bluuebunny/crossref_metadata_2025 huggingface dataset:
Presence of the P2RY8-CRLF2 rearrangement is associated with a poor prognosis in non–high-risk precursor B-cell acute lymphoblastic leukemia in children treated according to the ALL-BFM 2000 protocol
Authors: Cario Gunnar , Zimmermann Martin , Romey Renja , Gesk Stefan , Vater Inga , Harbott Jochen , Schrauder André , Moericke Anja , Izraeli Shai , Akasaka Takashi , Dyer Martin J. S. , Siebert Reiner , Schrappe Martin , Stanulla Martin
Published: April 2010

High-level expression of the cytokine receptor-like factor 2 gene, CRLF2, in precursor B-cell acute lymphoblastic leukemia (pB-ALL) was shown to be caused by a translocation involving the IGH@ locus or a deletion juxtaposing CRLF2 with the P2RY8 promoter. To assess its possible prognostic value, CRLF2 expression was analyzed in 555 childhood pB-ALL patients treated according to the Acute Lymphoblastic Leukemia Berlin-Frankfurt-Münster 2000 (ALL-BFM 2000) protocol. Besides CRLF2 rearrangements, high-level CRLF2 expression was seen in cases with supernumerary copies of the CRLF2 locus. On the basis of the detection of CRLF2 rearrangements, a CRLF2 high-expression group (n = 49) was defined. This group had a 6-year relapse incidence of 31% plus or minus 8% compared with 11% plus or minus 1% in the CRLF2 low-expression group (P = .006). This difference was mainly attributable to an extremely high incidence of relapse (71% ± 19%) in non–high-risk patients with P2RY8-CRLF2 rearrangement. The assessment of CRLF2 aberrations may therefore serve as new stratification tool in Berlin-Frankfurt-Münster–based protocols by identifying additional high-risk patients who may benefit from an intensified and/or targeted treatment.
Systematic cytokine receptor profiling reveals GM-CSF as a novel TLR-independent activator of human plasmacytoid predendritic cells
Authors: Ghirelli Cristina , Zollinger Raphaël , Soumelis Vassili
Published: April 2010

Human plasmacytoid predendritic cells (pDCs) can be activated during microbial infection through Toll-like receptor engagement. They are also involved in nonmicrobial inflammatory diseases, but their activation pathways in this context remain elusive. To identify Toll-like receptor-independent pDC activators, we performed a systematic analysis of cytokine receptors on primary human pDCs. Six receptors were expressed both at mRNA and protein levels: interleukin-3 receptor (IL-3R), IL-6R, IL-10R, IL-18R, interferon-γ receptor, and granulocyte-macrophage colony-stimulating factor (GM-CSF) receptor. Only GM-CSF and IL-3 were able to efficiently promote pDC survival and induce their differentiation into dendritic cells. Allogeneic naive CD4 T cells primed with GM-CSF–activated pDCs produced more interferon-γ and less IL-4 and IL-10 compared with IL-3–activated pDCs, indicating a shift in the Th1/Th2 balance. Our data point at a novel function of GM-CSF, which may serve as a link between a pathologic inflammatory environment, pDC activation, and the modulation of CD4 T-cell responses.
Cystic fibrosis and survival to 40 years: a case–control study
Authors: Simmonds N.J. , MacNeill S.J. , Cullinan P. , Hodson M.E.
Published: April 2010

The clinical course of patients with cystic fibrosis (CF) is variable and probably determined by many interacting factors. We aimed to examine the influence of early social and clinical factors on long-term survival.

A case–control study of adult CF patients was used to compare long-term survivors (aged ≥40 yrs) with patients who died before reaching 30 yrs of age. Each case (n = 78) was matched by birth date with at least one control (n = 152), after exclusion of “late diagnosis” patients. Probability-weighted logistic regression models were used to identify influences on survival.

Factors resulting in increased probabilities of survival included high body mass index (OR 1.76, 95% CI 1.40–2.22), forced expiratory volume in 1 s (OR per 5% increase 1.54, 95% CI 1.32–1.80), and forced vital capacity (OR per 5% increase 1.54, 95% CI 1.33–1.78) at transfer to the adult clinic and the exclusive use of oral antibiotics (OR 8.31, 95% CI 3.02–22.88). Factors resulting in decreased probabilities of survival werePseudomonas aeruginosaacquisition (OR 0.18, 95% 0.05–0.65) or pneumothorax before transfer to the adult clinic (OR 0.02, 95% CI 0.004–0.08) and referral from a paediatric clinic in a deprived area (OR 0.13, 95% CI 0.04–0.38).

Long-term survival is associated with the clinical features present by the time of referral to an adult clinic. Even “early-diagnosis” disease appears to have different phenotypes, possibly independent of CF gene function, that have different survival patterns.
Osteopontin promotes host defense duringKlebsiella pneumoniae-induced pneumonia
Authors: van der Windt G.J.W. , Hoogerwerf J.J. , de Vos A.F. , Florquin S. , van der Poll T.
Published: April 2010

Klebsiellapneumoniaeis a common cause of nosocomial pneumonia. Osteopontin (OPN) is a phosphorylated glycoprotein involved in inflammatory processes, some of which is mediated by CD44. The aim of this study was to determine the role of OPN duringK. pneumoniae-induced pneumonia.

Wild-type (WT) and OPN knockout (KO) mice were intranasally infected with 104colony forming units ofK. pneumoniae, or administeredKlebsiellalipopolysaccharides (LPS). In addition, recombinant OPN (rOPN) was intranasally administered to WT and CD44 KO mice.

