bluuebunny/crossref_metadata_2025_split huggingface dataset:
Available Potential Energy and Irreversible Mixing in the Meridional Overturning Circulation
Authors: Hughes Graham O. , Hogg Andrew Mc C. , Griffiths Ross W. 
Published: July 2009

Abstract
The overturning circulation of the global oceans is examined from an energetics viewpoint. A general framework for stratified turbulence is used for this purpose; first, it highlights the importance of available potential energy in facilitating the transfer of kinetic energy to the background potential energy (defined as the adiabatically rearranged state with no motion). Next, it is shown that it is the rate of transfer between different energy reservoirs that is important for the maintenance of the ocean overturning, rather than the total amount of potential or kinetic energy. A series of numerical experiments is used to assess which energy transfers are significant in the overturning circulation. In the steady state, the rate of irreversible diapycnal mixing is necessarily balanced by the production of available potential energy sourced from surface buoyancy fluxes. Thus, the external inputs of available potential energy from surface buoyancy forcing and of kinetic energy from other sources (such as surface winds and tides, and leading to turbulent mixing) are both necessary to maintain the overturning circulation.
Effect of Finite Spatial Resolution on the Turbulent Energy Spectrum Measured in the Coastal Ocean Bottom Boundary Layer
Authors: Hackett Erin E. , Luznik Luksa , Katz Joseph , Osborn Thomas R. 
Published: July 2009

AbstractThe effect of finite spatial resolution on the measured energy spectrum is examined via a parametric study using in situ particle image velocimetry (PIV) measurements performed in the bottom boundary layer on the Atlantic continental shelf. Two-dimensional (2D) box spatial filters of various scales are applied to the data, and these filtered distributions are used to compute 1D energy spectra in both frequency and wavenumber domains. It is found that energy levels are attenuated by more than 15% at all length scales that are smaller than 10 times the scale of the filter. Filtering both in the direction of the spectrum as well as perpendicular to it contributes to the extent of attenuation, the latter via implicit integration over all wavenumbers. At scales larger than that of the filter, Gaussian, nonlinear Butterworth, and median filters attenuate less energy than the box filter. When frequency spectra are converted using Taylor’s hypothesis, wave energy appears in wavenumber space at a location different than its true physical scale, which is much larger than the filter sizes. Consequently, wave energy is not attenuated and dominates over the turbulence through this spectral range. Because wave energy and turbulence respond differently to the filtering, modified spectral slopes at the transition between wave- and turbulence-dominated regions occur, resulting in inordinately steep spectral slopes. Finally, removal of the pressure-coherent part of the velocity signal is not sufficient to reveal the turbulence within the wave peak spectral range. Remaining energy in this range is still dominated by much larger scales.
Identification of novel antigens with induced immune response in monoclonal gammopathy of undetermined significance
Authors: Blotta Simona , Tassone Pierfrancesco , Prabhala Rao H. , Tagliaferri Piersandro , Cervi David , Amin Samir , Jakubikova Jana , Tai Yu-Tzu , Podar Klaus , Mitsiades Constantine S. , Zullo Alessandro , Franco Brunella , Anderson Kenneth C. , Munshi Nikhil C. 
Published: July 2009

Abstract
The transformation from monoclonal gammopathy of undetermined significance (MGUS) to multiple myeloma (MM) is thought to be associated with changes in immune processes. We have therefore used serologic analysis of recombinant cDNA expression library to screen the sera of MGUS patients to identify tumor-associated antigens. A total of 10 antigens were identified, with specific antibody responses in MGUS. Responses appeared to be directed against intracellular proteins involved in cellular functions, such as apoptosis (SON, IFT57/HIPPI), DNA and RNA binding (ZNF292, GPATCH4), signal transduction regulators (AKAP11), transcriptional corepressor (IRF2BP2), developmental proteins (OFD1), and proteins of the ubiquitin-proteasome pathway (PSMC1). Importantly, the gene responsible for the oral-facial-digital type I syndrome (OFD1) had response in 6 of 29 (20.6%) MGUS patients but 0 of 11 newly diagnosed MM patients. Interestingly, 3 of 11 (27.2%) MM patients after autologous stem cell transplantations showed responses to OFD1. We have confirmed T-cell responses against OFD1 in MGUS and observed down-regulation of GLI1/PTCH1 and p-β-catenin after OFD1 knock-down with specific siRNA, suggesting its functional role in the regulation of Hh and Wnt pathways. These findings demonstrate OFD1 as an important immune target and highlight its possible role in signal transduction and tumorigenesis in MGUS and MM.
How I treat the antiphospholipid syndrome
Authors: Giannakopoulos Bill , Krilis Steven A. 
Published: July 2009

