bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observing Surf-Zone Dispersion with Drifters
Authors: Spydell Matthew , Feddersen Falk , Guza R. T. , Schmidt W. E. 
Published: January 2008

AbstractSurf-zone dispersion is studied using drifter observations collected within about 200 m of the shoreline (at depths of less than about 5 m) on a beach with approximately alongshore uniform bathymetry and waves. There were about 70 individual drifter releases, each 10–20 min in duration, on two consecutive days. On the first day, the sea-swell significant wave height Hs was equal to 0.5 m and mean alongshore currents |υ| were moderate (&lt;0.1 m s−1). On the second day, the obliquely incident waves were larger, with Hs equal to 1.4 m, and at some surf-zone locations |υ| was greater than 0.5 m s−1. The one-particle diffusivity was larger, with larger waves and stronger currents. On both days, the one-particle diffusivity tensor is nonisotropic and time-dependent. The major axis is initially parallel to the cross-shore direction, but after a few wave periods it is aligned with the alongshore direction. In both the along- and cross-shore directions, the asymptotic diffusivity is reached sooner within, rather than seaward of, the surf zone. Two-particle statistics indicate that relative dispersion grows like D2(t) ∼ t3/2 and that the relative diffusivity is scale-dependent as μ ∼ l2/3, with l being the particle separation. The observed scalings differ from 2D inertial-subrange scalings [D2(t) ∼ t3 and μ ∼ l4/3]. Separations have a non-Gaussian self-similar distribution that is independent of time. The two-particle statistics are consistent with a nonconstant-coefficient diffusion equation for the separation probability density functions. The dispersion is explained by neither irrotational surface gravity waves nor shear dispersion. The observations imply the existence of a 2D eddy field with 5–50-m length scales, the source of which is speculated to be alongshore gradients in breaking-wave height associated with finite crest lengths.
Long Barotropic Waves Generated by a Storm Crossing Topography
Authors: Vennell Ross 
Published: January 2008

Abstract
Storms crossing topography are shown to radiate long surface gravity waves. The waves are transients generated by changes in the depth-dependent amplitude of the atmospherically forced pressure wave beneath a storm. This generation mechanism for long waves, known as “meteorological tsunamis” or rissaga, does not appear to have been previously discussed. The transients have periods equal to the passage time of the storm, of order 30 min for small fast-moving storms. A 1D model is used to give the amplitudes of the transient waves generated by a small fast-moving storm crossing a topographic step on to a continental shelf and across a ridge. Large transients are generated by storms whose translation speed is subcritical in deep water and supercritical in shallow water, that is, faster than the shallow-water wave speed. Surprisingly, when the depth difference between the deep water and the continental shelf is large, a gentle transition from deep to shallow water over 10 storm widths only slightly reduces the amplitudes of the transients. The influence of a finite-width shelf on the enhancement of coastal storm surge is also discussed. A 2D numerical model illustrates the topographic transients generated by sub- and supercritical storms moving across a ridge. Topographic transients are suggested as a source of energy for seiches on shelves and within embayments. The energy may come from a storm crossing the adjacent continental slope and possibly from distant open-ocean storms crossing multiple ridges and seamounts.
Extending pathways based on gene lists using InterPro domain signatures
Authors: Hahne Florian , Mehrle Alexander , Arlt Dorit , Poustka Annemarie , Wiemann Stefan , Beissbarth Tim 
Published: January 2008

Abstract

Background
High-throughput technologies like functional screens and gene expression analysis produce extended lists of candidate genes. Gene-Set Enrichment Analysis is a commonly used and well established technique to test for the statistically significant over-representation of particular pathways. A shortcoming of this method is however, that most genes that are investigated in the experiments have very sparse functional or pathway annotation and therefore cannot be the target of such an analysis. The approach presented here aims to assign lists of genes with limited annotation to previously described functional gene collections or pathways. This works by comparing InterPro domain signatures of the candidate gene lists with domain signatures of gene sets derived from known classifications, e.g. KEGG pathways.

Results
In order to validate our approach, we designed a simulation study. Based on all pathways available in the KEGG database, we create test gene lists by randomly selecting pathway genes, removing these genes from the known pathways and adding variable amounts of noise in the form of genes not annotated to the pathway. We show that we can recover pathway memberships based on the simulated gene lists with high accuracy. We further demonstrate the applicability of our approach on a biological example.

