bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model Estimates of the Land and Ocean Contributions to Biospheric Carbon and Water Fluxes Using MODIS Satellite Data
Authors: Alton Paul B. , Bodin Per E. 
Published: March 2011

Abstract
Land and ocean are often treated separately in modeling studies despite their close links through the carbon, water, and energy cycles. However, biospheric models, particularly when used in conjunction with recent satellite datasets, provide a new, fully coupled, global perspective. The current investigation uses a new version of the Grid Enabled Integrated Earth system (GENIE-SF) to compare both the magnitude and the seasonal and zonal variation in water flux [evaporation E and precipitation (PPT)] and carbon flux [net primary productivity (NPP)] above land and ocean. GENIE-SF contains state-of-the-art representations of photosynthesis and is driven by the phenological cycles of leaf area index (LAI) and marine chlorophyll concentration, both recorded with the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite sensors. The current study reveals the striking uniformity of the ocean–atmosphere carbon and water flux exchange, both temporally and spatially, compared to the corresponding land–atmosphere exchange. Although biospheric annual NPP (108 ± 27 GtC yr−1) is split almost equally between land (52% ± 9%) and ocean (48% ± 9%), the oceanic contribution to biospheric annual E exceeds that of the land by a factor of 6.7 ± 1.7. Simulations conducted over a 50-yr period (1951–2000) suggest that a 16% increase in land NPP, owing mainly to CO2 fertilization, may be partially offset by a decline in marine productivity.
Serum Bone Biomarkers and Oral/Systemic Bone Loss in Humans
Authors: Payne J.B. , Stoner J.A. , Lee H.-M. , Nummikoski P.V. , Reinhardt R.A. , Golub L.M. 
Published: March 2011

We recently reported that subantimicrobial-dose doxycycline (SDD) significantly reduced serum bone-resorption biomarkers in subgroups of post-menopausal women. We hypothesize that changes in serum bone biomarkers are associated not only with systemic bone mineral density (BMD) changes, but also with alveolar bone changes over time. One hundred twenty-eight eligible post-menopausal women with periodontitis and systemic osteopenia were randomly assigned to receive SDD or placebo tablets twice daily for two years, adjunctive to periodontal maintenance. Sera were analyzed for bone biomarkers. As expected, two-year changes in a serum bone biomarker were significantly associated with systemic BMD loss at the lumbar spine (osteocalcin, bone-turnover biomarker, p = 0.0002) and femoral neck (osteocalcin p = 0.0025). Two-year changes in serum osteocalcin and serum pyridinoline-crosslink fragment of type I collagen (ICTP; bone-resorption biomarker) were also significantly associated with alveolar bone density loss (p < 0.0001) and alveolar bone height loss (p = 0.0008), respectively. Thus, we have shown that serum bone biomarkers are associated with not only systemic BMD loss, but with alveolar bone loss as well. Clinical Trial Registration Information: Protocol registered at ClinicalTrials.gov, NCT00066027. Abbreviations: bone mineral density (BMD), bone-specific alkaline phosphatase (BSAP), computer-assisted densitometric image analysis (CADIA), confidence interval (CI), deoxypyridinoline-containing degradation fragment of the C-terminal telopeptide region of type I collagen (CTX), coefficient of variation (CV), dual-energy x-ray absorptiometry (DXA), pyridinoline-crosslink-containing degradation fragment of the C-terminal telopeptide region of type I collagen (ICTP), and subantimicrobial-dose doxycycline (SDD).
Ongoing Positive Effect of Platelet-Rich Plasma Versus Corticosteroid Injection in Lateral Epicondylitis
Authors: Gosens Taco , Peerbooms Joost C. , van Laar Wilbert , den Oudsten Brenda L. 
Published: March 2011

