bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative study on antioxidant properties of carrot juice stabilised by high‐intensity pulsed electric fields or heat treatments
Authors: Quitão‐Teixeira Luciano José , Odriozola‐Serrano Isabel , Soliva‐Fortuny Robert , Mota‐Ramos Afonso , Martín‐Belloso Olga
Published: October 2009

BACKGROUND:The effect of high‐intensity pulsed electric field (HIPEF) processing (35 kV cm−1for 1500 µs using 6‐µs bipolar pulses at 200 Hz) on the antioxidant features (vitamin C, β‐carotene, total phenolic compounds and antioxidant capacity) of carrot juice as well as on peroxidase activity was investigated and compared to the observed in heat pasteurised juices (90 °C for 60 s or 30 s) having the fresh juice as a reference.

RESULTS:HIPEF and heat‐treated carrot juices had higher β‐carotene and lower vitamin C contents than the untreated juices immediately after processing. The antioxidant capacity of the juices was significantly modified neither by HIPEF nor by thermal treatments. POD activity decreased drastically (≥93.3%) after processing irrespective of the treatment applied. Vitamin C and β‐carotene content decreased throughout the storage following an exponential trend (R2= 0.801–0.984) with degradation rates between 1.7 × 10−2and 3.5 × 10−2day−1. Vitamin C and β‐carotene contents were better maintained in HIPEF‐treated than in heat‐pasteurised juices throughout the storage. Total phenolic content and the antioxidant capacity of the HIPEF‐treated juice did not substantially differ from that of the thermally treated juice for 56 days.

CONCLUSION:HIPEF processing may help to achieve fresh‐like carrot juices with increased amounts of health‐related phytochemicals. Copyright © 2009 Society of Chemical Industry
Impact of postoperative irradiation after non‐curative resection of hilar biliary cancer
Authors: Kobayashi Shogo , Nagano Hiroaki , Marubashi Shigeru , Takeda Yutaka , Tanemura Masahiro , Konishi Koji , Yoshioka Yasuo , Inoue Takehiro , Doki Yuichiro , Mori Masaki
Published: October 2009

Background

The aim of this retrospective study was to determine the effect of surgical margin on the outcome of postoperative radiotherapy (RT) in patients with resected hilar biliary cancer.

Methods

The study subjects were 87 patients with hilar biliary cancer resected surgically before 2008. Based on the Japanese Society of Biliary Surgery (JSBS) criteria for diagnosis of biliary cancer, the surgical margin status was categorized as margin 1 (histopathologically margin negative, but cancer cells identified within 5 mm from the margin), margin 2 (histopathologically margin positive), and margin 0 (other margin status).

Results

The surgical margin was 1 or 2 in 44 patients and 21 of these patients underwent RT. The 3‐year overall survival and progression‐free survival rates of the RT and non‐RT groups were 47% and 23% (P = 0.0392), and 49% and 19% (P = 0.0197), respectively. Univariate and multivariate analyses identified RT as the only factor that influenced survival. Subgroup analysis showed that the effect of RT was dependent on pathologically negative lymph node metastasis and positive margin (margin 2).

Conclusion

Postoperative RT is beneficial for patients with margins 1 and 2, especially those who are lymph node metastasis negative and have histopathologically positive margin. J. Surg. Oncol. 2009;100:657–662. © 2009 Wiley‐Liss, Inc.
Relationship of polymorphism of the tandem repeat sequence in the thymidylate synthase gene and the survival of stage III colorectal cancer patients receiving adjuvant 5‐flurouracil‐based chemotherapy
Authors: Park Chi‐Min , Lee Woo Yong , Chun Ho‐Kyung , Cho Yong Beom , Yun Hae Ran , Heo Jin Seok , Yun Seong Hyeon , Kim Hee Cheol
Published: October 2009

Background

The aim of this study was to determine whether the different polymorphisms in the thymidylate synthase (TS) gene, novel G>C single nucleotide polymorphism (SNP) and variable number of tandem repeat (VNTR), may be related with disease‐free survival (DFS) in patients with stage III colorectal cancer receiving adjuvant chemotherapy.

