bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of proteinases from the midgut of Rhipicephalus (Boophilus) microplus involved in the generation of antimicrobial peptides
Authors: Cruz Carlos E , Fogaça Andréa C , Nakayasu Ernesto S , Angeli Cláudia B , Belmonte Rodrigo , Almeida Igor C , Miranda Antônio , Miranda Maria Terêsa M , Tanaka Aparecida S , Braz Glória R , Craik Charles S , Schneider Eric , Caffrey Conor R , Daffre Sirlei 
Published: July 2010

Abstract

Background
Hemoglobin is a rich source of biologically active peptides, some of which are potent antimicrobials (hemocidins). A few hemocidins have been purified from the midgut contents of ticks. Nonetheless, how antimicrobials are generated in the tick midgut and their role in immunity is still poorly understood. Here we report, for the first time, the contribution of two midgut proteinases to the generation of hemocidins.

Results
An aspartic proteinase, designated BmAP, was isolated from the midgut of Rhipicephalus (Boophilus) microplus using three chromatographic steps. Reverse transcription-quantitative polymerase chain reaction revealed that BmAP is restricted to the midgut. The other enzyme is a previously characterized midgut cathepsin L-like cysteine proteinase designated BmCL1. Substrate specificities of native BmAP and recombinant BmCL1 were mapped using a synthetic combinatorial peptide library and bovine hemoglobin. BmCL1 preferred substrates containing non-polar residues at P2 subsite and polar residues at P1, whereas BmAP hydrolysed substrates containing non-polar amino acids at P1 and P1'.

Conclusions
BmAP and BmCL1 generate hemocidins from hemoglobin alpha and beta chains in vitro. We postulate that hemocidins may be important for the control of tick pathogens and midgut flora.
Characterisation of the Binding Properties of Bacillus Thuringiensis 18 Toxin on Leukaemic Cells
Authors: Wong Rebecca SY , Mohamed Shar M , Nadarajah Vishna D , Tengku Ibrahim Azmi T 
Published: July 2010

AbstractBackgroundVarious strains ofBacillus thuringiensis(Bt) have been found to produce parasporal proteins that are cytotoxic to human cancer cells. This study aims to establish the binding affinity of purified Bt 18 toxin for CEM-SS (T lymphoblastic leukaemia cell line), to determine if competition exists between the toxin and commercial anticancer drugs for the binding site on CEM-SS and to localise the binding site of the toxin on CEM-SS.MethodsIn homologous competitive binding study, the purified toxin was labelled with biotin and allowed to compete with unlabelled toxin for binding sites on CEM-SS and its dissociation constant (Kd) was determined. Comparisons were made with CCRF-SB, CCRF-HSB-2 and MCF-7. In heterologous competitive binding study, biotinylated toxin competition was determined with two other Bt toxins (crude Btj and crude Bt 22) and anticancer drugs (cisplatin, doxorubicin, etoposide, navelbine and methotrexate). To localise the binding site under the confocal microscope, the biotinylated toxin was tagged with FITC-conjugated streptavidin.ResultsHomologous competitive binding assays revealed decreasing binding affinity of Bt 18 toxin for CEM-SS, CCRF-SB, and CCRF-HSB-2 with Kd of 8.44 nM, 14.98 nM and 17.71 nM respectively. Kd for MCF-7 was not determined as the inhibitory concentration (IC50) was not reached. Heterologous competitive study showed little competition (< 30%) between biotinylated Bt 18 toxin and all test compounds used. Confocal microscopy revealed binding of toxin at the periphery of the cell.ConclusionsIt was postulated that purified Bt 18 toxin binds on the cell surface of CEM-SS and the mechanism of cell death may differ from that of Btj toxin, Bt 22 toxin and all five anticancer drugs used in this study, since it did not significantly compete with these compounds for the same binding site.
Economic results of a palivizumab seasonal prophylaxis using a cohorting software and vial sharing
Authors: Coletta Elio , Coppolino Salvatore , Federico Febronia , Fulia Francesco 
Published: July 2010

Abstract

Background
Respiratory syncytial virus is the most important pathogen in lower respiratory tract infection in infants and young children. In high-risk populations it may develop severe, sometimes fatal, lower respiratory tract infections. A proportion of these infants require admission to intensive care units due to the severity of the condition and the level of care needed. Furthermore, we must consider the possible increased risk of asthma following RSV infection in infancy.

Methods
The aim of this work is to show how we strictly coordinated, during the 2008-2009 RSV season, the delivery of prophylaxis while minimising drug cost through vial sharing and cohorting infants with a software performed through Visual Basic programming system.

Results
By using this method we have been able to obtain a saving of the 29.2% compared to the theoretical amount. No infant requested hospitalisation for a RSV infection.

