bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells
Authors: Juelke Kerstin , Killig Monica , Luetke-Eversloh Merlin , Parente Eliana , Gruen Joachim , Morandi Barbara , Ferlazzo Guido , Thiel Andreas , Schmitt-Knosalla Isabela , Romagnani Chiara 
Published: May 2010

AbstractHuman natural killer (NK) cells comprise 2 main subsets, CD56bright and CD56dim cells, that differ in function, phenotype, and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK-cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon-γ after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK-cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK-cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors.
Identification of archaeal proteins that affect the exosome function in vitro
Authors: Luz Juliana S , Ramos Celso RR , Santos Márcia CT , Coltri Patricia P , Palhano Fernando L , Foguel Debora , Zanchin Nilson IT , Oliveira Carla C 
Published: May 2010

Abstract

Background
The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.

Results
Here, we show that the proteins PaSBDS and PaNip7, which bind preferentially to poly-A and AU-rich RNAs, respectively, affect the Pyrococcus abyssi exosome activity in vitro. PaSBDS inhibits slightly degradation of a poly-rA substrate, while PaNip7 strongly inhibits the degradation of poly-A and poly-AU by the exosome. The exosome inhibition by PaNip7 appears to depend at least partially on its interaction with RNA, since mutants of PaNip7 that no longer bind RNA, inhibit the exosome less strongly. We also show that FITC-labeled PaNip7 associates with the exosome in the absence of substrate RNA.

Conclusions
Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism.
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
Authors: Zhu Qianqian , Miecznikowski Jeffrey C , Halfon Marc S 
Published: May 2010

AbstractBackgroundConcomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the performance of various methods.ResultsWe generated a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive versus negative fold change. We use this new "Platinum Spike" dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset.ConclusionsWe present updated best-route methods for Affymetrix GeneChip analysis and demonstrate that the degree of "imbalance" in gene expression has a significant effect on the performance of these methods.
Conditional expression of Spry1 in neural crest causes craniofacial and cardiac defects
Authors: Yang Xuehui , Kilgallen Sean , Andreeva Viktoria , Spicer Douglas B , Pinz Ilka , Friesel Robert 
Published: May 2010

Abstract

Background
Growth factors and their receptors are mediators of organogenesis and must be tightly regulated in a temporal and spatial manner for proper tissue morphogenesis. Intracellular regulators of growth factor signaling pathways provide an additional level of control. Members of the Sprouty family negatively regulate receptor tyrosine kinase pathways in several developmental contexts. To gain insight into the role of Spry1 in neural crest development, we analyzed the developmental effects of conditional expression of Spry1 in neural crest-derived tissues.

Results
Here we report that conditional expression of Spry1 in neural crest cells causes defects in craniofacial and cardiac development in mice. Spry1;Wnt1-Cre embryos die perinatally and exhibit facial clefting, cleft palate, cardiac and cranial nerve defects. These defects appear to be the result of decreased proliferation and increased apoptosis of neural crest and neural crest-derived cell populations. In addition, the domains of expression of several key transcription factors important to normal craniofacial and cardiac development including AP2, Msx2, Dlx5, and Dlx6 were reduced in Spry1;Wnt1-Cre transgenic embryos.

Conclusion
Collectively, these data suggest that Spry1 is an important regulator of craniofacial and cardiac morphogenesis and perturbations in Spry1 levels may contribute to congenital disorders involving tissues of neural crest origin.
Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv
Authors: Målen Hiwa , Pathak Sharad , Søfteland Tina , de Souza Gustavo A , Wiker Harald G 
Published: May 2010