Abstract
This article discusses how we approach medical decision making in the treatment of the various facets of the antiphospholipid syndrome (APS), including secondary prophylaxis in the setting of venous and arterial thrombosis, as well as treatment for the prevention of recurrent miscarriages and fetal death. The role of primary thromboprophylaxis is also discussed in depth. Great emphasis is given to incorporating the most up-to-date and relevant evidence base both from the APS literature, and from large, recent, randomized controlled trials (RCTs) of primary and secondary thrombotic prophylaxis in the general population setting (ie, the population that has not been specifically investigated for APS).
A novel binding site for ADAMTS13 constitutively exposed on the surface of globular VWF
Authors: Zanardelli Sara , Chion Alain C. K. , Groot Evelyn , Lenting Peter J. , McKinnon Thomas A. J. , Laffan Mike A. , Tseng Michelle , Lane David A. 
Published: July 2009

AbstractADAMTS13 metalloprotease regulates the multimeric size of von Willebrand factor (VWF) by cleaving the Tyr1605-Met1606 bond in the VWF A2 domain. The mechanisms of VWF recognition by ADAMTS13 have yet to be fully resolved. Most studies have focused on the role of exosites within the VWF A2 domain, involved in interaction with the ADAMTS13 spacer domain. In the present study, we expressed different C-terminal domain VWF fragments and evaluated their binding to ADAMTS13 and its truncated mutants, MDTCS and del(TSP5-CUB). Using plate binding assay and surface plasmon resonance, we identified a novel ADAMTS13 binding site (KD ∼ 86 nM) in the region of VWF spanning residues 1874 to 2813, which includes the VWF D4 domain and that interacts with the C-terminal domains of ADAMTS13. We show that the interaction occurs even when VWF is in static conditions, assumed to be globular and where the VWF A2 domain is hidden. We demonstrate that C-terminal VWF fragments, as well as an antibody specifically directed toward the VWF D4 domain, inhibit VWF proteolysis by ADAMTS13 under shear conditions. We propose that this novel VWF C-terminal binding site may participate as the initial step of a multistep interaction ultimately leading to proteolysis of VWF by ADAMTS13.
Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites
Authors: Noda Satoko , Hongoh Yuichi , Sato Tomoyuki , Ohkuma Moriya 
Published: July 2009

AbstractBackgroundThe microbial community in the gut of termites is responsible for the efficient decomposition of recalcitrant lignocellulose. Prominent features of this community are its complexity and the associations of prokaryotes with the cells of cellulolytic flagellated protists. Bacteria in the order Bacteroidales are involved in associations with a wide variety of gut protist species as either intracellular endosymbionts or surface-attached ectosymbionts. In particular, ectosymbionts exhibit distinct morphological patterns of the associations. Therefore, these Bacteroidales symbionts provide an opportunity to investigate not only the coevolutionary relationships with the host protists and their morphological evolution but also how symbiotic associations between prokaryotes and eukaryotes occur and evolve within a complex symbiotic community.ResultsMolecular phylogeny of 31 taxa of Bacteroidales symbionts from 17 protist genera in 10 families was examined based on 16S rRNA gene sequences. Their localization, morphology, and specificity were also examined by fluorescent in situ hybridizations. Although a monophyletic grouping of the ectosymbionts occurred in three related protist families, the symbionts of different protist genera were usually dispersed among several phylogenetic clusters unique to termite-gut bacteria. Similar morphologies of the associations occurred in multiple lineages of the symbionts. Nevertheless, the symbionts of congeneric protist species were closely related to one another, and in most cases, each host species harbored a unique Bacteroidales species. The endosymbionts were distantly related to the ectosymbionts examined so far.ConclusionThe coevolutionary history of gut protists and their associated Bacteroidales symbionts is complex. We suggest multiple independent acquisitions of the Bacteroidales symbionts by different protist genera from a pool of diverse bacteria in the gut community. In this sense, the gut could serve as a reservoir of diverse bacteria for associations with the protist cells. The similar morphologies are considered a result of evolutionary convergence. Despite the complicated evolutionary history, the host-symbiont relationships are mutually specific, suggesting their cospeciations at the protist genus level with only occasional replacements.
Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Authors: Do Jin Hwan , Yamaguchi Rui , Miyano Satoru 
Published: July 2009

Abstract

Background
The thermotolerance of Aspergillus fumigatus plays a critical role in mammalian and avian infections. Thus, the identification of its adaptation mechanism to higher temperature is very important for an efficient anti-fungal drug development as well as fundamental understanding of its pathogenesis. We explored the temporal transcription regulation structure of this pathogenic fungus under heat shock conditions using the time series microarray data reported by Nierman et al. (Nature 2005, 438:1151-1156).

