bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early findings of prospective anti‐HLA donor specific antibodies monitoring study in pancreas transplantation: Indiana University Health Experience
Authors: Mujtaba Muhammad A. , Fridell Jonathan A. , Higgins Nancy , Sharfuddin Asif A. , Yaqub Muhammad S. , Kandula Praveen , Chen Jeanne , Mishler Dennis P. , Lobashevsky Andrew , Book Benita , Powelson John , Taber Tim E. 
Published: September 2012

AbstractThe significance of donor‐specific antibodies (DSA) is not well known in the setting of pancreas transplantation. Since December 2009, we prospectively followed pancreas transplant patients with single‐antigen‐luminex‐bead testing at one, two, three, six, and then every six months for the first two yr. Thirty‐five of the 92 patients that underwent pancreas transplantation (13 pancreas‐alone [PTA], 20 with a kidney [SPK], and two after a kidney [PAK]) agreed to participate in study. Median age at transplant was 45 yr and follow‐up was 23 months. Majority were Caucasian (n = 33) and male (n = 18). Rabbit anti‐thymocyte globulin induction was used. Median HLA‐mismatch was 4.2 ± 1.1. Eight patients (7SPK, 1PAK) developed post‐transplant DSA at median follow‐up of 76 d (26–119), 1 SPK had pre‐formed DSA. Seven patients had both class I and class II DSA, one with class I and one with class II only. Mean peak class I DSA‐MFI was 3529 (±1456); class II DSA‐MFI was 5734 (±3204) whereas cumulative DSA MFI (CI + CII) was 9264 (±4233). No difference was observed in the patient and donor demographics among patients with and without DSA. One patient in non‐DSA group developed acute cellular rejection of pancreas. From our data it appears that post‐transplant DSA in pancreas allograft recipients may not impact the early‐pancreatic allograft outcomes. The utility of prospective DSA monitoring in pancreatic transplant patients needs further evaluation and long‐term follow‐up.
Use of the ThinPrep Imaging System for internal quality control of cervical cytology
Authors: Heard T. , Chandra A. , Culora G. , Gupta S. S. , Herbert A. , Morgan M. 
Published: September 2012

T. Heard, A. Chandra, G. Culora, S.S. Gupta, A. Herbert and M. Morgan  Use of the ThinPrep Imaging System for internal quality control of cervical cytologyObjective:  To audit the use of the ThinPrep Imaging System (TIS) for internal quality control (IQC) in the place of rapid review (RR), and to compare its performance with routine primary screening.Method:  During 9 months, 16 462 ThinPrep slides were processed by TIS. Slides were initially reviewed using the TIS review scope, as recommended by the manufacturer: 22 fields of view were observed and, if considered abnormal, a full microscopic review was conducted using the review scope. Different biomedical scientists (BMSs), working on each procedure in rotation, performed batches of TIS‐assisted quality control and routine primary screening independently on unmarked slides. Any slides with abnormalities detected by either method were referred to a consultant pathologist or advanced BMS practitioner for a final report. TIS results were compared with both previous records of RR and routine primary screening carried out on the same slides. We used the UK terminology in which ‘dyskaryosis’ is equivalent to squamous intraepithelial lesion (SIL) and borderline to atypical (including squamous and glandular cells).Results:  TIS preview detected significantly more high‐grade dyskaryosis compared with RR during the previous 4 years: 2.0–4.2 compared with 0.1–1.8 detected per 1000 slides (P = 0.0001). TIS and routine screening were equivalent in sensitivity and specificity for the final cytology result, but BMSs were significantly more likely to classify slides as dyskaryotic rather than borderline when using TIS compared with routine screening. Referrals for potentially high‐grade abnormalities detected by TIS‐assisted IQC alone found 28 biopsies of at least cervical intraepithelial neoplasia grade 2 (CIN2+), whereas 15 CIN2+ biopsies were found on routine screening but missed using TIS. There was no significant change in the rates of inadequate tests, high‐ or low‐grade cytological abnormalities, or positive predictive value for CIN2+ when TIS was in use.Conclusions:  Screening with TIS was more sensitive than RR for IQC, providing a rescreening method equivalent to routine primary screening in overall accuracy.
Role of DNA methylation in growth and differentiation in Physcomitrella patens and characterization of cytosine DNA methyltransferases
Authors: Malik Garima , Dangwal Meenakshi , Kapoor Sanjay , Kapoor Meenu 
Published: September 2012

