bluuebunny/crossref_metadata_2025_split huggingface dataset:
Putting chromatin immunoprecipitation into context
Authors: Zecchini Vincent , Mills Ian G. 
Published: February 2009

AbstractChromatin immunoprecipitation (ChIP), when paired with sequencing or arrays, has become a method of choice for the unbiased identification of genomic‐binding sites for transcription factors and epigenetic marks in various model systems. The data generated is often then interpreted by groups seeking to link these binding sites to the expression of adjacent or distal genes, and more broadly to the evolution of species, cell fate/differentiation or even cancer development. Against this backdrop is an ongoing debate over the relative importance DNA sequence versus chromatin structure and modification in the regulation of gene expression (Anon. 2008a Nature 454: 795; Anon. 2008b Nature 454: 711–715; Henikoff et al. 2008 Science 322: 853; Madhani et al. 2008 Science 322: 43–44). Rationally there is a synergy between the two and the goal of a biologist is to characterise both comprehensively enough to explain a cellular phenotype or a developmental process. If this is truly our goal then the critical factor in good science is an awareness of the constraints and potential of the biological models used. The reality however is often that this discussion is polarised by funding imperatives and the need to align to a transcription factor or epigenetic camp. This article will discuss the extrapolations involved in using ChIP data to draw conclusions about these themes and the discoveries that have resulted. J. Cell. Biochem. 107: 19–29, 2009. © 2009 Wiley‐Liss, Inc.
Size exclusion chromatography coupled to electrospray ionization mass spectrometry for analysis and quantitative characterization of arsenic interactions with peptides and proteins
Authors: Schmidt Anne‐Christine , Fahlbusch Benjamin , Otto Matthias 
Published: February 2009

AbstractArsenic‐binding proteins are of toxicological importance since enzymatic activities can be blocked by arsenic interactions. In the present work, a novel methodology based on size exclusion chromatography coupled to electrospray ionization mass spectrometry (SEC‐ESI‐MS) was developed with special emphasis to preserve the intact proteins and their arsenic bindings. The eluent composition of 25 mMTris/HCl, pH 7.5, with the addition of 100‐mM NaCl optimized for SEC with UV detection provided the highest SEC separation efficiency, but was not compatible with the ESI‐MS because of the non‐volatility of the buffer substance and of the salt additive. In order to find the best compromise between chromatographic separation and ionization of the arsenic‐binding proteins, buffer type and concentration, pH value, portion of organic solvent in the SEC eluent as well as the flow rate were varied. In the optimized procedure five different arsenic‐binding peptides and proteins (glutathione, oxytocin, aprotinin, α‐lactalbumin, thioredoxin) covering a molar mass range of 0.3–14 kDa could be analyzed using 75% 10‐mM ammonium formate, pH 5.0/25% acetonitrile (v : v) as eluent and a turbo ion spray source operated at 300 °C and 5.5 kV. A complete differentiation of all peptides and proteins involved in the arsenic‐binding studies as well as of their arsenic‐bound forms has become feasible by means of the extracted ion chromatograms (XIC) of the mass spectrometric detection. The new method offered the possibility to estimate equilibrium constants for the reaction of phenylarsine oxide with different thiol‐containing biomolecules by means of the XIC peak areas of reactants and products. Limits of detection in the range of 2–10 µM were obtained by SEC‐ESI‐MS for the individual proteins. Copyright © 2009 John Wiley & Sons, Ltd.
A reanalysis climatology of cool‐season tornado environments over southern Australia
Authors: Kounkou R. , Mills G. , Timbal B. 
Published: February 2009