Conclusions
Such a model ensures all patients to receive appropriate immunization and thus positively influencing the cost-benefit of palivizumab prophylaxis. We hope that our model of care delivery will be of use to other hospitals.
Trait-stratified genome-wide association study identifies novel and diverse genetic associations with serologic and cytokine phenotypes in systemic lupus erythematosus
Authors: Kariuki Silvia N , Franek Beverly S , Kumar Akaash A , Arrington Jasmine , Mikolaitis Rachel A , Utset Tammy O , Jolly Meenakshi , Crow Mary K , Skol Andrew D , Niewold Timothy B 
Published: July 2010

Abstract
Introduction
Systemic lupus erythematosus (SLE) is a highly heterogeneous disorder, characterized by differences in autoantibody profile, serum cytokines, and clinical manifestations. SLE-associated autoantibodies and high serum interferon alpha (IFN-α) are important heritable phenotypes in SLE which are correlated with each other, and play a role in disease pathogenesis. These two heritable risk factors are shared between ancestral backgrounds. The aim of the study was to detect genetic factors associated with autoantibody profiles and serum IFN-α in SLE.

Methods
We undertook a case-case genome-wide association study of SLE patients stratified by ancestry and extremes of phenotype in serology and serum IFN-α. Single nucleotide polymorphisms (SNPs) in seven loci were selected for follow-up in a large independent cohort of 538 SLE patients and 522 controls using a multi-step screening approach based on novel metrics and expert database review. The seven loci were: leucine-rich repeat containing 20 (LRRC20); protein phosphatase 1 H (PPM1H); lysophosphatidic acid receptor 1 (LPAR1); ankyrin repeat and sterile alpha motif domain 1A (ANKS1A); protein tyrosine phosphatase, receptor type M (PTPRM); ephrin A5 (EFNA5); and V-set and immunoglobulin domain containing 2 (VSIG2).

Results
SNPs in the LRRC20, PPM1H, LPAR1, ANKS1A, and VSIG2 loci each demonstrated strong association with a particular serologic profile (all odds ratios > 2.2 and P < 3.5 × 10-4). Each of these serologic profiles was associated with increased serum IFN-α. SNPs in both PTPRM and LRRC20 were associated with increased serum IFN-α independent of serologic profile (P = 2.2 × 10-6 and P = 2.6 × 10-3 respectively). None of the SNPs were strongly associated with SLE in case-control analysis, suggesting that the major impact of these variants will be upon subphenotypes in SLE.

Conclusions
This study demonstrates the power of using serologic and cytokine subphenotypes to elucidate genetic factors involved in complex autoimmune disease. The distinct associations observed emphasize the heterogeneity of molecular pathogenesis in SLE, and the need for stratification by subphenotypes in genetic studies. We hypothesize that these genetic variants play a role in disease manifestations and severity in SLE.
ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67
Authors: Tuominen Vilppu J , Ruotoistenmäki Sanna , Viitanen Arttu , Jumppanen Mervi , Isola Jorma 
Published: July 2010

Abstract
Introduction
Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections.

Methods
The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n = 50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n = 50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients.

Results
The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r = 0.98). Using the median Ki-67 labeling index (20%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n = 123, P = 0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website.

Conclusions
We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens.
APCAP - activated protein C in acute pancreatitis: a double-blind randomized human pilot trial
Authors: Pettilä Ville , Kyhälä Lea , Kylänpää Marja-Leena , Leppäniemi Ari , Tallgren Minna , Markkola Antti , Puolakkainen Pauli , Repo Heikki , Kemppainen Esko 
Published: July 2010

Abstract
Introduction
Previous human studies have shown low activity of protein C (APC) in severe acute pancreatitis (SAP). This, together with the findings in animal models, suggests that activated protein C (APC) may protect against pancreatic injury and ameliorate the disease. We, therefore, evaluated its effect on multiple organ dysfunction (MOD) measured by the SOFA (Sequential Organ Failure Assessment) and on organ-failure-free days, and the safety of APC in SAP.

Methods
A prospective double blind randomized pilot study was use. The study occurred in one university hospital tertiary intensive care unit (ICU) with eight beds. The patients were chosen according to the following inclusion criteria: 1) Those admitted to the hospital < 96 h from the onset of pain, 2) Those who had a three-fold increase in serum amylase over normal upper range or/and in whom computed tomography (CT) verification of SAP was noted, 3) Those who had one or more organ dysfunction (OD), and 4) Those in whom less than 48 hours had passed since their first OD. Of a total of 215 adult patients with SAP screened between June 2003 and August 2007, 158 fulfilled the study inclusion criteria. After exclusions 32 patients were randomized to the study. The intervention consisted of APC (N = 16) administered intravenously for 96 hours with a dose of 24 μg/kg/hour or placebo (N = 16) with a similar infusion rate. The sample size for the study was calculated according to the primary end-point: the change in SOFA during study drug infusion (Days 0 and 5). Comparisons between the study groups were performed using patient-related changes and calculation of difference in means (DIM, 95% CIs) and regarding categorical variables with Fisher's exact test. For all comparisons P < 0.05 was considered significant.

