bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-Seeded Collagen Matrix–Supported Autologous Chondrocyte Transplantation (ACT-CS)
Authors: Steinwachs Matthias , Peterson Lars , Bobic Vladimir , Verdonk Peter , Niemeyer Philipp 
Published: February 2012

Objective: Autologous chondrocyte transplantation has become an established therapy for full-thickness cartilage defects. Cell-seeded collagen matrix–supported autologous chondrocyte transplantation (ACT-CS) has been introduced as a modification of conventional ACT, which allows easier handling and is intended to combine the advantages of using a cell suspension (i.e., cell viability and mitotic activity) with the stability and self-containment provided by a matrix of biomaterials. Unlike other techniques and products, this seeding step can be easily applied using a porcine collagen type I/III membrane and autologous chondrocytes in an operating room setting. Although some suturing is required, this technique provides the distinct advantage of not requiring a water-tight seal of the bilayer membrane, as is required using the classic cell suspension technique. Comparable to other modifications of ACT, the ACT-CS procedure requires a specific surgical technique that focuses on the following important details: (1) accurate debridement of the cartilage defect; (2) preparation of the cells, and seeding and containment of the cells within the transplantation site; and (3) sealing and suturing around the defect. Design: A consensus meeting of leading European orthopedic surgeons specializing in cartilage repair was convened to discuss and standardize the surgical aspects of this technique. Results & Conclusions: The present article describes and discusses the adoption of these best surgical practices for implementing the ACT-CS technique, including more detailed descriptions of each phase of the surgery in order to standardize and optimize patient outcomes.
What Patients Expect About Autologous Chondrocyte Implantation (ACI) for Treatment of Cartilage Defects at the Knee Joint
Authors: Niemeyer Philipp , Porichis Stella , Salzmann Gian , Südkamp Norbert P. 
Published: February 2012

Objective: Although autologous chondrocyte implantation (ACI) has become an established surgical treatment for cartilage defects of the knee, little is known about what patients expect about this surgery. Design: A total of 150 patients who underwent ACI for cartilage defects at the knee were assigned to the present study and asked about their expectations and estimation concerning the ACI procedure. Patients were asked to answer 4 questions of a web-based questionnaire concerning their expectations on clinical outcome and on factors they considered relevant for clinical outcome. Results: A total of 118 (79%) returned questionnaires. Mean patient age was 32.6 years and mean defects size was 4.1 cm2. A proportion of 70% ( n = 83) of patients expected pain-free sports participation as a result of the ACI surgery, including 24 patients who expected to return to high-impact sports without any restrictions. Only 12.7% expected a reduction but persistence of pain during everyday activities. Concerning factors that influence outcome, the majority of the patients (55.1%) considered defect characteristics (i.e., size and location) most important for clinical outcome, whereas only a small proportion of patients considered rehabilitation (7.6%), cell quality (10.2%), or prior surgeries (4.2%) more relevant for final outcome. Conclusion: The present study illustrates that expectations of ACI patients are demanding and quite high. The ACI technique seems generally considered to be able to restore pain-free sports participation. Patients do not seem to be aware of all factors of possible importance concerning clinical outcome.
Response of Chondrocytes to Local Mechanical Injury in an Ex Vivo Model
Authors: Lyman Jeffrey R. , Chappell Jonathan D. , Morales Teresa I. , Kelley Scott S. , Lee Greta M. 
Published: February 2012