Methods

The study included 201 patients with pathologic TNM stage III colon cancer who received adjuvant 5‐fluorouracil (5‐FU)‐based chemotherapy after surgery. DNA was extracted from fresh tumor tissue and sequenced. Patients with TS genotypes of 2R3G, 3C3G, or 3G3G were assigned to a high expression group, and those with 2R2R, 2R3C, or 3C3C, to a low expression group.

Results

Frequencies of the TS tandem repeat polymorphisms among the tumor genotypes were 6.0% in 2R2R, 25.4% in 2R3R, and 68.7% in 3R3R. The low expression group included 52 patients (25.9%), and the high expression group included 149 patients (74.1%). Groups classified according to possession of VNTR, SNP, and low‐ or high‐expression genotypes did not differ significantly in DFS. In multivariate analysis, only tumor stage showed significant prognostic value (hazard ratio (HR) 2.05, 95% CI = 1.24–3.37, P = 0.005).

Conclusions

TS polymorphisms do not predict clinical outcome of colorectal cancer patients treated with adjuvant 5‐FU‐based chemotherapy. J. Surg. Oncol. 2010;101:22–27. © 2009 Wiley‐Liss, Inc.
Diagnosis of second head and neck tumors in primary laryngeal SCC is an indicator of overall survival and not associated with poorer overall survival: A single centre study in 987 patients
Authors: Farhadieh Ross Darius , Salardini Arash , Yang Jia Lin , Russell Pamela , Smee Robert
Published: October 2009

Objectives

Second primary tumors (SPTs) have been implicated in poor overall survival (OS) of head and neck squamous cell carcinomas (HNSCCs). Confusion remains regarding their actual incidence and prognostic impact. This study assessed the incidence of SPTs; the SPT diagnostic time lag; the impact on OS; and the mean annual risk.

Methods

Nine hundred eighty seven consecutive patients treated for primary larynx SCC (1967–2004) were analyzed in this study. 96.3% and 91.4% of patients reached a minimum follow‐up period of 3 and 5 years.

Results

Two hundred eight (21.1%) patients were diagnosed with SPTs. One hundred forty three (14.5%) patients developed upper aero‐digestive tract (UAD)‐SPTs, 83 (8.4%) were HNSCCs, 56 (5.7%) were lung, and 4 (0.41%) were esophageal‐SPTs. Survival analysis demonstrated clear superior OS rates for the UAD‐SPT (P < 0.008) and HNSCC–SPT (P < 0.001) groups. A comparison of survival of subgroups showed lung/esophagus to have a poorer survival when compared to all other subgroups. OS after diagnosis of an SPT was poorer when compared with no‐SPT group (P < 0.001). The mean annual risk of developing UAD‐SPTs was 2.4%.

Conclusion

These results suggest that HNSCC–SPT should not be viewed as an adverse prognostic factor. Reclassifications of UAD‐SPTs into HNSCC–SPT and non‐HNSCC–SPT better reflects their clinical behavior and prognosis. J. Surg. Oncol. 2010;101:72–77. © 2009 Wiley‐Liss, Inc.
The impact of anatomical resection for hepatocellular carcinoma that meets the milan criteria
Authors: Kamiyama Toshiya , Nakanishi Kazuaki , Yokoo Hideki , Kamachi Hirofumi , Matsushita Michiaki , Todo Satoru
Published: October 2009

Background

The aim of this study was to analyze the impact of anatomical resection for hepatocellular carcinoma (HCC) that meets the Milan criteria.

Methods

Between 1990 and 2006, 322 consecutive patients with HCC who met the Milan criteria underwent curative resection (R0) and were classified into two groups: Group A (patients with a single HCC, with a tumor diameter of 5 cm or less) and Group B (patients with multiple tumors, no more than three tumor nodules, each with a diameter of 3 cm or less). Patient survival (PS), recurrence‐free survival rates (RFS), and risk factors were analyzed.