AbstractIt is of great interest to assess the likely changes in occurrence of extreme weather events such as those associated with severe convective storms in future (changed) climates. However, while events such as tornadoes cannot be resolved by climate models, or even the higher‐resolution operational numerical weather prediction (NWP) models, it has been shown that some of the environments in which they occur can be predicted. In Australia, the so‐called cool‐season tornado (CST) environment is defined as the area where the forecast 700 hPa Surface Lifted Index and the surface to 1‐km vertical wind shear exceed specified thresholds. CST threat area forecasts are issued with each operational mesoscale NWP forecast by the Australian Bureau of Meteorology. In this paper, the application of this diagnostic indicator of CST occurrence to typical climate model resolutions is tested using the NCEP/NCAR and ERA‐40 reanalysis data sets. The techniques used to apply the diagnostic to these data sets are described, together with the calibration necessary to specify separate thresholds for each analysis set. Using these thresholds 40‐year climatologies of CST risk over Australia are constructed for each reanalysis data set. It is shown that the two data sets indicate very similar spatial distributions of risk. Trends in frequency of occurrence are problematic, with significant discontinuities in frequency after the introduction of satellite sounding data in 1979, with an increased frequency, but little trend in numbers, of CST environments since that time. Relating inter‐annual variations in the frequency of CST environments to large‐scale circulation indices show little relation with regional sea surface temperature anomalies or with the Southern Oscillation Index, but showed significant negative correlation with the Southern Annular Mode Index. Copyright © 2009 Royal Meteorological Society
Use of the standardized precipitation index (SPI) and a modified SPI for shaping the drought probabilities over Turkey
Authors: Türkeş Murat , Tatlı Hasan 
Published: February 2009

AbstractThis paper suggests a new methodology for the Standardized Precipitation Index (SPI), for studying different aspects of drought events in Turkey, including intensity, frequency and identifying the spatial and temporal patterns. The classical SPI is locally defined; for instance, for monthly scale or running means, a drought event would begin when the precipitation amount is below its long‐term average. However, the proposed method considers the local‐time means of the precipitation series by fitting an upper and a lower envelope to precipitation data to obtain the SPI values, thus it explicitly assesses a dry (or wet) spell of weather.When we consider the climatological/meteorological features of precipitation and the physical geographical controls of the climate over Turkey, it is found that the proposed method is more capable of estimating the probability of dry or wet conditions for a station's monthly precipitation totals (or running means) than if the SPI values are obtained using the classical method. Comparisons of the probability values calculated for the long‐term series and various time scales have revealed that the proposed method successfully estimates and/or well represents the various precipitation anomalies, particularly the wet and dry extremes. For instance, the probabilities of monthly values obtained by the proposed SPI method being above normal, below normal, near normal (i.e. normal) and extremely dry are more realistic and reasonable than those found by the classical SPI method. In conclusion, one can apply the proposed SPI methodology for determining and monitoring droughts of other semi‐arid, dry sub‐humid and semi‐humid climate regions, where the precipitation series show high seasonality and year‐to‐year variability, such as in the Mediterranean macro‐climate region. Copyright © 2009 Royal Meteorological Society
Climatic forcing of glacier thinning on the mountains of equatorial East Africa
Authors: Hastenrath Stefan 
Published: February 2009

AbstractEquatorial glaciers are particularly climate sensitive components of the environment and their area shrinkage is spectacular, but the quantitative appraisal of climatic forcing requires information on net balance and changing ice thickness. Unique in the tropical belt, observations of mass budget and surface topography have been gathered by decades‐long monitoring on Mount Kenya, particularly its largest, the Lewis Glacier. More limited information on ice thickness change is available for the summit of Kilimanjaro. Sensitivity analyses with constant precipitation, net allwave radiation and relative humidity serve to explore the sensible and latent heat transfer processes; humidity change riding on that of temperature providing the more substantial energy contribution to ablation. For Lewis Glacier it is found that with air some 0.7 °C cooler the mass budget could reach equilibrium. Observations on the secular evolution of air temperature and humidity in the areas of Mount Kenya and Rwenzori show compatible magnitudes, although contribution by radiative forcing cannot be excluded. For the summit of Kilimanjaro, above the mean freezing level, where ablation is limited to sublimation, turbulent heat transfer processes associated with temperature differences cannot account for the imbalance of the mass budget, and solar radiation forcing continues to be important for both the ice thinning and the lateral retreat of ice cliffs. Copyright © 2009 Royal Meteorological Society
Damage and degenerative changes in menisci‐covered and exposed tibial osteochondral regions after simulated landing impact compression—a porcine study
Authors: Yeow Chen Hua , Lau Swee Ting , Lee Peter Vee Sin , Goh James Cho Hong 
Published: February 2009