Background: Our goal was to set up an ex vivo culture system to assess whether cartilage wounding (partial-thickness defects) can induce morphological changes in neighboring chondrocytes and whether these cells can translocate to the surface of the defect. Methods: Two-millimeter partial-depth defects were created in human osteochondral explants followed by culture for up to 4 weeks. Frozen sections of defects and defect-free regions were labeled using immunofluorescence for a plasma membrane protein, CD44, and actin with TRITC-phalloidin. Viable nuclei were detected with Hoechst 33342. Differential interference contrast (DIC), confocal, and transmission electron microscopy (TEM) were used to examine process extension. Results: Significant changes in cell morphology occurred in response to wounding in the superficial and deep cartilage zones. These included cell flattening, polarization of the actin cytoskeleton, extension of pseudopods projecting towards the edge of the defect, and interactions of these filopodia with collagen fibers. Cell density decreased progressively in the 300-µm zone adjacent to the defect to an average of approximately 25% to 35% after 3 weeks. Concomitant increases in cell density in the defect margin were observed. By contrast, minimal changes were seen in the middle cartilage zone. Conclusions: These novel observations strongly suggest active cartilage cell responses and movements in response to wounding. It is proposed that cartilage cells use contact guidance on fibrillated collagen to move into and populate defect areas in the superficial and deep zones.
O157:H7 and O104:H4 Vero/Shiga toxin-producing Escherichia coli outbreaks: respective role of cattle and humans
Authors: Piérard Denis , De Greve Henri , Haesebrouck Freddy , Mainil Jacques 
Published: February 2012

AbstractAn enteroaggregative Verotoxin (Vtx)-producingEscherichia colistrain of serotype O104:H4 has recently been associated with an outbreak of haemolytic-uremic syndrome and bloody diarrhoea in humans mainly in Germany, but also in 14 other European countries, USA and Canada. This O104:H4E. colistrain has often been described as an enterohaemorrhagicE. coli(EHEC), i.e. a Vtx-producingE. coliwith attaching and effacing properties. Although both EHEC and the German O104:H4E. colistrains indeed produce Vtx, they nevertheless differ in several other virulence traits, as well as in epidemiological characteristics. For instance, the primary sources and vehicles of typical EHEC infections in humans are ruminants, whereas no animal reservoir has been identified for enteroaggregativeE. coli(EAggEC). The present article is introduced by a brief overview of the main characteristics of Vtx-producingE. coliand EAggEC. Thereafter, the O104:H4E. colioutbreak is compared to typical EHEC outbreaks and the virulence factors and host specificity of EHEC and EAggEC are discussed. Finally, a renewed nomenclature of Vtx-producingE. coliis proposed to avoid more confusion in communication during future outbreaks and to replace the acronym EHEC that only refers to a clinical condition.
Repertoire of Escherichia coli agonists sensed by innate immunity receptors of the bovine udder and mammary epithelial cells
Authors: Porcherie Adeline , Cunha Patricia , Trotereau Angelina , Roussel Perrine , Gilbert Florence B , Rainard Pascal , Germon Pierre 
Published: February 2012

Abstract

Escherichia coli is a frequent cause of clinical mastitis in dairy cows. It has been shown that a prompt response of the mammary gland after E. coli entry into the lumen of the gland is required to control the infection, which means that the early detection of bacteria is of prime importance. Yet, apart from lipopolysaccharide (LPS), little is known of the bacterial components which are detected by the mammary innate immune system. We investigated the repertoire of potential bacterial agonists sensed by the udder and bovine mammary epithelial cells (bMEC) during E. coli mastitis by using purified or synthetic molecular surrogates of bacterial agonists of identified pattern-recognition receptors (PRRs). The production of CXCL8 and the influx of leucocytes in milk were the readouts of reactivity of stimulated cultured bMEC and challenged udders, respectively. Quantitative PCR revealed that bMEC in culture expressed the nucleotide oligomerization domain receptors NOD1 and NOD2, along with the Toll-like receptors TLR1, TLR2, TLR4, and TLR6, but hardly TLR5. In line with expression data, bMEC proved to react to the cognate agonists C12-iE-DAP (NOD1), Pam3CSK4 (TLR1/2), Pam2CSK4 (TLR2/6), pure LPS (TLR4), but not to flagellin (TLR5). As the udder reactivity to NOD1 and TLR5 agonists has never been reported, we tested whether the mammary gland reacted to intramammary infusion of C12-iE-DAP or flagellin. The udder reacted to C12-iE-DAP, but not to flagellin, in line with the reactivity of bMEC. These results extend our knowledge of the reactivity of the bovine mammary gland to bacterial agonists of the innate immune system, and suggest that E. coli can be recognized by several PRRs including NOD1, but unexpectedly not by TLR5. The way the mammary gland senses E. coli is likely to shape the innate immune response and finally the outcome of E. coli mastitis.
ICGE: an R package for detecting relevant clusters and atypical units in gene expression
Authors: Irigoien Itziar , Sierra Basilio , Arenas Concepcion 
Published: February 2012

