bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomechanical Evaluation of Knotless Anatomical Double-Layer Double-Row Rotator Cuff Repair
Authors: Hepp Pierre , Osterhoff Georg , Engel Thomas , Marquass Bastian , Klink Thomas , Josten Christoph 
Published: March 2009

Background The layered configuration of the rotator cuff tendon is not taken into account in classic rotator cuff tendon repair techniques. Hypothesis The mechanical properties of (1) the classic double-row technique, (2) a double-layer double-row (DLDR) technique in simple suture configuration, and (3) a DLDR technique in mattress suture configuration are significantly different. Study Design Controlled laboratory study. Methods Twenty-four sheep shoulders were assigned to 3 repair groups of full-thickness infraspinatus tears: group 1, traditional double-row repair; group 2, DLDR anchor repair with simple suture configuration; and group 3, DLDR knotless repair with mattress suture configuration. After ultrasound evaluation of the repair, each specimen was cyclically loaded with 10 to 100 N for 50 cycles. Each specimen was then loaded to failure at a rate of 1 mm/s. Results There were no statistically significant differences among the 3 testing groups for the mean footprint area. The cyclic loading test revealed no significant difference among the 3 groups with regard to elongation. For the load-to-failure test, groups 2 and 3 showed no differences in ultimate tensile load when compared with group 1. However, when compared to group 2, group 3 was found to have significantly higher values regarding ultimate load, ultimate elongation, and energy absorbed. Conclusion The DLDR fixation techniques may provide strength of initial repair comparable with that of commonly used double-row techniques. When compared with the knotless technique with mattress sutures, simple suture configuration of DLDR repair may be too weak. Knotless DLDR rotator cuff repair may (1) restore the footprint by the use of double-row principles and (2) enable restoration of the shape and profile. Clinical Relevance Double-layer double-row fixation in mattress suture configuration has initial fixation strength comparable with that of the classic double-row fixation and so may potentially improve functional results of rotator cuff repair.
Thrombophilic patterns of coagulation factors in lupus
Authors: Dhar JP , Andersen J , Essenmacher L , Ager J , Bentley G , Sokol RJ 
Published: March 2009

Our aim was to better define the coagulation abnormalities in patients with systemic lupus erythematosus who had thrombosis or high-risk clinical settings for thrombosis. Clinical and laboratory data of 111 patients with lupus referred for coagulation assessment because of thrombosis, pregnancy loss or high-risk clinical settings for thrombosis were reviewed retrospectively. Increased activity of procoagulant factors and decreased activity of anti-coagulant factors were observed well above the expected 5% prevalence. All comparisons were significant at the P < 0.001 level. Anticardiolipin antibodies were present in 70.5% of patients tested (55/78) in this high-risk group, but usually in low titres. Platelet hyperfunction was detected in the majority of patients tested (85.7%, 78/91). Hypercoagulability in lupus is complex and is better defined by assessing multiple haemostatic factors in addition to platelet function. Platelet hyperfunction contributes significantly to thrombophilia in lupus and this is the key finding of our study.
Association of the HLA-G 14 bp polymorphism with systemic lupus erythematosus
Authors: Veit TD , Cordero EAA , Mucenic T , Monticielo OA , Brenol JCT , Xavier RM , Delgado-Cañedo A , Chies JAB 
Published: March 2009

Human leukocyte antigen-G (HLA-G) is a nonclassical class I major histocompatibility complex molecule which is induced at the course of inflammatory pathologies, and its expression has been suggested as a possible mechanism of tissue protection against autoimmune inflammatory responses, therefore acting as a mechanism of immune surveillance. We investigated the influence of the 14 bp polymorphism of the HLA-G gene on systemic lupus erythematosus (SLE) by analyzing 293 patients with SLE and 460 healthy controls. The patient’s group was not in Hardy–Weinberg equilibrium, presenting an excess of heterozygotes ( P = 0.014). The heterozygote group exhibited lower systemic lupus erythematosus disease activity indexes than the homozygous deletion group and the homozygous insertion group (mean value = 2.29 against 2.97 and 3.4, respectively, P = 0.035). Photosensitive patients showed a higher frequency of heterozygotes and an equivalent lower frequency of homozygotes for deletion; on the other hand, patients without arthritis presented a higher frequency of heterozygotes than the arthritis group and also a lower frequency of the del/del genotype. Overall, our results support the idea of a role of the HLA-G insertion/deletion polymorphism and therefore a role for the HLA-G molecule, on the pathology of SLE.
Clinical and immunological manifestations in 624 SLE patients in Saudi Arabia
Authors: Al Arfaj AS , Khalil N 
Published: March 2009