Epigenetic mechanisms such as DNA methylation are known to regulate important developmental processes in higher eukaryotes. However, little is known about the necessity and role of this process in early land plants. Using the methyltransferase (MTase) inhibitor zebularine (1‐(β‐d‐ribofuranosyl)‐1,2‐dihydropyrimidine‐2‐one), the impact of loss of genome‐wide methylation on the overall development in Physcomitrella patens was analyzed. It is observed that various aspects of growth and differentiation during gametophyte development become aberrant. A search for the core molecular components of methylation machinery, cytosine DNA MTases, revealed the presence of seven loci in the P. patens genome. Five of the loci code for MTases that are similar to corresponding proteins in higher plants, while two MTases appear specific to P. patens and are closely related to human DNMT3a and DNMT3b, respectively. These proteins possess all the conserved catalytic motifs characteristic of MTases and a domain of unknown function, DUF3444. Association of these highly conserved motifs with a DUF has not been reported in any of the MTases known so far. All the seven genes are differentially but ubiquitously expressed in gametophytes at low levels. Subcellular localization of GFP‐fused proteins shows patterns of distribution that can be correlated with their putative cellular functions. This work bridges the knowledge of MTases in P. patens and makes this simple model plant accessible for studies on epigenetic aspects that remain intractable in higher plants.
Synergistic effects of ocean acidification and warming on overwintering pteropods in the Arctic
Authors: Lischka Silke , Riebesell Ulf 
Published: September 2012

AbstractOcean acidification and warming will be most pronounced in the Arctic Ocean. Aragonite shell‐bearing pteropods in the Arctic are expected to be among the first species to suffer from ocean acidification. Carbonate undersaturation in the Arctic will first occur in winter and because this period is also characterized by low food availability, the overwintering stages of polar pteropods may develop into a bottleneck in their life cycle. The impacts of ocean acidification and warming on growth, shell degradation (dissolution), and mortality of two thecosome pteropods, the polar Limacina helicina and the boreal L. retroversa, were studied for the first time during the Arctic winter in the Kongsfjord (Svalbard). The abundance of L. helicina and L. retroversa varied from 23.5 to 120 ind m−2 and 12 to 38 ind m−2, and the mean shell size ranged from 920 to 981 μm and 810 to 823 μm, respectively. Seawater was aragonite‐undersaturated at the overwintering depths of pteropods on two out of ten days of our observations. A 7‐day experiment [temperature levels: 2 and 7 °C, pCO2 levels: 350, 650 (only for L. helicina) and 880 μatm] revealed a significant pCO2 effect on shell degradation in both species, and synergistic effects between temperature and pCO2 for L. helicina. A comparison of live and dead specimens kept under the same experimental conditions indicated that both species were capable of actively reducing the impacts of acidification on shell dissolution. A higher vulnerability to increasing pCO2 and temperature during the winter season is indicated compared with a similar study from fall 2009. Considering the species winter phenology and the seasonal changes in carbonate chemistry in Arctic waters, negative climate change effects on Arctic thecosomes are likely to show up first during winter, possibly well before ocean acidification effects become detectable during the summer season.
Crystal structure and DNA‐binding mode of Klebsiella pneumoniae primosomal PriB protein
Authors: Huang Yen‐Hua , Lo Yu‐Hua , Huang Wenya , Huang Cheng‐Yang 
Published: September 2012

PriB is a primosomal DNA replication protein required for the re‐initiation of replication in bacteria. In this study, we investigated the gene expression of PriB in Klebsiella pneumoniae (KpPriB) and characterized the gene product through crystal structural and functional analyses. Quantitative polymerase chain reaction analysis (Q‐PCR) indicated that the 104‐aa priB was expressed in K. pneumoniae with a CT value of 22.4. The crystal structure of KpPriB (Protein Data Bank entry: 4APV) determined at a resolution of 2.1 Å was similar to that of Escherichia coli PriB (EcPriB). KpPriB formed a single complex with single‐stranded DNA (ssDNA) of different lengths, suggesting a highly cooperative process. Structure‐based mutational analysis revealed that substitution at K18, F42, R44, W47, K82, K84, or K89 but not R34 in KpPriB had a significant effect on both ssDNA and double‐stranded DNA (dsDNA) binding. Based on these findings, the known ssDNA interaction sites of PriB were expanded to include R44 and F42, thus allowing nucleic acids to wrap around the whole PriB protein.
Helicobacter pylori Induces Increased Expression of Toll‐Like Receptors and Decreased Toll‐Interacting Protein in Gastric Mucosa that Persists Throughout Gastric Carcinogenesis
Authors: Pimentel‐Nunes Pedro , Gonçalves Nádia , Boal‐Carvalho Inês , Afonso Luís , Lopes Paula , Roncon‐Albuquerque Roberto , Henrique Rui , Moreira‐Dias Luís , Leite‐Moreira Adelino F. , Dinis‐Ribeiro Mário 
Published: September 2012

