bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergence of Hormones, Inflammation, and Energy-Related Factors: A Novel Pathway of Cancer Etiology
Authors: Slattery Martha L. , Fitzpatrick F.A. 
Published: November 2009

AbstractColorectal cancer (CRC) is a multifactorial disease with several hypothesized etiologic factors including inflammatory processes; hormones such as estrogen, androgen, and insulin; and energy-related factors. We present evidence that integrates these elements in a pathway we call the convergence of hormones, inflammation, and energy-related factors (CHIEF). First, given the physiology of the gut, substantial epidemiologic and molecular data support the hypothesis that activation of innate immunity in the normal gut mucosa by various environmental agents (commensal bacteria, dietary antigens, mucosal irritants, pathogens) and endogenous factors such as estrogen, androgens, and insulin levels provokes basal inflammation as an underlying factor of the association of insulin, estrogen, and energy-related factors with CRC. Second, critical genes involved in this pathway, e.g., phosphatase tensin homologue on chromosome 10 (PTEN) and serine threonine kinase 11 (STK11)/LKB1, are tumor suppressor genes often mutated in intestinal cancer or CRC. Third, laboratory experiments show that cellular PTEN and STK11/LKB1 tumor suppressor enzymes are vulnerable to inactivation by redox-active species, especially chemically reactive lipid mediators of inflammation and redox stress. Epidemiologic data further support the underlying proposal that CHIEF comprises important elements of CRC risk. Although this discussion of the CHIEF pathway focuses on CRC, we believe that this pathway may play an important role in the etiology of other cancers as well.
Autofluorescence-Guided Surveillance for Oral Cancer
Authors: Jayaprakash Vijayvel , Sullivan Maureen , Merzianu Mihai , Rigual Nestor R. , Loree Thom R. , Popat Saurin R. , Moysich Kirsten B. , Ramananda Soumya , Johnson Timothy , Marshall James R. , Hutson Alan D. , Mang Thomas S. , Wilson Brian C. , Gill Steven R. , Frustino Jennifer , Bogaards Arjen , Reid Mary E. 
Published: November 2009

Abstract
Early detection of oral premalignant lesions (OPL) and oral cancers (OC) is critical for improved survival. We evaluated if the addition of autofluorescence visualization (AFV) to conventional white-light examination (WLE) improved the ability to detect OPLs/OCs. Sixty high-risk patients, with suspicious oral lesions or recently diagnosed untreated OPLs/OCs, underwent sequential surveillance with WLE and AFV. Biopsies were obtained from all suspicious areas identified on both examinations (n = 189) and one normal-looking control area per person (n = 60). Sensitivity, specificity, and predictive values were calculated for WLE, AFV, and WLE + AFV. Estimates were calculated separately for lesions classified by histopathologic grades as low-grade lesions, high-grade lesions (HGL), and OCs. Sequential surveillance with WLE + AFV provided a greater sensitivity than WLE in detecting low-grade lesions (75% versus 44%), HGLs (100% versus 71%), and OCs (100% versus 80%). The specificity in detecting OPLs/OCs decreased from 70% with WLE to 38% with WLE + AFV. Thirteen of the 76 additional biopsies (17%) obtained based on AFV findings were HGLs/OCs. Five patients (8%) were diagnosed with a HGL/OC only because of the addition of AFV to WLE. In seven patients, additional HGL/OC foci or wider OC margins were detected on AFV. Additionally, AFV aided in the detection of metachronous HGL/OC in 6 of 26 patients (23%) with a history of previously treated head and neck cancer. Overall, the addition of AFV to WLE improved the ability to detect HGLs/OCs. In spite of the lower specificity, AFV + WLE can be a highly sensitive first-line surveillance tool for detecting OPLs/OCs in high-risk patients.
Significant Compositional Techniques in the Psalms: Evidence for the Use of Number as an Organizing Principle
Authors: Labuschagne Casper 
Published: November 2009