Results
No serious bleeding was detected clinically or by CT scans in either group. No significant difference in SOFA score change between the APC and placebo groups was found (difference in means (DIM) +2.3, 95% CI -0.7 to +5.3). Treatment with APC was associated with an increase in serum levels of both total and conjugated bilirubin. No differences in ventilator-free days, in renal replacement therapy-free days, in vasopressor-free days, or in days alive outside the hospital were detected.

Conclusions
No serious bleeding or differences in the evolution of MOD were detected between APC and the placebo. Instead we found an increase in serum bilirubin in the APC group compared to the placebo group in patients with SAP.

Trial registration
ClinicalTrials.gov NCT01017107.
Salvage Regimens With Autologous Transplantation for Relapsed Large B-Cell Lymphoma in the Rituximab Era
Authors: Gisselbrecht Christian , Glass Bertram , Mounier Nicolas , Singh Gill Devinder , Linch David C. , Trneny Marek , Bosly Andre , Ketterer Nicolas , Shpilberg Ofer , Hagberg Hans , Ma David , Brière Josette , Moskowitz Craig H. , Schmitz Norbert 
Published: July 2010

PurposeSalvage chemotherapy followed by high-dose therapy and autologous stem-cell transplantation (ASCT) is the standard treatment for relapsed diffuse large B-cell lymphoma (DLBCL). Salvage regimens have never been compared; their efficacy in the rituximab era is unknown.Patients and MethodsPatients with CD20+DLBCL in first relapse or who were refractory after first-line therapy were randomly assigned to either rituximab, ifosfamide, etoposide, and carboplatin (R-ICE) or rituximab, dexamethasone, high-dose cytarabine, and cisplatin (R-DHAP). Responding patients received high-dose chemotherapy and ASCT.ResultsThe median age of the 396 patients enrolled (R-ICE, n = 202; R-DHAP, n = 194) was 55 years. Similar response rates were observed after three cycles of R-ICE (63.5%; 95% CI, 56% to 70%) and R-DHAP (62.8%; 95 CI, 55% to 69%). Factors affecting response rates (P < .001) were refractory disease/relapse less than versus more than 12 months after diagnosis (46% v 88%, respectively), International Prognostic Index (IPI) of more than 1 versus 0 to 1 (52% v 71%, respectively), and prior rituximab treatment versus no prior rituximab (51% v 83%, respectively). There was no significant difference between R-ICE and R-DHAP for 3-year event-free survival (EFS) or overall survival. Three-year EFS was affected by prior rituximab treatment versus no rituximab (21% v 47%, respectively), relapse less than versus more than 12 months after diagnosis (20% v 45%, respectively), and IPI of 2 to 3 versus 0 to 1 (18% v 40%, respectively). In the Cox model, these parameters were significant (P < .001).ConclusionIn patients who experience relapse more than 12 months after diagnosis, prior rituximab treatment does not affect EFS. Patients with early relapses after rituximab-containing first-line therapy have a poor prognosis, with no difference between the effects of R-ICE and R-DHAP.
Senior-Friendly Emergency Department Care: An Environmental Assessment
Authors: Kelley Mary Lou , Parke Belinda , Jokinen Nancy , Stones Michael , Renaud Donna 
Published: July 2010

Objectives To assess the environment of an emergency department (ED) and its impact on care of adults aged 75 and over, using a ‘senior-friendly’ conceptual framework that included the physical environment, social climate, hospital policies and procedures, and wider health care system. Methods In this focused ethnography, we collected and analysed data from the ED of a regional acute care hospital located in Ontario, Canada from October 2007 to January 2008. Data collection included interviews with seniors or their proxy decision-makers, staff and key community informants; on-site observations; a staff survey; and hospital administrative data. Data sets were individually analysed and a synthesis of findings developed to formulate recommendations for policy, practice and education. Results Staff expressed their vision of providing senior-friendly care. However, the ED was fast-paced, overcrowded, chaotic and lacked orientation and wayfinding cues, as well as appropriate equipment and furniture, all of which created barriers to providing appropriate care. Seniors' expectations often went unmet and staff expressed moral angst at recognizing unmet needs. Some hospital policies and procedures compounded these difficulties, including hallway practice, lack of off-hour access to multidisciplinary health care professionals, and the inability of patients to access food and drink. Better communication and coordination between the ED and other components of the health care system are needed. Conclusions The ED is an important part of seniors' health care. Changes to policy and practices, and enhanced education must occur to better meet the complex health care needs of seniors. This assessment provides a method that can be replicated elsewhere to generate site-specific recommendations and initiate capacity development processes to enhance senior-friendly care.
‘Not quite Jericho, but more doors than there used to be’. Staff views of the impact of ‘modernization’ on boundaries around adult critical care services in England
Authors: Durand Mary , Hutchings Andrew , Black Nick , Green Judith 
Published: July 2010

