bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening forIL28Bgene variants identifies predictors of hepatitis C therapy success
Authors: Doehring Alexandra , Hofmann Wolf Peter , Schlecker Christina , Zeuzem Stefan , Susser Simone , Geisslinger Gerd , Sarrazin Christoph , Lötsch Jörn
Published: November 2010

Background

Recent research has shown that genetic variation in the IL28B gene predicts both chronicity of HCV infection and sustained virological response (SVR) to antiviral standard therapy. Because HCV affects 170 million people worldwide and is a leading cause of cirrhosis and hepatocellular carcinoma, screening for prognostic factors in routine clinical practice requires rapid and reliable assays.

Methods

The frequencies of gene polymorphisms IL28B rs8099917, rs12979860 and rs12980275 were investigated in two cohorts of 89 and 187 unrelated HCV-infected Caucasian patients and 195 non-infected participants. This was carried out by means of newly developed sensitive Pyrosequencing™ screening assays.

Results

The minor alleles were more frequent in patients ( n=276) than in controls ( n=195), with odds ratios (recessive hereditary model) of 2.2–11.6, indicating a moderate to large genotype effect size. The positive predictive values of the minor alleles for chronicity of HCV infection were 68.3%, 64.8% and 65.8% for rs8099917, rs12979860 and rs12980275, respectively. The minor alleles were also more frequent in patients who had a non-SVR ( n=49) than in SVR patients ( n=40), with odds ratios of 1.1–3.5 showing a small to moderate genotype effect size. The positive predictive values for non-SVR were 56.9%, 79.2% and 74% for rs8099917, rs12979860 and rs12980275, respectively.

Conclusions

With the screening for IL28B polymorphisms rs12980275, rs8099917 and rs12979860, which are associated with HCV chronicity and with reduced SVR rates, an important prognostic factor of the therapy of chronic hepatitis C can be easily diagnosed.
Online Games for the Next Generation of Workers
Authors: Mysirlaki Sofia , Paraskeva Fotini
Published: November 2010

The â??Next Generation
Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach
Authors: Shameer Khader , Pugalenthi Ganesan , Kandaswamy Krishna Kumar , Suganthan Ponnuthurai N. , Archunan Govindaraju , Sowdhamini Ramanathan
Published: November 2010

3-dimensional domain swapping is a mechanism where two or more protein molecules form higher order oligomers by exchanging identical or similar subunits. Recently, this phenomenon has received much attention in the context of prions and neurodegenerative diseases, due to its role in the functional regulation, formation of higher oligomers, protein misfolding, aggregation etc. While 3-dimensional domain swap mechanism can be detected from three-dimensional structures, it remains a formidable challenge to derive common sequence or structural patterns from proteins involved in swapping. We have developed a SVM-based classifier to predict domain swapping events using a set of features derived from sequence and structural data. The SVM classifier was trained on features derived from 150 proteins reported to be involved in 3D domain swapping and 150 proteins not known to be involved in swapped conformation or related to proteins involved in swapping phenomenon. The testing was performed using 63 proteins from the positive dataset and 63 proteins from the negative dataset. We obtained 76.33% accuracy from training and 73.81% accuracy from testing. Due to high diversity in the sequence, structure and functions of proteins involved in domain swapping, availability of such an algorithm to predict swapping events from sequence and structure-derived features will be an initial step towards identification of more putative proteins that may be involved in swapping or proteins involved in deposition disease. Further, the top features emerging in our feature selection method may be analysed further to understand their roles in the mechanism of domain swapping.
The Use of Soluble Transferrin Receptor in the Detection of rHuEPO abuse in Sports
Authors: McGrowder Donovan , Brown Paul , Alexander-Lindo Ruby Lisa , Budall Shirley , Irving Rachael , Gordon Lorenzo
Published: November 2010

Erythropoietin (EPO) increases the number of circulating erythrocytes and muscle oxygenation. The recombinant forms of EPO have indiscriminately been used by athletes, mainly in endurance sports to increase their erythrocytes concentration, thus generating a better delivery of oxygen to the muscle tissue. The administration of recombinant human erythropoietin (rHuEPO) except for therapeutic use was prohibited by the International Olympic Committee (IOC) and its unauthorized use considered as doping. In the last few years, a number of studies using parameters indicative of accelerated erythropoiesis have investigated a number of indirect methods for the detection of rHuEPO abuse. No single indirect marker has been found that can satisfactorily demonstrated rHuEPO misuse. Soluble transferrin receptor (sTfR) is a new marker of iron status and erythropoietic activity. It has been included in multivariable blood testing models for the detection of performance enhancing EPO abuse in sports. Indirect markers of altered erythropoiesis give reliable evidence of current or discontinued rHuEPO usage. This review describes the physical, biological and pharmacokinetic properties of endogenous EPO and its recombinant form. It also discusses the available strategies for the detection of rHuEPO abuse in sports, involving the use of sTfR concentration directly or in mathematical multivariate models.
Morphological Changes and Immunohistochemical Expression of RAGE and its Ligands in the Sciatic Nerve of Hyperglycemic Pig (Sus Scrofa)
Authors: Juranek Judyta K. , Aleshin Alexey , Rattigan Eileen M. , Johnson Lynne , Qu Wu , Song Fei , Ananthakrishnan Radha , Quadri Nosirudeen , Yan Shi Du , Ramasamy Ravichandran , Schmidt Ann Marie , Geddis Matthew S.
Published: November 2010