Background: Platelet-rich plasma (PRP) has been shown to be a general stimulation for repair and 1-year results showed promising success percentages. Purpose: This trial was undertaken to determine the effectiveness of PRP compared with corticosteroid injections in patients with chronic lateral epicondylitis with a 2-year follow-up. Study Design: Randomized controlled trial; Level of evidence, 1. Methods: The trial was conducted in 2 Dutch teaching hospitals. One hundred patients with chronic lateral epicondylitis were randomly assigned to a leukocyte-enriched PRP group (n = 51) or the corticosteroid group (n = 49). Randomization and allocation to the trial group were carried out by a central computer system. Patients received either a corticosteroid injection or an autologous platelet concentrate injection through a peppering needling technique. The primary analysis included visual analog scale (VAS) pain scores and Disabilities of the Arm, Shoulder and Hand (DASH) outcome scores. Results: The PRP group was more often successfully treated than the corticosteroid group ( P < .0001). Success was defined as a reduction of 25% on VAS or DASH scores without a reintervention after 2 years. When baseline VAS and DASH scores were compared with the scores at 2-year follow-up, both groups significantly improved across time (intention-to-treat principle). However, the DASH scores of the corticosteroid group returned to baseline levels, while those of the PRP group significantly improved (as-treated principle). There were no complications related to the use of PRP. Conclusion: Treatment of patients with chronic lateral epicondylitis with PRP reduces pain and increases function significantly, exceeding the effect of corticosteroid injection even after a follow-up of 2 years. Future decisions for application of PRP for lateral epicondylitis should be confirmed by further follow-up from this trial and should take into account possible costs and harms as well as benefits.
The PhaSeal® system: Impact of its use on workplace contamination and duration of chemotherapy preparation
Authors: Favier B , Labrosse H , Gilles-Afchain L , Cropet C , Perol D , Chaumard N , Latour JF , Hild P 
Published: March 2011

Purpose. The primary objective of this study was to compare the levels of environmental contamination before and after the introduction of PhaSeal® (closed-system drug transfer device) in two hospital pharmacies. Our secondary objective was to assess the impact of the device on the duration of drug preparation compared to procedures involving the use of needles and syringes. Methods. The study involved two French hospitals, which prepared antineoplastic chemotherapy using a biological safety cabinet and an isolator. Five skilled pharmacy technicians at each hospital prepared a total of 100 chemotherapy preparations using the standard procedure and 100 using the PhaSeal® system. To control for possible contamination occurring in the course of the procedure, we used fluorescein which becomes fluorescent when exposed to UV light. To reply the second objective, we timed the duration of the different steps of the manipulation. Results. Our findings showed a major reduction in the contamination of the work environment when using the PhaSeal® system for drug preparation. Reduction rates higher than 93% were obtained, whatever the type of protection used. On the duration of preparation, our results indicate that this duration would be approximately 1 h longer for the preparation of 100 samples. Conclusion. In conclusion, this study clearly establishes the benefit of using PhaSeal® for protecting the staff members who work with hazardous agents. It also indicates that the duration of drug preparation is not impacted by the use of the system.
Long-term risk factor management after inpatient cardiac rehabilitation by means of a structured post-care programme
Authors: Harb Birgit M , Wonisch Manfred , Brandt Dieter , Müller Rudolf 
Published: March 2011

Background: Initiation of a long-term improvement of cardiac risk factors is one of the major aims of a cardiac rehabilitation/secondary prevention programme. Methods and participants: The Health Guide collected data in terms of cardiac risk factors: blood pressure, resting pulse, total cholesterol, LDL cholesterol, body weight, physical activity and number of cigarettes at admission and discharge after a stationary rehabilitation programme and every 3 months. After 12 months the Health Guides were returned. In the prospective study 2664 patients (71.8% men, age: MV = 62.94 years, SD = 9.96; 28% women, MV = 67.59 years, SD = 9.53) with coronary heart disease (CHD) were included. Results: All cardiac risk factors documented by the Health Guide improved during the cardiac rehabilitation programme. After one year, risk factors were significantly lower than at admission, apart from total cholesterol. The individual goal in terms of body weight and LDL cholesterol was partially achieved after the rehabilitation programme and maintained after one year. In the investigation years, 2004–2007, the cholesterol and blood pressure were significantly lower than in the years 2000–2003. Conclusion: The use of a Health Guide resulted in an improved long-term effect of a cardiac rehabilitation/secondary prevention programme. It is a simple and cheap intervention and can help in the guidance of the patients.
MUC1-C oncoprotein suppresses reactive oxygen species–induced terminal differentiation of acute myelogenous leukemia cells
Authors: Yin Li , Wu Zekui , Avigan David , Rosenblatt Jacalyn , Stone Richard , Kharbanda Surender , Kufe Donald 
Published: March 2011

