bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Labrador Sea Convection on the North Atlantic Meridional Overturning Circulation
Authors: Pickart Robert S. , Spall Michael A. 
Published: September 2007

Abstract
The overturning and horizontal circulations of the Labrador Sea are deduced from a composite vertical section across the basin. The data come from the late-spring/early-summer occupations of the World Ocean Circulation Experiment (WOCE) AR7W line, during the years 1990–97. This time period was chosen because it corresponded to intense wintertime convection—the deepest and densest in the historical record—suggesting that the North Atlantic meridional overturning circulation (MOC) would be maximally impacted. The composite geostrophic velocity section was referenced using a mean lateral velocity profile from float data and then subsequently adjusted to balance mass. The analysis was done in depth space to determine the net sinking that results from convection and in density space to determine the diapycnal mass flux (i.e., the transformation of light water to Labrador Sea Water). The mean overturning cell is calculated to be 1 Sv (1 Sv ≡ 106 m3 s−1), as compared with a horizontal gyre of 18 Sv. The total water mass transformation is 2 Sv. These values are consistent with recent modeling results. The diagnosed heat flux of 37.6 TW is found to result predominantly from the horizontal circulation, both in depth space and density space. These results suggest that the North Atlantic MOC is not largely impacted by deep convection in the Labrador Sea.
Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements
Authors: Lan Hui , Carson Rachel , Provart Nicholas J , Bonner Anthony J 
Published: September 2007

AbstractBackgroundArabidopsis thalianais the model species of current plant genomic research with a genome size of 125 Mb and approximately 28,000 genes. The function of half of these genes is currently unknown. The purpose of this study is to infer gene function in Arabidopsis using machine-learning algorithms applied to large-scale gene expression data sets, with the goal of identifying genes that are potentially involved in plant response to abiotic stress.ResultsUsing in house and publicly available data, we assembled a large set of gene expression measurements forA. thaliana. Using those genes of known function, we first evaluated and compared the ability of basic machine-learning algorithms to predict which genes respond to stress. Predictive accuracy was measured using ROC50and precision curves derived through cross validation. To improve accuracy, we developed a method for combining these classifiers using a weighted-voting scheme. The combined classifier was then trained on genes of known function and applied to genes of unknown function, identifying genes that potentially respond to stress. Visual evidence corroborating the predictions was obtained using electronic Northern analysis. Three of the predicted genes were chosen for biological validation. Gene knockout experiments confirmed that all three are involved in a variety of stress responses. The biological analysis of one of these genes (At1g16850) is presented here, where it is shown to be necessary for the normal response to temperature and NaCl.ConclusionSupervised learning methods applied to large-scale gene expression measurements can be used to predict gene function. However, the ability of basic learning methods to predict stress response varies widely and depends heavily on how much dimensionality reduction is used. Our method of combining classifiers can improve the accuracy of such predictions – in this case, predictions of genes involved in stress response in plants – and it effectively chooses the appropriate amount of dimensionality reduction automatically. The method provides a useful means of identifying genes inA. thalianathat potentially respond to stress, and we expect it would be useful in other organisms and for other gene functions.
Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering
Authors: Zhang Wei , Li Li , Li Xia , Jiang Wei , Huo Jianmin , Wang Yadong , Lin Meihua , Rao Shaoqi 
Published: September 2007