Conclusion
Results based on simulation and data analysis show that domain based pathway enrichment analysis is a very sensitive method to test for enrichment of pathways in sparsely annotated lists of genes. An R based software package domainsignatures, to routinely perform this analysis on the results of high-throughput screening, is available via Bioconductor.
MacroH2A1 knockdown effects on the Peg3 imprinted domain
Authors: Choo Jung Ha , Kim Jeong Do , Kim Joomyeong 
Published: January 2008

Abstract

Background
MacroH2A1 is a histone variant that is closely associated with the repressed regions of chromosomes. A recent study revealed that this histone variant is highly enriched in the inactive alleles of Imprinting Control Regions (ICRs).

Results
The current study investigates the potential roles of macroH2A1 in genomic imprinting by lowering the cellular levels of the macroH2A1 protein. RNAi-based macroH2A1 knockdown experiments in Neuro2A cells changed the expression levels of a subset of genes, including Peg3 and Usp29 of the Peg3 domain. The expression of these genes was down-regulated, rather than up-regulated, in response to reduced protein levels of the potential repressor macroH2A1. This down-regulation was not accompanied with changes in the DNA methylation status of the Peg3 domain.

Conclusion
MacroH2A1 may not function as a transcriptional repressor for this domain, but that macroH2A1 may participate in the heterochromatin formation with functions yet to be discovered.
Single nucleotide polymorphisms (SNPs) are highly conserved in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques
Authors: Street Summer L , Kyes Randall C , Grant Richard , Ferguson Betsy 
Published: January 2008

Abstract

Background

Macaca fascicularis (cynomolgus or longtail macaques) is the most commonly used non-human primate in biomedical research. Little is known about the genomic variation in cynomolgus macaques or how the sequence variants compare to those of the well-studied related species, Macaca mulatta (rhesus macaque). Previously we identified single nucleotide polymorphisms (SNPs) in portions of 94 rhesus macaque genes and reported that Indian and Chinese rhesus had largely different SNPs. Here we identify SNPs from some of the same genomic regions of cynomolgus macaques (from Indochina, Indonesia, Mauritius and the Philippines) and compare them to the SNPs found in rhesus.

Results
We sequenced a portion of 10 genes in 20 cynomolgus macaques. We identified 69 SNPs in these regions, compared with 71 SNPs found in the same genomic regions of 20 Indian and Chinese rhesus macaques. Thirty six (52%) of the M. fascicularis SNPs were overlapping in both species. The majority (70%) of the SNPs found in both Chinese and Indian rhesus macaque populations were also present in M. fascicularis. Of the SNPs previously found in a single rhesus population, 38% (Indian) and 44% (Chinese) were also identified in cynomolgus macaques. In an alternative approach, we genotyped 100 cynomolgus DNAs using a rhesus macaque SNP array representing 53 genes and found that 51% (29/57) of the rhesus SNPs were present in M. fascicularis. Comparisons of SNP profiles from cynomolgus macaques imported from breeding centers in China (where M. fascicularis are not native) showed they were similar to those from Indochina.

Conclusion
This study demonstrates a surprisingly high conservation of SNPs between M. fascicularis and M. mulatta, suggesting that the relationship of these two species is closer than that suggested by morphological and mitochondrial DNA analysis alone. These findings indicate that SNP discovery efforts in either species will generate useful resources for both macaque species. Identification of SNPs that are unique to regional populations of cynomolgus macaques indicates that location-specific SNPs could be used to distinguish monkeys of uncertain origin. As an example, cynomolgus macaques obtained from 2 different breeding centers in China were shown to have Indochinese ancestry.
Humoral response to HspX and GlcB to previous and recent infection by Mycobacterium tuberculosis
Authors: Rabahi Marcelo Fouad , Junqueira-Kipnis Ana Paula , dos Reis Michelle Cristina Guerreiro , Oelemann Walter , Conde Marcus Barreto 
Published: January 2008

Abstract

Background
Tuberculosis (TB) remains a major world health problem. Around 2 billions of people are infected by Mycobacterium tuberculosis, the causal agent of this disease. This fact accounts for a third of the total world population and it is expected that 9 million people will become infected each year. Only approximately 10% of the infected people will develop disease. However, health care workers (HCW) are continually exposed to the bacilli at endemic sites presenting increased chance of becoming sick. The objective of this work was to identify LTBI (latent tuberculosis infection) among all asymptomatic HCW of a Brazilian Central Hospital, in a three year follow up, and evaluate the humoral response among HCW with previous and recent LTBI to recombinant HspX and GlcB from M. tuberculosis.