The aim of our project was to study the effect of streptozotocin (STZ)–-induced hyperglycemia on sciatic nerve morphology, blood plasma markers and immunohistochemical expression of RAGE (the Receptor for Advanced Glycation End-products), and its ligands–-S100B and Carboxymethyl Lysine (CML)-advanced glycation endproduct (AGE) in the laboratory pig. Six months after STZ–-injections, blood plasma measurements, morphometric analysis of sciatic nerve fiber density, immunofluorescent distribution of potential molecular neuropathy contributors, ELISA measurement of plasma AGE level and HPLC analysis of sciatic nerve levels of one of the pre-AGE and the glycolysis intermediate products–-methylglyoxal (MG) were performed. The results of our study revealed that STZ–-injected animals displayed elevated levels of plasma glucose, gamma glutamyl transferase (GGT) and triglycerides. The sciatic nerve of STZ-injected pigs revealed significantly lower numbers of small-diameter myelinated fibers, higher immunoreactivity for RAGE and S100B and increased levels of MG as compared to control animals. Our results correspond to clinical findings in human patients with hyperglycemia/diabetes-evoked peripheral neuropathy and suggest that the domestic pig may be a suitable large animal model for the study of mechanisms underlying hyperglycemia-induced neurological complications in the peripheral nerve and may serve as a relevant model for the pre-clinical assessment of candidate drugs in neuropathy.
A Method to Detect Differential Gene Expression in Cross-Species Hybridization Experiments at Gene and Probe Level
Authors: Chen Ying , Wu Rebekah , Felton James , Rocke David M. , Chakicherla Anu
Published: November 2010

Motivation

Whole genome microarrays are increasingly becoming the method of choice to study responses in model organisms to disease, stressors or other stimuli. However, whole genome sequences are available for only some model organisms, and there are still many species whose genome sequences are not yet available. Cross-species studies, where arrays developed for one species are used to study gene expression in a closely related species, have been used to address this gap, with some promising results. Current analytical methods have included filtration of some probes or genes that showed low hybridization activities. But consensus filtration schemes are still not available.

Results

A novel masking procedure is proposed based on currently available target species sequences to filter out probes and study a cross-species data set using this masking procedure and gene-set analysis. Gene-set analysis evaluates the association of some priori defined gene groups with a phenotype of interest. Two methods, Gene Set Enrichment Analysis (GSEA) and Test of Test Statistics (ToTS) were investigated. The results showed that masking procedure together with ToTS method worked well in our data set. The results from an alternative way to study cross-species hybridization experiments without masking are also presented. We hypothesize that the multi-probes structure of Affymetrix microarrays makes it possible to aggregate the effects of both well-hybridized and poorly-hybridized probes to study a group of genes. The principles of gene-set analysis were applied to the probe-level data instead of gene-level data. The results showed that ToTS can give valuable information and thus can be used as a powerful technique for analyzing cross-species hybridization experiments.

Availability

Software in the form of R code is available at http://anson.ucdavis.edu/~ychen/cross-species.html

Supplementary Data

Supplementary data are available at http://anson.ucdavis.edu/~ychen/cross-species.html
Suicide Note Classification Using Natural Language Processing: A Content Analysis
Authors: Pestian John , Nasrallah Henry , Matykiewicz Pawel , Bennett Aurora , Leenaars Antoon
Published: November 2010

Suicide is the second leading cause of death among 25–34 year olds and the third leading cause of death among 15–25 year olds in the United States. In the Emergency Department, where suicidal patients often present, estimating the risk of repeated attempts is generally left to clinical judgment. This paper presents our second attempt to determine the role of computational algorithms in understanding a suicidal patient's thoughts, as represented by suicide notes. We focus on developing methods of natural language processing that distinguish between genuine and elicited suicide notes. We hypothesize that machine learning algorithms can categorize suicide notes as well as mental health professionals and psychiatric physician trainees do. The data used are comprised of suicide notes from 33 suicide completers and matched to 33 elicited notes from healthy control group members. Eleven mental health professionals and 31 psychiatric trainees were asked to decide if a note was genuine or elicited. Their decisions were compared to nine different machine-learning algorithms. The results indicate that trainees accurately classified notes 49% of the time, mental health professionals accurately classified notes 63% of the time, and the best machine learning algorithm accurately classified the notes 78% of the time. This is an important step in developing an evidence-based predictor of repeated suicide attempts because it shows that natural language processing can aid in distinguishing between classes of suicidal notes.
Diagnostic Markers for Tuberculosis Ascites: A Preliminary Study
Authors: Kashyap Rajpal S. , Saha Sonali M. , Nagdev Khushboo J. , Kelkar Sanjeevani S. , Purohit Hemant J. , Taori Girdhar M. , Daginawala Hatim F.
Published: November 2010

Objective

The diagnosis of tuberculosis (TB) ascites is problematic. Delay in the diagnosis and treatment of TB ascites are considered to be major factors that contribute to the high mortality of TB. This study identifies specific protein markers in ascitic fluid which will be useful in diagnosis of TB ascites.

Methods

We used Two-Dimensional Electrophoresis, liquid chromatography-mass spectrometry/mass spectrometry, immunoblot analysis and Enzyme Linked Immunosorbent assay (ELISA) as a comprehensive quantitative proteomic screening system for the diagnosis of TB ascites.

Results

The screen identified several antigens of interest: a 30-kilodalton (kDa) protein that demonstrated significant homology to the antigen 85B and 85C (Ag 85) complex; a 65-kDa protein that corresponded to Mycobacterium tuberculosis (MTB) heat shock protein 65 (65-kDa HSP), Rv0440; a 14-kDa protein and 71-kDa protein that exhibits an amino acid sequence identical to that of MTB heat shock protein 14 (14-kDa HSP), GroES; and MTB heat shock protein 71 (71-kDa HSP), Rv0350 respectively. ELISA confirmed that TB ascites patients were consistently positive for these antigens at higher rates than non-TB ascites patients.