AbstractThis article directs attention to a largely unobserved, and grossly ignored, aspect of the biblical writings in general and of the Psalms in particular: their numerical features. It shall be demonstrated that in composing their texts, the biblical writers used specific numbers as an organizing principle to shape their texts and as a means of imbuing them with symbolic significance. In doing so, they employed a variety of numerical techniques, in which 7 and 11, symbolizing 'fullness' and 'comprehensiveness', play a crucial role as ordering devices. Evidence is adduced to show that the scribes also used the divine name numbers 17 and 26 in various ways to symbolically express God's presence and to give prominence to their texts. Approaching the book of Psalms from this perspective provides us with a new key to unlock and understand the compositional architecture of the psalms and the five books of the Psalter. These claims are substantiated by a discussion of sufficient examples to illustrate that the psalms are interrelated numerical compositions and that the book of Psalms is a sophisticated, meticulously designed work of art, shaped primarily by numerical considerations.
On the Maximum Observed Wind Speed in a Randomly Sampled Hurricane
Authors: Solow Andrew R. 
Published: November 2009

Abstract
There is considerable interest in detecting a long-term trend in hurricane intensity possibly related to large-scale ocean warming. This effort is complicated by the paucity of wind speed measurements for hurricanes occurring in the early part of the observational record. Here, results are presented regarding the maximum observed wind speed in a sparsely randomly sampled hurricane based on a model of the evolution of wind speed over the lifetime of a hurricane.
Great Plains Drought in Simulations of the Twentieth Century
Authors: McCrary Rachel R. , Randall David A. 
Published: November 2009

Abstract
Coupled global circulation models (CGCMs) have been widely used to explore potential future climate change. Before these climate projections can be trusted, the ability of the models to simulate present-day climate must be assessed. This study evaluates the ability of three CGCMs that participated in the Fourth Assessment Report of the Intergovernmental Panel on Climate Change to simulate long-term drought over the Great Plains region with the same frequency and intensity as was observed during the twentieth century. The three models evaluated in this study are the Geophysical Fluid Dynamics Laboratory Coupled Model, version 2.0 (CM2.0); the National Centers for Atmospheric Research Community Climate System Model, version 3 (CCSM3); and third climate configuration of the Met Office Unified Model (HadCM3).
The models are shown to capture the broad features of the climatology of the Great Plains, with maximum precipitation occurring in early summer, as observed. However, all of the models overestimate annual precipitation rates. Also, in CCSM3, precipitation and evapotranspiration experience unrealistic decreases between the months of June and August.
Long-term droughts are found in each simulation of the twentieth century that are comparable in duration, severity, and spatial extent as has been observed. However, the processes found to be associated with simulated long-term droughts vary among the models. In both CM2.0 and HadCM3, low-frequency variations in Great Plains precipitation are found to correspond with low-frequency variations in tropical Pacific SSTs. In CCSM3, on the other hand, there appears to be no significant correlation between tropical Pacific SST variability and Great Plains precipitation. Strong land–atmosphere coupling in CCSM3 may explain the persistence of long-term droughts in this model.
Shallow and Deep Latent Heating Modes over Tropical Oceans Observed with TRMM PR Spectral Latent Heating Data
Authors: Takayabu Yukari N. , Shige Shoichi , Tao Wei-Kuo , Hirota Nagio 
Published: November 2009

Abstract
Three-dimensional distributions of the apparent heat source (Q1) − radiative heating (QR) estimated from Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) utilizing the spectral latent heating (SLH) algorithm are analyzed. Mass-weighted and vertically integrated Q1 − QR averaged over the tropical oceans is estimated as ∼72.6 J s−1 (∼2.51 mm day−1) and that over tropical land is ∼73.7 J s−1 (∼2.55 mm day−1) for 30°N–30°S. It is shown that nondrizzle precipitation over tropical and subtropical oceans consists of two dominant modes of rainfall systems: deep systems and congestus. A rough estimate of the shallow-heating contribution against the total heating is about 46.7% for the average tropical oceans, which is substantially larger than the 23.7% over tropical land.
Although cumulus congestus heating linearly correlates with SST, deep-mode heating is dynamically bounded by large-scale subsidence. It is notable that a substantial amount of rain, as large as 2.38 mm day−1 on average, is brought from congestus clouds under the large-scale subsiding circulation. It is also notable that, even in the region with SSTs warmer than 28°C, large-scale subsidence effectively suppresses the deep convection, with the remaining heating by congestus clouds.
The results support that the entrainment of mid–lower-tropospheric dry air, which accompanies the large-scale subsidence, is the major factor suppressing the deep convection. Therefore, a representation of the realistic entrainment is very important for proper reproduction of precipitation distribution and the resultant large-scale circulation.
A New Procedure Based on Surface Renewal Analysis to Estimate Sensible Heat Flux: A Case Study over Grapevines
Authors: Castellví F. , Snyder R. L. 
Published: November 2009