DuringKlebsiellapneumonia, WT mice displayed elevated pulmonary and plasma OPN levels. OPN KO and WT mice showed similar pulmonary bacterial loads 6 h after infection; thereafter,Klebsiellaloads were higher in lungs of OPN KO mice and the mortality rate in this group was higher than in WT mice. Early neutrophil recruitment into the bronchoalveolar space was impaired in the absence of OPN after intrapulmonary delivery of eitherKlebsiellabacteria orKlebsiellaLPS. Moreover, rOPN induced neutrophil migration into the bronchoalveolar space, independent from CD44.In vitro, OPN did not affectK. pneumoniaegrowth or neutrophil function.

In conclusion, OPN levels were rapidly increased in the bronchoalveolar space duringK. pneumoniaepneumonia, where OPN serves a chemotactic function towards neutrophils, thereby facilitating an effective innate immune response.
Pulmonary artery pressure limits exercise capacity at high altitude
Authors: Naeije R. , Huez S. , Lamotte M. , Retailleau K. , Neupane S. , Abramowicz D. , Faoro V.
Published: April 2010

Altitude exposure is associated with decreased exercise capacity and increased pulmonary vascular resistance (PVR).

Echocardiographic measurements of pulmonary haemodynamics and a cardiopulmonary exercise test were performed in 13 healthy subjects at sea level, in normoxia and during acute hypoxic breathing (1 h, 12% oxygen in nitrogen), and in 22 healthy subjects after acclimatisation to an altitude of 5,050 m. The measurements were obtained after randomisation, double-blinded to the intake of placebo or the endothelin A receptor blocker sitaxsentan (100 mg·day−1for 7 days). Blood and urine were sampled for renal function measurements.

Normobaric as well as hypobaric hypoxia increased PVR and decreased maximum workload and oxygen uptake (V′O2,max). Sitaxsentan decreased PVR in acute and chronic hypoxia (both p<0.001), and partly restoredV′O2,max, by 30 % in acute hypoxia (p<0.001) and 10% in chronic hypoxia (p<0.05). Sitaxsentan-induced changes in PVR andV′O2,maxwere correlated (p = 0.01). Hypoxia decreased glomerular filtration rate and free water clearance, and increased fractional sodium excretion. These indices of renal function were unaffected by sitaxsentan intake.

Selective endothelin A receptor blockade with sitaxsentan improves mild pulmonary hypertension and restores exercise capacity without adverse effects on renal function in hypoxic normal subjects.
Is tidal expiratory flow limitation predictive of sleep-related disorders in the elderly?
Authors: Guillot M. , Costes F. , Sforza E. , Maudoux D. , Bertoletti L. , Barthélémy J.C. , Roche F.
Published: April 2010

Sleep-related disorders represent an important health burden and their prevalence increases with age. In patients with snoring or sleepiness, the presence of expiratory flow limitation (EFL), determinedviathe negative expiratory pressure (NEP) method, is related to the apnoea/hypopnoea index (AHI). In this study, we examined whether EFL can be used to predict obstructive sleep apnoea syndrome (OSAS) in healthy asymptomatic older subjects.

A group of 72-yr-old subjects (n = 448, 44% males) with a mean body mass index of 25.5±3.8 kg·m−2were examined. All subjects underwent spirometry, NEP (-5 cmH2O, sitting position) and ventilatory polygraphy (VP).

Spirometry was within normal values in 88% of the group and EFL was present in 143 (32%) subjects with a higher prevalence in females (89 out of 249versus54 out of 199 in females and males, respectively). VP showed an AHI<15 h−1in 238 subjects (53%) and OSAS with an AHI ≥15 h−1in 47%. EFL was found in 15% of subjects with OSAS. Consequently, EFL had low sensitivity and specificity in the prediction of OSAS (31.4% and 67.7%, respectively).

We conclude that the prevalence of EFL is elevated in healthy older subjects and cannot be used to predict the presence of sleep-related disorders in an older population.
The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori
Authors: Douillard François P , Ryan Kieran A , Lane Michael C , Caly Delphine L , Moore Stanley A , Penn Charles W , Hinds Jason , O'Toole Paul W
Published: April 2010

Background

Helicobacter pylori is the causative agent for gastritis, and peptic and duodenal ulcers. The bacterium displays 5-6 polar sheathed flagella that are essential for colonisation and persistence in the gastric mucosa. The biochemistry and genetics of flagellar biogenesis in H. pylori has not been fully elucidated. Bioinformatics analysis suggested that the gene HP0256, annotated as hypothetical, was a FliJ homologue. In Salmonella, FliJ is a chaperone escort protein for FlgN and FliT, two proteins that themselves display chaperone activity for components of the hook, the rod and the filament.

Results

Ablation of the HP0256 gene in H. pylori significantly reduced motility. However, flagellin and hook protein synthesis was not affected in the HP0256 mutant. Transmission electron transmission microscopy revealed that the HP0256 mutant cells displayed a normal flagellum configuration, suggesting that HP0256 was not essential for assembly and polar localisation of the flagella in the cell. Interestingly, whole genome microarrays of an HP0256 mutant revealed transcriptional changes in a number of genes associated with the flagellar regulon and the cell envelope, such as outer membrane proteins and adhesins. Consistent with the array data, lack of the HP0256 gene significantly reduced adhesion and the inflammatory response in host cells.