AbstractBackgroundToll‐like receptors (TLR) are essential for Helicobacter pylori (HP) recognition. Their role in the progression of gastric lesions leading to cancer is not established.AimTo evaluate for the first time in humans the expression of TLR2, TLR4, and TLR5, as well as the expression of other related molecules in the entire sequence of gastric lesions.MethodsBiopsy samples (n = 80, 48% HP+) from normal mucosa, HP gastritis, metaplasia, dysplasia or adenocarcinoma were obtained from 44 patients. mRNA quantification of TLR2, TLR4, TLR5, Toll‐interacting protein (TOLLIP), PPAR‐γ, NF‐κB, TNF‐α, COX‐1, COX‐2, and CDX‐2 was performed by real‐time RT‐PCR. TLR2, TLR4, and TLR5 protein expression was quantified by immunohistochemistry.ResultsWhen compared to normal mucosa (1.0 arbitrary unit (AU)), HP gastritis presented higher expression of TLR2 (2.23 ± 0.36 AU), TLR4 (1.92 ± 0.40 AU) and TNF‐α (2.14 ± 0.50 AU) and lower TOLLIP and PPARγ expression (0.72 ± 0.12 AU, p < .05 all genes). Metaplasia and dysplasia/carcinoma presented higher expression of TLR2 (1.66 ± 0.46 and 1.48 ± 0.20 AU, respectively, p < .05), lower expression of TOLLIP (0.66 ± 0.09 and 0.52 ± 0.04 AU, p < .05) and PPARγ (0.73 ± 0.12 and 0.63 ± 0.10 AU, p < .05). The significant trend for decrease in TOLLIP and PPARγ was associated with increasing levels of CDX‐2 from normal mucosa to carcinoma (p < .05), translating that in diffuse and higher TLRs protein expression (p < .05).ConclusionGastric carcinogenesis is associated with decreasing levels of TLRs inhibitors and elevated TLRs levels throughout all the spectrum of lesions. Future studies should investigate if modulation of these receptors activity may influence gastric carcinogenesis and tumor progression.
The Pathogenic Potential of Helicobacter pullorum: Possible Role for the Type VI Secretion System
Authors: Sirianni Andrea , Kaakoush Nadeem O. , Raftery Mark J. , Mitchell Hazel M. 
Published: September 2012

AbstractBackgroundHelicobacter pullorum is a putative enterohepatic pathogen that has been associated with hepatobiliary and gastrointestinal diseases in chickens and in humans. The pathogenic potential of H. pullorum NCTC 12826 was investigated.MethodsAdherence and gentamicin protection assays and scanning electron microscopy were performed to quantitate and visualise H. pullorum adherence and invasion. Proteomics coupled with mass spectrometry was employed to characterise the secretome of H. pullorum.ResultsHelicobacter pullorum was able to adhere to the Caco‐2 intestinal epithelial cell line with a mean attachment value of 1.98 ± 0.16% and invade Caco‐2 cells with a mean invasion value of 0.25 ± 0.02%. The in vitro adherence and invasion assays were confirmed with scanning electron microscopy, which showed that H. pullorum can adhere to host cells through flagellum–microvillus interaction and invade causing a membrane‐ruffling effect. One hundred and thirty‐seven proteins were identified, of which 33 were bioinformatically predicted to be secreted. Further functional classifications revealed six putative virulence and colonisation factors, which included cell‐binding factor 2, flagellin, secreted protein Hcp, valine‐glycine repeat protein G, a type VI secretion protein, and a protease. Protein threading of H. pullorum Hcp and subsequent 3D‐Blast searches revealed structural similarities between Hcp and endocytic vesicle coat proteins, suggesting the type VI secretion system of H. pullorum may interact with endocytic vesicles.ConclusionsThis study has shown that H. pullorum has the ability to adhere to and invade human cells and secrete factors that may contribute to the pathogenic potential of H. pullorum.
Use of a United States‐based laboratory as a hematopathology reference center for a developing country: logistics and results
Authors: Deetz C. O. , Scott M. G. , Ladenson J. H. , Seyoum M. , Hassan A. , Kreisel F. H. , Nguyen T. T. , Frater J. L. 
Published: September 2012