AbstractBackgroundIt becomes increasingly clear that our current taxonomy of clinical phenotypes is mixed with molecular heterogeneity. Of vital importance for refined clinical practice and improved intervention strategies is to define the hidden molecular distinct diseases using modern large-scale genomic approaches. Microarray omics technology has provided a powerful way to dissect hidden genetic heterogeneity of complex diseases. The aim of this study was thus to develop a bioinformatics approach to seek the transcriptional features leading to the hidden subtyping of a complex clinical phenotype. The basic strategy of the proposed method was to iteratively partition in two ways sample and feature space with super-paramagnetic clustering technique and to seek for hard and robust gene clusters that lead to a natural partition of disease samples and that have the highest functionally conceptual consensus evaluated with Gene Ontology.ResultsWe applied the proposed method to two publicly available microarray datasets of diffuse large B-cell lymphoma (DLBCL), a notoriously heterogeneous phenotype. A feature subset of 30 genes (38 probes) derived from analysis of the first dataset consisting of 4026 genes and 42 DLBCL samples identified three categories of patients with very different five-year overall survival rates (70.59%, 44.44% and 14.29% respectively;p= 0.0017). Analysis of the second dataset consisting of 7129 genes and 58 DLBCL samples revealed a feature subset of 13 genes (16 probes) that not only replicated the findings of the important DLBCL genes (e.g.JAW1andBCL7A), but also identified three clinically similar subtypes (with 5-year overall survival rates of 63.13%, 34.92% and 15.38% respectively;p= 0.0009) to those identified in the first dataset. Finally, we built a multivariate Cox proportional-hazards prediction model for each feature subset and definedJAW1as one of the most significant predictor (p= 0.005 and 0.014; hazard ratios = 0.02 and 0.03, respectively for two datasets) for both DLBCL cohorts under study.ConclusionOur results showed that the proposed algorithm is a promising computational strategy for peeling off the hidden genetic heterogeneity based on transcriptionally profiling disease samples, which may lead to an improved diagnosis and treatment of cancers.
Leishmania amazonensisinfection impairs differentiation and function of human dendritic cells
Authors: Favali Cecilia , Tavares Natália , Clarêncio Jorge , Barral Aldina , Barral-Netto Manoel , Brodskyn Claudia 
Published: September 2007

AbstractDendritic cells (DCs) are of utmost importance in initiating an immune response and may also function as targets for pathogens. The presence of pathogens inside DCs is likely to impair their functions and thus, influence immune responses. In the present report, we evaluated the impact of the presence of Leishmania amazonensis during differentiation and maturation of human monocyte-derived DCs. The presence of live L. amazonensis parasites during DC differentiation led to a significant decrease in CD80 (92%) and CD1a (56%) expression and an increase in CD86 (56%) cell surface expression. Phenotypic changes were accompanied by a lower secretion of IL-6, observed after 6 days of DC differentiation in the presence of L. amazonensis. DCs differentiated in the presence of L. amazonensis were used as APC in an autologous coculture, and lower amounts of IFN-γ were obtained compared with control DCs differentiated in the absence of parasites. The effect of heat-killed parasites, but not of Leishmania antigen, during DC differentiation and maturation was similar to that observed with viable parasites. During maturation, the presence of live L. amazonensis parasites, but not of soluble Leishmania antigen, led to a decrease in IL-6 and IL-10 production. In this way, we observed that the parasite is able to abrogate full DC differentiation, causing a delay in the immune response and likely, favoring its establishment in human hosts.
Ginsenoside Re Reduces Insulin Resistance through Inhibition of c-Jun NH2-Terminal Kinase and Nuclear Factor-κB
Authors: Zhang Zhiguo , Li Xiaoying , Lv Wenshan , Yang Yisheng , Gao Hong , Yang Jun , Shen Yun , Ning Guang 
Published: September 2007

AbstractGinsenoside Re (Re), a compound derived from Panax ginseng, shows an antidiabetic effect. However, the molecular basis of its action remains unknown. We investigated insulin signaling and the antiinflammatory effect by Re in 3T3-L1 adipocytes and in high-fat diet (HFD) rats to dissect its anti-hyperglycemic mechanism. Glucose uptake was measured in 3T3-L1 cells and glucose infusion rate determined by clamp in HFD rats. The insulin signaling cascade, including insulin receptor (IR) β-subunit, IR substrate-1, phosphatidylinositol 3-kinase, Akt and Akt substrate of 160 kDa, and glucose transporter-4 translocation are examined. Furthermore, c-Jun NH2-terminal kinase (JNK), MAPK, and nuclear factor (NF)-κB signaling cascades were also assessed. The results show Re increases glucose uptake in 3T3-L1 cells and glucose infusion rate in HFD rats. The activation of insulin signaling by Re is initiated at IR substrate-1 and further passes on through phosphatidylinositol 3-kinase and downstream signaling cascades. Moreover, Re demonstrates an impressive suppression of JNK and NF-κB activation and inhibitor of NF-κBα degradation. In conclusion, Re reduces insulin resistance in 3T3-L1 adipocytes and HFD rats through inhibition of JNK and NF-κB activation.
CR6-Interacting Factor 1 Represses the Transactivation of Androgen Receptor by Direct Interaction
Authors: Suh Ji Ho , Shong Minho , Choi Hueng-Sik , Lee Keesook 
Published: September 2007