Results

Univariate analysis revealed that in Group A, anatomical resection was the significant factor related to PS, while anatomical resection was that related to RFS. Multivariate analysis showed that in Group A, anatomical resection was a significant favorite factor associated with PS and RFS. Univariate analysis for Group B revealed that anatomical resection was the significant factor related to PS, while that related to RFS was the anatomical resection. Multivariate analysis showed that anatomical resection was a significant favorite factor for only RFS in Group B.

Conclusion

Anatomical resection improved the surgical outcome of the patients with HCC which met the Milan criteria. J. Surg. Oncol. 2010;101:54–60. © 2009 Wiley‐Liss, Inc.
Liver transplantation versus liver resection for the treatment of hepatocellular carcinoma
Authors: Lee Kyung Keun , Kim Dong Goo , Moon In Sung , Lee Myung Duk , Park Jung Hyun
Published: October 2009

Purpose

Liver resection (LR) and liver transplantation (LT) are considered the only two potentially curative treatments for hepatocellular carcinoma (HCC). Recently, there has been an intense debate as to whether LR or LT is the optimal initial treatment for patients with Child A or B cirrhosis. The aim of this study was to compare the results of LR and LT in patients with HCC and with Child A or B cirrhosis in a single center over a 10‐year period.

Method

Seventy‐eight patients were treated with LT and 130 were treated with LR. We evaluated patient characteristics, short‐term results such as hospital stay, postoperative complication, mortality, and long‐term results such as overall and recurrence‐free survival and recurrence.

Results

The hospital stay of the LT group was significantly longer than that of the LR group (P < 0.001). The postoperative complication rate and the early operative mortality rate were similar between the two groups. The overall survival rate was higher after LT than it was after LR, but not to a statistically significant degree (P = 0.267). The recurrence‐free survival rate was significantly higher after LT than it was after LR (P = 0.002). Within and beyond the Milan criteria, the overall survival rate was higher after LT than it was after LR, but not to a statistically significant degree. The recurrence‐free survival rate was significantly higher after LT than it was after LR in the patients within Milan criteria (P < 0.001). HCC recurred more frequently after resection (51.5%) than it did after transplantation (29.5%) (P < 0.001), and HCC recurrence developed in the liver more frequently after LR than it did after LT (P = 0.002). However, after recurrence, LR had better survival than LT did, but not to a statistically significant degree (P = 0.177).

Conclusion

LT should be considered as the primary treatment in patients with HCC within the Milan criteria. LR is recommended for patients with HCC beyond the Milan criteria. The LT group showed a significantly lower recurrence rate than the LR group. However, in the case of recurrence, the LT group showed a poorer long‐term outcome than the LR group. J. Surg. Oncol. 2010;101:47–53. © 2009 Wiley‐Liss, Inc.
Purely vertical upbeat nystagmus in bilateral posterior canal benign paroxysmal positional vertigo: A case report
Authors: Beyea Jason A. , Parnes Lorne S.
Published: October 2009

Vertical nystagmus occurs in patients with central vestibular system pathology. Lesions of the pons, medulla, and cerebellum lead to vertical nystagmus. Given this association, vertical nystagmus is considered pathognomonic in nature. We present a case of benign paroxysmal positional vertigo (BPPV) with positive Dix‐Hallpike bilaterally, but also with upbeat purely vertical nystagmus in the straight back head hanging position. Computed tomography imaging of the typically pathologic structures in vertical nystagmus (brainstem/posterior fossa) revealed normal anatomy. We propose this case as an instance of peripheral‐associated purely vertical nystagmus without central pathology, while building on our previous understanding of BPPV physiology. Laryngoscope, 2010
Genome‐wide transcriptome analyses reveal p53 inactivation mediated loss of miR‐34a expression in malignant peripheral nerve sheath tumours
Authors: Subramanian Subbaya , Thayanithy Venugopal , West Robert B , Lee Cheng‐Han , Beck Andrew H , Zhu Shirley , Downs‐Kelly Erinn , Montgomery Kelli , Goldblum John R , Hogendoorn Pancras CW , Corless Christopher L , Oliveira Andre M , Dry Sarah M , Nielsen Torsten O , Rubin Brian P , Fletcher Jonathan A , Fletcher Christopher DM , van de Rijn Matt
Published: October 2009