Conclusion

The 65-kDa HSP, 71-kDa HSP, 14-kDa HSP and Ag 85 complex proteins may serve as very useful diagnostic markers for TB ascites.
The Negative Impact of Imatinib Mesylate Therapy Prior to Allogeneic Hematopoietic Stem Cell Transplantation in Patients with Chronic Myeloid Leukemia
Authors: Al-Anazi K.A. , Chaudhri N. , Al-Mohareb F.I. , Al-Zahrani H.A. , Al-Omar H.M. , Al-Shanqeeti A. , Sahovic E. , Sharif F.Z. Al , Mohamed S.Y. , Rasheed W. , Beihani A. , Hejazi A. , Zaidi Z. , Morshid M. , Seth P. , El-Tayeb K.I. , Nassar A. , Bakr M. , Jafar S. Abu , Othman I.A. , Abdulwahab A. , Al-Sultan O. , Aljurf M.D.
Published: November 2010

Background

In patients with chronic myeloid leukemia subjected to allogeneic hematopoietic stem cell transplant, the possible negative impact of imatinib therapy in the pre-transplant period is still controversial.

Methods and materials

A retrospective study of patients with chronic myeloid leukemia who received allogeneic hematopoietic stem cell transplant between January 2004 and December 2006 at King Faisal Specialist Hospital and Research Centre in Riyadh was conducted. The results of patients who received hydroxyurea or interferon-α (group A) prior to transplant were compared with those of patients who received imatinib therapy (group B). Both groups of patients received the same conditioning therapy and graft versus host disease prophylaxis.

Results

Survival was shorter and mortality rate was higher in group B compared to group A patients. Both acute and chronic graft versus host disease were not only more frequent but also more severe and extensive in group B. Viral, bacterial and fungal infections were more predominant and more serious in group B compared to group A.

Conclusions

In patients with chronic myeloid leukemia who are subjected to hematopoietic stem cell transplant, prior therapy with imatinib mesylate may have an adverse outcome in terms of survival, graft versus host disease and post-transplant infectious complications.
The Induction of Circulating, ACAID-Inducing Monocytes Requires CCR2/CCL2-Dependent Migration of Circulating F4/80+ Cells into the Anterior Chamber
Authors: Cone Robert E , Chattopadhyay Subhasis , Pais Roshan , Bhowmick Sourojit , Sharafieh Roshanak , Lemire Yen , O'rourke James
Published: November 2010

To determine the origin of peripheral blood mononuclear cells (PBMC) that activate regulatory T cells in anterior chamber-associated immune deviation (ACAID), fluorescein-labeled PBMC were intravenously injected into mice before the mice received an intracameral injection of antigen. Six-24 hr after intracameral injection, fluorescein-labeled PBMC increased in the iris. Twenty-four-48 hr labeled cells decreased in the iris and increased in the thymus and spleen. The entry of the labeled PBMC into the anterior chamber and subsequent production of PBMC that transfer ACAID required the expression of CCR2 by the PBMC and the production of the chemokine CCL2 by the recipient of the PBMC. The results suggest that the intracameral injection of antigen induces i) the infiltration of F4/80+ PBMC into the AC, ii) where these PBMC are converted to a regulatory phenotype, and iii) recirculate to activate T cells that suppress cell-mediated immunity.
Southeast Pacific stratocumulus clouds, precipitation and boundary layer structure sampled along 20° S during VOCALS-REx
Authors: Bretherton C. S. , Wood R. , George R. C. , Leon D. , Allen G. , Zheng X.
Published: November 2010

Abstract. Multiplatform airborne, ship-based, and land-based observations from 16 October–15 November 2008 during the VOCALS Regional Experiment (REx) are used to document the typical structure of the Southeast Pacific stratocumulus-topped boundary layer and lower free troposphere on a~transect along 20° S between the coast of Northern Chile and a buoy 1500 km offshore. Strong systematic gradients in clouds, precipitation and vertical structure are modulated by synoptically and diurnally-driven variability. The boundary layer is generally capped by a strong (10–12 K), sharp inversion. In the coastal zone, the boundary layer is typically 1 km deep, fairly well mixed, and topped by thin, nondrizzling stratocumulus with accumulation-mode aerosol and cloud droplet concentrations exceeding 200 cm−3. Far offshore, the boundary layer depth is typically deeper (1600 m) and more variable, and the vertical structure is usually decoupled. The offshore stratocumulus typically have strong mesoscale organization, much higher peak liquid water paths, extensive drizzle, and cloud droplet concentrations below 100 cm−3, sometimes with embedded pockets of open cells with lower droplet concentrations. The lack of drizzle near the coast is not just a microphysical response to high droplet concentrations; smaller cloud depth and liquid water path than further offshore appear comparably important. Moist boundary layer air is heated and mixed up along the Andean slopes, then advected out over the top of the boundary layer above adjacent coastal ocean regions. Well offshore, the lower free troposphere is typically much drier. This promotes strong cloud-top radiative cooling and stronger turbulence in the clouds offshore. In conjunction with a slightly cooler free troposphere, this may promote stronger entrainment that maintains the deeper boundary layer seen offshore. Winds from ECMWF and NCEP operational analyses have an rms difference of only 1 m s−1 from collocated airborne leg-mean observations in the boundary layer and 2 m s−1 above the boundary layer. This supports the use of trajectory analysis for interpreting REx observations. Two-day back-trajectories from the 20° S transect suggest that eastward of 75° W, boundary layer (and often free-tropospheric) air has usually been exposed to South American coastal aerosol sources, while at 85° W, neither boundary-layer or free-tropospheric air has typically had such contact.
Sensitivity of global cloud condensation nuclei concentrations to primary sulfate emissions parameterizations
Authors: Luo G. , Yu F.
Published: November 2010