Abstract
Acute myeloid leukemia (AML) cells are characterized by unlimited self-renewal and an impaired capacity to undergo terminal differentiation. The MUC1 oncoprotein is aberrantly expressed in AML cells; however, there has been no evidence for involvement of MUC1 in myeloid leukemogenesis. Cell-penetrating peptide inhibitors of the MUC1-C subunit block its oligomerization and thereby oncogenic function. The present results demonstrate that treatment of human MOLM-14 and MV4-11 AML cells with these inhibitors is associated with arrest of growth, induction of late apoptosis/necrosis, and loss of self-renewal capacity. Similar results were obtained with primary blasts from patients with AML. Inhibition of MUC1-C was associated with increases in reactive oxygen species (ROS) and depletion of glutathione. Increases in ROS have been linked to induction of hematopoietic cell differentiation along the myeloid lineage. In this regard, inhibition of MUC1-C was associated with induction of a terminally differentiated myeloid phenotype in AML cell lines and primary blasts by an ROS-dependent mechanism. These findings indicate that MUC1-C function is of importance to AML cell self-renewal and that inhibition of MUC1-C represents a potential therapeutic approach to induce terminal differentiation of AML cells.
From an old remedy to a magic bullet: molecular mechanisms underlying the therapeutic effects of arsenic in fighting leukemia
Authors: Chen Sai-Juan , Zhou Guang-Biao , Zhang Xiao-Wei , Mao Jian-Hua , de Thé Hugues , Chen Zhu 
Published: March 2011

AbstractArsenic had been used in treating malignancies from the 18th to mid-20th century. In the past 3 decades, arsenic was revived and shown to be able to induce complete remission and to achieve, when combined with all-trans retinoic acid and chemotherapy, a 5-year overall survival of 90% in patients with acute promyelocytic leukemia driven by the t(15;17) translocation-generated promyelocytic leukemia–retinoic acid receptor α (PML-RARα) fusion. Molecularly, arsenic binds thiol residues and induces the formation of reactive oxygen species, thus affecting numerous signaling pathways. Interestingly, arsenic directly binds the C3HC4 zinc finger motif in the RBCC domain of PML and PML-RARα, induces their homodimerization and multimerization, and enhances their interaction with the SUMO E2 conjugase Ubc9, facilitating subsequent sumoylation/ubiquitination and proteasomal degradation. Arsenic-caused intermolecular disulfide formation in PML also contributes to PML-multimerization. All-trans retinoic acid, which targets PML-RARα for degradation through its RARα moiety, synergizes with arsenic in eliminating leukemia-initiating cells. Arsenic perturbs a number of proteins involved in other hematologic malignancies, including chronic myeloid leukemia and adult T-cell leukemia/lymphoma, whereby it may bring new therapeutic benefits. The successful revival of arsenic in acute promyelocytic leukemia, together with modern mechanistic studies, has thus allowed a new paradigm to emerge in translational medicine.
HIV-specific CD8+ T cells from HIV+ individuals receiving HAART can be expanded ex vivo to augment systemic and mucosal immunity in vivo
Authors: Chapuis Aude G. , Casper Corey , Kuntz Steve , Zhu Jia , Tjernlund Annelie , Diem Kurt , Turtle Cameron J. , Cigal Melinda L. , Velez Roxanne , Riddell Stanley , Corey Lawrence , Greenberg Philip D. 
Published: March 2011