Malignant peripheral nerve sheath tumours (MPNSTs) are aggressive soft tissue tumours that occur either sporadically or in patients with neurofibromatosis type 1. The malignant transformation of the benign neurofibroma to MPNST is incompletely understood at the molecular level. We have determined the gene expression signature for benign and malignant PNSTs and found that the major trend in malignant transformation from neurofibroma to MPNST consists of the loss of expression of a large number of genes, rather than widespread increase in gene expression. Relatively few genes are expressed at higher levels in MPNSTs and these include genes involved in cell proliferation and genes implicated in tumour metastasis. In addition, a gene expression signature indicating p53 inactivation is seen in the majority of MPNSTs. Subsequent microRNA profiling of benign and malignant PNSTs indicated a relative down‐regulation of miR‐34a in most MPNSTs compared to neurofibromas. In vitro studies using the cell lines MPNST‐14 (NF1 mutant) and MPNST‐724 (from a non‐NF1 individual) show that exogenous expression of p53 or miR‐34a promotes apoptotic cell death. In addition, exogenous expression of p53 in MPNST cells induces miR‐34a and other miRNAs. Our data show that p53 inactivation and subsequent loss of expression of miR‐34a may significantly contribute to the MPNST development. Collectively, our findings suggest that deregulation of miRNAs has a potential role in the malignant transformation process in peripheral nerve sheath tumours. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Age, stage, and radiotherapy, but not primary tumor site, affects the outcome of patients with malignant rhabdoid tumors
Authors: Sultan Iyad , Qaddoumi Ibrahim , Rodríguez‐Galindo Carlos , Nassan Anwar Al , Ghandour Khalil , Al‐Hussaini Maysa
Published: October 2009

Background

Malignant rhabdoid tumors (MRTs) are aggressive and often fatal; the Surveillance, Epidemiology, and End Results (SEER) database offers an opportunity to study this rare malignancy.

Methods

From the SEER database, we extracted records of patients with a reported diagnosis of MRT and analyzed them for clinical features and survival rates by univariate and multivariate analyses.

Results

For the 229 patients included in our data, who were diagnosed from 1986 to 2005, primary tumors were located in the central nervous system (CNS) (35%), kidneys (20%), and extra‐renal non‐cranial sites (ERNC‐MRTs) (45%). Most patients with renal and CNS tumors were less than 18 years old (87% and 96%, respectively) while more than half of the patients with ERNC‐MRTs (61%) were adults. Among staged tumors, 23% were localized, 34% regional, and 43% distant. Renal tumors had significantly more metastatic disease (47%; P = 0.006) than ERNC‐MRTs. The estimated 5‐year survival for the entire group was 33 ± 3.4% (SE). Univariate and multivariate analyses showed that age at diagnosis (2–18 years), localized stage of tumors, and use of radiotherapy were significantly associated with improved survival. Adults had a better outcome than young children (<2 years old) but a poorer outcome than older children (2–18 years old); tumor stage, but not radiotherapy use, affected outcome in adults. The survival and prognostic factors of children diagnosed before and after 2000 did not differ significantly.

Conclusion

Our population‐based study indicates that age at diagnosis, tumor stage, and use of radiotherapy favorably impact survival rates of patients with MRTs. Pediatr Blood Cancer 2010; 54:35–40. © 2009 Wiley‐Liss, Inc.
Processing and properties of PLA/thermoplastic starch/montmorillonite nanocomposites
Authors: Arroyo O.H. , Huneault M.A. , Favis B.D. , Bureau M.N.
Published: October 2009

