bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extranodal marginal zone lymphoma of the ocular adnexa
Authors: Stefanovic Alexandra , Lossos Izidore S. 
Published: April 2009

Abstract
Lymphomas of the ocular adnexa are a heterogeneous group of malignancies, composing approximately 1% to 2% of non-Hodgkin lymphomas (NHLs) and 8% of extranodal lymphomas. The most common subtype, accounting for up to 80% of cases of primary ocular adnexal lymphoma, is marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) type. In the recent past, there have been significant advances in our understanding of the clinical characteristics, morphology and phenotype, etiology, pathogenesis, diagnosis, natural history, treatment approaches, outcome, and prognostic factors of this disease entity. Novel immunologic and molecular techniques have aided in the distinction between MALT lymphoma and other lymphoproliferative disorders and led to the identification of tissue markers of prognostic significance. Modern imaging modalities provide invaluable tools for accurate staging and treatment planning. Besides radiotherapy and chemotherapy, a variety of new treatment options have emerged in the management of patients with ocular adnexal MALT lymphoma, especially monoclonal antibody therapy and antibiotic therapy against Chlamydia psittaci, which has been associated with the pathogenesis of ocular adnexal lymphomas in some parts of the world. In this review, we present a state-of-the-art summary of ocular adnexal MALT lymphomas.
Impact of donor CMV status on viral infection and reconstitution of multifunction CMV-specific T cells in CMV-positive transplant recipients
Authors: Zhou Wendi , Longmate Jeff , Lacey Simon F. , Palmer Joycelynne M. , Gallez-Hawkins Ghislaine , Thao Lia , Spielberger Ricardo , Nakamura Ryotaro , Forman Stephen J. , Zaia John A. , Diamond Don J. 
Published: April 2009

AbstractReconstitution of cytomegalovirus (CMV)–specific CD8+ T cells is essential to the control of CMV infection in CMV-positive recipients (R+) after allogeneic hematopoietic stem cell transplantation (HCT). Six-color flow cytometry was used to assess the functional profile of CMV-specific CD8+ T cells in 62 of 178 R+ HCT recipients followed virologically for CMV reactivation. R+ recipients receiving grafts from CMV-negative donors (D−; D−/R+) reconstituted fewer multifunctional CD8+ T cells expressing tumor necrosis factor-α (TNF-α), macrophage inflammatory protein-1β (MIP-1β), and CD107 in addition to interferon-γ (IFN-γ), compared with D+/R+ recipients. Unlike monofunctional CD8+ T cells secreting IFN-γ, which were abundantly generated during CMV reactivation in D−/R+ recipients, the relative lack of multifunctional CD8+ T cells persisted until at least 1 year post-HCT. D−/R+ recipients were more likely to require recurrent and prolonged use of antivirals. These findings were robust to statistical adjustment for pretransplant factors, as well as for posttransplant factors including graft-versus-host disease (GVHD) and its treatment by steroids. These analyses suggest that D+/R+ transplants, on average, generate higher levels of multifunctional CMV-specific T cells and require less antiviral therapy compared with D−/R+ HCT recipients. These results highlight the benefit of D+ donors in improving outcomes of R+ HCT recipients by reducing the duration and recurrent need of antiviral treatment, aided by increased levels of multifunctional CMV-specific T cells.
Imaging of the diffusion of single band 3 molecules on normal and mutant erythrocytes
Authors: Kodippili Gayani C. , Spector Jeff , Sullivan Caitlin , Kuypers Frans A. , Labotka Richard , Gallagher Patrick G. , Ritchie Ken , Low Philip S. 
Published: April 2009