Conclusions

We conclude that HP0256 is not a functional counterpart of FliJ in H. pylori. However, it is required for full motility and it is involved, possibly indirectly, in expression of outer membrane proteins and adhesins involved in pathogenesis and adhesion.
A rich TILLING resource for studying gene function in Brassica rapa
Authors: Stephenson Pauline , Baker David , Girin Thomas , Perez Amandine , Amoah Stephen , King Graham J , Østergaard Lars
Published: April 2010

Background

The Brassicaceae family includes the model plant Arabidopsis thaliana as well as a number of agronomically important species such as oilseed crops (in particular Brassica napus, B. juncea and B. rapa) and vegetables (eg. B. rapa and B. oleracea).

Separated by only 10-20 million years, Brassica species and Arabidopsis thaliana are closely related, and it is expected that knowledge obtained relating to Arabidopsis growth and development can be translated into Brassicas for crop improvement. Moreover, certain aspects of plant development are sufficiently different between Brassica and Arabidopsis to warrant studies to be carried out directly in the crop species. However, mutating individual genes in the amphidiploid Brassicas such as B. napus and B. juncea may, on the other hand, not give rise to expected phenotypes as the genomes of these species can contain up to six orthologues per single-copy Arabidopsis gene. In order to elucidate and possibly exploit the function of redundant genes for oilseed rape crop improvement, it may therefore be more efficient to study the effects in one of the diploid Brassica species such as B. rapa. Moreover, the ongoing sequencing of the B. rapa genome makes this species a highly attractive model for Brassica research and genetic resource development.

Results

Seeds from the diploid Brassica A genome species, B. rapa were treated with ethyl methane sulfonate (EMS) to produce a TILLING (Targeting Induced Local Lesions In Genomes) population for reverse genetics studies. We used the B. rapa genotype, R-o-18, which has a similar developmental ontogeny to an oilseed rape crop. Hence this resource is expected to be well suited for studying traits with relevance to yield and quality of oilseed rape. DNA was isolated from a total of 9,216 M2 plants and pooled to form the basis of the TILLING platform. Analysis of six genes revealed a high level of mutations with a density of about one per 60 kb. This analysis also demonstrated that screening a 1 kb amplicon in just one third of the population (3072 M2 plants) will provide an average of 68 mutations and a 97% probability of obtaining a stop-codon mutation resulting in a truncated protein. We furthermore calculated that each plant contains on average ~10,000 mutations and due to the large number of plants, it is predicted that mutations in approximately half of the GC base pairs in the genome exist within this population.

Conclusions

We have developed the first EMS TILLING resource in the diploid Brassica species, B. rapa. The mutation density in this population is ~1 per 60 kb, which makes it the most densely mutated diploid organism for which a TILLING population has been published. This resource is publicly available through the RevGenUK reverse genetics platform http://revgenuk.jic.ac.uk.
The obesity gene, TMEM18, is of ancient origin, found in majority of neuronal cells in all major brain regions and associated with obesity in severely obese children
Authors: Almén Markus Sällman , Jacobsson Josefin A , Shaik Jafar HA , Olszewski Pawel K , Cedernaes Jonathan , Alsiö Johan , Sreedharan Smitha , Levine Allen S , Fredriksson Robert , Marcus Claude , Schiöth Helgi B
Published: April 2010

Background

TMEM18 is a hypothalamic gene that has recently been linked to obesity and BMI in genome wide association studies. However, the functional properties of TMEM18 are obscure.

Methods

The evolutionary history of TMEM18 was inferred using phylogenetic and bioinformatic methods. The gene's expression profile was investigated with real-time PCR in a panel of rat and mouse tissues and with immunohistochemistry in the mouse brain. Also, gene expression changes were analyzed in three feeding-related mouse models: food deprivation, reward and diet-induced increase in body weight. Finally, we genotyped 502 severely obese and 527 healthy Swedish children for two SNPs near TMEM18 (rs6548238 and rs756131).

Results

TMEM18 was found to be remarkably conserved and present in species that diverged from the human lineage over 1500 million years ago. The TMEM18 gene was widely expressed and detected in the majority of cells in all major brain regions, but was more abundant in neurons than other cell types. We found no significant changes in the hypothalamic and brainstem expression in the feeding-related mouse models. There was a strong association for two SNPs (rs6548238 and rs756131) of the TMEM18 locus with an increased risk for obesity (p = 0.001 and p = 0.002).

Conclusion

We conclude that TMEM18 is involved in both adult and childhood obesity. It is one of the most conserved human obesity genes and it is found in the majority of all brain sites, including the hypothalamus and the brain stem, but it is not regulated in these regions in classical energy homeostatic models.
Same-visit HIV testing in Trinidad and Tobago
Authors: Duke Violet , Samiel Sheila , Musa David , Ali Cameile , Chang-Kit Catherine , Warner Cynthia
Published: April 2010

Background

The Ministry of Health (hereafter, Ministry) of Trinidad and Tobago is responsible for delivery of all health services in the country. The Ministry takes responsibility for direct delivery of care in the public sector and has initiated a process whereby those seeking HIV test results could obtain confidential reports during a single-visit to a testing location. The Ministry requested technical assistance with this process from the Caribbean Epidemiology Centre (CAREC). The United States Centers for Disease Control and Prevention (CDC) played an important role in this process through its partnership with CAREC.

Methods

Under the technical guidance of CAREC and CDC, the Ministry organized a technical working group which included representatives from key national HIV program services and technical assistance partners. This working group reviewed internationally-recognized best practices for HIV rapid testing and proposed a program that could be integrated into the national HIV programs of Trinidad and Tobago. The working group wrote a consensus protocol, defined certification criteria, prepared training materials and oversaw implementation of "same-visit" HIV testing at two pilot sites.