AbstractGrapevines are grown on a range of soils and in different climates. Depending on the desired final product and method of harvesting, the trellis system, and hence vineyard architecture, varies dramatically. Consequently, the crop coefficients used to estimate vineyard evapotranspiration from reference evapotranspiration are less universal than for other crops. Evapotranspiration measurements are often limited because of a lack of fetch and unavailability of vine parameters required as input. In this paper, a new procedure based on surface renewal (SR) analysis was derived to estimate sensible heat flux over the grapevines. A two-dimensional sonic anemometer operating close to the canopy can provide the inputs required to estimate the sensible heat flux and the work of expansion of the air parcels under constant pressure. Regardless of the stability conditions, the SR estimates were comparable to those determined using the eddy covariance (EC) method providing a root-mean-square error of 14 W m−2 for all data. Thus, the procedure is low cost and makes SR a simpler method than EC to estimate latent heat flux as the residual of the energy balance equation in moderately tall and heterogeneous crops. The experiment was carried out at a site influenced by regional advection of sensible heat flux.
The Instability of the Thermohaline Circulation in a Low-Order Model
Authors: Colin de Verdière Alain 
Published: November 2009

Abstract
Although the instability of the thermohaline circulation has been widely observed in numerical ocean models, theoretical advances have been hindered by the nonlinearity of heat and salt transports, a circulation governed by lateral temperature, and salinity gradients. Because the instability occurs initially in polar waters through the formation of haloclines and the halt of convection, any explanatory model must have at least a surface and a deep layer. The model proposed here (two surface boxes above a deep one) reduces to a 2 degrees-of-freedom dynamical system when convection is active and 3 degrees when it is interrupted. The instability that is induced by a negative freshwater perturbation in polar waters has three stages. The first stage is a rapid 5-yr adjustment to a transient thermal attractor that results from an approximate balance between heat advection and air–sea heat fluxes. The second stage is a slow evolution that self-organizes near this attractor, which preconditions the instability, as it can be shown that the circulation becomes more sensitive to changes in salinity gradients than in temperature gradients. The slow O(100 yr) growth of salinity in the subtropics is the critical precursor of the instability while at the same time the subpolar salinity rises against the initial perturbation to stabilize the system by increasing the overturning and restoring convection. When the overturning becomes smaller than the value at the unstable fixed point, the third stage occurs, which is when the subpolar salinity decreases at last on a fast O(10 yr) time scale, precipitating the fall of the overturning. During the last two stages of the instability, the horizontal thermal gradient increases, but its stabilizing effect is just barely unable to prevent the outcome. The return to stability occurs frequently through a regime of multidecadal oscillations with intermittent convection. The hypothesis of mixed boundary conditions has been relaxed by coupling the ocean box model to an atmospheric energy balance model to show that the coupling increases the stability of the oceanic circulation; however, the precursors of the instability are unchanged.
Automated summaries of serious adverse events in the hepatitis C antiviral long-term treatment against cirrhosis trial
Authors: Bell Margaret C , Robuck Patricia R , Wright Elizabeth C , Mihova Marina S , Hofmann Charlotte , De Santo Jennifer L , Milstein Susan L , Richtmyer Pamela A , Shelton Janel L , Cormier Maureen , King Debra L , Park Choon J , Molchen Wallis A , Park Yoon , Kelley Michelle 
Published: November 2009