AbstractMembrane-spanning proteins may interact with a variety of other integral and peripheral membrane proteins via a diversity of protein-protein interactions. Not surprisingly, defects or mutations in any one of these interacting components can impact the physical and biological properties on the entire complex. Here we use quantum dots to image the diffusion of individual band 3 molecules in the plasma membranes of intact human erythrocytes from healthy volunteers and patients with defects in one of their membrane components, leading to well-known red cell pathologies (hereditary spherocytosis, hereditary elliptocytosis, hereditary hydrocytosis, Southeast Asian ovalocytosis, and hereditary pyropoikilocytosis). After characterizing the motile properties of the major subpopulations of band 3 in intact normal erythrocytes, we demonstrate that the properties of these subpopulations of band 3 change significantly in diseased cells, as evidenced by changes in the microscopic and macroscopic diffusion coefficients of band 3 and in the compartment sizes in which the different band 3 populations can diffuse. Because the above membrane abnormalities largely arise from defects in other membrane components (eg, spectrin, ankyrin), these data suggest that single particle tracking of band 3 might constitute a useful tool for characterizing the general structural integrity of the human erythrocyte membrane.
dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation
Authors: Hariharan Manoj , Scaria Vinod , Brahmachari Samir K 
Published: April 2009

Abstract

Background
MicroRNAs (miRNAs) regulate several biological processes through post-transcriptional gene silencing. The efficiency of binding of miRNAs to target transcripts depends on the sequence as well as intramolecular structure of the transcript. Single Nucleotide Polymorphisms (SNPs) can contribute to alterations in the structure of regions flanking them, thereby influencing the accessibility for miRNA binding.

Description
The entire human genome was analyzed for SNPs in and around predicted miRNA target sites. Polymorphisms within 200 nucleotides that could alter the intramolecular structure at the target site, thereby altering regulation were annotated. Collated information was ported in a MySQL database with a user-friendly interface accessible through the URL: http://miracle.igib.res.in/dbSMR.

Conclusion
The database has a user-friendly interface where the information can be queried using either the gene name, microRNA name, polymorphism ID or transcript ID. Combination queries using 'AND' or 'OR' is also possible along with specifying the degree of change of intramolecular bonding with and without the polymorphism. Such a resource would enable researchers address questions like the role of regulatory SNPs in the 3' UTRs and population specific regulatory modulations in the context of microRNA targets.
Identifying set-wise differential co-expression in gene expression microarray data
Authors: Cho Sung Bum , Kim Jihun , Kim Ju Han 
Published: April 2009

Abstract

Background
Previous differential coexpression analyses focused on identification of differentially coexpressed gene pairs, revealing many insightful biological hypotheses. However, this method could not detect coexpression relationships between pairs of gene sets. Considering the success of many set-wise analysis methods for microarray data, a coexpression analysis based on gene sets may elucidate underlying biological processes provoked by the conditional changes. Here, we propose a differentially coexpressed gene sets (dCoxS) algorithm that identifies the differentially coexpressed gene set pairs between conditions.

Results
dCoxS is a two-step analysis method. In each condition, dCoxS measures the interaction score (IS), which represents the expression similarity between two gene sets using Renyi relative entropy. When estimating the relative entropy, multivariate kernel density estimation was used to model gene-gene correlation structure. Statistical tests for the conditional difference between the ISs determined the significance of differential coexpression of the gene set pair. Simulation studies supported that the IS is a representative measure of similarity between gene expression matrices. Single gene coexpression analysis of two publicly available microarray datasets detected no significant results. However, the dCoxS analysis of the datasets revealed differentially coexpressed gene set pairs related to the biological conditions of the datasets.

Conclusion
dCoxS identified differentially coexpressed gene set pairs not found by single gene analysis. The results indicate that set-wise differential coexpression analysis is useful for understanding biological processes induced by conditional changes.
Non-replication of an association of CTNNBL1polymorphisms and obesity in a population of Central European ancestry
Authors: Vogel Carla IG , Greene Brandon , Scherag André , Müller Timo D , Friedel Susann , Grallert Harald , Heid Iris M , Illig Thomas , Wichmann H-Erich , Schäfer Helmut , Hebebrand Johannes , Hinney Anke 
Published: April 2009

Abstract

Background
A recent genome-wide association (GWA) study of U.S. Caucasians suggested that eight single nucleotide polymorphisms (SNPs) in CTNNBL1 are associated with obesity and increased fat mass. We analysed the respective SNPs in data from our previously published GWA for early onset obesity (case-control design), in GWA data from a population-based cohort of adults, and in an independent family-based obesity study. We investigated whether variants in CTNNBL1 (including rs6013029) and in three other genes (SH3PXD2B, SLIT3 and FLJ42133,) were associated with obesity.