Methods
Four hundred and thirty seven HCW were screened and classified into three different groups according to tuberculin skin test (TST) status: uninfected, previous LTBI and recent LTBI. ELISA test were performed to determine the humoral immune response to HspX and GlcB.

Results
The levels of IgG and IgM against the HspX and GlcB antigens were the same among HCW with recent and previous LTBI, as well as among non infected HCW. However, the IgM levels to HspX was significantly higher among HCW with recent LTBI (OD = 1.52 ± 0.40) than among the uninfected (OD = 1.09 ± 0.50) or subjects with previous LTBI (OD = 0.96 ± 0.51) (p < 0.001).

Conclusion
IgG and IgM humoral responses to GlcB antigens were similar amongst all studied groups; nevertheless IgM levels against HspX were higher among the recent LTBI/HCW.
A novel RUNX2 missense mutation predicted to disrupt DNA binding causes cleidocranial dysplasia in a large Chinese family with hyperplastic nails
Authors: Tang Shaohua , Xu Qiyu , Xu Xueqin , Du Jicheng , Yang Xuemei , Jiang Yusheng , Wang Xiaoqin , Speck Nancy , Huang Taosheng 
Published: January 2008

Abstract

Background
Cleidocranial dysplasia (CCD) is a dominantly inherited disease characterized by hypoplastic or absent clavicles, large fontanels, dental dysplasia, and delayed skeletal development. The purpose of this study is to investigate the genetic basis of Chinese family with CCD.

Methods
Here, a large Chinese family with CCD and hyperplastic nails was recruited. The clinical features displayed a significant intrafamilial variation. We sequenced the coding region of the RUNX2 gene for the mutation and phenotype analysis.

Results
The family carries a c.T407C (p.L136P) mutation in the DNA- and CBFβ-binding Runt domain of RUNX2. Based on the crystal structure, we predict this novel missense mutation is likely to disrupt DNA binding by RUNX2, and at least locally affect the Runt domain structure.

Conclusion
A novel missense mutation was identified in a large Chinese family with CCD with hyperplastic nails. This report further extends the mutation spectrum and clinical features of CCD. The identification of this mutation will facilitate prenatal diagnosis and preimplantation genetic diagnosis.
Antitumor activity and mechanisms of action of total glycosides from aerial part of Cimicifuga dahurica targeted against hepatoma
Authors: Tian Ze , Si Jianyong , Chang Qi , Zhou Liang , Chen Shilin , Xiao Peigen , Wu Erxi 
Published: January 2008

Abstract

Background
Medicinal plant is a main source of cancer drug development. Some of the cycloartane triterpenoids isolated from the aerial part of Cimicifuga dahurica showed cytotoxicity in several cancer cell lines. It is of great interest to examine the antiproliferative activity and mechanisms of total triterpenoid glycosides of C. dahurica and therefore might eventually be useful in the prevention or treatment of Hepatoma.

Methods
The total glycosides from the aerial part (TGA) was extracted and its cytotoxicity was evaluated in HepG2 cells and primary cultured normal mouse hepatocytes by an MTT assay. Morphology observation, Annexin V-FITC/PI staining, cell cycle analysis and western blot were used to further elucidate the cytotoxic mechanism of TGA. Implanted mouse H22 hepatoma model was used to demonstrate the tumor growth inhibitory activity of TGA in vivo.

Results
The IC50 values of TGA in HepG2 and primary cultured normal mouse hepatocytes were 21 and 105 μg/ml, respectively. TGA induced G0/G1 cell cycle arrest at lower concentration (25 μg/ml), and triggered G2/M arrest and apoptosis at higher concentrations (50 and 100 μg/ml respectively). An increase in the ratio of Bax/Bcl-2 was implicated in TGA-induced apoptosis. In addition, TGA inhibited the growth of the implanted mouse H22 tumor in a dose-dependent manner.