AbstractBackgroundMembrane- and membrane-associated proteins are important for the pathogenicity of bacteria. We have analysed the content of these proteins in virulentMycobacterium tuberculosisH37Rv using Triton X-114 detergent-phase separation for extraction of lipophilic proteins, followed by their identification with high resolution mass spectrometry.ResultsIn total, 1417 different proteins were identified.In silicoanalysis of the identified proteins revealed that 248 proteins had at least one predicted trans-membrane region. Also, 64 of the identified proteins were predicted lipoproteins, and 54 proteins were predicted as outer membrane proteins. Three-hundred-and-ninety-five of the observed proteins, including 91 integral membrane proteins were described for the first time. Comparison of abundance levels of the identified proteins was performed using the exponentially modified protein abundance index (emPAI) which takes into account the number of the observable peptides to the number of experimentally observed peptide ions for a given protein. The outcome showed that among the membrane-and membrane-associated proteins several proteins are present with high relative abundance. Further, a close examination of the lipoprotein LpqG (Rv3623) which is only detected in the membrane fractions ofM. tuberculosisbut not inM. bovis, revealed that the homologous gene inM. bovislack the signal peptide and lipobox motif, suggesting impaired export to the membrane.ConclusionsAltogether, we have identified a substantial proportion of membrane- and membrane-associated proteins ofM. tuberculosisH37Rv, compared the relative abundance of the identified proteins and also revealed subtle differences between the different members of theM. tuberculosiscomplex.
Assessment of insulin resistance by a 13C glucose breath test: a new tool for early diagnosis and follow-up of high-risk patients
Authors: Mizrahi Meir , Lalazar Gadi , Adar Tomer , Raz Itamar , Ilan Yaron 
Published: May 2010

Abstract

Background/Aims
Insulin resistance (IR) plays an important role in the pathogenesis of diabetes and non-alcoholic fatty liver disease (NAFLD). Current methods for insulin resistance detection are cumbersome, or not sensitive enough for early detection and follow-up. The BreathID® system can continuously analyse breath samples in real-time at the point-of-care. Here we determined the efficacy of the BreathID® using the 13C-Glucose breath test (GBT) for evaluation of insulin resistance.

Methods
Twenty healthy volunteers were orally administered 75 mg of 13C-glucose 1-13C. An oral glucose tolerance test (OGTT) was performed immediately; followed by serum glucose and insulin level determinations using GBT. GBT and OGTT were repeated following exercise, which alters insulin resistance levels.

Results
Within-subject correlations of GBT parameters with serum glucose and serum insulin levels were high. Before and after exercise, between-subjects correlations were high between the relative insulin levels and the % dose recoveries at 90 min (PDR 90), and the cumulative PDRs at 60 min (CPDR 60). Pairwise correlations were identified between pre-exercise Homeostasis Model Assessment (HOMA) IR at 90 min and PDR 90; HOMA B (for beta cell function) 120 and CPDR 30; HOMA IR 60 and peak time post-exercise; and HOMA B 150 with PDR 150.

Conclusions
The non-invasive real-time BreathID® GBT reliably assesses changes in liver glucose metabolism, and the degree of insulin resistance. It may serve as a non-invasive tool for early diagnosis and follow up of patients in high-risk groups.
A case of gangliocytic paraganglioma in the ampulla of Vater
Authors: Kwon Junsik , Lee Seung Eun , Kang Mee Joo , Jang Jin-Young , Kim Sun-Whe 
Published: May 2010

Abstract

Background
Duodenal gangliocytic paraganglioma is an extremely rare tumor and few cases have been reported to date.

Case presentation
The authors report a case of gangliocytic paraganglioma verified by post-op pathology after pancreaticoduodenectomy for a tumor in the ampulla of Vater. The 56-year-old male patient concerned visited our emergency room with melena that started one week prior to hospitalization. The patient was diagnosed to have a tumor in the ampulla of Vater with bleeding on its surface. However post-op, he was diagnosed as having gangliocytic paraganglioma by immunohistochemistry.

Conclusion
This tumor has precise clinical implications, and if continuous follow up is conducted after careful diagnosis and surgical treatment, invasive major operations, such as, radical pancreaticoduodenectomy can be avoided.
Skin Test Reactivity to Indoor Allergens Correlates with Asthma Severity in Jeddah, Saudi Arabia
Authors: Koshak Emad A 
Published: May 2010

Abstract

Background
There is increased emphasis on the role of indoor allergens in asthma.