Methods
The GWA studies were carried out using Affymetrix® SNP Chips with approximately 500,000 markers each. In the families, SNP rs6013029 was genotyped using the TaqMan® allelic discrimination assay. The German case-control GWA included 487 extremely obese children and adolescents and 442 healthy lean individuals. The adult GWA included 1,644 individuals from a German population-based study (KORA). The 775 independent German families consisted of extremely obese children and adolescents and their parents.

Results
We found no evidence for an association of the reported variants in CTNNBL1 with early onset obesity or increased BMI. Further, in our family-based study we found no evidence for over-transmission of the rs6013029 risk-allele T to obese children. Additionally, we found no evidence for an association of SH3PXD2B, SLIT3 and FLJ42133 variants in our two GWA samples.

Conclusion
We detected no confirmation of the recent association of variants in CTNNBL1 with obesity in a population of Central European ancestry.
Patient satisfaction with healthcare provided by family doctors: primary dimensions and an attempt at typology
Authors: Marcinowicz Ludmila , Chlabicz Slawomir , Grebowski Ryszard 
Published: April 2009

Abstract

Background
Patient satisfaction is a complex and difficult concept to measure, thus precluding the use of exclusively quantitative methods for its description. The purpose of this survey was firstly to identify particular healthcare dimensions that determine a patient's satisfaction or dissatisfaction; and secondly to attempt to typologise the patients' responses based on their evaluation of healthcare.

Methods
Using a qualitative research design, thirty-six in-depth interviews with patients of family physicians were conducted: four patients from each of 9 family practices in different regions of Poland were interviewed. The main outcome measure was factors associated with patient satisfaction/dissatisfaction.

Results
In their evaluations of their contacts with family doctors, the patients cited mostly issues concerning interpersonal relationships with the doctor. Nearly 40% of the statements referred to this aspect of healthcare, with nearly equal proportions of positive and negative comments. The second most frequent category of responses concerned contextual factors (21%) that related to conditions of medical service, with two-thirds of the evaluations being negative. Statements concerning the doctor's competencies (12.9%) and personal qualities (10.5%) were less common.

Conclusion
To improve the quality of healthcare, family doctors should take special care to ensure the quality of their interactions with patients.
Equity and coverage of insecticide-treated bed nets in an area of intense transmission of Plasmodium falciparum in Tanzania
Authors: Bernard Jubilate , Mtove George , Mandike Renata , Mtei Frank , Maxwell Caroline , Reyburn Hugh 
Published: April 2009

Abstract

Background
There is no clear consensus on the most sustainable and effective distribution strategy for insecticide treated bed nets (ITNs). Tanzania has been a leader in social marketing but it is still not clear if this can result in high and equitable levels of coverage.

Methods
A cluster-randomized survey of ITN and bed net ownership and use was conducted in a rural area exposed to intense Plasmodium falciparum transmission in NE Tanzania where ITN distribution had been subject to routine delivery of national strategies and episodic free distribution through local clinics. Data were collected on household assets to assess equity of ITN coverage and a rapid diagnostic test for malaria (RDT) was performed in all ages.

Results
Among 598 households in four villages the use of any or insecticidal bed nets in children less than five years of age was 71% and 54% respectively. However there was a 19.8% increase in the number of bed nets per person (p < 0.001) and a 13.4% increase in the number of insecticidal nets per person (p < 0.001) for each quintile increase in household asset score. The odds of being RDT-positive were reduced by more than half in the least poor compared to the poorest households (OR 0.49, 95% CI 0.35–0.70). Poorer households had paid less for their nets and acquired them more recently, particularly from non-commercial sources, and bed nets in the least poor households were less likely to be insecticidal compared to nets in the poorest households (OR 0.44, 95% CI 0.26–0.74).