AbstractThe capacity of menisci‐covered and exposed tibial osteochondral regions in resisting impact‐induced damage and degeneration is not fully understood. This study sought to evaluate damage and degenerative changes in these regions upon a single simulated landing impact. We hypothesized that the menisci‐covered regions are more susceptible to damage and degeneration than their exposed counterparts. Menisci‐covered and exposed tibial osteochondral explants were extracted from fresh porcine hind legs and placed in culture up to 14 days. Impact compression, based on a single 10‐Hz haversine, was performed at Day 1. Control (non‐impact) and impacted explants were randomly selected for cell viability assessment, glycoaminoglycan and collagen content assays, histology, immunohistochemistry, and micro‐computed tomography. When subjected to 2‐mm displacement compression, exposed explants achieved a significantly higher peak impact stress (p < 0.05) than menisci‐covered explants. No significant difference in cell viability, glycoaminoglycan and collagen content, and Mankin scores (p > 0.05) was observed between both explant groups. Both groups were observed with reduced proteoglycan and type II collagen staining at Day 14; the exposed group was noted with increased cartilage volume at Days 7–14. The inferior resistance of menisci‐covered regions, against impact‐induced damage and degeneration, is a potential factor that may contribute to the meniscectomy model of osteoarthritis. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 1100–1108, 2009
Clay dispersion and its relation to surface charge in a paddy soil of the Red River Delta, Vietnam
Authors: Nguyen Minh N. , Dultz Stefan , Kasbohm Jörn , Le Duc 
Published: February 2009

AbstractDispersion is an important issue for clay leaching in soils. In paddy soils of the Red River Delta (RRD), flooding with fresh water and relatively high leaching rates can accelerate dispersion and the translocation of clay. For the clay fraction of the puddled horizon of a typical paddy soil of the RRD, the effect of various cations and anions as well as humic acid (HA) at different pH values on the surface charge (SC) were quantified and the dispersion properties were determined in test tubes and described by the C50 value.In the <2 µm fraction, dominated by illite, the proportion of 2:1 vs. 1:1 clay minerals is 5:1. The organic‐C content of the clay fraction is 2.2%. Surface charge was found to be highly pH‐dependent. At pH 8 values of –32 and at pH 1 of –8 mmolc kg–1 were obtained. Complete dispersion was observed at pH > 4, where SC is > –18 mmolc kg–1. The flocculation efficiency of Ca strongly depends on the pH. At pH 4, the C50 value is 0.33, 0.66 at pH 5, and 0.90 mmol L–1 at pH 6. At pH 6, close to realistic conditions of paddy soils, the effect of divalent cations on the SC and flocculation decreases in the order: Pb > Cu > Cd > FeII > Zn > Ca > MnII > Mg; FeII was found to have a slightly stronger effect on flocculation than Ca. An increase in concentrations of Ca, MnII, and Mg from 0 to 1 mmol L–1 resulted in a change in SC from –25 to approx. –15 mmolc kg–1. In comparison, the divalent heavy‐metal cations Pb, Cu, Cd, and Zn were found to neutralize the SC more effectively. At a Pb concentration of 1 mmol L–1, the SC is –2 mmolc kg–1. From pH 3 to 5, the dispersion of the clay fraction is facilitated rather by SO$ _4^{2-} $ than by Cl–, which can be explained by the higher affinity of SO$ _4^{2-} $ to the positively charged sites. With an increase of the amount of HA added, the SC continuously shifts to more negative values, and higher concentrations of cations are needed for flocculation. At pH 3, where flocculation is usually observed, the presence of HA at a concentration of 40 mg L–1 resulted in a dispersion of the clay fraction. While high anion concentrations and the presence of HA counteract flocculation by making the SC more negative, FeII and Ca (C50 at pH 6 = 0.8 and 0.9 mmol L–1, respectively) are the main factors for the flocculation of the clay fraction.For FeII and Ca, the most common cations in soil solution, the C50 values were found to be relatively close together at pH 4, 5, and 6, respectively. Depending on the specific mineralogical composition of the clay fraction, SC is a suitable measure for the determination of dispersion properties and for the development of methods to keep clay particles in the soil in the flocculated state.
The influence of a Gene expression profile on breast cancer decisions
Authors: Henry Leonard R. , Stojadinovic Alexander , Swain Sandra M. , Prindiville Sheila , Cordes Rose , Soballe Peter W. 
Published: February 2009