Results

A Ministry-of-Health-supported program of "same-visit" HIV testing has been established in Trinidad and Tobago. This program provides confidential testing that is independent of laboratory confirmation. The program allows clients who want to know their HIV status to obtain this information during a single-visit to a testing location. Testers who are certified to provide testing on behalf of the Ministry are also counselors. Non-laboratory personnel have been trained to provide HIV testing in non-laboratory locations. The program includes procedures to assure uniform quality of testing across multiple testing sites. Several procedural and training documents were developed during implementation of this program. This report contains links to those documents.

Conclusions

The Ministry of Health has implemented a program of "same-visit" HIV testing in Trinidad and Tobago. This program provides clients confidential HIV test reports during a single visit to a testing location. The program is staffed by non-laboratory personnel who are trained to provide both testing and counseling in decentralized (non-laboratory) settings. This approach may serve as a model for other small countries.
Molecular mechanisms of HIV-1 persistence in the monocyte-macrophage lineage
Authors: Le Douce Valentin , Herbein Georges , Rohr Olivier , Schwartz Christian
Published: April 2010

The introduction of the highly active antiretroviral therapy (HAART) has greatly improved survival. However, these treatments fail to definitively cure the patients and unveil the presence of quiescent HIV-1 reservoirs like cells from monocyte-macrophage lineage. A purge, or at least a significant reduction of these long lived HIV-1 reservoirs will be needed to raise the hope of the viral eradication. This review focuses on the molecular mechanisms responsible for viral persistence in cells of the monocyte-macrophage lineage. Controversy on latency and/or cryptic chronic replication will be specifically evoked. In addition, since HIV-1 infected monocyte-macrophage cells appear to be more resistant to apoptosis, this obstacle to the viral eradication will be discussed. Understanding the intimate mechanisms of HIV-1 persistence is a prerequisite to devise new and original therapies aiming to achieve viral eradication.
Human herpesvirus-8 in northwestern China: epidemiology and characterization among blood donors
Authors: Wang Xing , He Bin , Zhang Zhaoxia , Liu Tao , Wang Hui , Li Xu , Zhang Qiong , Lan Ke , Lu Xiaomei , Wen Hao
Published: April 2010

Background

Human herpes virus 8 (HHV-8) is the etiologic agent associated with development of classical, AIDS-related, iatrogenic, and endemic Kaposi's sarcoma (KS). Several studies provide strong evidence that HHV-8 can be transmitted by blood transfusion. We evaluated the seroprevalence and potential risk factors of HHV-8 infection in blood donors in one region. We surveyed HHV-8 infection among 4461 blood donors in Xinjiang, China, a unique endemic area for HHV-8 and KS.

Results

The HHV-8 seroprevalence was higher in local minority groups which comprise most KS cases in China, than in Han people. HHV-8 prevalence was 18.6% in the Han ethnic group, 25.9% in Uygur subjects, 29.2% in Kazak subjects, 36.8% in Mongolian subjects, and 21.9% in other ethnic groups. In several subgroups, the time of donation of whole blood seemed to be a risk factor. In HHV-8-seropositive subjects, a larger fraction of local minorities (23.9%) had high HHV-8 titers than that of Han subjects (9.2%). HHV-8 infection was associated with ethnicity and residence.

Conclusion

HHV-8 seroprevalence was significantly high among blood donors in Xinjiang, where the prevalence of KS correlates with HHV-8 prevalence and titers in Uygur and Kazak ethnic groups. Blood exposure represented by the frequency of blood donation indicated a possible blood-borne transmission route of HHV-8 in Xinjiang. Detecting anti-HHV-8 antibodies before donation in this region is therefore important.
Mobile Air Quality Studies (MAQS)-an international project
Authors: Groneberg David A , Scutaru Cristian , Lauks Mathias , Takemura Masaya , Fischer Tanja C , Kölzow Silvana , van Mark Anke , Uibel Stefanie , Wagner Ulrich , Vitzthum Karin , Beck Fabian , Mache Stefanie , Kreiter Carolin , Kusma Bianca , Friedebold Annika , Zell Hanna , Gerber Alexander , Bock Johanna , Al-Mutawakl Khaled , Donat Johannes , Geier Maria Victoria , Pilzner Carolin , Welker Pia , Joachim Ricarda , Bias Harald , Götting Michael , Sakr Mohannad , Addicks Johann P , Börger Julia-Annik , Jensen Anna-Maria , Grajewski Sonja , Shami Awfa , Neye Niko , Kröger Stefan , Hoffmann Sarah , Kloss Lisa , Mayer Sebastian , Puk Clemens , Henkel Ulrich , Rospino Robert , Schilling Ute , Krieger Evelyn , Westphal Gesa , Meyer-Falcke Andreas , Hupperts Hagen , de Roux Andrés , Tropp Salome , Weiland Marco , Mühlbach Janette , Steinberg Johannes , Szerwinski Anne , Falahkohan Sepiede , Sudik Claudia , Bircks Anna , Noga Oliver , Dickgreber Nicolas , Dinh Q Thai , Golpon Heiko , Kloft Beatrix , Groneberg Rafael Neill B , Witt Christian , Wicker Sabine , Zhang Li , Springer Jochen , Kütting Birgitta , Mingomataj Ervin C , Fischer Axel , Schöffel Norman , Unger Volker , Quarcoo David
Published: April 2010