Abstract. The impact of primary sulfate emissions on cloud condensation nuclei (CCN) concentrations, one of the major uncertainties in global CCN predictions, depends on the fraction of sulfur mass emitted as primary sulfate particles (fsulfate), the fraction of primary sulfate mass distributed into the nucleation mode particles (fnucl), and the nucleation and growth process in the ambient atmosphere. Here, we use a global size-resolved aerosol microphysics model recently developed to study how the different parameterizations of primary sulfate emission affect particle properties and CCN abundance. Different from previous studies, we use the ion-mediated nucleation scheme to calculate tropospheric particle formation and explicitly simulate the condensation of low volatile secondary organic gas (in addition to H2SO4 gas) on nucleated particles. Our simulations show a compensation effect of nucleation to primary sulfate emission. We find that the change of fnucl from 5% to 15% has a more significant impact on the simulated particle number budget than that of fsulfate within the range of 2.5–5%. An increase of fsulfate from 0% to 2.5% (with fnucl = 5%) does not improve the agreement between simulated and observed annual mean number concentrations of particles >10 nm at 21 stations but further increase of either fsulfate from 2.5% to 5% (with fnucl = 5%) or fnucl from 5% to 15% (with fsulfate = 2.5%) substantially deteriorates the agreement. For fsulfate of 2.5%–5% and fnucl of 5%, our simulations indicate that the global CCN at supersaturation of 0.2 increases by 8–11% in the boundary layer and 3–5% in the whole troposphere (compared to the case with fsulfate = 0). Our derived impact of primary sulfate emission on global CCN abundance is about a factor of ∼3–7 smaller than those found in previous studies.
Ergosterol, arabitol and mannitol as tracers for biogenic aerosols in the Eastern Mediterranean
Authors: Burshtein N. , Lang Yona N. , Rudich Y.
Published: November 2010

Abstract. Aerosols containing biological components can have a significant effect on human health by causing primarily irritation, infection and allergies. Specifically, airborne fungi can cause a wide array of adverse responses in humans depending on the type and quantity present. In this study we used chemical biomarkers for analyzing fungi-containing aerosols in the eastern Mediterranean region during the year 2009 in order to quantify annual fungal abundances. The prime marker for fungi used in this study was ergosterol, and its concentrations were compared with those of mannitol and arabitol, which were recently suggested to also correlate with fungal spores concentrations (Bauer et al., 2008a). Back trajectory analysis, inorganic ions, humidity and temperature were used in an attempt to identify sources as well as the dependence on seasonal and environmental conditions. We found that the ambient concentrations of ergosterol, arabitol and mannitol range between 0 and 2.73 ng m−3, 1.85 and 58.27 ng m−3, 5.57 and 138.03 ng m−3, respectively. The highest levels for all biomarkers were during the autumn, probably from local terrestrial sources, as deduced from the inorganic ions and back trajectory analysis. Significant correlations were observed between arabitol and mannitol during the entire year except for the winter months. Both sugars correlated with ergosterol only during the spring and autumn. We conclude that mannitol and arabitol might not be specific biomarkers for fungi and that the observed correlations during spring and autumn may be attributed to high levels of vegetation during spring blossoms and autumn decomposition.
Annual variation of methane emissions from forested bogs in West Siberia (2005–2009): a case of high CH4 and precipitation rate in the summer of 2007
Authors: Sasakawa M. , Ito A. , Machida T. , Tsuda N. , Niwa Y. , Davydov D. , Fofonov A. , Arshinov M.
Published: November 2010

Abstract. We have been conducting continuous measurements of CH4 and CO2 on a network of towers (JR-STATION: Japan–Russia Siberian Tall Tower Inland Observation Network) located in taiga, steppe, and wetland biomes of Siberia. Here we describe measurements from two forested bog sites, Karasevoe (KRS; 58°15′ N, 82°25′ E) and Demyanskoe (DEM; 59°47′ N, 70°52′ E), in West Siberia from 2005 to 2009. Although both CH4 and CO2 accumulation (ΔCH4 and ΔCO2) during nighttime (duration of 7 h beginning 21:30 LST) at KRS in July 2007 showed an anomalously high concentration, the higher ratios of ΔCH4/ΔCO2 compared with those in other years indicate that a considerably more CH4 flux occurred relative to the CO2 flux in response to large precipitation recorded in 2007 (~2.7 mm d−1 higher than the climatological 1979–1998 base). Estimated seasonal CH4 fluxes based on the ratio of ΔCH4/ΔCO2 and the CASA 3-hourly CO2 flux for the 2005–2009 period exhibited a seasonal variation with a maximum in July at both sites. Annual values of the CH4 emission from the forested bogs around KRS (approx. 7.8×104 km2) calculated from a process-based ecosystem model, Vegetation Integrative Simulator for Trace gases (VISIT), showed inter-annual variation of 0.54, 0.31, 0.94, 0.44, and 0.41 Tg CH4 yr−1 from 2005 to 2009, respectively, with the highest values in 2007. It was assumed in the model that the area flooded with water is proportional to the cumulative anomaly in monthly precipitation rate.
Ethics of primate use
Authors: Prescott M. J.
Published: November 2010

