAL, 1.6 mm; DBL, 1.5 mm); moreover, the aCPRT group showed a significantly smaller GR increase (0.5 mm) and a greater DBL gain (3.1 mm) compared to the GTR group (2 and 2.4 mm, respectively; P <0.05).Conclusions: Both the GTR and aCPRT treatments produce additional clinical benefits over OFD alone. Moreover, the aCPRT technique can minimize post‐surgical GR and produce better defect bone‐level improvement.
Comparison Between Micro‐ and Macrosurgical Techniques for the Treatment of Localized Gingival Recessions Using Coronally Positioned Flaps and Enamel Matrix Derivative
Authors: Andrade Patrícia F. , Grisi Márcio F.M. , Marcaccini Andrea M. , Fernandes Patrícia G. , Reino Danilo M. , Souza Sérgio L.S. , Taba Mário , Palioto Daniela B. , Novaes Arthur B. 
Published: June 2010

Background: The aim of this study is to compare the macro‐ and microsurgery techniques for root coverage using a coronally positioned flap (CPF) associated with enamel matrix derivative (EMD).Methods: Thirty patients were selected for the treatment of localized gingival recessions (GRs) using CPF associated to EMD. Fifteen patients were randomly assigned to the test group (TG), and 15 patients were randomly assigned to the control group (CG). The microsurgical approach was performed in the TG, and the conventional macrosurgical technique was performed in the CG. The clinical parameters evaluated before surgery and after 6 months were GR, probing depth, relative clinical attachment level, width of keratinized tissue (WKT), and thickness of keratinized tissue (TKT). The discomfort evaluation was performed 1 week postoperative.Results: There were no statistically significant differences between groups for all parameters at baseline. At 6 months, there was no statistically significant difference between the techniques in achieving root coverage. The percentage of root coverage was 92% and 83% for TG and CG, respectively. After 6 months, there was a statistically significant increase of WKT and TKT in TG only. Both procedures were well tolerated by all patients.Conclusions: The macro‐ and microsurgery techniques provided a statistically significant reduction in GR height. After 6 months, there was no statistically significant difference between the techniques regarding root coverage, and the microsurgical technique demonstrated a statistically significant increase in WKT and TKT.
A Systematic Review of Clinical Efficacy of Adjunctive Antibiotics in the Treatment of Smokers With Periodontitis
Authors: Angaji Mahdi , Gelskey Shirley , Nogueira‐Filho Getulio , Brothwell Doug 
Published: June 2010

Background: The aim of this study is to systematically review the evidence of the efficacy of adjunctive antibiotic therapy to periodontal therapy in smokers with periodontitis.Methods: A search was conducted for randomized clinical trials (RCTs) with durations ≥6 months that compared periodontal therapy with and without adjunctive antibiotics for the treatment of periodontitis in smokers. Data sources primarily included PubMed with MeSH terms and free text as well as EMBASE, SCOPUS, and the Cochrane Central Register of Controlled Clinical Trials. In addition, a hand search of selected periodontal journals, bibliographies, and review articles was conducted. Independent reviewers were assigned to make independent searches and quality assessments (MA and DB) of the included studies, and disagreements were resolved by discussion.Results: Five RCTs were selected for quantitative and qualitative assessments. Little evidence was found that supported the use of antibiotic therapy in conjunction with surgical periodontal therapy in smokers. With respect to non‐surgical therapy, consistent improvements in clinical attachment level (CAL) gain and probing depth (PD) reduction was reported after the use of a 250‐mg azithromycin tablet in one study. Adjunctive doxycycline gel and minocycline microspheres statistically improved CAL gain (in one RCT) and PD reduction (in one RCT), respectively. However, the risk of bias in all studies was estimated as high. Also, inadequate and inconsistent data precluded performing meta‐analyses.Conclusions: The present systematic review concludes that the evidence for an additional benefit of adjunctive antibiotic therapy in smokers with chronic periodontitis is insufficient and inconclusive. Additional well‐designed RCTs are required to assess the effect of antibiotics in conjunction with periodontal treatments in smokers.
The selection of aptamers specific for membrane molecular targets
Authors: Janas Teresa , Janas Tadeusz 
Published: June 2010