Objectives: To explore staff perceptions of the impact of ‘modernization’ on the organization, delivery and culture of adult critical care services in England. ‘Modernization’ policies aimed to alter the boundaries around critical care and create a comprehensive, seamless service. Methods: Seven hospitals (three teaching and four district general hospitals) in three critical care networks participated. In-depth interviews were conducted with a purposive sample of 45 critical care staff. Data were analysed thematically. Results: The boundaries around critical care were generally perceived to be less fixed than previously. The reframing of ‘internal walls’ within hospitals was associated with the introduction of outreach teams, new hospital-wide remits for intensive care unit (ICU) staff and the greater integration of allied health professionals into the critical care team. Transformation of services was challenged by practicalities including the need for additional staff, and a ‘them and us’ attitude between ICU and ward staff. ‘External walls’ between hospitals were breached where local clinical networks were perceived to have successfully improved communication and joint working. This was facilitated by effective leadership, availability of network-associated funds, the identification of common problems and evidence of benefit from cooperation. However, barriers existed and there was some scepticism among staff as to whether critical care can ever be entirely ‘without walls’. Conclusions: Policies to remove boundaries around adult critical care are perceived to have had a dramatic impact on the organization of the service. Considerable progress was reported towards developing comprehensive critical care services both within and between hospitals.
Connective tissue growth factor expression in endocrine tumors is associated with high stromal expression of α-smooth muscle actin
Authors: Cunningham Janet L , Tsolakis Apostolos V , Jacobson Annica , Janson Eva T 
Published: July 2010

ObjectiveComplications due to fibrosis development are common in patients with well-differentiated endocrine carcinomas in the small intestine (ileal carcinoids). Connective tissue growth factor (CTGF) expression in ileal carcinoids may be related to this fibrosis development. This study aimed to examine CTGF expression in relation to local myofibroblast differentiation in a large series of ileal carcinoids and in different types of endocrine tumors.MethodsImmunoreactivity (IR) for CTGF and α-smooth muscle actin (α-SMA), a marker for myofibroblasts, was compared in serial tumor tissue sections from 42 patients with ileal carcinoids and from 80 patients with other endocrine tumors. Western blot was performed on an additional 21 patients with ileal carcinoids.ResultsCTGF IR was present in >50% of tumor cells in all 42 ileal carcinoids and in 2 out of 14 endocrine pancreatic tumors, 4 out of 6 rectal carcinoids, and 1 out of 5 lung carcinoids. Tumors with abundant CTGF expression also displayed α-SMA IR in stromal fibroblast-like cells, whereas other endocrine tumors displayed less or no CTGF and α-SMA IR. Protein bands corresponding to full-length CTGF (36–42 kDa) were detected in protein lysates from ileal carcinoids.ConclusionCTGF is uniquely prevalent in ileal carcinoids when compared with most other endocrine tumor types. Immunoreactive cells are adjacent areas with increased fibrovascular stroma that express α-SMA. This supports a potential role for CTGF in myofibroblast-mediated fibrosis associated with ileal carcinoids, and indicates that CTGF should be investigated as a target for future therapy.
Statistical Analysis of Nondisjunction Assays in Drosophila
Authors: Zeng Yong , Li Hua , Schweppe Nicole M , Hawley R Scott , Gilliland William D 
Published: July 2010

AbstractMany advances in the understanding of meiosis have been made by measuring how often errors in chromosome segregation occur. This process of nondisjunction can be studied by counting experimental progeny, but direct measurement of nondisjunction rates is complicated by not all classes of nondisjunctional progeny being viable. For X chromosome nondisjunction in Drosophila female meiosis, all of the normal progeny survive, while nondisjunctional eggs produce viable progeny only if fertilized by sperm that carry the appropriate sex chromosome. The rate of nondisjunction has traditionally been estimated by assuming a binomial process and doubling the number of observed nondisjunctional progeny, to account for the inviable classes. However, the correct way to derive statistics (such as confidence intervals or hypothesis testing) by this approach is far from clear. Instead, we use the multinomial-Poisson hierarchy model and demonstrate that the old estimator is in fact the maximum-likelihood estimator (MLE). Under more general assumptions, we derive asymptotic normality of this estimator and construct confidence interval and hypothesis testing formulae. Confidence intervals under this framework are always larger than under the binomial framework, and application to published data shows that use of the multinomial approach can avoid an apparent type 1 error made by use of the binomial assumption. The current study provides guidance for researchers designing genetic experiments on nondisjunction and improves several methods for the analysis of genetic data.