AbstractBackgroundGene expression technologies have opened up new ways to diagnose and treat cancer and other diseases. Clustering algorithms are a useful approach with which to analyze genome expression data. They attempt to partition the genes into groups exhibiting similar patterns of variation in expression level. An important problem associated with gene classification is to discern whether the clustering process can find a relevant partition as well as the identification of new genes classes. There are two key aspects to classification: the estimation of the number of clusters, and the decision as to whether a new unit (gene, tumor sample...) belongs to one of these previously identified clusters or to a new group.Resultsis a user-friendly package which provides many functions related to this problem: identify the number of clusters using mixed variables, usually found by applied biomedical researchers; detect whether the data have a cluster structure; identify whether a new unit belongs to one of the pre-identified clusters or to a novel group, and classify new units into the corresponding cluster. The functions in the ICGE package are accompanied by help files and easy examples to facilitate its use.ConclusionsWe demonstrate the utility of ICGE by analyzing simulated and real data sets. The results show that ICGE could be very useful to a broad research community.
Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis
Authors: Wang Yang , Liu Chong , Fang Ying , Liu Xiaoli , Li Wentao , Liu Shuqing , Liu Yingyu , Liu Yuxi , Charreyre Catherine , Audonnet Jean-Christophe , Chen Pin , He Qigai 
Published: February 2012

AbstractBackgroundHaemophilus parasuis(H. parasuis) is the etiological agent of Glässer's disease in pigs. Currently, the molecular basis of this infection is largely unknown. The innate immune response is the first line of defense against the infectious disease. Systematical analysis on host innate immune response to the infection is important for understanding the pathogenesis of the infectious microorganisms.ResultsA total of 428 differentially expressed (DE) genes were identified in the porcine alveolar macrophages (PAMs) 6 days afterH. parasuisinfection. These genes were principally related to inflammatory response, immune response, microtubule polymerization, regulation of transcript and signal transduction. Through the pathway analysis, the significant pathways mainly concerned with cell adhesion molecules, cytokine-cytokine receptor interaction, complement and coagulation cascades, toll-like receptor signaling pathway, MAPK signaling pathway, suggesting that the host took different strategies to activate immune and inflammatory response uponH. parasuisinfection. The global interactions network and two subnetworks of the proteins encoded by DE genes were analyzed by using STRING. Further immunostimulation analysis indicated that mRNA levels of S100 calcium-binding protein A4 (S100A4) and S100 calcium-binding protein A6 (S100A6) in porcine PK-15 cells increased within 48 h and were sustained after administration of lipopolysaccharide (LPS) and Poly (I:C) respectively. Thes100a4ands100a6genes were found to be up-regulated significantly in lungs, spleen and lymph nodes inH. parasuisinfected pigs. We firstly cloned and sequenced the porcinecoronin1agene. Phylogenetic analysis showed that poCORONIN 1A belonged to the group containing theBos taurussequence. Structural analysis indicated that the poCORONIN 1A contained putative domains of Trp-Asp (WD) repeats signature, Trp-Asp (WD) repeats profile and Trp-Asp (WD) repeats circular profile at the N-terminus.ConclusionsOur present study is the first one focusing on the response of porcine alveolar macrophages toH. parasuis. Our data demonstrate a series of genes are activated uponH. parasuisinfection. The observed gene expression profile could help screening the potential host agents for reducing the prevalence ofH. parasuisand further understanding the molecular pathogenesis associated withH. parasuisinfection in pigs.
Identification of novel microRNAs in Hevea brasiliensisand computational prediction of their targets
Authors: Gébelin Virginie , Argout Xavier , Engchuan Worrawat , Pitollat Bertrand , Duan Cuifang , Montoro Pascal , Leclercq Julie 
Published: February 2012

Abstract

Background
Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. They negatively regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs (mRNAs). In Hevea brasiliensis, environmental and harvesting stresses are known to affect natural rubber production. This study set out to identify abiotic stress-related miRNAs in Hevea using next-generation sequencing and bioinformatic analysis.