Our objective was to study the demographic, clinical, laboratory features, therapy, and outcome of systemic lupus erythematosus (SLE) patients. In this retrospective study, which covered a 27-year period (1980–2006), 624 SLE patients referring to King Khalid University hospital, Riyadh were included. There were 566 females and 58 males (9.8:1) with a mean age of 34.3 (range 8–71) years and mean age at disease onset of 25.3 years (range 0.08–67). The mean disease duration was 9.3 years (range 0.3–30). The most common disease manifestations were hematological abnormalities (82.7%), arthritis (80.4%), and mucocutaneous symptoms (64.3%). The prevalence of malar rash was 47.9%, discoid rash 17.6%, photosensitivity 30.6%, oral ulcers 39.1%, serositis 27.4%, nephritis 47.9%, and neuropsychiatric manifestations 27.6%. Lymphopenia (40.3%), anti-Ro (53.1%), anti-La (26.6%), anti-Sm (41.6%), anticardiolipin IgG (49.7%), and IgM (33.5%) antibodies were highly prevalent. Antinuclear antibodies were detected in 99.7% and anti-DNA in 80.1% patients. Low C3 and C4 were observed in 45.4% and 42.2%, respectively. Therapy included oral steroids (96.2%), IV cyclophosphamide (34.1%) and azathioprine (32.1%) along with other drugs. Long-term remission was achieved in 82.4%, disease was active in 2.6%, renal failure occurred in 4.3% requiring dialysis, 6.7% lost follow up and 4.0% patients died. Infections (48%) and active SLE (36%) were the common causes of death. The 5- and 10-year patient survival rate was 98% and 97%, respectively. This study suggests that, in our patients, SLE manifests with features similar to SLE patients from other Arab countries and Caucasia. In comparison to Caucasians, higher prevalence of anti-Ro antibodies is observed in our study, in some Middle-Eastern and Asian countries; this may likely be due to inter-ethnic variation owing to genetic differences. Our 5-year patient survival rate was similar to that of western countries, while 10-year survival rate was better than that of most places.
Copy number variation in African Americans
Authors: McElroy Joseph P , Nelson Matthew R , Caillier Stacy J , Oksenberg Jorge R 
Published: March 2009

AbstractBackgroundCopy number variants (CNVs) have been identified in several studies to be associated with complex diseases. It is important, therefore, to understand the distribution of CNVs within and among populations. This study is the first report of a CNV map in African Americans.ResultsEmploying a SNP platform with greater than 500,000 SNPs, a first-generation CNV map of the African American genome was generated using DNA from 385 healthy African American individuals, and compared to a sample of 435 healthy White individuals. A total of 1362 CNVs were identified within African Americans, which included two CNV regions that were significantly different in frequency between African Americans and Whites (17q21 and 15q11). In addition, a duplication was identified in 74% of DNAs derived from cell lines that was not present in any of the whole blood derived DNAs.ConclusionThe Affymetrix 500 K array provides reliable CNV mapping information. However, using cell lines as a source of DNA may introduce artifacts. The duplication identified in high frequency in Whites and low frequency in African Americans on chromosome 17q21 reflects haplotype specific frequency differences between ancestral groups. The generation of the CNV map will be a valuable tool for identifying disease associated CNVs in African Americans.
Erratum to: Gene expression and isoform variation analysis using Affymetrix exon arrays
Authors: Bemmo Amandine , Benovoy David , Kwan Tony , Gaffney Daniel J , Jensen Roderick V , Majewski Jacek 
Published: March 2009

Abstract
Correction to Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J: Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics 2008, 9: 529.
Biocomputational prediction of non-coding RNAs in model cyanobacteria
Authors: Voß Björn , Georg Jens , Schön Verena , Ude Susanne , Hess Wolfgang R 
Published: March 2009

Abstract

Background
In bacteria, non-coding RNAs (ncRNA) are crucial regulators of gene expression, controlling various stress responses, virulence, and motility. Previous work revealed a relatively high number of ncRNAs in some marine cyanobacteria. However, for efficient genetic and biochemical analysis it would be desirable to identify a set of ncRNA candidate genes in model cyanobacteria that are easy to manipulate and for which extended mutant, transcriptomic and proteomic data sets are available.