SummaryIntroductionWith proper logistical support and sponsorship, a laboratory in an industrialized nation might be able to act as a reference laboratory for clinicians based in a developing country.MethodsWe built on previous experience in the clinical laboratory to see whether a specialized histopathology service (hematopathology) could be provided to a developing country without the expertise or experience to do it in country.ResultsOver an 13‐year period, 582 cases from 579 individuals were analyzed. Principal pathologic findings included acute leukemia in 84 cases (14%), dyspoiesis in one or more of the hematopoietic lineages in 65 cases (11%, including three cases with high‐grade myelodysplasia), 23 cases (4%) with findings suspicious for a chronic myeloproliferative disorder, 35 cases (6%) with findings suspicious for a lymphoproliferative disorder, and infectious organisms (presumably Leishmania in most instances) in 9 (1%) of cases. Specimens from 45 cases (8%) were unsatisfactory owing to extreme hemodilution and/or specimen degeneration.ConclusionWith proper support, a medical laboratory in an industrialized nation may serve as a reference facility for a developing nation. The use of existing infrastructure may be remarkably effective to achieve optimal turnaround time. Although the lack of ancillary studies and follow‐up biopsies limit the ability to achieve a definitive diagnosis in many cases, this must be viewed in the context of the limited ability to diagnose or manage hematopoietic neoplasia in developing nations.
Label‐free mass spectrometry‐based quantification of hemagglutinin and neuraminidase in influenza virus preparations and vaccines
Authors: Getie‐Kebtie Melkamu , Sultana Ishrat , Eichelberger Maryna , Alterman Michail 
Published: September 2012

Please cite this paper as: Getie‐Kebtie et al. (2012) Label‐free mass spectrometry‐based quantification of hemagglutinin and neuraminidase in influenza virus preparations and vaccines. Influenza and Other Respiratory Viruses 7(4), 521–530.Background  Influenza vaccination is the primary method for preventing influenza and its severe complications. An accurate rapid method to determine hemagglutinin (HA) concentration would facilitate reference antigen preparation and consequently expedite availability of seasonal as well as pandemic vaccines.Objective  The goal of this study was to develop a label‐free mass spectrometry (MS) based method that enables simultaneous identification and quantification of HA, neuraminidase (NA), and other viral proteins and protein contaminations in influenza vaccine or virus preparations.Methods  The method presented is based on LC/MSE analysis of vaccine or virus preparations tryptic digests spiked with a known amount of protein standard from which a universal response factor is generated and applied to calculate the concentration of proteins identified in the mixture.Results  We show that, with the use of an appropriate internal standard, the label‐free MS‐based protein quantification method is applicable for simultaneous identification and absolute quantification of HA and identification and relative quantification of other influenza proteins as well as protein impurities in influenza vaccines and virus preparations. We show that different subtype recombinant HA is preferred internal standard that provides the most accurate results in absolute quantification of HAs and other influenza proteins. We applied this method to measure the absolute quantity of HA as well as relative quantities of other viral proteins and impurities in preparations of whole virus and monovalent vaccine, providing data to demonstrate strain‐dependent differences in the amount of NA.Conclusion  The label‐free MS method presented here is ideally suited for timely preparation of reference material needed for potency testing of seasonal and pandemic vaccines.
Botrytis cinerea mutants deficient in d‐galacturonic acid catabolism have a perturbed virulence on Nicotiana benthamiana and Arabidopsis, but not on tomato
Authors: Zhang Lisha , van Kan Jan A. L. 
Published: September 2012