Thermoplastic starch (TPS) and polylactic acid (PLA) were compounded with natural montmorillonite (MMT) using a twin‐screw extrusion process to investigate the structure and properties of these nanocomposites and to examine the use of water to enhance clay exfoliation. Tensile and essential work of fracture measurements were performed on standard dumbbell shape samples and on double notched samples to determine the effect of MMT and PLA/TPS interfacial modification on the mechanical and fracture properties of the materials. The nanocomposite structure was investigated using X‐Ray diffraction, transmission electron microscopy, and atomic force microscopy. Differential scanning calorimetric analysis was performed on the materials to determine the effect of TPS and MMT on PLA crystallization and physical aging. It was found that the TPS can intercalate the clay structure and that the clay was preferentially located in the TPS phase or at the blend interface. This led to an improvement in tensile modulus and strength and to a reduction in fracture toughness. POLYM. COMPOS., 2010. © 2009 Society of Plastics Engineers
Vibration joining of fiber‐reinforced thermosets
Authors: Beiss T. , Menacher M. , Feulner R. , Huelder G. , Osswald T.A.
Published: October 2009

Adhesive bonding is known to be particularly suitable for thermoset composites with continuous fiber reinforcement as it does not interrupt the fibers because of drilled holes. The frequently used two‐part adhesives often require long curing times for the chemical reaction. At the Institute of Polymer Technology (LKT), a vibration‐assisted hot melt bonding technique (vibration joining) was developed, which offers short cycle times and represents a modification of hot melt bonding, using the machine technology from vibration welding. It is suitable to join thermoplastics with thermoset materials or thermosets using a thermoplastic interlayer, by taking advantage of short cycle time and good lap shear strength, compared to bonding with reactive adhesives. Polym Compos 2009 POLYM. COMPOS., 31:1205–1212, 2010. © 2009 Society of Plastics Engineers
The influence of fiber formation conditions on the structure and properties of nanocomposite alginate fibers containing tricalcium phosphate or montmorillonite
Authors: Boguń Maciej , Rabiej Stanisław
Published: October 2009

The authors devised conditions for the formation of nanocomposite calcium alginate fibers containing tricalcium phosphate (TCP) or montmorillonite (MMT). The rheological, sorptive, and strength properties of these fibers, as well as their porous and supramolecular structures were subjected to analysis. It has been concluded that the presence of nanoadditives in the material of alginate fibers decreases their susceptibility to distortion in the drawing stage. The obtained fibers are characterized by an even distribution of the nanoadditive on the fiber surface. POLYM. COMPOS., 31:1321–1331, 2010. © 2009 Society of Plastics Engineers
A “fluorescence switch” technique increases the sensitivity of proteomic detection and identification of S‐nitrosylated proteins
Authors: Tello Daniel , Tarín Carlos , Ahicart Patricia , Bretón‐Romero Rosa , Lamas Santiago , Martínez‐Ruiz Antonio
Published: October 2009

Protein S‐nitrosylation is a reversible post‐translational modification of protein cysteines that is increasingly being considered as a signal transduction mechanism. The “biotin switch” technique marked the beginning of the study of the S‐nitrosoproteome, based on the specific replacement of the labile S‐nitrosylation by a more stable biotinylation that allowed further detection and purification. However, its application for proteomic studies is limited by its relatively low sensitivity. Thus, typical proteomic experiments require high quantities of protein extracts, which precludes the use of this method in a number of biological settings. We have developed a “fluorescence switch” technique that, when coupled to 2‐DE proteomic methodologies, allows the detection and identification of S‐nitrosylated proteins by using limited amounts of starting material, thus significantly improving the sensitivity. We have applied this methodology to detect proteins that become S‐nitrosylated in endothelial cells when exposed to S‐nitroso‐L‐cysteine, a physiological S‐nitrosothiol, identifying already known S‐nitrosylation targets, as well as proteins that are novel targets. This “fluorescence switch” approach also allowed us to identify several proteins that are denitrosylated by thioredoxin in cytokine‐activated RAW264.7 (murine macrophage) cells. We believe that this method represents an improvement in order to approach the identification of S‐nitrosylated proteins in physiological conditions.
Tagging of Escherichia coli proteins with new cassettes allowing in vivo systematic fluorescent and luminescent detection, and purification from physiological expression levels
Authors: Wahl Astrid , Hubert Pierre , Sturgis James N. , Bouveret Emmanuelle
Published: October 2009