Due to an increasing awareness of the potential hazardousness of air pollutants, new laws, rules and guidelines have recently been implemented globally. In this respect, numerous studies have addressed traffic-related exposure to particulate matter using stationary technology so far. By contrast, only few studies used the advanced technology of mobile exposure analysis. The Mobile Air Quality Study (MAQS) addresses the issue of air pollutant exposure by combining advanced high-granularity spatial-temporal analysis with vehicle-mounted, person-mounted and roadside sensors. The MAQS-platform will be used by international collaborators in order 1) to assess air pollutant exposure in relation to road structure, 2) to assess air pollutant exposure in relation to traffic density, 3) to assess air pollutant exposure in relation to weather conditions, 4) to compare exposure within vehicles between front and back seat (children) positions, and 5) to evaluate "traffic zone"-exposure in relation to non-"traffic zone"-exposure.

Primarily, the MAQS-platform will focus on particulate matter. With the establishment of advanced mobile analysis tools, it is planed to extend the analysis to other pollutants including NO2, SO2, nanoparticles and ozone.
Does opening a milk bank in a neonatal unit change infant feeding practices? A before and after study
Authors: Utrera Torres María Isabel , Medina López Carmen , Vázquez Román Sara , Alonso Díaz Clara , Cruz-Rojo Jaime , Fernández Cooke Elisa , Pallás Alonso Carmen R
Published: April 2010

Background

Donor human milk banks are much more than simple centers for collection, storage, processing, and distribution of donor human milk, as they cover other aspects and represent a real opportunity to promote and support breastfeeding. The aim of our study is to assess the impact that opening a human milk bank has had on the proportion of infants receiving exclusive breast milk at discharge and other aspects related to feeding children with birth weight < or = 1500 g or < 32 weeks gestation admitted to the neonatal unit.

Methods

The study included babies of < or = 1500 g or < 32 weeks gestation. Fifty infants born from February to July in 2006, before the opening of the human milk bank, and 54 born from February to July in 2008, after its opening, met inclusive criteria. We collected data about days of hospital stay, hours of life when feeding was started, hours of life when full enteral feeding was attained, the type of milk received during admission, and the type of feeding on discharge.

Results

Children born in 2008 commenced feeding 16 hours earlier than those born in 2006 (p = 0.00). The proportion of infants receiving exclusive breast milk at discharge was 54% in 2006 and 56% in 2008 (p = 0.87). The number of days they received their mother's own milk during the first 28 days of life was 24.2 days in 2006, compared to 23.7 days in 2008 (p = 0.70). In 2006, 60% of infants received infant formula at least once in the first 28 days of life, compared to 37% in 2008 (p = 0.01).

Conclusions

The opening of a donor human milk bank in a neonatal unit did not reduce the proportion of infants exclusively fed with breast milk at discharge, but did reduce the proportion of infants that received infant formula during the first four weeks of life. Also, having donor human milk available enables commencement of enteral feeding earlier.
Protocol: fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato
Authors: Ricardi Martiniano M , González Rodrigo M , Iusem Norberto D
Published: April 2010

Background

Searching thoroughly for plant cis-elements corresponding to transcription factors is worthwhile to reveal novel gene activation cascades. At the same time, a great deal of research is currently focused on epigenetic events in plants. A widely used method serving both purposes is chromatin immunoprecipitation, which was developed for Arabidopsis and other plants but is not yet operational for tomato (Solanum lycopersicum), a model plant species for a group of economically important crops.

Results

We developed a chromatin immunoprecipitation protocol suitable for tomato by adjusting the parameters to optimise in vivo crosslinking, purification of nuclei, chromatin extraction, DNA shearing and precipitate analysis using real-time PCR. Results were obtained with two different antibodies, five control loci and two normalisation criteria.

Conclusion

Here we provide a chromatin immunoprecipitation procedure for tomato leaves that could be combined with high-throughput sequencing to generate a detailed map of epigenetic modifications or genome-wide nucleosome positioning data.
Remnant of a non-patent ductus arteriosus mimicking traumatic thoracic aorta transection: a case report
Authors: Apostolakis Efstratios E , Baikoussis Nikolaos G , Kalogeropoulou Christina , Koletsis Efstratios , Koniari Ioanna , Karnabatidis Dimitrios , Karanikolas Menelaos
Published: April 2010

We present an interesting case of a 53-year-old man with a non-patent ductus arteriosus erroneously diagnosed as acute thoracic aorta transection after a car accident. The aortography revealed a "rupture" of the linear inner curve of the aorta in the isthmus area, as well as a protrusion of the aortic lumen in the corresponding area. During the followed thoracotomy an intact thoracic aorta and the remnant of a non-patent ligamentum arteriosum were found. It is the first reported case and we review all the possible entities which may give a false-positive image of traumatic aortic transection.
Evolution of T-cell clonality in a patient with Ph-negative acute lymphocytic leukemia occurring after interferon and imatinib therapy for Ph-positive chronic myeloid leukemia
Authors: Wang Liang , Zhu Kanger , Zha Xianfeng , Chen Shaohua , Yang Lijian , Chen Si , Li Yangqiu
Published: April 2010

Introduction

The development of Philadelphia chromosome (Ph) negative acute leukemia/myelodysplastic syndrome (MDS) in patients with Ph-positive chronic myeloid leukemia (CML) is very rare. The features of restrictive usage and absence of partial T cell clones have been found in patients with CML. However, the T-cell clonal evolution of Ph-negative malignancies during treatment for CML is still unknown.