Abstract. This article provides an overview of the ethical issues raised by the use of non-human primates (NHPs) in research involving scientific procedures which may cause pain, suffering, distress or lasting harm. It is not an exhaustive review of the literature and views on this subject, and it does not present any conclusions about the moral acceptability or otherwise of NHP research. Rather the aim has been to identify the ethical issues involved and to provide guidance on how these might be addressed, in particular by carefully examining the scientific rationale for NHP use, implementing fully the 3Rs principle of Russell and Burch (1959) and applying a robust "harm-benefit assessment" to research proposals involving NHPs.
Local flux-profile relationships of wind speed and temperature in a canopy layer in atmospheric stable conditions
Authors: Zhang G. , Leclerc M. Y. , Karipot A.
Published: November 2010

Abstract. The particularities of the physics of the canopy layer pose challenges to the determination and use of traditional universal functions so helpful in the atmospheric surface layer. Progress toward "universal-like functions" such as those provided by Monin-Obukhov similarity theory for the canopy layer has been modest. One of the challenges lies in that the assumptions underlying Monin-Obukhov similarity theory do not hold within a canopy layer. This paper thus examines the local flux-profile relations for wind (Φm) and for temperature (Φh). It uses three different stability parameters, i.e., h/L(h) at tree top, local z/L(z), and the local bulk Richardson number (Ri), within a tall forest canopy in nighttime stable (indicated by h/L(h) > 0) conditions. Results suggest that the in-canopy Φm can be described using the local Richardson number Ri. Furthermore, Φm is found to increase linearly with Ri in the upper canopy layer for |Ri| < 1. When local |Ri| > 1, |Φm| decreases with |Ri| in a power function, a result consistent for all levels of measurements within the canopy. When both local Φh and local Ri are positive, i.e., the local downward turbulent heat flux is consistent with the local temperature gradient, the local Φh increases with the local Ri when Ri < 1. However, Φh does not change with Ri (or much more scattered) when Ri > 1. The relationship between local Φh and Ri disappears when counter-gradient heat transfer occurs in strongly stable conditions. A self-correlation analysis is used to examine the influence of self-correlation and the physical meaning of these relationships.
Long-term CH3Br and CH3Cl flux measurements in temperate salt marshes
Authors: Blei E. , Heal M. R. , Heal K. V.
Published: November 2010

Abstract. Fluxes of CH3Br and CH3Cl and their relationship with potential drivers such as sunlight, temperature and soil moisture, were monitored at fortnightly to monthly intervals for more than two years at two contrasting temperate salt marsh sites in Scotland. Manipulation experiments were conducted to further investigate possible links between drivers and fluxes. Fluxes followed both seasonal and diurnal trends with highest fluxes during summer days and lowest (negative) fluxes during winter nights. Mean (± 1 sd) annually and diurnally-weighted net emissions from the two sites were found to be 300 ± 44 ng m−2 h−1 for CH3Br and 662 ± 266 ng m−2 h−1 for CH3Cl. The fluxes from this work are similar to findings from this and other research groups for salt marshes in cooler, higher latitude climates, but lower than values from salt marshes in the Mediterranean climate of southern California. Statistical analysis generally did not demonstrate a strong link between temperature or sunlight levels and methyl halide fluxes, although it is likely that temperatures have a weak direct influence on emissions, and both certainly have indirect influence via the annual and daily cycles of the vegetation. CH3Cl flux magnitudes from different measurement locations depended on the plant species enclosed whereas such dependency was not discernible for CH3Br fluxes. In 14 out of 18 collars with vegetation CH3Br and CH3Cl net fluxes were significantly positively correlated. The CH3Cl/CH3Br net-emission mass ratio was 2.2, a magnitude lower than mass ratios of global methyl halide budgets (~22) or emissions from tropical rainforests (~60). This is likely due to preference for CH3Br production by the relatively high bromine content in the salt marsh plant material. Extrapolation based solely on data from this study yields salt marsh contributions of 0.5–3.2% and 0.05–0.33%, respectively, of currently-estimated total global production of CH3Br and CH3Cl, but actual global contributions likely lie between these values and those derived from southern California.
ESCIMO.spread – a spreadsheet-based point snow surface energy balance model to calculate hourly snow water equivalent and melt rates for historical and changing climate conditions
Authors: Strasser U. , Marke T.
Published: November 2010

Abstract. This paper describes the spreadsheet-based point energy balance model ESCIMO.spread which simulates the energy and mass balance as well as melt rates at the snow surface. The model makes use of hourly recordings of temperature, precipitation, wind speed, relative humidity, and incoming global and longwave radiation. The effect of potential climate change on the seasonal evolution of the snow cover can be estimated by modifying the time series of observed temperature and precipitation by means of adjustable parameters. Model output is graphically visualized in hourly and daily diagrams. The results compare well with weekly measured snow water equivalent (SWE). The model is easily portable and adjustable, and runs particularly fast: an hourly calculation of a one winter season is instantaneous on a standard computer. ESCIMO.spread can be obtained from the authors on request.
GEOCLIM reloaded (v 1.0): a new coupled earth system model for past climate change
Authors: Arndt S. , Regnier P. , Goddéris Y. , Donnadieu Y.
Published: November 2010