AbstractMost HIV+ individuals require lifelong highly active antiretroviral therapy (HAART) to suppress HIV replication, but fail to eliminate the virus in part because of residual replication in gut-associated lymphoid tissues (GALT). Naturally elicited HIV-specific CD8+ T cells generated in the acute and chronic infectious phases exhibit antiviral activity, but decrease in number after HAART. Therapeutic vaccines represent a potential strategy to expand cellular responses, although previous efforts have been largely unsuccessful, conceivably because of a lack of responding HIV-specific central-memory CD8+ T cells (Tcm). To determine whether patients receiving HAART possess CD8+ T cells with Tcm qualities that are amenable to augmentation, HIV-specific CD8+ T-cell clones were derived from HIV-reactive CD28+CD8+ T-cell lines isolated from 7 HIV+ HAART-treated patients, expanded ex vivo, and reinfused into their autologous host. Tracking of the cells in vivo revealed that clones could persist for ≥ 84 days, maintain expression and/or re-express CD28, up-regulate CD62L, secrete IL-2, proliferate on cognate Ag encounter and localize to the rectal mucosa. These results suggest some infused cells exhibited phenotypic and functional characteristics shared with Tcm in vivo, and imply that more effective therapeutic vaccination strategies targeting CD8+ Tcm in patients on HAART might provide hosts with expanded, long-lasting immune responses not only systemically but also in GALT. This study is registered at www.clinicaltrials.gov as NCT00110578.
KL-6 concentration in pulmonary epithelial lining fluid is a useful prognostic indicator in patients with acute respiratory distress syndrome
Authors: Kondo Tomohiro , Hattori Noboru , Ishikawa Nobuhisa , Murai Hiroshi , Haruta Yoshinori , Hirohashi Nobuyuki , Tanigawa Koichi , Kohno Nobuoki 
Published: March 2011

Abstract

Background
KL-6 is a mucin-like glycoprotein expressed on the surface of alveolar type II cells. Elevated concentrations of KL-6 in serum and epithelial lining fluid (ELF) in patients with acute respiratory distress syndrome (ARDS) have been previously reported; however, kinetics and prognostic significance of KL-6 have not been extensively studied. This study was conducted to clarify these points in ARDS patients.

Methods
Thirty-two patients with ARDS who received mechanical ventilation under intubation were studied for 28 days. ELF and blood were obtained from each patient at multiple time points after the diagnosis of ARDS. ELF was collected using a bronchoscopic microsampling procedure, and ELF and serum KL-6 concentrations were measured.

Results
KL-6 levels in ELF on days 0 to 3 after ARDS diagnosis were significantly higher in nonsurvivors than in survivors, and thereafter, there was no difference in concentrations between the two groups. Serum KL-6 levels did not show statistically significant differences between nonsurvivors and survivors at any time point. When the highest KL-6 levels in ELF and serum sample from each patient were examined, KL-6 levels in both ELF and serum were significantly higher in nonsurvivors than in survivors. The optimal cut-off values were set at 3453 U/mL for ELF and 530 U/mL for serum by receiver operating characteristic (ROC) curve analyses. Patients with KL-6 concentrations in ELF higher than 3453 U/mL or serum concentrations higher than 530 U/mL had significantly lower survival rates up to 90 days after ARDS diagnosis.

Conclusions
ELF and serum KL-6 concentrations were found to be good indicators of clinical outcome in ARDS patients. Particularly, KL-6 levels in ELF measured during the early period after the diagnosis were useful for predicting prognosis in ARDS patients.
FGF signalling through RAS/MAPK and PI3K pathways regulates cell movement and gene expression in the chicken primitive streak without affecting E-cadherin expression
Authors: Hardy Katharine M , Yatskievych Tatiana A , Konieczka JH , Bobbs Alexander S , Antin Parker B 
Published: March 2011

Abstract

Background
FGF signalling regulates numerous aspects of early embryo development. During gastrulation in amniotes, epiblast cells undergo an epithelial to mesenchymal transition (EMT) in the primitive streak to form the mesoderm and endoderm. In mice lacking FGFR1, epiblast cells in the primitive streak fail to downregulate E-cadherin and undergo EMT, and cell migration is inhibited. This study investigated how FGF signalling regulates cell movement and gene expression in the primitive streak of chicken embryos.

Results
We find that pharmacological inhibition of FGFR activity blocks migration of cells through the primitive streak of chicken embryos without apparent alterations in the level or intracellular localization of E-cadherin. E-cadherin protein is localized to the periphery of epiblast, primitive streak and some mesodermal cells. FGFR inhibition leads to downregulation of a large number of regulatory genes in the preingression epiblast adjacent to the primitive streak, the primitive streak and the newly formed mesoderm. This includes members of the FGF, NOTCH, EPH, PDGF, and canonical and non-canonical WNT pathways, negative modulators of these pathways, and a large number of transcriptional regulatory genes. SNAI2 expression in the primitive streak and mesoderm is not altered by FGFR inhibition, but is downregulated only in the preingression epiblast region with no significant effect on E-cadherin. Furthermore, over expression of SNAIL has no discernable effect on E-cadherin protein levels or localization in epiblast, primitive streak or mesodermal cells. FGFR activity modulates distinct downstream pathways including RAS/MAPK and PI3K/AKT. Pharmacological inhibition of MEK or AKT indicate that these downstream effectors control discrete and overlapping groups of genes during gastrulation. FGFR activity regulates components of several pathways known to be required for cell migration through the streak or in the mesoderm, including RHOA, the non-canonical WNT pathway, PDGF signalling and the cell adhesion protein N-cadherin.