Objective

To investigate the dynamic change of clonal proliferation of T cell receptor (TCR) Vα and Vβ subfamilies in one CML patient who developed Ph-negative acute lymphoblastic leukemia (ALL) after interferon and imatinib therapy.

Methods

The peripheral blood mononuclear cells (PBMC) samples were collected at the 3 time points (diagnosis of Ph-positive chronic phase (CP) CML, developing Ph-negative ALL and post inductive chemotherapy (CT) for Ph-negative ALL, respectively). The CDR3 size of TCR Vα and Vβ repertoire were detected by RT-PCR. The PCR products were further analyzed by genescan to identify T cell clonality.

Results

The CML patient who achieved complete cytogenetic remission (CCR) after 5 years of IFN-α therapy suddenly developed Ph-negative ALL 6 months following switch to imatinib therapy. The expression pattern and clonality of TCR Vα/Vβ T cells changed in different disease stages. The restrictive expression of Vα/Vβ subfamilies could be found in all three stages, and partial subfamily of T cells showed clonal proliferation. Additionally, there have been obvious differences in Vα/Vβ subfamily of T cells between the stages of Ph-positive CML-CP and Ph-negative ALL. The Vα10 and Vβ3 T cells evolved from oligoclonality to polyclonality, the Vβ13 T cells changed from bioclonality to polyclonality, when Ph-negative ALL developed.

Conclusions

Restrictive usage and clonal proliferation of different Vα/Vβ subfamily T cells between the stages of Ph-positive CP and Ph-negative ALL were detected in one patient. These changes may play a role in Ph- negative leukemogenesis.
Improved resolution in Bayesian lithology/fluid inversion from prestack seismic data and well observations: Part 1 — Methodology
Authors: Ulvmoen Marit , Omre Henning
Published: April 2010

The focus of our study is lithology/fluid inversion with spatial coupling from prestack seismic amplitude variation with offset (AVO) data and well observations. The inversion is defined in a Bayesian setting where the complete solution is the posterior model. The prior model for the lithology/fluid (LF) characteristics is defined as a profile Markov random-field model with lateral continuity. Each vertical profile is further given as an inhomogeneous Markov-chain model upward through the reservoir. The likelihood model is defined by profile, and it relates the LF characteristics to the seismic data via a set of elastic material parameters and a convolution model. The likelihood model is approximated. The resulting approximate posterior model is explored using an efficient block Gibbs simulation algorithm. The inversion approach is evaluated on a synthetic realistic 2D reservoir. Seismic AVO data and well observations are integrated in a consistent manner to obtain predictions of the LF characteristics with associated uncertainty statements. The predictions appear very reliable despite the approximation of the posterior model, and errors in seismic data are the major contributions to the uncertainty. Resolution of the inversion is improved considerably by using a spatially coupled prior LF model, and LF units of [Formula: see text] thick can be identified even with a seismic signal-to-noise ratio of two. The inversion results appear robust toward varying model parameter values in the prior model as a result of the discretization of LF characteristics and seismic data with good spatial coverage.
The Role of Some Functional Equations in Decision Analysis
Authors: Abbas Ali E. , Aczél János
Published: April 2010

This paper presents some functional equations that have played an essential role in the characterization of utility and probability functions in decision analysis. We survey some previous results with improvements and derive several new results. We also discuss some simple methods for the solution of these equations and highlight some subtle points about their use. We show that one functional equation can determine several unknown functions within it, and that relaxing differentiability and requiring only continuity of the functions leads to generalizations of many well-known results in utility and Bayesian probability theory.
An Empirical Investigation of Private Label Supply by National Label Producers
Authors: Chen Jack (Xinlei) , Narasimhan Om , John George , Dhar Tirtha
Published: April 2010

Private labels (PLs) are ubiquitous in several categories, including groceries, apparel, and appliances. However, existing empirical work has not examined the differential impact of various upstream supply arrangements for PL products or the strategic motives for PL supply. To do so requires one to model the interaction between private and national label (NL) products both upstream and downstream while accounting for strategic behavior on the part of manufacturers and retailers and retaining essential differences between NL and PL products. We build a model that satisfies these requirements and lets us answer our two research questions: First, can an NL firm profit from being an outsourced PL supplier? Second, what are the upstream and downstream impacts of different PL supply arrangements?

We answer these questions by modeling private labels as homogenous products at wholesale, but as differentiated products at retail. In contrast, national label products are differentiated at both wholesale and retail levels. Using structural model estimates for fluid milk in a major metropolitan area, we conduct three counterfactual experiments. We find that both NL producers and retailers profit from adding private labels. We also find that a vertically integrated supply of PL leads to lower prices for end consumers.
For a Few Cents More: Why Supersize Unhealthy Food?
Authors: Dobson Paul W. , Gerstner Eitan
Published: April 2010

Health-care experts believe that increases in portion sizes served by food vendors contribute to the obesity epidemic. This paper shows that food vendors can profit handsomely by using supersizing strategies where regular portion sizes are priced sufficiently high to discourage price-conscious consumers from selecting them, and the prices for enlarging food portions are set so low that these customers are tempted to order the larger portion sizes and overeat. Setting aside the impact of obesity on health-care costs, we show that using supersizing to steer customers toward consuming excessive amounts of food can destroy value from a social perspective; thus this social value destruction trap adds another justification for pressuring food vendors to reduce supersizing for unhealthy food. As a public policy response, we consider how “moderating policies” may counter these effects through measures designed specifically to encourage eating in moderation by applying supersizing bans, taxes, and warnings.
Demand Estimation with Social Interactions and the Implications for Targeted Marketing
Authors: Hartmann Wesley R.
Published: April 2010