Background Even though adverse event (AE) collection and official accounting are mandatory for clinical trials, there are limited detailed guidelines specifying how to summarize the event for reporting in a timely and expeditious manner. This article details the AE and serious adverse event (SAE) reporting summary developed for a large multi-center National Institutes of Health (NIH)-sponsored clinical trial. Purpose To review and analyze the large volume of AE data reported by 10 sites (806 SAEs and 19,034 AEs from August 2000 to May 2007) the automated SAE summary was developed. It was designed to ensure timeliness and clarity in the complex process of AE review and reporting. Methods The AE and SAE case report forms (CRFs) as well as the automated SAE summary were developed within a database management system developed by the Data Coordinating Center (DCC) which allowed for web-based data entry at the DCC and 10 sites and offered immediate overall and site-specific reports accessible by the DCC, site, and NIH project staff. Results The automated SAE summary pulled data from multiple CRFs to create a succinct and informative summary and allowed for prompt and easy reporting to the regulatory agencies. The summary was adaptable to the needs of reviewers because of the availability of multiple search options.
Evidence for a cross-talk between human neutrophils and Th17 cells
Authors: Pelletier Martin , Maggi Laura , Micheletti Alessandra , Lazzeri Elena , Tamassia Nicola , Costantini Claudio , Cosmi Lorenzo , Lunardi Claudio , Annunziato Francesco , Romagnani Sergio , Cassatella Marco A. 
Published: November 2009

AbstractInterleukin-17A (IL-17A) and IL-17F are 2 of several cytokines produced by T helper 17 cells (Th17), which are able to indirectly induce the recruitment of neutrophils. Recently, human Th17 cells have been phenotypically characterized and shown to express discrete chemokine receptors, including CCR2 and CCR6. Herein, we show that highly purified neutrophils cultured with interferon-γ plus lipopolysaccharide produce the CCL2 and CCL20 chemokines, the known ligands of CCR2 and CCR6, respectively. Accordingly, supernatants from activated neutrophils induced chemotaxis of Th17 cells, which was greatly suppressed by anti-CCL20 and anti-CCL2 antibodies. We also discovered that activated Th17 cells could directly chemoattract neutrophils via the release of biologically active CXCL8. Consistent with this reciprocal recruitment, neutrophils and Th17 cells were found in gut tissue from Crohn disease and synovial fluid from rheumatoid arthritis patients. Finally, we report that, although human Th17 cells can directly interact with freshly isolated or preactivated neutrophils via granulocyte-macrophage colony-stimulating factor, tumor necrosis factor-α, and interferon-γ release, these latter cells cannot be activated by IL-17A and IL-17F, because of their lack of IL-17RC expression. Collectively, our results reveal a novel chemokine-dependent reciprocal cross-talk between neutrophils and Th17 cells, which may represent a useful target for the treatment of chronic inflammatory diseases.
Information-theoretic gene-gene and gene-environment interaction analysis of quantitative traits
Authors: Chanda Pritam , Sucheston Lara , Liu Song , Zhang Aidong , Ramanathan Murali 
Published: November 2009

Abstract

Background
The purpose of this research was to develop a novel information theoretic method and an efficient algorithm for analyzing the gene-gene (GGI) and gene-environmental interactions (GEI) associated with quantitative traits (QT). The method is built on two information-theoretic metrics, the k-way interaction information (KWII) and phenotype-associated information (PAI). The PAI is a novel information theoretic metric that is obtained from the total information correlation (TCI) information theoretic metric by removing the contributions for inter-variable dependencies (resulting from factors such as linkage disequilibrium and common sources of environmental pollutants).

Results
The KWII and the PAI were critically evaluated and incorporated within an algorithm called CHORUS for analyzing QT. The combinations with the highest values of KWII and PAI identified each known GEI associated with the QT in the simulated data sets. The CHORUS algorithm was tested using the simulated GAW15 data set and two real GGI data sets from QTL mapping studies of high-density lipoprotein levels/atherosclerotic lesion size and ultra-violet light-induced immunosuppression. The KWII and PAI were found to have excellent sensitivity for identifying the key GEI simulated to affect the two quantitative trait variables in the GAW15 data set. In addition, both metrics showed strong concordance with the results of the two different QTL mapping data sets.

