bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of DNA polymerase β from Danio rerio by overexpression in E. coli using the in vivo/in vitro compatible pIVEX plasmid
Authors: Ishido Tomomi , Yamazaki Naoshi , Ishikawa Mitsuru , Hirano Ken 
Published: November 2011

Abstract

Background
Eukaryotic DNA polymerase β (pol β), the polymerase thought to be responsible for DNA repair synthesis, has been extensively characterized in rats and humans. However, pol β has not been purified or enzymatically characterized from the model fish species Danio rerio (zebrafish). We used the in vitro/in vivo dual expression system plasmid, pIVEX, to express Danio rerio pol β (Danio pol β) for biochemical characterization.

Results

Danio pol β encoded by the in vitro/in vivo-compatible pIVEX plasmid was expressed in E. coli BL21(DE3), BL21(DE3)pLysS, and KRX, and in vitro as a C-terminal His-tagged protein. Danio pol β expressed in vitro was subject to proteolysis; therefore, bacterial overexpression was used to produce the protein for kinetic analyses. KRX cells were preferred because of their reduced propensity for leaky expression of pol β. The cDNA of Danio rerio pol β encodes a protein of 337 amino acids, which is 2-3 amino acids longer than other pol β proteins, and contains a P63D amino acid substitution, unlike mammalian pol βs. This substitution lies in a hairpin sequence within an 8-kDa domain, likely to be important in DNA binding. We performed extensive biochemical characterization of Danio pol β in comparison with rat pol β, which revealed its sensitivity to metal ion activators (Mn2+ and Mg2+), its optimum salt concentration (10 mM KCl and 50 mM NaCl), alkaline pH optimum (pH 9.0), and low temperature optimum (30°C). Substituting Mn2+ for Mg2+ resulted in 8.6-fold higher catalytic efficiency (k
cat/K
m).

Conclusions
Our characterization of pol β from a model fish organism contributes to the study of the function and evolution of DNA polymerases, which are emerging as important cellular targets for chemical intervention in the development of anticancer agents.
Toxicity and cosmesis outcomes after single fraction partial breast irradiation in early stage breast cancer
Authors: Pinnarò Paola , Arcangeli Stefano , Giordano Carolina , Arcangeli Giorgio , Impiombato Fabrizio Ambesi , Pinzi Valentina , Iaccarino Giuseppe , Soriani Antonella , Landoni Valeria , Strigari Lidia 
Published: November 2011

Abstract

Background
To report the clinical outcome after a Single Shot 3D-CRT PBI (SSPBI) in breast cancer patients after conservative surgery (ClinicalTrials.gov Identifier: NCT01316328).

Methods
A dose of 18Gy (in the first 4 patients) and 21Gy (in the remaining 60 patients) was prescribed in a single session and delivered to the index area (i.e. the area of breast including the primary tumor bed and the surrounding tissue) using 3D-CRT with patients in prone position. Acute and late toxicity was assessed using the National Cancer Institute's CTC for Adverse Events. Cosmesis was defined based on modified Harvard criteria. Differences between dosimetric or clinical parameters of patients with/without G2 or more late toxicity or unsatisfactory (poor or fair) cosmetic outcome were evaluated with the Mann-Whitney test. Odds ratios and 95% confidence interval were calculated for cosmesis and fibrosis. Univariate and multivariate analyses(UVA/MVA) were used to determine covariates associated with an increase in fibrosis or fat necrosis rate.

Results
Sixty four patients were enrolled. With a median follow-up of 3 years, G2 and G3 subcutaneous fibrosis was detected in 20(31%) and in 8(13%) patients, and ≥G2 fat necrosis was observed in 2(3%) patients. Good to excellent, fair and poor cosmesis was observed in 38(59%), 23(36%) and 3(5%) patients, respectively. Based on UVA, the breast volume receiving more than 21Gy (V21Gy) was found to be a predictor of the ≥G1 or ≥G2 fibrosis/fat necrosis. Based on MVA, V21Gy was confirmed as a predictor for ≥G1 fibrosis/fat necrosis, the results correlated as a trend for ≥G2. Cosmesis was correlated with whole breast (WB) mean dose (p = 0.030).