Results
The estimated transcription regulation structure of A. fumigatus shows that the heat shock proteins are strongly negatively associated with central metabolic pathway genes such as the tricarboxylic acid cycle (TCA cycle) and carbohydrate metabolism. It was 60 min and 120 min, respectively, after the growth temperature changes from 30°C (corresponding to environments of tropical soil) to 37°C and 48°C (corresponding to temperatures in the human body and compost, respectively) that some of genes in TCA cycle were started to be upregulated. In these points, most of heat shock proteins showed lowest expression level after heat shocks. Among the heat shock proteins, the HSP30 (AFU6G06470), a single integral plasma membrane heat shock protein, presented most active role in transcription regulation structure in both heat shock conditions of 37°C and 48°C. The metabolic genes associated with multiple genes in the gene regulation network showed a tendency to have opposite expression patterns of heat shock proteins. The role of those metabolic genes was second regulator in the coherent feed-forward loop type of regulation structure having heat shock protein as its first regulator. This type of regulation structure might be very advantageous for the thermal adaptation of A. fumigatus under heat shock because a small amount of heat shock proteins can rapidly magnify their regulation effect on target genes. However, the coherent feed-forward loop type of regulation of heat shock proteins with metabolic genes became less frequent with increasing temperature. This might be the reason for dramatic increase in the expression of heat shock proteins and the number of heat shock response genes at heat shock of 48°C.

Conclusion
We systemically analysed the thermal adaption mechanism of A. fumigatus by state space model with times series microarray data in terms of transcription regulation structure. We suggest for the first time that heat shock proteins might efficiently regulate metabolic genes using the coherent feed-forward loop type of regulation structure. This type of regulation structure would also be efficient for adjustment to the other stresses requiring rapid change of metabolic mode as well as thermal adaptation.
Hmrbase: a database of hormones and their receptors
Authors: Rashid Mamoon , Singla Deepak , Sharma Arun , Kumar Manish , Raghava Gajendra PS 
Published: July 2009

Abstract

Background
Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors.

Description
This manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information.

Conclusion
Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, DrugPedia linkage etc. Hmrbase is available online for public from http://crdd.osdd.net/raghava/hmrbase/.
Integrin α6Bβ4 inhibits colon cancer cell proliferation and c-Myc activity
Authors: Dydensborg Anders Bondo , Teller Inga C , Groulx Jean-François , Basora Nuria , Paré Fréderic , Herring Elizabeth , Gauthier Rémy , Jean Dominique , Beaulieu Jean-François 
Published: July 2009

AbstractBackgroundIntegrins are known to be important contributors to cancer progression. We have previously shown that the integrin β4 subunit is up-regulated in primary colon cancer. Its partner, the integrin α6 subunit, exists as two different mRNA splice variants, α6A and α6B, that differ in their cytoplasmic domains but evidence for distinct biological functions of these α6 splice variants is still lacking.MethodsIn this work, we first analyzed the expression of integrin α6A and α6B at the protein and transcript levels in normal human colonic cells as well as colorectal adenocarcinoma cells from both primary tumors and established cell lines. Then, using forced expression experiments, we investigated the effect of α6A and α6B on the regulation of cell proliferation in a colon cancer cell line.ResultsUsing variant-specific antibodies, we observed that α6A and α6B are differentially expressed both within the normal adult colonic epithelium and between normal and diseased colonic tissues. Proliferative cells located in the lower half of the glands were found to predominantly express α6A, while the differentiated and quiescent colonocytes in the upper half of the glands and surface epithelium expressed α6B. A relative decrease of α6B expression was also identified in primary colon tumors and adenocarcinoma cell lines suggesting that the α6A/α6B ratios may be linked to the proliferative status of colonic cells. Additional studies in colon cancer cells showed that experimentally restoring the α6A/α6B balance in favor of α6B caused a decrease in cellular S-phase entry and repressed the activity of c-Myc.ConclusionThe findings that the α6Bβ4 integrin is expressed in quiescent normal colonic cells and is significantly down-regulated in colon cancer cells relative to its α6Aβ4 counterpart are consistent with the anti-proliferative influence and inhibitory effect on c-Myc activity identified for this α6Bβ4 integrin. Taken together, these findings point out the importance of integrin variant expression in colon cancer cell biology.
Artificial arterial blood pressure artifact models and an evaluation of a robust blood pressure and heart rate estimator
Authors: Li Qiao , Mark Roger G , Clifford Gari D 
Published: July 2009