Abstract. We present a new version of the coupled Earth system model GEOCLIM. The new release, GEOCLIM reloaded, links the existing atmosphere and weathering modules to a novel, temporally and spatially resolved model of the global ocean circulation, which provides a physical framework for a mechanistic description of the marine biogeochemical dynamics of carbon, nitrogen, phosphorus and oxygen. The ocean model is also coupled to a fully formulated, vertically resolved diagenetic model. GEOCLIM reloaded is thus a unique tool to investigate the short- and long-term feedbacks between climatic conditions, continental inputs, ocean biogeochemical dynamics and diagenesis. A complete and detailed description of the resulting Earth system model and its new features is first provided. The performance of GEOCLIM reloaded is then evaluated by comparing steady-state simulation under present-day conditions with a comprehensive set of oceanic data and existing global estimates of bio-element cycling in the pelagic and benthic compartments.
Photogrammetric determination of spatio-temporal velocity fields at Glaciar San Rafael in the Northern Patagonian Icefield
Authors: Maas H.-G. , Casassa G. , Schneider D. , Schwalbe E. , Wendt A.
Published: November 2010

Abstract. Glaciar San Rafael in the Northern Patagonian Icefield, with a length of 46 km and an ice area of 722 km2, is the lowest latitude tidewater outlet glacier in the world and one of the fastest and most productive glaciers in southern South America in terms of iceberg flux. In a joint project of the TU Dresden and CECS, spatio-temporal velocity fields in the region of the glacier front were determined in a campaign in austral spring of 2009. Monoscopic terrestrial image sequences were recorded with an intervallometer mode high resolution digital camera over several days. In these image sequences, a large number of glacier surface points were tracked by subpixel accuracy feature tracking techniques. Scaling and georeferencing of the trajectories obtained from image space tracking was performed via a multi-station GPS-supported photogrammetric network. The technique allows for tracking hundreds of glacier surface points at a measurement accuracy in the order of one decimeter and an almost arbitrarily high temporary resolution. The results show velocities of up to 16 m per day. No significant tidal signals could be observed. Our velocities are in agreement with earlier measurements from theodolite and satellite interferometry performed in 1986–1994, suggesting that the current thinning of 3.5 m/y at the front is not due to dynamic thinning but rather by enhanced melting.
Mechanical Characterization of Thin Films by Use of Atomic Force Acoustic Microscopy
Authors: Kopycinska‐Müller Malgorzata , Striegler Andre , Köhler Bernd , Wolter Klaus‐Jürgen
Published: November 2010

The atomic force acoustic microscopy (AFAM) technique has been used to determine elastic properties of films with thicknesses decreasing from several hundreds of nanometers to several nanometers. It has been shown that metal films as thin as 50 nm can be characterized directly without the need to consider the influence of the substrate. For films with thicknesses ranging from about 30 to 50 nm, measurement parameters can be chosen such as to allow characterization of the elastic properties of either the film or the film–substrate interface. This attribute has been combined with the ability of the method to obtain qualitative stiffness images to show variations in the film–substrate adhesion. The AFAM technique has been also used to determine the indentation modulus of thin films of silicon oxide with thicknesses ranging from 7 to 28 nm. In this case, elastic properties of the substrate had to be considered. The examples of the applications of the AFAM method reported here for characterization of elastic properties of very thin films have shown that this technique has the lateral and depth resolution required to characterize the very thin films used nowadays in microelectronics industry.
Copper(II) Acetate/Oxygen‐Mediated Nucleophilic Addition and Intramolecular CH Activation/CN or CC Bond Formation: One‐Pot Synthesis of Benzimidazoles or Quinazolines
Authors: He Hua‐Feng , Wang Zhi‐Jing , Bao Weiliang
Published: November 2010

Diarylcarbodiimides or benzylphenylcarbodiimides are converted to 1,2‐disubstituted benzimidazoles or 1,2‐disustituted quinazolines via addition/intramolecular CH bond activation/C‐N or CC bond forming reaction using copper(II) acetate/oxygen [Cu(OAc)2/O2] as the oxidant at 100 °C in one‐pot cascade procedure.
Heterogeneous Selective Oxidation of Alkenes to α,β‐ Unsaturated Ketones over Coordination Polymer MIL‐101
Authors: Maksimchuk Nataliya V. , Kovalenko Konstantin A. , Fedin Vladimir P. , Kholdeeva Oxana A.
Published: November 2010

The mesoporous metal‐organic framework MIL‐101 is an efficient heterogeneous catalyst for the selective allylic oxidation of alkenes with tert‐butyl hydroperoxide. The selectivity towards α,β‐unsaturated ketones reaches 86–93%. The temperature of the catalyst activation strongly affects the ketone yield. MIL‐101 is stable to chromium leaching, behaves as a true heterogeneous catalyst, can be easily recovered by filtration, and can be reused several times without loss of the catalytic performance.
Brachydactyly type A1 with short humerus and associated skeletal features
Authors: Lacombe Didier , Delrue Marie‐Ange , Rooryck Caroline , Morice‐Picard Fanny , Arveiler Benoît , Maugey‐Laulom Brigitte , Mundlos Stefan , Toutain Annick , Chateil Jean‐François
Published: November 2010

We report on a three‐generation family affected with an osteochondrodysplasia transmitted as an autosomal dominant trait. The phenotype consists of short humerus, curved radius with accessory ossification centre at the proximal third of ulna, variable short stature and brachydactyly, and has not been reported to the best of our knowledge. The brachydactyly falls into the brachydactyly A1 category (especially short 2nd, 4th, and 5th middle phalanges). A unique feature in one family member is triphalangeal thumbs. Vertebrae are normal. Mental development is normal and deafness is seen in some of the family members. A mutation was excluded by sequencing the entire coding regions of the IHH gene encoding the Indian Hedgehog protein and the GDF5 gene. This condition is a novel chondrodyplasia phenotype or possibly one end of the spectrum of the brachydactyly A1. © 2010 Wiley‐Liss, Inc.
A Neurological Comparative Study of the Harp Seal (Pagophilus groenlandicus) and Harbor Porpoise (Phocoena phocoena) Brain
Authors: Walløe Solveig , Eriksen Nina , Dabelsteen Torben , Pakkenberg Bente
Published: November 2010