Results
Here we have used comparative genome analysis for the biocomputational prediction of ncRNA genes and other sequence/structure-conserved elements in intergenic regions of the three unicellular model cyanobacteria Synechocystis PCC6803, Synechococcus elongatus PCC6301 and Thermosynechococcus elongatus BP1 plus the toxic Microcystis aeruginosa NIES843. The unfiltered numbers of predicted elements in these strains is 383, 168, 168, and 809, respectively, combined into 443 sequence clusters, whereas the numbers of individual elements with high support are 94, 56, 64, and 406, respectively. Removing also transposon-associated repeats, finally 78, 53, 42 and 168 sequences, respectively, are left belonging to 109 different clusters in the data set. Experimental analysis of selected ncRNA candidates in Synechocystis PCC6803 validated new ncRNAs originating from the fabF-hoxH and apcC-prmA intergenic spacers and three highly expressed ncRNAs belonging to the Yfr2 family of ncRNAs. Yfr2a promoter-luxAB fusions confirmed a very strong activity of this promoter and indicated a stimulation of expression if the cultures were exposed to elevated light intensities.

Conclusion
Comparison to entries in Rfam and experimental testing of selected ncRNA candidates in Synechocystis PCC6803 indicate a high reliability of the current prediction, despite some contamination by the high number of repetitive sequences in some of these species. In particular, we identified in the four species altogether 8 new ncRNA homologs belonging to the Yfr2 family of ncRNAs. Modelling of RNA secondary structures indicated two conserved single-stranded sequence motifs that might be involved in RNA-protein interactions or in the recognition of target RNAs. Since our analysis has been restricted to find ncRNA candidates with a reasonable high degree of conservation among these four cyanobacteria, there might be many more, requiring direct experimental approaches for their identification.
Comparative genomics of lactic acid bacteria reveals a niche-specific gene set
Authors: O'Sullivan Orla , O'Callaghan John , Sangrador-Vegas Amaia , McAuliffe Olivia , Slattery Lydia , Kaleta Pawel , Callanan Michael , Fitzgerald Gerald F , Ross R Paul , Beresford Tom 
Published: March 2009

Abstract

Background
The recently sequenced genome of Lactobacillus helveticus DPC4571 [1] revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM [2]. This led us to hypothesise that a group of genes could be determined which could define an organism's niche.

Results
Taking 11 fully sequenced lactic acid bacteria (LAB) as our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we demonstrated that the presence or absence of certain genes involved in sugar metabolism, the proteolytic system, and restriction modification enzymes were pivotal in suggesting the niche of a strain. We identified 9 niche specific genes, of which 6 are dairy specific and 3 are gut specific. The dairy specific genes identified in Lactobacillus helveticus DPC4571 were lhv_1161 and lhv_1171, encoding components of the proteolytic system, lhv_1031 lhv_1152, lhv_1978 and lhv_0028 encoding restriction endonuclease genes, while bile salt hydrolase genes lba_0892 and lba_1078, and the sugar metabolism gene lba_1689 from Lb. acidophilus NCFM were identified as gut specific genes.

Conclusion
Comparative analysis revealed that if an organism had homologs to the dairy specific geneset, it probably came from a dairy environment, whilst if it had homologs to gut specific genes, it was highly likely to be of intestinal origin.
We propose that this "barcode" of 9 genes will be a useful initial guide to researchers in the LAB field to indicate an organism's ability to occupy a specific niche.
Nitric oxide synthase 2A (NOS2A) polymorphisms are not associated with invasive pneumococcal disease
Authors: Payton Antony , Payne Debbie , Mankhambo Limangeni A , Banda Daniel L , Hart C Anthony , Ollier William ER , Carrol Enitan D 
Published: March 2009

Abstract

Background

Streptococcus pneumoniae (pneumococcus) is responsible for over one million deaths per year, with young children, the elderly and immunocompromised individuals being most at risk. Approximately half of East African children have been reported to be asymptomatic carriers of pneumococcus with invasive infection occurring after the disruption of the respiratory membrane which is believed to be caused by the host immune response. Racial incidence of invasive pneumococcal disease (IPD) is higher in certain populations even after adjusting for environmental factors suggesting a genetic component to disease susceptibility. The nitric oxide synthase 2A (NOS2A) gene is responsible for the production of nitric oxide under pathological conditions including host defence against bacterial infection. Nitric oxide is a modulator of apoptotic and inflammatory cascades and endothelial permeability. We hypothesised that genetic variants within this gene may predispose to disease risk and survival.