Results
Deep sequencing of small RNAs was carried out on plantlets subjected to severe abiotic stress using the Solexa technique. By combining the LeARN pipeline, data from the Plant microRNA database (PMRD) and Hevea EST sequences, we identified 48 conserved miRNA families already characterized in other plant species, and 10 putatively novel miRNA families. The results showed the most abundant size for miRNAs to be 24 nucleotides, except for seven families. Several MIR genes produced both 20-22 nucleotides and 23-27 nucleotides. The two miRNA class sizes were detected for both conserved and putative novel miRNA families, suggesting their functional duality. The EST databases were scanned with conserved and novel miRNA sequences. MiRNA targets were computationally predicted and analysed. The predicted targets involved in "responses to stimuli" and to "antioxidant" and "transcription activities" are presented.

Conclusions
Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs when the complete genome is not yet available. Our study provided additional information for evolutionary studies and revealed potentially specific regulation of the control of redox status in Hevea.
Methylation of the KEAP1 gene promoter region in human colorectal cancer
Authors: Hanada Naoyuki , Takahata Takenori , Zhou Qiliang , Ye Xulu , Sun Ruowen , Itoh Jugoh , Ishiguro Atsushi , Kijima Hiroshi , Mimura Junsei , Itoh Ken , Fukuda Shinsaku , Saijo Yasuo 
Published: February 2012

Abstract

Background
The Keap1-Nrf2 pathway has been reported to be impaired in several cancers. However, the status of Keap1-Nrf2 system in human colorectal cancer (CRC) has not been elucidated.

Methods
We used colorectal cancer (CRC) cell lines and surgical specimens to investigate the methylation status of the KEAP1 promoter region as well as expression of Nrf2 and its downstream antioxidative stress genes, NQO-1 and AKR1C1.

Results
DNA sequencing analysis indicated that all mutations detected were synonymous, with no amino acid substitutions. We showed by bisulfite genomic sequencing and methylation-specific PCR that eight of 10 CRC cell lines had hypermethylated CpG islands in the KEAP1 promoter region. HT29 cells with a hypermethylated KEAP1 promoter resulted in decreased mRNA and protein expression but unmethylated Colo320DM cells showed higher expression levels. In addition, treatment with the DNA methyltransferase inhibitor 5-Aza-dC combined with the histone deacetylase inhibitor trichostatin A (TSA) increased KEAP1 mRNA expression. These result suggested that methylation of the KEAP1 promoter regulates its mRNA level. Time course analysis with the Nrf2-antioxidant response element (ARE) pathway activator t-BHQ treatment showed a rapid response within 24 h. HT29 cells had higher basal expression levels of NQO-1 and AKR1C1 mRNA than Colo320DM cells. Aberrant promoter methylation of KEAP1 was detected in 53% of tumor tissues and 25% of normal mucosae from 40 surgical CRC specimens, indicating that cancerous tissue showed increased methylation of the KEAP1 promoter region, conferring a protective effect against cytotoxic anticancer drugs.

Conclusion
Hypermethylation of the KEAP1 promoter region suppressed its mRNA expression and increased nuclear Nrf2 and downstream ARE gene expression in CRC cells and tissues.
The economic impact of stroke in The Netherlands: the €-restore4stroke study
Authors: van Eeden Mitchel , van Heugten Caroline M , Evers Silvia MAA 
Published: February 2012

Abstract

Background
Stroke has a considerable socio-economic impact worldwide and is the leading cause of disabilities in the Western world. Economic studies of stroke focus merely on physical aspects and clinical interventions. To our current knowledge there is no comprehensive economic study investigating the economic impact of stroke including psychological and social aspects. The €-Restore4Stroke project, part of a large comprehensive research programme Restore4Stroke, aims to investigate the total economic impact of stroke in the Netherlands.