AbstractCR6-interacting factor 1 (CRIF1) was previously identified as a nuclear protein that interacts with members of the Gadd45 family and plays a role as a negative regulator in cell growth. However, the nuclear function of CRIF1 remains largely unknown. In this study, we demonstrate that CRIF1 acts as a novel corepressor of the androgen receptor (AR) in prostatic cells. Transient transfection studies show that CRIF1 specifically represses AR transcriptional activation of target promoters in a dose-dependent manner. Additionally, CRIF1 is recruited with AR to the endogenous AR target promoters. In vivo and in vitro protein interaction assays reveal that CRIF1 directly interacts with AR via the activation function-1 domain of AR. Interestingly, both the N-terminal and C-terminal half-regions of CRIF1 are independently capable of interacting with and repressing the transactivation of AR. CRIF1 represses AR transactivation through competition with AR coactivators. In addition, the CRIF1-mediated inhibition of AR transactivation involves the recruitment of histone deacetylase 4. Down-regulation of CRIF1 by small interfering RNA increases the transactivation of AR and the mRNA level of the AR target gene prostate-specific antigen, whereas the overexpression of CRIF1 decreases the prostate-specific antigen mRNA level. Finally, the overexpression of CRIF1 inhibits the androgen-induced proliferation and cell cycle progression of prostate cancer cells. Taken together, these results suggest that CRIF1 acts as an AR corepressor and may play an important role in the regulation of AR-positive growth of prostate cancer.
Influence of ScaI and Natriuretic Peptide (NP) Clearance Receptor Polymorphisms of the NP System on NP Concentration in Chronic Heart Failure
Authors: Vassalle Cristina , Andreassi Maria Grazia , Prontera Concetta , Fontana Marianna , Zyw Luc , Passino Claudio , Emdin Michele 
Published: September 2007

AbstractBackground: Genetic variants related to the natriuretic peptide (NP) system [ScaI mutated allele (A1) of the atrial NP (ANP) gene and the C variant of the natriuretic peptide clearance receptor (NPRC) gene] have been identified as independent risk factors for cardiovascular morbidity and mortality. Despite the importance of NPs in heart failure (HF), the role of these polymorphisms in HF has not been evaluated.Methods: We screened 124 HF patients [mean (SD), age 66 (12) years, 100 men, ejection fraction 32% (10%), New York Heart Association (NYHA) class I–II 65, III–IV 59] for NP concentrations [ANP, brain NP (BNP) and amino-terminal pro-BNP (NT-proBNP)] and for the ScaI and NPRC variants.Results: ScaI polymorphism had no effect on NP concentration in the NYHA I–II subgroup. Conversely, in severe HF, A1 carriers had higher ANP (P ≤0.05), BNP (P &lt;0.01), and NT-proBNP (P &lt;0.01) than A2A2 patients. After multivariate adjustment, A1 presence remained an independent predictor for increased NP. Regarding NPRC polymorphism in mild HF, higher ANP (P &lt;0.05) and BNP (P &lt;0.05) were observed in CC than A allele carriers. After multivariate adjustment, however, this association did not remain significant. In severe HF, the NPRC polymorphism had no effect on NP.Conclusions: The ScaI polymorphism of the ANP gene might be an important additive genetic factor influencing neurohormonal activation and disease progression in severe HF. The NPRC polymorphism is not an independent determinant of NP concentration in HF.
Applications of Nanobiotechnology in Clinical Diagnostics
Authors: Jain Kewal K 
Published: September 2007