Methods
A cohort of 299 children with IPD (221 meningitis, 41 pneumonia and 37 with bacteraemia) and 931 age matched controls from Malawi were used in this study. We investigated nine haplotype tagging single nucleotide polymorphisms within the NOS2A gene and compared the presence or absence of the minor alleles in cases and controls and survivors and non-survivors within the cases.

Results
We observed no significant associations between cases and controls or with survival in either all IPD cases or in the separate analysis of meningitis cases. A near significant association was obtained for the comparison of rs8078340 in cases and controls (p-value, 0.078). However, results were unadjusted for multiple testing.

Conclusion
Our results suggest that polymorphic variation within the NOS2A gene does not influence invasive pneumococcal disease susceptibility or survival.
Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins
Authors: Heikkinen Outi , Seppala Raili , Tossavainen Helena , Heikkinen Sami , Koskela Harri , Permi Perttu , Kilpeläinen Ilkka 
Published: March 2009

Abstract

Background

Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of infections from mild respiratory tract infections to life-threatening states as sepsis. Recent emergence of S. aureus strains resistant to numerous antibiotics has created a need for new antimicrobial agents and novel drug targets. S. aureus PrsA is a membrane associated extra-cytoplasmic lipoprotein which contains a parvulin-type peptidyl-prolyl cis-trans isomerase domain. PrsA is known to act as an essential folding factor for secreted proteins in Gram-positive bacteria and thus it is a potential target for antimicrobial drugs against S. aureus.

Results
We have solved a high-resolution solution structure of the parvulin-type peptidyl-prolyl cis-trans isomerase domain of S. aureus PrsA (PrsA-PPIase). The results of substrate peptide titrations pinpoint the active site and demonstrate the substrate preference of the enzyme. With detailed NMR spectroscopic investigation of the orientation and tautomeric state of the active site histidines we are able to give further insight into the structure of the catalytic site. NMR relaxation analysis gives information on the dynamic behaviour of PrsA-PPIase.

Conclusion
Detailed structural description of the S. aureus PrsA-PPIase lays the foundation for structure-based design of enzyme inhibitors. The structure resembles hPin1-type parvulins both structurally and regarding substrate preference. Even though a wealth of structural data is available on parvulins, the catalytic mechanism has yet to be resolved. The structure of S. aureus PrsA-PPIase and our findings on the role of the conserved active site histidines help in designing further experiments to solve the detailed catalytic mechanism.
Mammaglobin as a potential molecular target for breast cancer drug delivery
Authors: Zuo Lian , Li Ly , Wang Qian , Fleming Timothy P , You Shaojin 
Published: March 2009

Abstract

Background
Mammaglobin (MAM) has been used as a specific molecular marker for breast cancer diagnosis. Recently, several groups of researchers proposed a number of therapeutic strategies targeting this molecule. Some of the strategies are based upon an essential but not demonstrated hypothesis – mammaglobin is associated with the surface of breast cancer cells, which strongly disputes the therapeutic strategies.

Results
We conducted a computer-based predictive analysis and identified a small fragment at the N-end of MAM as a potential transmembrane domain. We provided several evidences to demonstrate the presence of the membrane-associated MAM. We isolated the membrane protein components from known MAM positive breast cancer cells (MDA-MB361 and MDA-MB415). We showed that about 22–64% of MAM proteins, depending upon the types of the cancer cells, directly attached on the membrane of breast cancer cells, by Western blotting assays. To directly visualize the presence of the membrane-bound MAM protein, we incubated the MAM positive cancer cells with FITC labeled anti-MAM antibody, and observed clear fluorescent signals on the surface of the cells. In studying the MAM protein distribution in human breast cancer tissues, we first identified two immunostain patterns that are associated with the membrane-bound MAM: the membrane stain pattern and luminary surface stain pattern. To test whether the membrane-associated MAM can serve as a molecular target for drug delivery, we conjugated anti-MAM antibody to human low-density lipoprotein (LDL) and loaded doxorubicin (Dox) in the core of LDL. Specific binding and cytotoxicity of the MAM targeted and Dox loaded LDL was tested in the MAM positive breast cancer cells in vitro.