The cetacean brain is well studied. However, few comparisons have been done with other marine mammals. In this study, we compared the harp seal (Pagophilus groenlandicus) and the harbor porpoise brain (Phocoena phocoena). Stereological methods were applied to compare three areas of interest: the entire neocortex and two subdivisions of the neocortex, the auditory and visual cortices. The total number of neurons and glial cells in the three regions was estimated. The main results showed that the harbor porpoise have an estimated 14.9 × 109 neocortical neurons and 34.8 × 109 neocortical glial cells, whereas the harp seal have 6.1 × 109 neocortical neurons and 17.5 × 109 neocortical glial cells. The harbor porpoise have significantly more neurons and glial cells in the auditory cortex than in the visual cortex, whereas the pattern was opposite for the harp seal. These results are the first to provide estimates of the number of neurons and glial cells in the neocortex of the harp seal and harbor porpoise brain and offer new data to the comparative field of mammalian brain evolution. Anat Rec, 2010. © 2010 Wiley‐Liss, Inc.
Enantioselective and Regioselective Organocatalytic Conjugate Addition of Malonates to Nitroenynes
Authors: Li Xiao‐Jiao , Peng Fang‐Zhi , Li Xiang , Wu Wen‐Tao , Sun Zhong‐Wen , Li Ying‐Mei , Zhang Shao‐Xiong , Shao Zhi‐Hui
Published: November 2010

The first catalytic asymmetric conjugate addition of 1,3‐dicarbonyl compounds to nitroenynes catalyzed by cinchona alkaloid‐based thiourea organocatalysts has been developed. The 1,4‐addition adducts were obtained solely, in moderate to good yields (up to 93 %) with good enantioselectivities (up to 99 % ee). This protocol affords a conceptually different entry to the precursors of pharmaceutically important chiral β‐alkynyl acid derivatives and synthetically useful chiral nitroalkynes. Notably, the protocol worked well with both aryl‐ and alkyl‐substituted alkynyl substrates.
Stereoselectivity in Trimethylenemethane (TMM) Diyl Mediated Cycloaddition Reaction to Angularly Fused Triquinanes
Authors: Yoon Yeokwon , Kang Taek , Lee Hee‐Yoon
Published: November 2010

A thorough study on the diastereoselectivity in the TMM diyl mediated [2+3] cycloaddition reaction of monosubstituted linear substrates to form angularly fused triquinanes was carried out. Substitution at position 3 provided complete diastereoselectivity, while positions 1 and 4 induced marginal stereoselectivity. Position 2 did not show any influence on the diastereoselectivity. Position 4 turned out to be incompatible with the cycloaddition reaction as the carbene intermediate underwent OSi bond insertion to form a dihydrofuran ring.
Fed‐batch culture of Escherichia coli for L‐valine production based on in silico flux response analysis
Authors: Park Jin Hwan , Kim Tae Yong , Lee Kwang Ho , Lee Sang Yup
Published: November 2010

We have previously reported the development of a 100% genetically defined engineered Escherichia coli strain capable of producing L‐valine from glucose with a high yield of 0.38 g L‐valine per gram glucose (0.58 mol L‐valine per mol glucose) by batch culture. Here we report a systems biological strategy of employing flux response analysis in bioprocess development using L‐valine production by fed‐batch culture as an example. Through the systems‐level analysis, the source of ATP was found to be important for efficient L‐valine production. There existed a trade‐off between L‐valine production and biomass formation, which was optimized for the most efficient L‐valine production. Furthermore, acetic acid feeding strategy was optimized based on flux response analysis. The final fed‐batch cultivation strategy allowed production of 32.3 g/L L‐valine, the highest concentration reported for E. coli. This approach of employing systems‐level analysis of metabolic fluxes in developing fed‐batch cultivation strategy would also be applicable in developing strategies for the efficient production of other bioproducts. Biotechnol. Bioeng. 2011; 108:934–946. © 2010 Wiley Periodicals, Inc.
Composition and Intraspecific Chemical Variability of the Essential Oil from Artemisia herba‐alba Growing Wild in a Tunisian Arid Zone
Authors: Mighri Hédi , Akrout Ahmed , El‐jeni Hajer , Zaidi Slah , Tomi Félix , Casanova Joseph , Neffati Mohamed
Published: November 2010

The intraspecific chemical variability of essential oils (50 samples) isolated from the aerial parts of Artemisia herba‐alba Asso growing wild in the arid zone of Southeastern Tunisia was investigated. Analysis by GC (RI) and GC/MS allowed the identification of 54 essential oil components. The main compounds were β‐thujone and α‐thujone, followed by 1,8‐cineole, camphor, chrysanthenone, trans‐sabinyl acetate, trans‐pinocarveol, and borneol. Chemometric analysis (k‐means clustering and PCA) led to the partitioning into three groups. The composition of two thirds of the samples was dominated by α‐thujone or β‐thujone. Therefore, it could be expected that wild plants of A. herba‐alba randomly harvested in the area of Kirchaou and transplanted by local farmers for the cultivation in arid zones of Southern Tunisia produce an essential oil belonging to the α‐thujone/β‐thujone chemotype and containing also 1,8‐cineole, camphor, and trans‐sabinyl acetate at appreciable amounts.
Chemical Composition, Seasonal Variation, and Biosynthetic Considerations of Essential Oils from Baccharis microdonta and B. elaeagnoides (Asteraceae)
Authors: Sayuri Viviane A. , Romoff Paulete , Fávero Oriana A. , Ferreira Marcelo J. P. , Lago João H. G. , Buturi Fátima O. S.
Published: November 2010