Conclusion
Marked inequity persists with the poorest households still experiencing the highest risk of malaria and the lowest ITN coverage. Abolition of this inequity within the foreseeable future is likely to require mass or targeted free distribution, but risks damaging what is otherwise an effective commercial market.
High level expression of the anti-retroviral protein APOBEC3G is induced by influenza A virus but does not confer antiviral activity
Authors: Pauli Eva-K , Schmolke Mirco , Hofmann Henning , Ehrhardt Christina , Flory Egbert , Münk Carsten , Ludwig Stephan 
Published: April 2009

Abstract
Human APOBEC3G is an antiretroviral protein that was described to act via deamination of retroviral cDNA. However, it was suggested that APOBEC proteins might act with antiviral activity by yet other mechanisms and may also possess RNA deamination activity. As a consequence there is an ongoing debate whether APOBEC proteins might also act with antiviral activity on other RNA viruses. Influenza A viruses are single-stranded RNA viruses, capable of inducing a variety of antiviral gene products. In searching for novel antiviral genes against these pathogens, we detected a strong induction of APOBEC3G but not APOBEC3F gene transcription in infected cells. This upregulation appeared to be induced by the accumulation of viral RNA species within the infected cell and occurred in an NF-κB dependent, but MAP kinase independent manner. It further turned out that APOBEC expression is part of a general IFNβ response to infection. However, although strongly induced, APOBEC3G does not negatively affect influenza A virus propagation.
Torsion of right middle lobe after a right upper lobectomy
Authors: Chen Chih-Hao , Hung Tzu-Ti , Chen Tung-Ying , Liu Hung-Chang 
Published: April 2009

Abstract
Lobar torsion after lung resection is a quite rare complication. A 50-year-old woman presented typical features on chest radiographs and CT(computed tomography) scan of lobar torsion after a right upper lobectomy. After emergency lobectomy of right middle lobe, the patient recovered well and discharged 10 days after the second operation.
LRP1 shedding in human brain: roles of ADAM10 and ADAM17
Authors: Liu Qiang , Zhang Juan , Tran Hien , Verbeek Marcel M , Reiss Karina , Estus Steven , Bu Guojun 
Published: April 2009

Abstract

Background
The low-density lipoprotein receptor-related protein 1 (LRP1) plays critical roles in lipid metabolism, cell survival, and the clearance of amyloid-β (Aβ) peptide. Functional soluble LRP1 (sLRP1) has been detected in circulating human placenta; however, whether sLRP1 is also present in the central nervous system is unclear.

Results
Here we show that abundant sLRP1 capable of binding its ligands is present in human brain tissue and cerebral spinal fluid (CSF). Interestingly, the levels of sLRP1 in CSF are significantly increased in older individuals, suggesting that either LRP1 shedding is increased or sLRP1 clearance is decreased during aging. To examine potential effects of pathological ligands on LRP1 shedding, we treated MEF cells with Aβ peptide and found that LRP1 shedding was increased. ADAM10 and ADAM17 are key members of the ADAM family that process membrane-associated proteins including amyloid precursor protein and Notch. We found that LRP1 shedding was significantly decreased in MEF cells lacking ADAM10 and/or ADAM17. Furthermore, forced expression of ADAM10 increased LRP1 shedding, which was inhibited by ADAM-specific inhibitor TIMP-3.

Conclusion
Our results demonstrate that LRP1 is shed by ADAM10 and ADAM17 and functional sLRP1 is abundantly present in human brain and CSF. Dysregulated LRP1 shedding during aging could alter its function and may contribute to the pathogenesis of AD.
Changes in S-100 protein serum levels in survivors of out-of-hospital cardiac arrest treated with mild therapeutic hypothermia: a prospective, observational study
Authors: Derwall Matthias , Stoppe Christian , Brücken David , Rossaint Rolf , Fries Michael 
Published: April 2009

Abstract
Introduction
Knowledge about the influence of current neuroprotective interventions on prognostic markers after survival from cardiac arrest is lacking. This study aimed to investigate the effects of mild therapeutic hypothermia on the release of the astroglial protein S-100 after cardiopulmonary resuscitation (CPR) in survivors of out-of-hospital cardiac arrest.