Conclusion
We first showed that some of MAM protein directly associated with the surface of breast cancer cells. The membrane-associated MAM protein may be utilized as a useful molecular marker for breast cancer targeted drug delivery.
Taurolidine reduces the tumor stimulating cytokine interleukin-1beta in patients with resectable gastrointestinal cancer: a multicentre prospective randomized trial
Authors: Braumann Chris , Gutt Carsten N , Scheele Johannes , Menenakos Charalambos , Willems Wilhelm , Mueller Joachim M , Jacobi Christoph A 
Published: March 2009

Abstract

Background
The effect of additional treatment strategies with antineoplastic agents on intraperitoneal tumor stimulating interleukin levels are unclear. Taurolidine and Povidone-iodine have been mainly used for abdominal lavage in Germany and Europe.

Methods
In the settings of a multicentre (three University Hospitals) prospective randomized controlled trial 120 patients were randomly allocated to receive either 0.5% taurolidine/2,500 IU heparin (TRD) or 0.25% povidone-iodine (control) intraperitoneally for resectable colorectal, gastric or pancreatic cancers. Due to the fact that IL-1beta (produced by macrophages) is preoperatively indifferent in various gastrointestinal cancer types our major outcome criterion was the perioperative (overall) level of IL-1beta in peritoneal fluid.

Results
Cytokine values were significantly lower after TRD lavage for IL-1beta, IL-6, and IL-10. Perioperative complications did not differ. The median follow-up was 50.0 months. The overall mortality rate (28 vs. 25, p = 0.36), the cancer-related death rate (17 vs. 19, p = .2), the local recurrence rate (7 vs. 12, p = .16), the distant metastasis rate (13 vs. 18, p = 0.2) as well as the time to relapse were not statistically significant different.

Conclusion
Reduced cytokine levels might explain a short term antitumorigenic intraperitoneal effect of TRD. But, this study analyzed different types of cancer. Therefore, we set up a multicentre randomized trial in patients undergoing curative colorectal cancer resection.

Trial registration
ISRCTN66478538
Comparison of intraoperative frozen section analysis for sentinel lymph node biopsy during breast cancer surgery for invasive lobular carcinoma and invasive ductal carcinoma
Authors: Horvath James W , Barnett Gary E , Jimenez Rafael E , Young Donn C , Povoski Stephen P 
Published: March 2009

AbstractBackgroundSentinel lymph node (SLN) biopsy is the standard of care for the surgical assessment of the axilla during breast cancer surgery. However, the diagnostic accuracy of intraoperative frozen section analysis for confirming metastatic involvement of SLNs in cases of invasive lobular carcinoma (ILC) versus that of invasive ductal carcinoma (IDC) has generated controversy secondary to a frequently low-grade cytologic appearance and an often discohesive pattern displayed by metastatic lymph nodes in ILC. In the current report, we present a comparison of intraoperative frozen section analysis for confirming the presence of metastatic disease within SLNs during breast cancer surgery for ILC and IDC.MethodsWe evaluated the results of 131 consecutive cases of ILC from 1997 to 2008 and 133 cases of IDC (selected by a random sequence generator program) from amongst 1163 consecutive cases of IDC from the same time period. All cases had at least one SLN that had both intraoperative frozen section analysis and confirmatory permanent section analysis performed.ResultsNo statistically significant difference was found in the sensitivity (67% vs. 75%, P = 0.385), specificity (100% vs. 100%), accuracy (86% vs. 92%, P = 0.172), false negative rate (33% vs. 25%, P = 0.385), negative predictive value (81% vs. 89%, P = 0.158), and positive predictive value (100% vs. 100%) for frozen section analysis for confirming the presence of metastatic disease within SLNs during breast cancer surgery for ILC and IDC.ConclusionSince there was no statistically significant difference in sensitivity, specificity, accuracy, false negative rate, negative predictive value, and positive predictive value between frozen section analysis of SLNs for patients with ILC and IDC, the clinical accuracy of confirming metastatic involvement of SLNs on frozen section analysis for ILC should not be considered inferior to the clinical accuracy for IDC. Therefore, frozen section analysis of all SLNs during breast cancer surgery in patients with ILC should remain the standard of care in order to reduce the risk of the need of a later, separate axillary lymph node dissection.