Objective
To examine the spectrum of skin test reactivity (sensitization) to indoor allergens and its correlation with asthma severity in Jeddah, Saudi Arabia.

Methods
Asthmatic patients referred to the allergy clinic at King Abdulaziz University Hospital (KAUH) in Jeddah were studied. Measures of clinical severity were adopted from national and international asthma guidelines. The degree of sensitization was assessed by the wheal size (positive ≥ 3 mm) from standard skin-prick tests for the following common indoor inhalant allergens: house dust mites (Dermatophagoides pteronyssinus [Dp] and Dermatophagoides farinae [Df]), cat, and cockroach.

Results
Skin test results from 113 of 151 (74.8%) asthmatic patients were positive for one or more allergens. The patients' ages ranged between 9 and 63 years (mean, 30 ± 13 years), and females constituted 65.5%. The predominant asthma severity level was moderate persistent (55.8%), followed by mild persistent (33.6%). The prevalences of sensitization to indoor allergens were as follows: Dp, 87% (3-25 mm [mean, 7 mm]); Df, 84% (3-20 mm [mean, 7 mm]); cat, 44% (3-15 mm [mean, 6 mm]); and cockroach, 33% (3-12 mm [mean, 4 mm]). Higher asthma severity levels were significantly correlated with the number of allergens with positive sensitization (R = 0.3, p < .001) and with the degree of sensitization to house dust mites (Dp [degrees of freedom {df} = 16, p < .001] and Df [df = 17, p < .01]) but not to cat (df = 10, p < .24) or cockroach (df = 8, p < .36).

Conclusions
Immunoglobulin E-mediated skin test reactivity to indoor allergens, particularly to house dust mites, was common in asthmatic patients from Jeddah at KAUH. Increased sensitization was associated with higher levels of asthma severity, which is compatible with the literature. This emphasizes the importance of identifying sensitization to relevant indoor allergens in the clinical evaluation of asthmatic persons.
Erythropoietic Protoporphyria Masquerading as Angioedema in a 4-Year-Old Female
Authors: Wang Helen C , Yousef Ejaz 
Published: May 2010

Abstract
Angioedema is a common presentation with a broad differential, including rare disorders with which an allergist must be familiar. Our objective was to report a case of swelling of the hands and feet mimicking angioedema with hepatomegaly in a 4-year-old girl. The patient was evaluated for painful swelling of the hands and feet after exposure to sun. Examination revealed edema and erythema of the extremities and hepatomegaly. Laboratory evaluation included elevated liver transaminases and plasma protoporphyrin, with normal urine porphyrins. Liver biopsy confirmed the diagnosis of erythropoietic protoporphyria, a disorder of heme biosynthesis in which patients may present with photosensitivity and angioedema. It is important for allergists to recognize this entity in patients with cutaneous disorders of unclear etiology in order to prevent possible life-threatening sequelae.
Prevalence and Severity of Asthma, Rhinitis, and Atopic Eczema in 13- to 14-Year-Old Schoolchildren from Southern Brazil
Authors: Neto Arnaldo C Porto , Annes Rafael D'Agostini , Wolff Nathalia MM , Klein Andréia P , dos Santos Francisco C , Dullius Juliana L , Gressler Marina , Muller Letícia S , Angonese Cristine F , Menna-Barreto Sérgio 
Published: May 2010

AbstractThe objective of this study was to investigate the prevalence and severity of asthma, rhinitis, and atopic eczema in schoolchildren from southern Brazil. A cross-sectional study was carried out with the International Study of Asthma and Allergies in Childhood phase III written questionnaire. The questionnaire was self-applied by 2,948 randomly selected schoolchildren aged 13 to 14 years. The lifetime prevalence rates of symptoms were as follows: wheezing, 40.8%; rhinitis, 40.7%; eczema, 13.6%; self-reported asthma, 14.6%; rhinitis, 31.4%; eczema, 13.4%. Rhinitis was reported by 55% of adolescents with current asthma (60% females vs 46.9% males). Girls 13 to 14 years of age had higher prevalence rates of asthma, rhinitis, and eczema than boys had. Atopic eczema was reported by 42.7% of girls and 31.4% of boys with asthma. The prevalence rates were statistically significant for symptoms of asthma, rhinitis, and atopic eczema in females. However, there were no statistically significant differences between the sexes in regard to reported asthma and bronchospasm induced by exercise.
Lack of Correlation between Severity of Clinical Symptoms, Skin Test Reactivity, and Radioallergosorbent Test Results in Venom-Allergic Patients
Authors: Warrington R.J. 
Published: May 2010