The chemical composition and seasonal variation throughout one year of the essential oils from leaves of Baccharis microdonta and B. elaeagnoides, collected in Campos do Jordão, SP, were investigated. The composition of the latter species has been described for the first time. By GC (RI) and GC/MS analysis, 43 compounds were identified, and a predominance of oxygenated sesquiterpene derivatives was found in both species. The main components of the B. microdonta oils were elemol (31; 11.7–30.6%), spathulenol (34; 4.7–9.1%), β‐caryophyllene (19; 3.7–6.2%), and germacrene D (24; 2.9–12.2%), and those of the B. elaeagnoides oils were 34 (10.1–21.5%), viridiflorol (35; 3.6–18.4%), 24 (0.9–13.8%), and 19 (3.5–9.4%). The identified compounds were grouped according to their respective C‐skeletons, and the percentages of occurrence of the C‐skeletons in the essential oils of leaves collected in the four seasons allowed identifying the preferential accumulation of different types of C‐skeletons as well as the seasonal variation of the biosynthetic routes over the studied period.
Antimicrobial Peptides and Their Superior Fluorinated Analogues: Structure–Activity Relationships as Revealed by NMR Spectroscopy and MD Calculations
Authors: Díaz M. Dolores , Palomino‐Schätzlein Martina , Corzana Francisco , Andreu Cecilia , Carbajo Rodrigo J. , del Olmo Marcellí , Canales‐Mayordomo Angeles , Pineda‐Lucena Antonio , Asensio Gregorio , Jiménez‐Barbero Jesús
Published: November 2010

The conformations of two synthetic pentapeptides with antimicrobial activity and their 4‐fluorophenylalanine (Pff)‐containing analogues (ArXArXAr‐NH2; Ar=Phe, Pff; X=Lys, Arg) have been studied. NMR experiments carried out both in aqueous fluoroalcohol solutions and SDS micelles permitted their interactions with membrane‐like environments to be explored. WaterLOGSY experiments and Mn2+‐based paramagnetic probes were also applied to assess their orientations with respect to the SDS micelles. In addition, pulse‐field gradient (PFG) diffusion NMR spectroscopy studies were conducted, under different experimental conditions (i.e., concentration, temperature) to characterize the possible changes in the peptides' aggregation states as a putative critical factor for their antimicrobial activity. Finally, molecular dynamics simulations on a variety of conformations showed the intrinsic flexibility of these peptides in both aqueous solutions and membrane‐mimetic systems.
Nanoscale Self‐Hosting of Molecular Spin‐States in the Intermediate Phase of a Spin‐Crossover Material
Authors: Bréfuel Nicolas , Collet Eric , Watanabe Hiroshi , Kojima Masaaki , Matsumoto Naohide , Toupet Loic , Tanaka Koichiro , Tuchagues Jean‐Pierre
Published: November 2010

A new spin‐crossover (SC) complex [FeIIH2L2‐Me][AsF6]2 has been synthesized, in which H2L2‐Me denotes the chirogenic hexadentate N6 Schiff‐base ligand bis{[(2‐methylimidazol‐4‐yl)methylidene]‐3‐aminopropyl}ethylenediamine. This complex has revealed a rich variety of phases during its two‐step thermal crossover, as well as photoinduced spin‐state switching. A high‐symmetry high‐spin (HS, S=2) phase, a low‐symmetry low‐spin (LS, S=0) phase, an intermediate phase characterized by an unprecedented lozenge pattern of 12 predominantly HS molecular crystallographic sites confining 18 predominantly LS molecular crystallographic sites, and a photoinduced low‐symmetry HS phase have been accurately evidenced by temperature‐dependent magnetic susceptibility, Mössbauer spectroscopy, and crystallographic studies. This variety of phases illustrates the multi‐stability of this system, which results from coupling between the electronic states and structural instabilities.
Surface Modification of Polymeric Micelles by Strain‐Promoted Alkyne–Azide Cycloadditions
Authors: Guo Jun , Chen Guojun , Ning Xinghai , Wolfert Margreet A. , Li Xiuru , Xu Bingqian , Boons Geert‐Jan
Published: November 2010

Organomicelles modified by surface dibenzylcyclooctyne moieties can conveniently be functionalized by strain‐promoted alkyne–azide cycloadditions. The ligation approach is highly efficient, does not require toxic reagents and is compatible with a wide variety of functional modules. Interactions of proteins with surface ligands of the micelles have been studied by AFM, which revealed that it leads to disassembly of the particles thereby providing a mechanism for triggered drug release.
Breakage Probability of Irregularly Shaped Particles by Impact Stressing
Authors: Aman Sergej , Tomas Jürgen , Kalman Haim
Published: November 2010

Bei der Prallbeanspruchung einzelner Partikel wurde die Verteilung der Bruchenergie untersucht. Als unregelmäßig geformte Partikel wurden Salzpartikel des Toten Meeres, Zuckerkristalle und kugelförmige Al2O3‐Granulate verwendet. Die Partikelform und das Kontaktverhalten beim Aufprall wurden mit Hilfe eines Halbkugel‐Modells angenähert. Basierend auf den Modellvorstellungen lassen sich alle gewonnen experimentellen Bruchwahrscheinlichkeitsverteilungen mit der Monte‐Carlo‐Methode simulieren. Die engen Größenklassen der getesteten Partikel werden durch breitere, logarithmische Normalverteilungen der halbkugelförmigen Rauigkeiten ersetzt. Die Simulation zeigt eine gute Übereinstimmung mit den experimentellen Ergebnissen.