Methods
Two trial-based economic evaluation studies will be conducted within the €-Restore4Stroke project: one focussing on a self-management intervention and one on an augmented cognitive behavioural therapy intervention. Both include cost-effectiveness analyses and cost-utility analyses as primary research methods. Furthermore, a cost-of-illness study investigating costs after stroke attached to a cohort study and a record linkage study in which four databases are linked to investigate patterns of health care consumption before and after stroke, are embedded in €-Restore4Stroke. All studies will be performed from a societal perspective. The primary outcome measure for the cost-effectiveness analysis is the increase in health status on the primary outcome scales. Within the cost-utility analysis, the primary outcome measure is quality-adjusted life years (QALYs) for which an indirect preference-based technique will be used. In the self-management study we will also look at the estimation of health effects on informal caregivers. Cost outcomes in the cost-of-illness study will be computed with a cost questionnaire and linkage of several databases will be used to derive outcomes in the record linkage study,

Discussion
€-Restore4Stroke will provide new insights and evidence for the economic impact of psychosocial consequences after stroke. Besides being innovative in various ways (i.e. focussing on the chronic phase after stroke and including personal factors as possible determinants of long-term re-integration including quality of life in a prospective longitudinal design), a major strength of €-Restore4Stroke is that we include impact on informal caregivers. The outcomes of this study will provide health care decision makers with valuable and necessary information regarding stroke care related decisions.

Trial registration

NTR3051 (RCT Self-management), NTR2999 (RCT Augmented Cognitive Behavioural Therapy)
Recombinant protein expression in Pichia pastoris strains with an engineered methanol utilization pathway
Authors: Krainer Florian W , Dietzsch Christian , Hajek Tanja , Herwig Christoph , Spadiut Oliver , Glieder Anton 
Published: February 2012

Abstract

Βackground
The methylotrophic yeast Pichia pastoris has become an important host organism for recombinant protein production and is able to use methanol as a sole carbon source. The methanol utilization pathway describes all the catalytic reactions, which happen during methanol metabolism. Despite the importance of certain key enzymes in this pathway, so far very little is known about possible effects of overexpressing either of these key enzymes on the overall energetic behavior, the productivity and the substrate uptake rate in P. pastoris strains.

Results
A fast and easy-to-do approach based on batch cultivations with methanol pulses was used to characterize different P. pastoris strains. A strain with MutS phenotype was found to be superior over a strain with Mut+ phenotype in both the volumetric productivity and the efficiency in expressing recombinant horseradish peroxidase C1A. Consequently, either of the enzymes dihydroxyacetone synthase, transketolase or formaldehyde dehydrogenase, which play key roles in the methanol utilization pathway, was co-overexpressed in MutS strains harboring either of the reporter enzymes horseradish peroxidase or Candida antarctica lipase B. Although the co-overexpression of these enzymes did not change the stoichiometric yields of the recombinant MutS strains, significant changes in the specific growth rate, the specific substrate uptake rate and the specific productivity were observed. Co-overexpression of dihydroxyacetone synthase yielded a 2- to 3-fold more efficient conversion of the substrate methanol into product, but also resulted in a reduced volumetric productivity. Co-overexpression of formaldehyde dehydrogenase resulted in a 2-fold more efficient conversion of the substrate into product and at least similar volumetric productivities compared to strains without an engineered methanol utilization pathway, and thus turned out to be a valuable strategy to improve recombinant protein production.

Conclusions
Co-overexpressing enzymes of the methanol utilization pathway significantly affected the specific growth rate, the methanol uptake and the specific productivity of recombinant P. pastoris MutS strains. A recently developed methodology to determine strain specific parameters based on dynamic batch cultivations proved to be a valuable tool for fast strain characterization and thus early process development.