Conclusion
TGA may potentially find use as a new therapy for the treatment of hepatoma.
Lumbar position sense and the risk of low back injuries in college athletes: a prospective cohort study
Authors: Silfies Sheri P , Cholewicki Jacek , Reeves N Peter , Greene Hunter S 
Published: January 2008

Abstract

Background
Impaired proprioception in the lumbar spine has often been reported in people with low back pain. However, no prospective studies exist to assert the cause and effect of this association. We hypothesized that athletes with a history of low back injury (LBI) would demonstrate poorer lumbar position sense (PS) than athletes without a history of LBI, and that this deficit would be a risk factor for future LBI.

Methods
This was a prospective cohort study with 2–3 year follow-up. Lumbar spine PS in the transverse plane was evaluated in 292 athletes using three tests: 1) passive and 2) active trunk repositioning, and 3) motion perception threshold. Mean absolute (accuracy) and variable (precision) errors were computed.

Results
There were no significant differences in the repositioning errors or motion perception threshold between athletes with and without a history of LBI or between those who did and did not get injured during the follow-up. Active trunk repositioning resulted in smaller errors than passive repositioning (1.6°± 0.8°) versus 2.1°± 1.0°) and 1.7°± 0.8°) versus 2.3°± 1.1°) for the absolute and relative errors, respectively).

Conclusion
Poor trunk PS in transverse plane is not associated with LBI in athletes, nor does it appear that poor trunk PS predisposes athletes to LBI.
Effectiveness of low-dose doxycycline (LDD) on clinical symptoms of Sjögren's Syndrome: a randomized, double-blind, placebo controlled cross-over study
Authors: Seitsalo Hubertus , Niemelä Raija K , Marinescu-Gava Magdalena , Vuotila Tuija , Tjäderhane Leo , Salo Tuula 
Published: January 2008

Abstract

Background
Matrix metalloproteinases (MMPs) are proteolytic enzymes that may contribute to tissue destruction in Sjögren's syndrome (SS). Low-dose doxycycline (LDD) inhibits MMPs. We evaluated the efficacy of LDD for the subjective symptoms in primary SS patients.
This was a randomized, double blind, placebo controlled cross-over study. 22 patients were randomly assigned to receive either 20 mg LDD or matching placebo twice a day for 10 weeks. The first medication period was followed by 10-week washout period, after which the patient received either LDD or placebo, depending on the first drug received, followed by the second washout period. Stimulated saliva flow rates and pH were measured before and after one and ten weeks of each medication and after washout periods. VAS scale was used to assess the effect of LDD and placebo on following six subjective symptoms: xerostomia; xerophtalmia; difficulty of swallowing; myalgia; arthralgia; and fatigue. The effect was evaluated for each medication and washout period separately.

Results
Overall, the effects of medications on subjective symptoms were minor. Wilcoxon test demonstrated increased fatigue with LDD during medication (p < 0.05). The differences may, however, reflect normal fluctuation of symptoms in SS patients.

Conclusion
LDD may not be useful in reducing the primary SS symptoms.
Biotin deficiency up-regulates TNF-α production in murine macrophages
Authors: Kuroishi Toshinobu , Endo Yasuo , Muramoto Koji , Sugawara Shunji 
Published: January 2008