Abstract
Background: Nanobiotechnologies are being applied to molecular diagnostics and several technologies are in development.
Methods: This review describes nanobiotechnologies that are already incorporated in molecular diagnostics or have potential applications in clinical diagnosis. Selected promising technologies from published literature as well as some technologies that are in commercial development but have not been reported are included.
Results: Nanotechnologies enable diagnosis at the single-cell and molecule levels, and some can be incorporated in current molecular diagnostic methods, such as biochips. Nanoparticles, such as gold nanoparticles and quantum dots, are the most widely used, but various other nanotechnological devices for manipulation at the nanoscale as well as nanobiosensors are also promising for potential clinical applications.
Conclusions: Nanotechnologies will extend the limits of current molecular diagnostics and enable point-of-care diagnostics, integration of diagnostics with therapeutics, and development of personalized medicine. Although the potential diagnostic applications are unlimited, the most important current applications are foreseen in the areas of biomarker discovery, cancer diagnosis, and detection of infectious microorganisms. Safety studies are needed for in vivo use. Because of its close interrelationships with other technologies, nanobiotechnology in clinical diagnosis will play an important role in the development of nanomedicine in the future.
Methylation-Sensitive High-Resolution Melting-Curve Analysis of the SNRPN Gene as a Diagnostic Screen for Prader-Willi and Angelman Syndromes
Authors: White Helen E , Hall Victoria J , Cross Nicholas CP 
Published: September 2007

Abstract
Background: Angelman syndrome (AS) and Prader-Willi syndrome (PWS) are 2 distinct neurodevelopmental disorders caused primarily by deficiency of specific parental contributions at an imprinted domain within the chromosomal region 15q11.2–13. Lack of paternal contribution results in PWS either by paternal deletion (approximately 70%) or maternal uniparental disomy (UPD) (approximately 25%). Most cases of AS result from the lack of a maternal contribution from this same region, by maternal deletion (70%) or paternal UPD (approximately 5%). Analysis of allelic methylation differences at the small nuclear ribonucleoprotein polypeptide N (SNRPN) locus differentiates the maternally and paternally inherited chromosome 15 and can be used as a diagnostic test for AS and PWS.
Methods: Methylation-sensitive high-resolution melting-curve analysis (MS-HRM) using the DNA binding dye EvaGreen was used to analyze methylation differences at the SNRPN locus in anonymized DNA samples from individuals with PWS (n = 39) or AS (n = 31) and from healthy control individuals (n = 95). Results from the MS-HRM assay were compared to those obtained by use of a methylation-specific PCR (MSP) protocol that is used commonly in diagnostic practice.
Results: With the MS-HRM assay 97.6% of samples were unambiguously assigned to the 3 diagnostic categories (AS, PWS, normal) by use of automated calling with an 80% confidence percentage threshold, and the failure rate was 0.6%. One PWS sample showed a discordant result for the MS-HRM assay compared to MSP data.
Conclusions: MS-HRM is a simple, rapid, and robust method for screening methylation differences at the SNRPN locus and could be used as a diagnostic screen for PWS and AS.
Development and Validation of an Automated Thawing and Mixing Workcell
Authors: Hawker Charles D , Roberts William L , DaSilva Antonio , Stam Gordon D , Owen William E , Curtis DeVirl , Choi Byung-Sang , Ring Terry A 
Published: September 2007

Abstract
Background: Working toward a goal of total laboratory automation, we are automating manual activities in our highest volume laboratory section. Because half of all specimens arriving in this laboratory section are frozen, we began by developing an automated workcell for thawing frozen specimens and mixing the thawed specimens to remove concentration gradients resulting from freezing and thawing.
Methods: We developed an initial robotic workcell that removed specimens from the transport system’s conveyor, blew high-velocity room temperature air at the tubes, mixed them, and replaced them on the conveyor. Aliquots of citrated plasma were frozen with thermocouples immersed in the tubes, and thawing times and temperatures were monitored. Completeness of mixing of thawed specimens was studied by careful removal of small aliquots from the uppermost layer of the upright tubes without disturbing tube contents and analysis of total protein and electrolytes.
Results: High velocity ambient air aimed directly at tubes ranging from 12 × 75 to 16 × 100 mm brought specimens to room temperature in a maximum of 23 min. Adequate mixing of the specimens by the workcell’s robot required only 2 approximate 126° movements from an upright starting point, a surprising observation, because laboratorians are usually trained to mix 10 or 20 times. We also observed that, in a frozen overfilled tube, resulting analyte concentrations will be lower because more concentrated solutes leak from the tube.
Conclusions: A high-throughput, automated thawing and mixing workcell was successfully built, validated, and installed on our automated transport and sorting system.
Influence of Test Method on Direct Shear Behavior of Segmental Retaining Wall Units
Authors: Bathurst Richard J. , Althoff Sebastian , Linnenbaum Peter 
Published: September 2007