AbstractPurposeThe Oncotype Dx® Recurrence Score (RS), is often employed in patients with estrogen receptor‐positive, node negative (ER+LN−) breast cancer. We investigated the impact of the RS on actual chemotherapy administration and the effect of the assay on a panel of breast oncology experts.Patients and MethodsThe prospective adjuvant chemotherapy recommendations (prior to RS) and actual adjuvant therapy (after RS) for consecutive patients with ER+LN− breast cancer were recorded. After 6 months and with the same information, a panel of five experts made adjuvant therapy recommendations with and without RS and rated the strength of their recommendations. Rates of panel consensus, recommendation changes, and changes in recommendation strength were compared.ResultsThere were 29 patients (28 women). RS results altered the plan for chemotherapy in 9 patients (31%); 7 of 13 patients (54%) initially recommended for chemotherapy did not receive it, and 2 of 16 (13%) received chemotherapy following initial recommendations against it. RS results changed the panel's chemotherapy recommendation in 7 patients (24%): 5 of 12 (42%) recommendations for changed to against, and 2 of 17 (12%) recommendations against changed to for chemotherapy. RS increased consensus by the panel 10%, but did not increase the reported strength in chemotherapy recommendations.ConclusionsRS results were associated with real‐world decision changes in 31% of patients and 24% of panel recommendations and increased panel consensus by 10%. However RS did not increase the strength of panelist's recommendations. J. Surg. Oncol. 2009;99:319–323. Published 2009 Wiley Periodicals, Inc.
Circulating form of human vascular adhesion protein‐1 (VAP‐1): Decreased serum levels in progression of colorectal cancer and predictive marker of lymphatic and hepatic metastasis
Authors: Toiyama Yuji , Miki Chikao , Inoue Yasuhiro , Kawamoto Aya , Kusunoki Masato 
Published: February 2009

AbstractBackground and ObjectivesVascular adhesion protein‐1 (VAP‐1) is an endothelial cell molecule that controls leukocyte tissue infiltration. Elevated serum soluble VAP‐1 (sVAP‐1) has been described in certain diseases with an inflammatory component. However, sVAP‐1 expression or function has not been studied in colorectal cancer. The present study determined the relationships between preoperative serum sVAP‐1 and clinicopathological features and prognosis in colorectal cancer.MethodsOne hundred patients with histologically proven colorectal cancer and 33 normal volunteers were included. Preoperative serum was collected, and sVAP‐1 levels were assayed by enzyme‐linked immunosorbent assay.ResultsMean sVAP‐1 level in patients was significantly higher than in controls, and decreased with disease progression. Mean sVAP‐1 level was significantly correlated with venous invasion, lymph node metastasis, distant metastasis including hepatic metastasis, and advanced TNM classification. Furthermore, sVAP‐1 was an independent marker for predicting lymph node or hepatic metastasis. Prognosis of patients with a lower sVAP‐1 level was significantly worse than those with elevated sVAP‐1.ConclusionsPreoperative low sVAP‐1 level is associated with poor prognosis in colorectal cancer. Measuring serum sVAP‐1 may provide valuable information in predicting patients with lymph node or hepatic metastasis. J. Surg. Oncol. 2009;99:368–372. © 2009 Wiley‐Liss, Inc.
Microsatellite DNA instability in nasal polyposis
Authors: Karatzanis Alexander D. , Tzortzaki Eleni , Samara Katerina D. , Neofytou Eirini , Zenk Johannes , Iro Heinrich , Siafakas Nikolaos , Velegrakis George A. 
Published: February 2009

AbstractObjective:Genetic alterations, such as microsatellite instability (MSI) and loss of heterozygosity (LOH), have been detected in various inflammatory diseases, providing evidence that acquired somatic mutations might play a role in the aetiopathogenesis of chronic inflammatory conditions. The aim of this study is to assess the presence of MSI and/or LOH in nasal cytology of patients with nasal polyps.Study Design:Prospective case‐controlled basic science experiment utilizing human blood and human nasal brush samples.Methods:Nasal brush samples and peripheral blood from 12 patients with nasal polyps were analyzed. DNA was extracted and analyzed for MSI and LOH using the following microsatellite markers: D2S2113, D6S344, D6S1002, D11S1253, D11S480, USAT24G1, and D13S273, harboring potential susceptibility genes for nasal polyposis. Microsatellite DNA analysis was also performed in 7 control subjects.Results:MSI or LOH were revealed in 3 specimens of the nasal polyps group. Among these there were 2 cases of LOH, one for marker D11S1273 and one for D13S273, and one case of MSI in marker USAT24G1. Each one of these alterations was detected in a different patient. None of the control subjects exhibited any genetic alterations in the 7 markers tested.Conclusions:This is the first time that microsatellite genetic alterations are reported in nasal disease. The presence of such alterations suggests that acquired genomic somatic mutations might play a role in the pathogenesis of nasal polyps. Laryngoscope, 2009
Identification of distant metastases with PET‐CT in patients with suspected recurrent head and neck cancer
Authors: Gourin Christine G. , Watts Tammara , Williams Hadyn T. , Patel Vijay S. , Bilodeau Paul A. , Coleman Teresa A. 
Published: February 2009