AbstractA growing number of RNA aptamers have been selected experimentally using the SELEX combinatorial approach, and these aptamers have several advantages over monoclonal protein antibodies or peptides with respect to their applications in medicine and nanobiotechnology. Relatively few successful selections have been reported for membrane molecular targets, in contrast to the situation with non-membrane molecular targets. This review compares the procedures and techniques used in selections against membrane proteins and membrane lipids. In the case of membrane proteins, the selections were performed against soluble protein fragments, detergent-membrane protein mixed micelles, whole cells, vesicles derived from cellular membranes, and enveloped viruses. Liposomes were used as an experimental system for the selection of aptamers against membrane lipids. RNA structure-dependent aptamer binding for rafts in lipid vesicles was reported. Based on the selected aptamers against DOPC and the amino acid tryptophan, a specific passive membrane transporter composed of RNA was constructed. The determination of the selectivity of aptamers appears to be a crucial step in a selection, but has rarely been fully investigated. The selections, which use whole cells or vesicles derived from membranes, can yield aptamers not only against proteins but also against membrane lipids.
R proteins as fundamentals of plant innate immunity
Authors: Głowacki Sylwester , Macioszek Violetta , Kononowicz Andrzej 
Published: June 2010

AbstractPlants are attacked by a wide spectrum of pathogens, being the targets of viruses, bacteria, fungi, protozoa, nematodes and insects. Over the course of their evolution, plants have developed numerous defense mechanisms including the chemical and physical barriers that are constitutive elements of plant cell responses locally and/or systemically. However, the modern approach in plant sciences focuses on the evolution and role of plant protein receptors corresponding to specific pathogen effectors. The recognition of an invader’s molecules could be in most cases a prerequisite sine qua non for plant survival. Although the predicted three-dimensional structure of plant resistance proteins (R) is based on research on their animal homologs, advanced technologies in molecular biology and bioinformatics tools enable the investigation or prediction of interaction mechanisms for specific receptors with pathogen effectors. Most of the identified R proteins belong to the NBS-LRR family. The presence of other domains (including the TIR domain) apart from NBS and LRR is fundamental for the classification of R proteins into subclasses. Recently discovered additional domains (e.g. WRKY) of R proteins allowed the examination of their localization in plant cells and the role they play in signal transduction during the plant resistance response to biotic stress factors. This review focuses on the current state of knowledge about the NBS-LRR family of plant R proteins: their structure, function and evolution, and the role they play in plant innate immunity.
The proliferation and differentiation of osteoblasts in co-culture with human umbilical vein endothelial cells: An improved analysis using fluorescence-activated cell sorting
Authors: Zhang Yu , Schedle Andreas , Matejka Michael , Rausch-Fan Xiaohui , Andrukhov Oleh 
Published: June 2010

AbstractThe interaction of osteoblasts and endothelial cells plays a pivotal role in osteogenesis. This interaction has been extensively studied using their direct co-culture in vitro. However, co-culture experiments require clear discrimination between the two different cell types in the mixture, but this was rarely achieved. This study is the first to use fluorescence-activated cell sorting (FACS) for the separation and quantitative analysis of the proliferation and differentiation of MG-63 cells grown in direct co-culture with human umbilical vein endothelial cells (HUVECs). The cells of the MG-63 cell line have properties consistent with the characteristics of normal osteoblasts. We labeled HUVECs with fluorescent antibody against CD31 and used FACS to measure the proportions of each cell type and to separate them based on their different fluorescence intensities. The rate of proliferation of the MG-63 cells was estimated based on a count of the total viable cells and the proportion of MG-63 cells in the mixture. The mRNA expression levels of the osteoblast differentiation markers alkaline phosphatase (ALP), collagen type 1 (Coll-1) and osteocalcin (OC) in the MG-63 cells were measured via real-time PCR after the separation via FACS. We found that HUVECs stimulated the proliferation of the MG-63 cells after 72 h of co-culture, and inhibited it after 120 h of co-culture. The mRNA expression levels of ALP and Coll-1 significantly increased, whereas that of OC significantly decreased in MG-63 after co-culture with HUVECs. Using FACS for the quantitative analysis of the proliferation and differentiation of osteoblasts directly interacting with endothelial cells could have merit for further co-culture research.