This paper develops a model for the estimation and analysis of demand in the context of social interactions. Decisions made by a group of customers are modeled to be an equilibrium outcome of an empirical discrete game, such that all group members must be satisfied with chosen outcomes. The game-theoretic approach assists estimation by allowing us to account for the endogeneity of group members' decisions while also serving as a managerial tool that can simulate equilibrium outcomes for the group when the firm alters the marketing mix to the group. The model builds upon the existing literature on empirical models of discrete games by introducing a random coefficients heterogeneity distribution. Monte Carlo simulations reveal that including the heterogeneity resolves the endogenous group formation bias commonly noted in the social interactions literature. By estimating the heterogeneous equilibrium model using Bayesian hierarchical Markov chain Monte Carlo, we can also recover some parameters at the individual level to evaluate group-specific characteristics and targeted marketing strategies. To validate the model and illustrate its implications, we apply it to a data set of groups of golfers. We find significant social interaction effects, such that 65% of the median customer value is attributable to the customer and the other 35% is attributable to the customer's affect on members of his group. We also consider targeted marketing strategies and show that group-level targeting increases profit by 1%, whereas targeting within groups can increase profitability by 20%. We recognize that customer backlashes to targeting could be greater when group members receive different offers, so we suggest some alternatives that could retain some of the profitability of within group targeting while avoiding customer backlashes.
Stock Market Response to Regulatory Reports of Deceptive Advertising: The Moderating Effect of Omission Bias and Firm Reputation
Authors: Wiles Michael A. , Jain Shailendra P. , Mishra Saurabh , Lindsey Charles
Published: April 2010

Whereas a growing body of research has examined the consumer-related implications of deceptive advertising, the stock market consequences stemming from the regulatory exposure of such infractions remain largely unexplored. In a step to address this gap, the current research examines the effect of regulatory reports of misleading ads on firm stock prices. Results from an event study, focusing on the pharmaceutical industry as the empirical context, show an average abnormal return of −0.91% associated with regulatory reports of deceptive advertising. Analysis of the abnormal returns, however, reveals that the stock market response to these reports is shaped by omission bias, in that investors penalize commission violations more than omission violations. Furthermore, firm reputation is found to moderate the penalty for commission violations. In addition, two experiments examine the effect of such violations on investor beliefs. The first helps elucidate the process mechanism underlying the observed stock market effects and the second provides insights regarding the reputation-omission bias interaction for firms committing repeat violations. Overall, our findings provide important theoretical, managerial, and public policy implications regarding the role of financial markets in regulating deceptive ad practices.
An Empirical Analysis of Assortment Similarities Across U.S. Supermarkets
Authors: Hwang Minha , Bronnenberg Bart J. , Thomadsen Raphael
Published: April 2010

This paper examines pairwise assortment similarities at U.S. supermarkets to understand how assortment composition and size are related to underlying factors that describe local store clientele, local competitive structure, and the retail outlets' characteristics. The top-selling items, which cumulatively make up 50% of sales, are sold at nearly every store, but other items are viewed as optional. We find that, within states, supermarkets owned by the same chain carry similar assortments and that the composition of their clientele and the presence of competing stores have effects on assortment similarity that are an order of magnitude smaller than ownership structure. In contrast, we find that, across states, supermarkets owned by the same chain do version their assortment. We explain this difference using extant work on the minimal efficient scale of supermarkets and on local demand effects. Furthermore, we investigate the distribution and role of regional brands. We find that regional brands are primarily distributed by small regional chains or independent stores. “Value” regional brands are primarily distributed by supermarket firms without store brands, whereas the distribution of “premium” regional brands is unrelated to the presence of store brands. We discuss our findings in the context of modeling assortment decisions and manufacturers designing distribution policies.
History of Forced Sex and Recent Sexual Risk Indicators Among Young Adult Males
Authors: Smith Laureen H. , Ford Jodi
Published: April 2010

CONTEXT: It is unclear whether young adult men who have ever been forced to have sex are at increased risk for sexual risk‐taking, and whether their risk differs according to the gender of the perpetrator.

METHODS: Data from 1,400 males aged 18–24 who participated in the 2002 National Survey of Family Growth were used to determine the prevalence of a history of forced sex and the context of each respondent’s most recent experience with such assaults. Logistic regression analyses were conducted to examine the relationship between victimization and having a recent indicator of sexual risk (e.g., having had sex in the past year with five or more female partners, a female injection‐drug user or an HIV‐positive female). Separate analyses were performed for coercion by females and coercion by males.

RESULTS: Six percent of men reported having been forced by a female perpetrator to have vaginal intercourse, while 1% said they had been forced by a male perpetrator to have oral or anal sex. Men had an elevated likelihood of having had one or more recent sexual risk indicators if they had ever been forced to have sex by a male (odds ratio, 6.9) or female (3.3). Verbal and physical forms of coercion and provision of alcohol and drugs were commonly used by perpetrators of both genders.