Summaryd‐Galacturonic acid is the most abundant monosaccharide component of pectic polysaccharides that comprise a significant part of most plant cell walls. Therefore, it is potentially an important nutritional factor for Botrytis cinerea when it grows in and through plant cell walls. The d‐galacturonic acid catabolic pathway in B. cinerea consists of three catalytic steps converting d‐galacturonic acid to pyruvate and l‐glyceraldehyde, involving two nonhomologous galacturonate reductase genes (Bcgar1 and Bcgar2), a galactonate dehydratase gene (Bclgd1) and a 2‐keto‐3‐deoxy‐l‐galactonate aldolase gene (Bclga1). Knockout mutants in each step of the pathway (ΔBcgar1/ΔBcgar2, ΔBclgd1 and ΔBclga1) showed reduced virulence on Nicotiana benthamiana and Arabidopsis thaliana leaves, but not on Solanum lycopersicum leaves. The cell walls of N. benthamiana and A. thaliana leaves were shown to have a higher d‐galacturonic acid content relative to those of S. lycopersicum. The observation that mutants displayed a reduction in virulence, especially on plants with a high d‐galacturonic acid content in the cell walls, suggests that, in these hosts, d‐galacturonic acid has an important role as a carbon nutrient for B. cinerea. However, additional in vitro growth assays with the knockout mutants revealed that B. cinerea growth is reduced when d‐galacturonic acid catabolic intermediates cannot proceed through the entire pathway, even when fructose is present as the major, alternative carbon source. These data suggest that the reduced virulence of d‐galacturonic acid catabolism‐deficient mutants on N. benthamiana and A. thaliana is not only a result of the inability of the mutants to utilize an abundant carbon source as nutrient, but also a result of the growth inhibition by catabolic intermediates.
Nitrogen metabolism and milk production in dairy cows fed semi‐restricted amounts of ryegrass–legume silage with birdsfoot trefoil (Lotus corniculatus L.) or white clover (Trifolium repens L.)
Authors: Eriksson T. , Norell L. , Nilsdotter‐Linde N. 
Published: September 2012

AbstractIn change‐over trials, mid‐lactation dairy cows were fed concentrate‐supplemented, isonitrogenous and isofibrous perennial ryegrass–legume silage diets that satisfied energy requirements but were suboptimal with respect to metabolizable protein supply. Legumes were either birdsfoot trefoil with low levels of condensed tannins (typical for hemiboreal conditions), or white clover. Averaged over two experimental years, birdsfoot trefoil–based silage resulted in lower digestibility (P < 0·001) of dry matter (50 g kg−1), organic matter (52 g kg−1), neutral detergent fibre (120 g kg−1) and nitrogen (24 g kg−1) and lower rumen total volatile fatty acid concentration (7 mm; P = 0·009). Milk protein yield was 36 g d−1 higher with birdsfoot trefoil silage (P = 0·002), while raw milk yield tended to be 0·8 kg d−1 higher (P = 0·06). Rumen ammonia concentration was similar between diets, but milk urea concentration (P < 0·001), urinary urea excretion (P = 0·002) and faecal‐N proportion (P = 0·001) were higher with birdsfoot trefoil silage. The results suggest that grass–birdsfoot trefoil silage produced in hemiboreal areas exhibits a protein‐sparing effect in dairy rations, despite a low condensed tannin content that is further diluted by companion grasses and ration concentrate proportion.
Oral Health Care for Patients with Epidermolysis Bullosa ‐ Best Clinical Practice Guidelines
Authors: Krämer Susanne M. , Serrano María Concepción , Zillmann Gisela , Gálvez Pablo , Araya Ignacio , Yanine Nicolás , Carrasco‐Labra Alonso , Oliva Patricio , Brignardello‐Petersen Romina , Villanueva Julio 
Published: September 2012

International Journal of Paediatric Dentistry 2012; 22 (Suppl. 1): 1–35Objective.  To provide the users with information on the current best practices for managing the oral health care of people living with EB.Methods.  A systematic literature search, in which the main topic is dental care in patients with Epidermolysis Bullosa, was performed. Consulted sources, ranging from 1970 to 2010, included MEDLINE, EMBASE, CINAHL, The Cochrane Library, DARE, and the Cochrane controlled trials register (CENTRAL). In order to formulate the recommendations of the selected studies the SIGN system was used. The first draft was analysed and discussed by clinical experts, methodologists and patients representatives on a two days consensus meeting. The resulting document went through an external review process by a panel of experts, other health care professionals, patient representatives and lay reviewers. The final document was piloted in three different centres in United Kingdom, Czech Republic and Argentina.Results.  The guideline is composed of 93 recommendations divided into 3 main areas: 1) Oral Care ‐ access issues, early referral, preventative strategies, management of microstomia, prescriptions and review appointments‐, 2) Dental treatment: general treatment modifications, radiographs, restorations, endodontics, oral rehabilitation, periodontal treatment, oral surgery and orthodontics‐, and 3) Anaesthetic management of dental treatment.Conclusions.  A preventive protocol is today's dental management approach of choice.