Conclusion
Our choice of a single dose of 21Gy significantly increased the treatment related toxicity. However, this should not discourage novel SSPBI approaches with lower equivalent doses.
Combination of optical spectroscopy and chemometric techniques—a possible way for on-line monitoring of spent nuclear fuel (SNF) reprocessing
Authors: Kirsanov D. , Babain V. , Agafonova-Moroz M. , Lumpov A. , Legin A. 
Published: November 2011

Abstract
UV-Vis spectroscopic measurements were performed in model mixtures simulating solutions obtained in the course of PUREX spent nuclear fuel reprocessing. Mixtures contained constant concentrations of nitric acid and uranium with varied content of neptunium and plutonium. Spectral data were processed with classical chemometric technique — PLS regression. This approach has shown significant improvement in analytical precision of actinides determination compared to standard univariate data processing. The combination of spectroscopic measurements with chemometric data processing shows good promise for the development of on-line spectroscopic techniques for SNF reprocessing monitoring.
Venous Thromboembolism in Patients with Membranous Nephropathy
Authors: Lionaki Sophia , Derebail Vimal K. , Hogan Susan L. , Barbour Sean , Lee Taewoo , Hladunewich Michelle , Greenwald Allen , Hu Yichun , Jennette Caroline E. , Jennette J. Charles , Falk Ronald J. , Cattran Daniel C. , Nachman Patrick H. , Reich Heather N. 
Published: November 2011

Summary

Background and objectives
The aims of this study were to determine the frequency of venous thromboembolic events in a large cohort of patients with idiopathic membranous nephropathy and to identify predisposing risk factors.

Design, setting, participants, & measurements
We studied patients with biopsy-proven membranous nephropathy from the Glomerular Disease Collaborative Network (n=412) and the Toronto Glomerulonephritis Registry (n=486) inception cohorts. The cohorts were pooled after establishing similar baseline characteristics (total n=898). Clinically apparent and radiologically confirmed venous thromboembolic events were identified. Potential risk factors were evaluated using multivariable logistic regression models.

Results
Sixty-five (7.2%) subjects had at least one venous thromboembolic event, and this rate did not differ significantly between registries. Most venous thromboembolic events occurred within 2 years of first clinical assessment (median time to VTE = 3.8 months). After adjusting for age, sex, proteinuria, and immunosuppressive therapy, hypoalbuminemia at diagnosis was the only independent predictor of a venous thromboembolic event. Each 1.0 g/dl reduction in serum albumin was associated with a 2.13-fold increased risk of VTE. An albumin level <2.8 g/dl was the threshold below which risk for a venous thromboembolic event was greatest.

Conclusions
We conclude that clinically apparent venous thromboembolic events occur in about 7% of patients with membranous nephropathy. Hypoalbuminemia, particularly <2.8 g/dl, is the most significant independent predictor of venous thrombotic risk.
Predictors of Sudden Cardiac Death
Authors: Shastri Shani , Tangri Navdeep , Tighiouart Hocine , Beck Gerald J. , Vlagopoulos Panagiotis , Ornt Daniel , Eknoyan Garabed , Kusek John W. , Herzog Charles , Cheung Alfred K. , Sarnak Mark J. 
Published: November 2011

Summary

Background and objectives
There are few data on risk factors for sudden cardiac death (SCD) in patients undergoing hemodialysis (HD). The study objective was to identify predictors associated with various causes of death in the Hemodialysis (HEMO) Study and to develop a prediction model for SCD using a competing risk approach.

Design, setting, participants, & measurements
In this analysis of 1745 HEMO participants, all-cause mortality was classified as SCD, non-SCD, and noncardiac death. Predictors for each cause of death were evaluated using cause-specific Cox proportional hazards models, and a competing risk approach was used to calculate absolute risk predictions for SCD.