Conclusions
In chicken embryos, FGF signalling regulates cell movement through the primitive streak by mechanisms that appear to be independent of changes in E-cadherin expression or protein localization. The positive and negative effects on large groups of genes by pharmacological inhibition of FGF signalling, including major signalling pathways and transcription factor families, indicates that the FGF pathway is a focal point of regulation during gastrulation in chicken.
Organization and evolution of hsp70clusters strikingly differ in two species of Stratiomyidae (Diptera) inhabiting thermally contrasting environments
Authors: Garbuz David G , Yushenova Irina A , Zatsepina Olga G , Przhiboro Andrey A , Bettencourt Brian R , Evgen'ev Michael B 
Published: March 2011

Abstract

Background
Previously, we described the heat shock response in dipteran species belonging to the family Stratiomyidae that develop in thermally and chemically contrasting habitats including highly aggressive ones. Although all species studied exhibit high constitutive levels of Hsp70 accompanied by exceptionally high thermotolerance, we also detected characteristic interspecies differences in heat shock protein (Hsp) expression and survival after severe heat shock. Here, we analyzed genomic libraries from two Stratiomyidae species from thermally and chemically contrasting habitats and determined the structure and organization of their hsp70 clusters.

Results
Although the genomes of both species contain similar numbers of hsp70 genes, the spatial distribution of hsp70 copies differs characteristically. In a population of the eurytopic species Stratiomys singularior, which exists in thermally variable and chemically aggressive (hypersaline) conditions, the hsp70 copies form a tight cluster with approximately equal intergenic distances. In contrast, in a population of the stenotopic Oxycera pardalina that dwells in a stable cold spring, we did not find hsp70 copies in tandem orientation. In this species, the distance between individual hsp70 copies in the genome is very large, if they are linked at all. In O. pardalina we detected the hsp68 gene located next to a hsp70 copy in tandem orientation. Although the hsp70 coding sequences of S. singularior are highly homogenized via conversion, the structure and general arrangement of the hsp70 clusters are highly polymorphic, including gross aberrations, various deletions in intergenic regions, and insertion of incomplete Mariner transposons in close vicinity to the 3'-UTRs.

Conclusions
The hsp70 gene families in S. singularior and O. pardalina evolved quite differently from one another. We demonstrated clear evidence of homogenizing gene conversion in the S. singularior hsp70 genes, which form tight clusters in this species. In the case of the other species, O. pardalina, we found no clear trace of concerted evolution for the dispersed hsp70 genes. Furthermore, in the latter species we detected hsp70 pseudogenes, representing a hallmark of the birth-and-death process.
RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization
Authors: Hruz Tomas , Wyss Markus , Docquier Mylene , Pfaffl Michael W , Masanetz Sabine , Borghi Lorenzo , Verbrugghe Phebe , Kalaydjieva Luba , Bleuler Stefan , Laule Oliver , Descombes Patrick , Gruissem Wilhelm , Zimmermann Philip 
Published: March 2011

Abstract

Background
RT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls. There is increasing evidence, however, that the expression of commonly used reference genes can vary significantly in certain contexts.

Results
Using the Genevestigator database of normalized and well-annotated microarray experiments, we describe the expression stability characteristics of the transciptomes of several organisms. The results show that a) no genes are universally stable, b) most commonly used reference genes yield very high transcript abundances as compared to the entire transcriptome, and c) for each biological context a subset of stable genes exists that has smaller variance than commonly used reference genes or genes that were selected for their stability across all conditions.

Conclusion
We therefore propose the normalization of RT-qPCR data using reference genes that are specifically chosen for the conditions under study. RefGenes is a community tool developed for that purpose. Validation RT-qPCR experiments across several organisms showed that the candidates proposed by RefGenes generally outperformed commonly used reference genes. RefGenes is available within Genevestigator at http://www.genevestigator.com.