Abstract
This paper reports the results of interface shear testing carried out to investigate the influence of test methodology on shear-displacement behavior of five different segmental (modular) masonry concrete block configurations. The tests were carried out in general conformance with existing ASTM and National Concrete Masonry Association test protocols. Three different normal load arrangements were investigated: (1) flexible airbag, (2) fixed vertical piston, and (3) an adjustable vertical piston. A video-extensometer camera device was used to record block deformations in the vertical plane during testing. The test results showed that the three load arrangements gave similar shear capacity failure envelopes for the frictional block system with flat concrete surfaces. For more typical block systems with concrete shear keys and trailing lips that exhibit dilatant interface shear behavior, or a system with shear pins, the most consistent test results were developed using the flexible airbag arrangement. The results of this paper can be used to guide the selection of the loading arrangement for conventional laboratory modular block shear testing.
Inputs and Analyses: An End User’s Perspective of Heat-Air-Moisture Data
Authors: Decareau Christopher P. , Kan Liyen , Piñon Joseph P. 
Published: September 2007

Abstract
Hygrothermal simulation programs (HSPs) have the potential to help the way building enclosures are designed if end users are convinced the results are reliable. However, HSPs suffer from a lack of manufacturer-specific material data. HSP users often “create” materials by scouring multiple sources for hygrothermal properties. To the less familiar HSP user, significant error can be introduced into simulations by using properties that are calculated from variable sources. Through a series of case studies, this paper illustrates how material properties can make a difference in hygrothermal calculations and, ultimately, material specification.
Validation of Oxidative Stability of Factory Fill and Alternative Engine Oils Using the Iron Catalyzed Oxidation Test
Authors: Fitamen Eric , Tiquet Laurent , Woydt Mathias 
Published: September 2007

Abstract
Oxidation resistance is one of the limiting factors for long drains, bionotox, LowSAP or NoSAP engine oils. The French iron catalyzed oxidation test (ICOT) uses 60 ppm iron acetylacetonate as diluted catalyst under an aeration of 10 L∕h at 170°C. The ICOT ranks the oxidation stability of oils according to three properties: a. the viscosity increase (e.g., max. Δη40°C&lt;100 % or Δη100°C&lt;100 %), b. the increase to an individual TAN (e.g., max. 7.5 mgKOH∕g) and c. the oxidative evaporation losses of max. 10 % at Δη=100 % due to oxidation. This paper describes the ICOT method standardized as GFC Lu 36T 03 and the obtainable accuracy. Also, results are compiled achieved with this test for factory fill engine oils as well as alternative prototype engine oils based on esters, blends of esters with hydrocarbons, and polyglycols.
Moisture Buffering Capacities of Five North American Building Materials
Authors: Wu Yang , Fazio Paul , Kumaran Mavinkal K. (Kumar) 
Published: September 2007

AbstractThe moisture buffering capacities of five building materials which are widely used in North America was investigated experimentally. An experiment to quantify the moisture buffering capacity of building materials was developed. Hygrothermal properties of these building materials, reported in this paper, include the density, thermal conductivity, equilibrium moisture content, water vapor permeability, water absorption coefficient, and air permeability. Moisture buffering test results showed that among these materials the fiberboard product has the best moisture buffering capacity, whereas plywood has the lowest among the building products tested.
Carbon Nanotubes for Electronic and Electrochemical Detection of Biomolecules
Authors: Kim S. N. , Rusling J. F. , Papadimitrakopoulos F. 
Published: September 2007

AbstractThe unique electronic and optical properties of carbon nanotubes, in conjunction with their size and mechanically robust nature, make these nanomaterials crucial to the development of next‐generation biosensing platforms. In this Review, we present recent innovations in carbon nanotube‐assisted biosensing technologies, such as DNA‐hybridization, protein‐binding, antibody‐antigen and aptamers. Following a brief introduction on the diameter‐ and chirality‐derived electronic characteristics of single‐walled carbon nanotubes, the discussion is focused on the two major schemes for electronic biodetection, namely biotransistor‐ and electrochemistry‐based sensors. Key fabrication methodologies are contrasted in light of device operation and performance, along with strategies for amplifying the signal while minimizing nonspecific binding. This Review is concluded with a perspective on future optimization based on array integration as well as exercising a better control in nanotube structure and biomolecular integration.