Results
During a median follow-up of 2.5 years, 808 patients died. Rates of SCD, non-SCD, and noncardiac death were 22%, 17%, and 61%, respectively. Predictors of various causes of death differ somewhat in HD patients. Age, diabetes, peripheral vascular disease, ischemic heart disease, serum creatinine, and alkaline phosphatase were independent predictors of SCD. The 3-year C-statistic for SCD was 0.75 (95% confidence interval, 0.70–0.79), and calibration was good (χ2=1.1; P=0.89). At years 3 and 5 of follow-up, the standard Cox model overestimated the risk for SCD as compared with the competing risk approach on the relative scale by 25% and 46%, respectively, and on the absolute scale by 2% and 6%, respectively.

Conclusions
Predictors of various causes of death differ in HD patients. The proposed prediction model for SCD accounts for competing causes of death. External validation of this model is required.
Adding Specialized Clinics for Remote-Dwellers with Chronic Kidney Disease
Authors: Wiebe Natasha , Klarenbach Scott W. , Chui Betty , Ayyalasomayajula Bharati , Hemmelgarn Brenda R. , Jindal Kailash , Manns Braden , Tonelli Marcello 
Published: November 2011

Summary

Background and objectives
This study aimed to determine whether opening a new clinic in a remote region would be a cost-effective means of improving care for remote-dwellers with CKD.

Design, setting, participants, & measurements
This study is a cost-utility analysis from a public payer’s perspective over a lifetime horizon, using administrative data from a large cohort of adults with stage 3b-4 CKD in Alberta, Canada. The association between the distance from each simulated patient’s residence and the practice location of the closest nephrologist and clinical outcomes (quality of care, hospitalization, dialysis, and death) were examined. A Markov 6-month cycle economic decision model was analyzed; estimates of the effect of a new clinic were based on the association between residence location, resource use, and outcomes. Costs are reported in 2009 Canadian dollars.

Results
The costs for equipping and operating a clinic for 321 remote-dwelling patients were estimated at $25,000 and $250,000/yr, respectively. The incremental cost-utility ratios (ICURs) ranged from $4000 to $8000/quality-adjusted life-year under most scenarios. However, if reducing distance to nephrologist care does not alter mortality or hospitalization among remote-dwellers, the cost-effectiveness becomes less attractive. All other one-way sensitivity analyses had negligible effects on the ICUR.

Conclusions
Given the low costs of equipping and operating new clinics, and the very attractive ICUR relative to other currently funded interventions, establishing new clinics for remote-dwellers could play an important role in efficiently improving outcomes for patients with CKD. High-quality controlled studies are required to confirm this hypothesis.
Crimes Against Humanity
Authors: Geyer Michael 
Published: November 2011

Abstract
While the term “crimes against humanity” retains some of its older meaning, in referring to particularly outrageous acts of violence that offend the conscience of civilized nations, defy values of the civilized world, and injure the prevailing sense of humanness, it has lately developed into a precise, if not entirely unequivocal, legal term in national and international penal law. The most recent definition declares crimes against humanity — on a par with genocide, war crimes, and the crime of aggression — as “most serious crimes of concern for the international community” (Rome Statute of the International Criminal Court, Art. 5).
Electrical Conductivity Depth Modelling with a Multireceiver EMI Sensor for Prospecting Archaeological Features
Authors: Saey Timothy , De Smedt Philippe , Meerschman Eef , Islam Mohammad Monirul , Meeuws Fun , Van De Vijver Ellen , Lehouck Alexander , Van Meirvenne Marc 
Published: November 2011

ABSTRACTMultiple apparent electrical conductivity (ECa) measurements with an electromagnetic induction (EMI) sensor frequently reveal analogue patterns caused by conductive features in the soil. A procedure was proposed to highlight different archaeological anomalies based on combinations of the simultaneous ECameasurements with the DUALEM‐21S instrument. After selection of a 3.5 ha study site, 0.79 ha has been recorded by archaeological excavation. Since the majority of the archaeological features were found between the plough layer and 1.0 m below the soil surface, a set of four equations were developed to model the EC within that predefined depth interval. This set of four equations employed the four depth response curves specific to the four DUALEM‐21S coil configurations. The modelled conductivity between 0.5 and 1.0 m () showed a larger variability across the archaeological features than the raw EC data. To quantify the added value of this modelled conductivity,and measured ECawere compared with the rasterized map of the archaeological traces. Finally, themap proved to be better able to distinguish between the archaeological features and the ‘empty’ background. This technique allowed the highlighting of vague anomalies in the simultaneous DUALEM‐21S ECameasurements. Copyright © 2011 John Wiley & Sons, Ltd.
Enhanced podcasts for teaching biochemistry to veterinary students
Authors: Gough Kevin C. 
Published: November 2011