AbstractBiotin, a water-soluble vitamin of the B complex, functions as a cofactor of carboxylases that catalyze an indispensable cellular metabolism. Although significant decreases in serum biotin levels have been reported in patients with chronic inflammatory diseases, the biological roles of biotin in inflammatory responses are unclear. In this study, we investigated the effects of biotin deficiency on TNF-α production. Mice were fed a basal diet or a biotin-deficient diet for 8 weeks. Serum biotin levels were significantly lower in biotin-deficient mice than biotin-sufficient mice. After i.v. administration of LPS, serum TNF-α levels were significantly higher in biotin-deficient mice than biotin-sufficient mice. A murine macrophage-like cell line, J774.1, was cultured in a biotin-sufficient or -deficient medium for 4 weeks. Cell proliferation and biotinylation of intracellular proteins were decreased significantly in biotin-deficient cells compared with biotin-sufficient cells. Significantly higher production and mRNA expression of TNF-α were detected in biotin-deficient J774.1 cells than biotin-sufficient cells in response to LPS and even without LPS stimulation. Intracellular TNF-α expression was inhibited by actinomycin D, indicating that biotin deficiency up-regulates TNF-α production at the transcriptional level. However, the expression levels of TNF receptors, CD14, and TLR4/myeloid differentiation protein 2 complex were similar between biotin-sufficient and -deficient cells. No differences were detected in the activities of the NF-κB family or AP-1. The TNF-α induction by biotin deficiency was down-regulated by biotin supplementation in vitro and in vivo. These results indicate that biotin deficiency may up-regulate TNF-α production or that biotin excess down-regulates TNF-α production, suggesting that biotin status may influence inflammatory diseases.
Chaperone-rich tumor cell lysate-mediated activation of antigen-presenting cells resists regulatory T cell suppression
Authors: Larmonier Nicolas , Cantrell Jessica , LaCasse Collin , Li Gang , Janikashvili Nona , Situ Elaine , Sepassi Marjan , Andreansky Samita , Katsanis Emmanuel 
Published: January 2008

AbstractCD4+CD25+ regulatory T lymphocytes (Tregs) critically contribute to the mechanisms of cancer-induced tolerance. These cells suppress anti-tumoral CD8+ and CD4+ T lymphocytes and can also restrain the function of APCs. We have previously documented the immunostimulatory effects of a chaperone-rich cell lysate (CRCL) anti-cancer vaccine. Tumor-derived CRCL induces tumor immunity in vivo, partly by promoting dendritic cell (DC) and macrophage activation. In the current study, we evaluated the effects of CD4+CD25+forkhead box P3+ Tregs isolated from mice bearing 12B1 bcr-abl+ leukemia on DC and macrophages that had been activated by 12B1-derived CRCL. CRCL-activated DC and macrophages resisted Treg suppression, as the production of proinflammatory cytokines, the activation of transcription factor NF-κB, and their immunostimulatory potential was unaffected by Tregs. Our results thus highlight CRCL as a powerful adjuvant endowed with the capacity to overcome tumor-induced Treg-inhibitory effects on APCs.
Gelatinases mediate neutrophil recruitment in vivo: evidence for stimulus specificity and a critical role in collagen IV remodeling
Authors: Reichel Christoph A , Rehberg Markus , Bihari Peter , Moser Christian M , Linder Stefan , Khandoga Andrej , Krombach Fritz 
Published: January 2008

AbstractIn the present study, the role of gelatinases [matrix metalloproteinase-2 and -9 (MMP-2 and -9)] for leukocyte rolling, adherence, and transmigration was analyzed in the mouse cremaster muscle under different inflammatory conditions including ischemia-reperfusion (I/R) and stimulation with MIP-1α or platelet-activating factor (PAF). Using zymography, we detected a significant elevation of MMP-9 activity in response to the stimuli applied, and MMP-2 expression was not altered. However, treatment with a specific MMP-2/-9 inhibitor significantly abrogated elevated MMP-9 activity. As observed by intravital microscopy, all inflammatory conditions induced a significant increase in numbers of adherent and transmigrated leukocytes (&gt;80% Ly-6G+ neutrophils). Blockade of gelatinases significantly diminished I/R- and MIP-1α-induced leukocyte adherence and subsequent transmigration, and upon stimulation with PAF, gelatinase inhibition had no effect on leukocyte adherence but selectively reduced leukocyte transmigration. Concomitantly, we observed an increase in microvascular permeability after I/R and upon stimulation with MIP-1α or PAF, which was almost completely abolished in the inhibitor-treated groups. Using immunofluorescence staining and confocal microscopy, discontinuous expression of collagen IV, a major substrate of gelatinases within the perivascular basement membrane (BM), was detected in postcapillary venules. Analysis of intensity profiles demonstrated regions of low fluorescence intensity, whose size was enlarged significantly after I/R and upon stimulation with MIP-1α or PAF as compared with unstimulated controls. However, this enlargement was abolished significantly after inhibition of gelatinases, respectively. In conclusion, these data demonstrate that gelatinases strictly regulate microvascular permeability and BM remodeling during the early inflammatory response, whereas concomitant leukocyte recruitment is mediated by these proteases in a stimulus-specific manner.