Methods
This was a prospective, observational study performed during a two-year period, involving medical emergency services and five collaborating hospitals at the city of Aachen, Germany. Sixty-eight subjects were enrolled by the emergency physician on duty by taking blood samples after successful attempts at resuscitation with return of spontaneous circulation (ROSC), followed by samples at 6, 12, 24, 72 and 120 hours post ROSC by the appropriate intensive care unit staff. Depending on the decision of the attending physician, subjects were cooled down to 33°C (n = 37) for 24 hours or were held at 37°C (n = 31). Patients were tracked for estimating mortality and gross neurological outcome for 14 days.

Results
S-100 levels in patients not receiving mild therapeutic hypothermia (normothermia (NT)) showed equivalent numbers as compared with cooled patients (mild therapeutic hypothermia (MTH)) on baseline (NT = 1.38 μg/l versus MTH = 1.30 μg/l; P = 0.886). S-100 levels on baseline were significantly lower in patients with a good neurological outcome at 14 days after the event in comparison to their peers with adverse outcome (P = 0.014). Although the difference in S-100 levels of MTH patients with adverse or favourable neurological outcome reached statistical significance, it did not in NT patients.

Conclusions
Although the predictive power of S-100 levels were best on admission but not at later time points, MTH had no influence on S-100 serum levels in survivors of non-traumatic out-of-hospital cardiac arrest in the particular setting of this investigation.
Conservation of core gene expression in vertebrate tissues
Authors: Chan Esther T , Quon Gerald T , Chua Gordon , Babak Tomas , Trochesset Miles , Zirngibl Ralph A , Aubin Jane , Ratcliffe Michael JH , Wilde Andrew , Brudno Michael , Morris Quaid D , Hughes Timothy R 
Published: April 2009

Abstract
Background
Vertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet show great diversity in morphology, habitat and behavior. Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates.

Results
We measured expression of all known and predicted genes across twenty tissues in chicken, frog and pufferfish. By combining the results with human and mouse data and considering only ten common tissues, we have found evidence of conserved expression for more than a third of unique orthologous genes. We find that, on average, transcription factor gene expression is neither more nor less conserved than that of other genes. Strikingly, conservation of expression correlates poorly with the amount of conserved nonexonic sequence, even using a sequence alignment technique that accounts for non-collinearity in conserved elements. Many genes show conserved human/fish expression despite having almost no nonexonic conserved primary sequence.

Conclusions
There are clearly strong evolutionary constraints on tissue-specific gene expression. A major challenge will be to understand the precise mechanisms by which many gene expression patterns remain similar despite extensive cis-regulatory restructuring.
Enriching balancing information using the unbalance covariance matrix
Authors: Jiffri S , Garvey S D , Rix A I J 
Published: April 2009

Traditionally, rotor balancing is performed based only on vibration readings from either a balancing machine or from a machine in which the rotor is being balanced in-situ. These readings cannot reflect the complete state of unbalance in the rotor. The reason for this is that higher frequency modes do not make a significant contribution to response in any one operating condition. The resolution of measuring instrumentation is always limited and, as demands grow for ever-improved balance quality, this instrumentation struggles more and more with reducing signal-to-noise ratios. When balance corrections are made to a rotor based only on these vibration readings, the components of unbalance that tend to excite only the higher modes of the original configuration can make a significant contribution to response if the properties of the stator change. This article presents a novel approach to robust balancing. It relies on the use of additional information in the form of a rotor unbalance covariance matrix. In theory, this covariance matrix could be obtained if a large sample from the population of all rotors of this type could be tested in a very high-quality (and high-speed) balancing machine. This suggestion is impracticable in all real situations. However, it is entirely conceivable that modelling of the manufacturing processes used to create the rotor could deliver this covariance matrix. This article begins by illustrating how such a covariance matrix might be obtained from modelling and then goes on to explain how the information within the covariance matrix can be combined with a set of measurements from a specific rotor to provide an improved estimate of the actual state of unbalance on that rotor. Examples are included to demonstrate the proposed robust balancing method.