Abstract

Purpose
To retrospectively examine the relation between skin test reactivity, venom-specific immunoglobulin E (IgE) antibody levels, and severity of clinical reaction in patients with insect venom allergy.

Method
Thirty-six patients (including 15 females) who presented with a history of allergic reactions to insect stings were assessed. The mean age at the time of the reactions was 33.4 ± 15.1 years (range, 4-76 years), and patients were evaluated 43.6 ± 90 months (range, 1-300 months) after the reactions. Clinical reactions were scored according to severity, from 1 (cutaneous manifestations only) to 3 (anaphylaxis with shock). These scores were compared to scores for skin test reactivity (0 to 5, indicating the log increase in sensitivity from 1 μg/mL to 0.0001 μg/mL) and radioallergosorbent test (RAST) levels (0 to 4, indicating venom-specific IgE levels, from undetectable to >17.5 kilounits of antigen per litre [kUA/L]).

Results
No correlation was found between skin test reactivity (Spearman's coefficient = 0.15, p = .377) or RAST level (Spearman's coefficient = 0.32, p = .061) and the severity of reaction. Skin test and RAST scores both differed significantly from clinical severity (p < .05), but there was a significant correlation between skin test reactivity and RAST score (p = .042). There was no correlation between skin test reactivity and time since reaction (Spearman's coefficient = 0.18, p = .294) nor between RAST and time since reaction (r = 0.1353, p = .438). Elimination of patients tested more than 12 months after their reaction still produced no correlation between skin test reactivity (p = .681) or RAST score (p = .183) and the severity of the clinical reaction.

Conclusion
In venom-allergic patients (in contrast to reported findings in cases of inhalant IgE-mediated allergy), there appears to be no significant correlation between the degree of skin test reactivity or levels of venom-specific IgE (determined by RAST) and the severity of the clinical reaction.
Nutrient control of eukaryote cell growth: a systems biology study in yeast
Authors: Gutteridge Alex , Pir Pınar , Castrillo Juan I , Charles Philip D , Lilley Kathryn S , Oliver Stephen G 
Published: May 2010

AbstractBackgroundTo elucidate the biological processes affected by changes in growth rate and nutrient availability, we have performed a comprehensive analysis of the transcriptome, proteome and metabolome responses of chemostat cultures of the yeast,Saccharomyces cerevisiae, growing at a range of growth rates and in four different nutrient-limiting conditions.ResultsWe find significant changes in expression for many genes in each of the four nutrient-limited conditions tested. We also observe several processes that respond differently to changes in growth rate and are specific to each nutrient-limiting condition. These include carbohydrate storage, mitochondrial function, ribosome synthesis, and phosphate transport. Integrating transcriptome data with proteome measurements allows us to identify previously unrecognized examples of post-transcriptional regulation in response to both nutrient and growth-rate signals.ConclusionsOur results emphasize the unique properties of carbon metabolism and the carbon substrate, the limitation of which induces significant changes in gene regulation at the transcriptional and post-transcriptional level, as well as altering how many genes respond to growth rate. By comparison, the responses to growth limitation by other nutrients involve a smaller set of genes that participate in specific pathways.See associated commentaryhttp://www.biomedcentral.com/1741-7007/8/62
Prospective randomized trial evaluating mandatory second look surgery with HIPEC and CRS vs. standard of care in patients at high risk of developing colorectal peritoneal metastases
Authors: Ripley Robert T , Davis Jeremy L , Kemp Clinton D , Steinberg Seth M , Toomey Mary Ann , Avital Itzhak 
Published: May 2010