Abstract

Background
Within the intensive care unit (ICU), arterial blood pressure (ABP) is typically recorded at different (and sometimes uneven) sampling frequencies, and from different sensors, and is often corrupted by different artifacts and noise which are often non-Gaussian, nonlinear and nonstationary. Extracting robust parameters from such signals, and providing confidences in the estimates is therefore difficult and requires an adaptive filtering approach which accounts for artifact types.

Methods
Using a large ICU database, and over 6000 hours of simultaneously acquired electrocardiogram (ECG) and ABP waveforms sampled at 125 Hz from a 437 patient subset, we documented six general types of ABP artifact. We describe a new ABP signal quality index (SQI), based upon the combination of two previously reported signal quality measures weighted together. One index measures morphological normality, and the other degradation due to noise. After extracting a 6084-hour subset of clean data using our SQI, we evaluated a new robust tracking algorithm for estimating blood pressure and heart rate (HR) based upon a Kalman Filter (KF) with an update sequence modified by the KF innovation sequence and the value of the SQI. In order to do this, we have created six novel models of different categories of artifacts that we have identified in our ABP waveform data. These artifact models were then injected into clean ABP waveforms in a controlled manner. Clinical blood pressure (systolic, mean and diastolic) estimates were then made from the ABP waveforms for both clean and corrupted data. The mean absolute error for systolic, mean and diastolic blood pressure was then calculated for different levels of artifact pollution to provide estimates of expected errors given a single value of the SQI.

Results
Our artifact models demonstrate that artifact types have differing effects on systolic, diastolic and mean ABP estimates. We show that, for most artifact types, diastolic ABP estimates are less noise-sensitive than mean ABP estimates, which in turn are more robust than systolic ABP estimates. We also show that our SQI can provide error bounds for both HR and ABP estimates.

Conclusion
The KF/SQI-fusion method described in this article was shown to provide an accurate estimate of blood pressure and HR derived from the ABP waveform even in the presence of high levels of persistent noise and artifact, and during extreme bradycardia and tachycardia. Differences in error between artifact types, measurement sensors and the quality of the source signal can be factored into physiological estimation using an unbiased adaptive filter, signal innovation and signal quality measures.
Possible roles of Epstein-Barr virus in Castleman disease
Authors: Chen Chih-Hao , Liu Hung-Chang , Hung Tzu-Ti , Liu Tsang-Pai 
Published: July 2009

Abstract

Background
Complete resection seemed to be curative in patients with Castleman disease of any location but the disease is likely to be reactive in its pathogenesis. The relation between Epstein-Barr virus and Castleman disease has not been elucidated. We tried to define the role of Epstein-Barr virus in the pathogenesis of Castleman disease.

Methods
20 cases of Castleman disease were retrospectively reviewed from 1993 to 2006. At least 2 to 4 representative sections of formalin-fixed, paraffin-embedded specimens from each patient were obtained to examine the presence of EBV and its localization by hematoxylin-eosin stain, immunohistochemistry, polymerase chain reaction and In-situ hybridization

Results
Hyaline-vascular type was diagnosed in 18 cases, plasma cell type in 1 and mixed type in 1 case. All of them were positive for Epstein-Barr virus confirmed by PCR. For tumors that EBER(Epstein-Barr early region) signals mainly localized in the germinal centers have increased vascularity than cases with EBER detected in inter-follicular areas.

Conclusion
There is a strong association between Castleman disease and Epstein-Barr virus. EBV may have a potential role in angiogenesis of Castleman disease. For smaller lesion with high activity of angiogenesis but not amenable for curative resection, anti-angiogenesis medications may have a potential role to control the disease.
Foot orthoses: how much customisation is necessary?
Authors: Menz Hylton B 
Published: July 2009

AbstractThe relative merit of customised versus prefabricated foot orthoses continues to be the subject of passionate debate among foot health professionals. Although there is currently insufficient evidence to reach definitive conclusions, a growing body of research literature suggests that prefabricated foot orthoses may produce equivalent clinical outcomes to customised foot orthoses for some conditions. Consensus guidelines for the prescription of customised foot orthoses need to be developed so that the hypothesised benefits of these devices can be thoroughly evaluated.