AbstractObjectives:To investigate the utility of positron‐emission tomography/computed tomography (PET‐CT) in identifying distant metastatic disease in patients with suspected recurrent head and neck squamous cell cancer (HNSCC).Study Design:Retrospective analysis.Methods:Retrospective analysis of 64 consecutive patients with suspected recurrent HNSCC following definitive treatment who underwent PET‐CT imaging were eligible for inclusion. Patients with previous known distant metastatic disease were excluded.Results:The majority of patients (81%) had TNM stage III or IV disease. PET‐CT was suspicious for pulmonary malignancy in 14 patients (22%) and indeterminate in 6 patients (9%). Pulmonary metastases or a new lung primary were present in 10 patients (16%): 7 of 14 patients with positive PET‐CT scans (50%) and 3 of 50 patients with negative or indeterminate PET‐CT scans (6%). Including nonpulmonary sites, the overall incidence of distant disease was 23% (15/64) with 20% (13/64) unsuspected prior to PET‐CT. The sensitivity and specificity of PET‐CT in predicting distant malignancy was 86% and 84%, respectively, with a positive predictive value of 60% and a negative predictive value of 95%. There was a significant correlation between standardized uptake value (SUV) on PET‐CT and positive histology, with a mean SUV of 8.5 (range, 4.7–16.2) in patients with distant metastases compared with a mean SUV of 2.9 (range, 1.9–4.2) in patients with benign pathology (r = 0.87, P < .0001).Conclusions:A significant number of patients with recurrent HNSCC have distant metastases at the time of recurrence. These data suggest that PET‐CT improves detection of metastatic disease in the high‐risk patient and should be performed as part of the routine evaluation of patients with suspected recurrence prior to salvage surgery. Laryngoscope, 2009
Voice handicap evaluation after supracricoid partial laryngectomy
Authors: Makeieff Marc , de la Breteque Amy , Guerrier B. , Giovanni A. 
Published: February 2009

AbstractObjectives:To gather information on the vocal and professional impact of supracricoid partial laryngectomy (SCPL).Study Design:Collection of quality of life data more than 12 months postsurgery, including expert‐rated patient voice assessment (GRBAS [grade, roughness, breathiness, asthenia, strain] scale), self voice assessment, Voice Handicap Index (VHI), and socioprofessional data.Patients:Sixty‐four patients were evaluated after SCPL. The surgical procedure had been conducted for initial stage T1b or T2 glottic carcinoma. All patients had no recurrence, were decanulated, and did not have any swallowing impairment. Thirty‐three patients were less than 60 years old and were professionally active at the time of surgery. The mean age was 48.5 years old (42–59 years old). Fifteen patients were working in the communications sector, so use of their voice was obligatory. Professional impact and VHI measurements were evaluated.Results:For patients with professional activities before surgery, 15/33 (45%) continued their activities, whereas 55% had to withdraw from or modify these activities. For patients with communications activities, 6/15 (40%) continued their activities, 4 (26.6%) adapted, and 5 (33.3%) withdrew from their professional activities. The mean VHI value was 51.2. The mean VHI values according to the dysphonic grade (1, 2, and 3) were 36.3, 50.7, and 52.9, respectively. The mean VHI values were 45.6, 58.6, and 53.2, respectively, for patients who pursued their professional activities, withdrew from or adapted their activities, and had no professional activities. Correlations were obtained between VHI and the dysphonic grade (P = .043), cessation of professional activities (P = .034), and the time elapsed since surgery (P = .046). VHI emotional and physical subscale scores were significantly higher for patients who had withdrawn from their professional activities or adapted them.Conclusions:Supracricoid partial laryngectomy can have a marked social and professional impact. Many patients have to withdraw from professional activities in which vocal involvement is essential. The potential postsurgical social voice impact should be taken into consideration before proposing this surgery, and it is essential to estimate the possible impacts of the vocal handicap according to the patient's professional or other activities. Laryngoscope, 2009