AbstractThe teaching of biochemistry within medical disciplines presents certain challenges; firstly to relay a large body of complex facts and abstract concepts, and secondly to motivate students that this relatively difficult topic is worth their time to study. Here, nutrient biochemistry was taught within a multidisciplinary module as part of an undergraduate veterinary curriculum. The teaching approach was initially focussed on a mixture of didactic lectures and student‐centred activities such as directed group/self learning. In subsequent years the core didactic lectures were replaced with enhanced podcasts covering the same material, along with the introduction of student presentations delivered within groups with both peer and facilitator assessment. These changes were accompanied by an increase in the time dedicated to this topic to allow sufficient time for students to work through podcasts and prepare presentations. The combination of these changes resulted in significant improvements in student performance within an in‐course biochemistry long essay. These changes in the teaching approach, and particularly the introduction of extensive podcasts, was well received by students who perceived the process of going through the podcasts as time consuming but allowing them flexibility in both the pace that they studied this topic as well as the location and times that they studied it. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 6, pp. 421–425, 2011
Building student proficiency with scientific literature using the Zotero reference manager platform
Authors: Kim Thomas 
Published: November 2011

AbstractWhile mastery of the scientific literature is a strongly desirable trait for undergraduate students, the sheer volume of the current literature has complicated the challenge of teaching scientific literacy. Part of the response to this ever‐increasing volume of resources includes formal instruction in the use of reference manager software while engaging students with the primary literature. This article describes the incorporation of the reference manager program Zotero into a chemical literature course to facilitate the use of digital resources and to better enable them to use proper citation skills in their technical writing. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 6, pp. 412–415, 2011
A Tale of Two Polymorphic Pharmaceuticals: Pyrithyldione and Propyphenazone and their 1937 Co‐crystal Patent
Authors: Lemmerer Andreas , Bernstein Joel , Griesser Ulrich J. , Kahlenberg Volker , Többens Daniel M. , Lapidus Saul H. , Stephens Peter W. , Esterhuysen Catharine 
Published: November 2011

AbstractA co‐crystal of two polymorphic active pharmaceutical ingredients (APIs), first reported and patented in 1937, has been prepared and thoroughly characterised, including crystal structure analysis. The existence of four crystal forms of one of the APIs, the sedative and hypnotic active pharmaceutical ingredient 3,3‐diethyl‐2,4(1H,3H)‐pyridinedione, pyrithyldione (PYR), and of three crystal forms of the co‐crystal‐forming second API, the non‐steroidal anti‐inflammatory drug 1,2‐dihydro‐1,5‐dimethyl‐4‐(1‐methylethyl)‐2‐phenyl‐3H‐pyrazol‐3‐one, propyphenazone (PROP), has been reported previously, but they have only been partly characterised. For both compounds, none of the metastable forms exist at room temperature. DSC, hot‐stage microscopy, X‐ray diffraction and powder synchrotron X‐ray diffraction were employed to characterise the polymorphic forms and to determine the crystal structures of forms I–III of PYR and forms I and II of PROP.
Effects of Vegetation Restoration on Soil Physical Properties in the Wind–Water Erosion Region of the Northern Loess Plateau of China
Authors: Li Wang , Yan Mu , Qingfeng Zhang , Zhikaun Jia 
Published: November 2011