Abstract

Background
The standard of care for colorectal peritoneal carcinomatosis is evolving from chemotherapy to cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) for patients with disease limited to the peritoneum. Peritoneal carcinomatosis from colorectal cancer treated with chemotherapy alone results in median survival of 5 to 13 months, whereas CRS with HIPEC for early peritoneal carcinomatosis from colorectal cancer resulted in median survival of 48-63 months and 5 year survival of 51%.
Completeness of cytoreduction and limited disease are associated with longer survival, yet early peritoneal carcinomatosis is undetectable by conventional imaging. Exploratory laparotomy can successfully identify early disease, but this approach can only be justified in patients with high risk of peritoneal carcinomatosis. Historical data indicates that patients presenting with synchronous peritoneal carcinomatosis, ovarian metastases, perforated primary tumor, and emergency presentation with bleeding or obstructing lesions are at high risk of peritoneal carcinomatosis. Approximately 55% of these patient populations will develop peritoneal carcinomatosis. We hypothesize that performing a mandatory second look laparotomy with CRS and HIPEC for patients who are at high risk for developing peritoneal carcinomatosis from colorectal cancer will lead to improved survival as compared to patients who receive standard of care with routine surveillance.

Methods/Design
This study is a prospective randomized trial designed to answer the question whether mandatory second look surgery with CRS and HIPEC will prolong overall survival compared to the standard of care in patients who are at high risk for developing peritoneal carcinomatosis from colorectal cancer (CRC). Patients with CRC at high risk for developing peritoneal carcinomatosis who underwent curative surgery and subsequently received standard of care adjuvant chemotherapy will be evaluated. The patients who remain without evidence of disease by imaging, physical examination, and tumor markers for 12 months after the primary operation will be randomized to mandatory second look surgery or standard-of-care surveillance. At laparotomy, CRS and HIPEC will be performed with intraperitoneal oxaliplatin with concurrent systemic 5-fluorouracil and leucovorin. Up to 100 patients will be enrolled to allow for 35 evaluable patients in each arm; accrual is expected to last 5 years.

Trial Registration
ClinicalTrials.gov ID: NCT01095523
Clinical outcomes for T1-2N0-1 oral tongue cancer patients underwent surgery with and without postoperative radiotherapy
Authors: Shim Su Jung , Cha Jihye , Koom Woong Sub , Kim Gwi Eon , Lee Chang Geol , Choi Eun Chang , Keum Ki Chang 
Published: May 2010

Abstract

Background
The aim of this study was to assess the results of curative surgery with and without radiotherapy in patients with T1-2N0-1 oral tongue squamous cell carcinoma (OSCC) and to evaluate survival and prognostic factors.

Methods
Retrospective analysis of 86 patients with T1-2N0-1 OSCC who received surgery between January 2000 and December 2006. Fourteen patients (16.3%) received postoperative radiotherapy (PORT). Patient characteristics, tumor characteristics, treatment modality, failure patterns, and survival rates were analyzed.

Results
The median follow-up was 45 months. The five-year overall survival (OS) and disease-free survival (DFS) rates were 80.8% and 80.2%, respectively. Higher tumor grade and invasion depth ≥ 0.5 cm were the significant prognostic factors affecting five-year OS and DFS (OS rate; 65% vs. 91%, p = 0.001 for grade; 66% vs. 92%, p = 0.01 for invasion depth: DFS rate; 69% vs. 88%, p = 0.005 for grade; 66% vs. 92%, p = 0.013 for invasion depth). In the risk group, there was no local failure in patients with postoperative radiotherapy.

Conclusions
In T1-2N0-1 OSCC, factors that affected prognosis after primary surgery were higher tumor grade and deep invasion depth over 0.5 cm. Postoperative radiotherapy should be considered in early oral tongue cancer patients with these high-risk pathologic features.