CONCLUSIONS: A better understanding of the pathways linking sexual victimization to sexual risk‐taking among men is needed. Clinicians working with young men should screen them for victimization and provide STD testing and referrals for counseling if abuse is suspected or disclosed.
Seven Direct Methods for Measuring HDL and LDL Cholesterol Compared with Ultracentrifugation Reference Measurement Procedures
Authors: Miller W Greg , Myers Gary L , Sakurabayashi Ikunosuke , Bachmann Lorin M , Caudill Samuel P , Dziekonski Andrzej , Edwards Selvin , Kimberly Mary M , Korzun William J , Leary Elizabeth T , Nakajima Katsuyuki , Nakamura Masakazu , Nilsson Göran , Shamburek Robert D , Vetrovec George W , Warnick G Russell , Remaley Alan T
Published: April 2010

Background: Methods from 7 manufacturers and 1 distributor for directly measuring HDL cholesterol (C) and LDL-C were evaluated for imprecision, trueness, total error, and specificity in nonfrozen serum samples.

Methods: We performed each direct method according to the manufacturer’s instructions, using a Roche/Hitachi 917 analyzer, and compared the results with those obtained with reference measurement procedures for HDL-C and LDL-C. Imprecision was estimated for 35 runs performed with frozen pooled serum specimens and triplicate measurements on each individual sample. Sera from 37 individuals without disease and 138 with disease (primarily dyslipidemic and cardiovascular) were measured by each method. Trueness and total error were evaluated from the difference between the direct methods and reference measurement procedures. Specificity was evaluated from the dispersion in differences observed.

Results: Imprecision data based on 4 frozen serum pools showed total CVs <3.7% for HDL-C and <4.4% for LDL-C. Bias for the nondiseased group ranged from −5.4% to 4.8% for HDL-C and from −6.8% to 1.1% for LDL-C, and for the diseased group from −8.6% to 8.8% for HDL-C and from −11.8% to 4.1% for LDL-C. Total error for the nondiseased group ranged from −13.4% to 13.6% for HDL-C and from −13.3% to 13.5% for LDL-C, and for the diseased group from −19.8% to 36.3% for HDL-C and from −26.6% to 31.9% for LDL-C.

Conclusions: Six of 8 HDL-C and 5 of 8 LDL-C direct methods met the National Cholesterol Education Program total error goals for nondiseased individuals. All the methods failed to meet these goals for diseased individuals, however, because of lack of specificity toward abnormal lipoproteins.
Crystal structure and bond valence of CaH2 from neutron powder diffraction data
Authors: Alonso José Antonio , Retuerto María , Sanchez-Benitez Javier , Fernández-Díaz Maria Teresa
Published: April 2010

The crystal structure of CaH2 has been studied from neutron powder diffraction (NPD) at 295 K in a non-deuterated sample; a good quality NPD pattern was obtained in spite of the hydrogen incoherent scattering. The structure was refined by the Rietveld method in the Pnma space group (No. 62), Z = 4, with unit-cell parameters a = 5.9600(1), b = 3.6006(7) and c = 6.8167(1) Å. The two kinds of crystallographically independent H atoms, H1 and H2, are located in tetrahedral and square-pyramidal cavities, respectively, while Ca ions are nine-fold coordinated to hydrogen atoms. The average 〈Ca—H1〉 and 〈Ca—H2〉 bond lengths are 2.279 and 2.544 Å, respectively. Bond valence calculations show that Ca—H1 bonds are under compressive stress, whereas Ca—H2 bonds undergo tensile stress in a structure with a relatively high global instability index. It is also remarkable that the displacement factors for H2 are significantly larger than for H1, suggesting an increased lability for the Ca—H2 bonds. We provide with an analysis of the isotope effect, by comparing the present results on CaH2 with literature data on CaD2; we indeed observe a higher distortion of the H1 and H2 coordination polyhedra with respect to the deuteride, as observed in other isostructural dihydrides.
Rhythmic Auditory Stimulation in Rehabilitation of Movement Disorders: A Review Of Current Research
Authors: Thaut Michael H. , Abiru Mutsumi
Published: April 2010

PHYSIOLOGICAL RESEARCH HAS SHOWN THAT AUDITORY rhythm has a profound effect on the motor system. Evidence shows that the auditory and motor system have a rich connectivity across a variety of cortical, subcortical, and spinal levels. The auditory system—a fast and precise processor or temporal information—projects into motor structures in the brain, creating entrainment between the rhythmic signal and the motor response. Based on these physiological connections, a large number of clinical studies have researched the effectiveness of rhythm and music to produce functional change in motor therapy for stroke, Parkinson's disease, traumatic brain injury, and other conditions. Results have been strong in favor of rhythmic auditory stimulation (RAS) to significantly improve gait and upper extremity function. Comparative studies also have shown RAS to be more effective than other sensory cues and other techniques in physical rehabilitation.
The Therapeutic Effects of Singing in Neurological Disorders
Authors: Wan Catherine Y. , Rüber Theodor , Hohmann Anja , Schlaug Gottfried
Published: April 2010

MUSIC MAKING (PLAYING AN INSTRUMENT OR SINGING) is a multimodal activity that involves the integration of auditory and sensorimotor processes. The ability to sing in humans is evident from infancy, and does not depend on formal vocal training but can be enhanced by training. Given the behavioral similarities between singing and speaking, as well as the shared and distinct neural correlates of both, researchers have begun to examine whether singing can be used to treat some of the speech-motor abnormalities associated with various neurological conditions. This paper reviews recent evidence on the therapeutic effects of singing, and how it can potentially ameliorate some of the speech deficits associated with conditions such as stuttering, Parkinson's disease, acquired brain lesions, and autism. By reviewing the status quo, it is hoped that future research can help to disentangle the relative contribution of factors to why singing works. This may ultimately lead to the development of specialized or "gold-standard" treatments for these disorders, and to an improvement in the quality of life for patients.