AbstractIn the northern Loess Plateau that has been severely affected by wind–water erosion, shifts from arable land to forest or grasslands have been promoted since 1998, using both native and introduced vegetation. However, there is little knowledge of the ecological consequences and effectiveness of the vegetation restoration in the region. Therefore, relationships between watershed‐scale soil physical properties and plant recovery processes were analyzed. The results show that soil physical properties such as bulk density, hydraulic conductivity, mean weight diameter, and the stability of >1 mm macro‐aggregates have been significantly ameliorated in the 0–20 cm soil layer under secondary natural grasslands. In contrast, re‐vegetation with introduced species such as Caragana korshinskii or Medicago sativa had adversely affected the soil physical properties, probably due to the deterioration of soil water conditions and lower organic matter inputs resulting from severe erosion. Reductions in bulk density and increases in saturated hydraulic conductivity could be used as indicators of soil structure amelioration since they are closely related to most other measured properties. Practical considerations for future re‐vegetation projects are suggested, particularly that native species with lower water consumption rates than the introduced species should be used to avoid further soil degradation.
Image characterization and classification by physical complexity
Authors: Zenil Hector , Delahaye Jean‐Paul , Gaucherel Cédric 
Published: November 2011

AbstractWe present a method for estimating the complexity of an image based on Bennett's concept of logical depth. Bennett identified logical depth as the appropriate measure of organized complexity, and hence as being better suited to the evaluation of the complexity of objects in the physical world. Its use results in a different, and in some sense a finer characterization than is obtained through the application of the concept of Kolmogorov complexity alone. We use this measure to classify images by their information content. The method provides a means for classifying and evaluating the complexity of objects by way of their visual representations. To the authors' knowledge, the method and application inspired by the concept of logical depth presented herein are being proposed and implemented for the first time. © 2011 Wiley Periodicals, Inc. Complexity, 2011
Alterations in picual extra virgin olive oils under different storage conditions
Authors: Samaniego‐Sánchez Cristina , Oliveras‐López Maria Jesus , Quesada‐Granados Jose Javier , Villalón‐Mir Marina , Serrana Herminia López‐Gª 
Published: November 2011

AbstractStorage conditions can affect the stability of extra virgin olive oil, with adverse results on quality. The aim of this study is to examine changes in the chemical composition and sensory characteristics of the oil resulting from prolonged storage at different temperatures and depending on the type of container. The influence on the quality of the oil was also considered, based on the analysis of quality parameters, the total phenol contents, changes in minority compounds, the variation of the trolox equivalent antioxidant capacity values (TEAC) and sensory features. At both room temperature (RT) and refrigerated temperature, all container types had the same surface area of exposure to light and air. All the oils stored showed losses in both qualitative properties and minor components, as well as antioxidant capacity and sensory features. This was especially true for oils stored in polyethylene terephthalate and glass, but less so for those stored in Tetra‐Brik®.
Evidence of frontotemporal structural hypoconnectivity in social anxiety disorder: A quantitative fiber tractography study
Authors: Baur Volker , Brühl Annette Beatrix , Herwig Uwe , Eberle Tanja , Rufer Michael , Delsignore Aba , Jäncke Lutz , Hänggi Jürgen 
Published: November 2011

AbstractInvestigation of the brain's white matter fiber tracts in social anxiety disorder (SAD) may provide insight into the underlying pathophysiology. Because models of pathological anxiety posit altered frontolimbic interactions, the uncinate fasciculus (UF) connecting (orbito‐) frontal and temporal areas including the amygdala is of particular interest. Microstructural alterations in parts of the UF have been reported previously, whereas examination of the UF as discrete fiber tract with regard to more large‐scale properties is still lacking. Diffusion tensor imaging was applied in 25 patients with generalized SAD and 25 healthy control subjects matched by age and gender. By means of fiber tractography, the UF was reconstructed for each participant. The inferior fronto‐occipital fasciculus (IFOF), originating from the frontal cortex similarly to the UF, was additionally included as control tract. Volume and fractional anisotropy (FA) were compared between the groups for both tracts. Volume of left and right UF was reduced in patients with SAD, reaching statistical significance for the left UF. Bilateral IFOF volume was not different between groups. A similar pattern was observed for FA. Reduced volume of the left UF in SAD fits well into pathophysiological models of anxiety, as it suggests deficient structural connectivity between higher‐level control areas in the orbitofrontal cortex and more basal limbic areas like the amygdala. The results point to a specific role of the left UF with regard to altered white matter volume in SAD. However, results should be replicated and functional correlates of altered UF volume be determined in future studies. Hum Brain Mapp, 2013. © 2011 Wiley Periodicals, Inc.