Conclusion
The KWII and PAI are promising metrics for analyzing the GEI of QT.
Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death
Authors: Park Jong-Yi , Kim Jae-Hwan , Choi Yun-Jung , Hwang Kyu-Chan , Cho Seong-Keun , Park Ho-Hyun , Paik Seung-Sam , Kim Teoan , Park ChanKyu , Lee Hoon Taek , Seo Han Geuk , Park Soo-Bong , Hwang Seongsoo , Kim Jin-Hoi 
Published: November 2009

Abstract

Background
Somatic cell nuclear transfer (scNT)-derived piglets have high rates of mortality, including stillbirth and postnatal death. Here, we examined severe malformed umbilical cords (MUC), as well as other organs, from nine scNT-derived term piglets.

Results
Microscopic analysis revealed complete occlusive thrombi and the absence of columnar epithelial layers in MUC (scNT-MUC) derived from scNT piglets. scNT-MUC had significantly lower expression levels of platelet endothelial cell adhesion molecule-1 (PECAM-1) and angiogenesis-related genes than umbilical cords of normal scNT piglets (scNT-N) that survived into adulthood. Endothelial cells derived from scNT-MUC migrated and formed tubules more slowly than endothelial cells from control umbilical cords or scNT-N. Proteomic analysis of scNT-MUC revealed significant down-regulation of proteins involved in the prevention of oxidative stress and the regulation of glycolysis and cell motility, while molecules involved in apoptosis were significantly up-regulated. Histomorphometric analysis revealed severe calcification in the kidneys and placenta, peliosis in the liver sinusoidal space, abnormal stromal cell proliferation in the lungs, and tubular degeneration in the kidneys in scNT piglets with MUC. Increased levels of apoptosis were also detected in organs derived from all scNT piglets with MUC.

Conclusion
These results suggest that MUC contribute to fetal malformations, preterm birth and low birth weight due to underlying molecular defects that result in hypoplastic umbilical arteries and/or placental insufficiency. The results of the current study demonstrate the effects of MUC on fetal growth and organ development in scNT-derived pigs, and provide important insight into the molecular mechanisms underlying angiogenesis during umbilical cord development.
Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach
Authors: Wang Ying , Brahmakshatriya Vinayak , Zhu Huifeng , Lupiani Blanca , Reddy Sanjay M , Yoon Byung-Jun , Gunaratne Preethi H , Kim Jong Hwan , Chen Rui , Wang Junjun , Zhou Huaijun 
Published: November 2009

AbstractBackgroundMicroRNAs (miRNAs) play critical roles in a wide spectrum of biological processes and have been shown to be important effectors in the intricate host-pathogen interaction networks. Avian influenza virus (AIV) not only causes significant economic losses in poultry production, but also is of great concern to human health. The objective of this study was to identify miRNAs associated with AIV infections in chickens.ResultsTotal RNAs were isolated from lung and trachea of low pathogenic H5N3 infected and non-infected SPF chickens at 4 days post-infection. A total of 278,398 and 340,726 reads were obtained from lung and trachea, respectively. And 377 miRNAs were detected in lungs and 149 in tracheae from a total of 474 distinct chicken miRNAs available at the miRBase, respectively. Seventy-three and thirty-six miRNAs were differentially expressed between infected and non-infected chickens in lungs and tracheae, respectively. There were more miRNAs highly expressed in non-infected tissues than in infected tissues. Interestingly, some of these differentially expressed miRNAs, including miR-146, have been previously reported to be associated with immune-related signal pathways in mammals.ConclusionTo our knowledge, this is the first study on miRNA gene expression in AIV infected chickens using a deep sequencing approach. During AIV infection, many host miRNAs were differentially regulated, supporting the hypothesis that certain miRNAs might be essential in the host-pathogen interactions. Elucidation of the mechanism of these miRNAs on the regulation of host-AIV interaction will lead to the development of new control strategies to prevent or treat AIV infections in poultry.