We designed cassettes allowing the systematic fusion of fluorescent or luminescent proteins preceded by the calmodulin binding peptide tag to the C–terminus of Escherichia coli proteins. The chromosomal insertion, and thus physiological expression level of these fusions, permits the study of protein localization by fluorescent microscopy and protein quantification, in vivo and dynamically in diverse conditions. Furthermore, the calmodulin binding peptide tag allows standard detection, affinity purification, and co–purification experiments. These cassettes are therefore very valuable for the versatility of experiments they make available for a given strain, from biochemistry to dynamic and in vivo studies.
Systematic prediction of human membrane receptor interactions
Authors: Qi Yanjun , Dhiman Harpreet K. , Bhola Neil , Budyak Ivan , Kar Siddhartha , Man David , Dutta Arpana , Tirupula Kalyan , Carr Brian I. , Grandis Jennifer , Bar‐Joseph Ziv , Klein‐Seetharaman Judith
Published: October 2009

Membrane receptor‐activated signal transduction pathways are integral to cellular functions and disease mechanisms in humans. Identification of the full set of proteins interacting with membrane receptors by high‐throughput experimental means is difficult because methods to directly identify protein interactions are largely not applicable to membrane proteins. Unlike prior approaches that attempted to predict the global human interactome, we used a computational strategy that only focused on discovering the interacting partners of human membrane receptors leading to improved results for these proteins. We predict specific interactions based on statistical integration of biological data containing highly informative direct and indirect evidences together with feedback from experts. The predicted membrane receptor interactome provides a system‐wide view, and generates new biological hypotheses regarding interactions between membrane receptors and other proteins. We have experimentally validated a number of these interactions. The results suggest that a framework of systematically integrating computational predictions, global analyses, biological experimentation and expert feedback is a feasible strategy to study the human membrane receptor interactome.
The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3‐D cell
Authors: Widjaja Yose Y. , Pang Chi Nam Ignatius , Li Simone S. , Wilkins Marc R. , Lambert Tim D.
Published: October 2009

Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3‐D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real‐time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein “twins” when they occur in multiple locations. Since the Interactorium permits multi‐level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net.
A novel S3S‐TAP‐tag for the isolation of T‐cell interaction partners of adhesion and degranulation promoting adaptor protein
Authors: Lehmann Roland , Meyer Johann , Schuemann Michael , Krause Eberhard , Freund Christian
Published: October 2009

The identification of modular units of cellular function is a major goal for proteomic research. Protein complexes represent important building blocks defining functionality and deciphering their composition remains a major challenge. Here, we have designed a new tandem affinity purification (TAP) tag (termed S3S‐tag) for the isolation of protein complexes. Specifically, the immune cell protein ADAP that regulates integrin adhesion was fused either C‐ or N‐terminally to the S3S‐tag. After retroviral transduction of a vector containing S3S‐tagged ADAP and internal ribosomal entry site encoded enhanced green fluorescent protein (eGFP), Jurkat T cells were sorted according to eGFP expression and further selected for expression of TAP‐tagged protein close to endogenous levels. The combination of a cleavable S‐tag and a Strep‐tag II allowed for the isolation of ADAP and associated proteins. Subsequently, stable isotope labeling with amino acids in cell culture‐based mass spectrometric analysis was performed to identify potentially specific interaction partners. Co‐purification of the known interaction partner Src kinase‐associated phosphoprotein of 55 kDa indicates the validity of our approach, while the identification of the ENA/VASP family member EVL, the guanine nucleotide exchange factor GEF‐H1 and the adaptor protein DOCK2 corroborates a link between ADAP‐mediated integrin regulation and the cytoskeleton.
A proteomic view of the facultatively chemolithoautotrophic lifestyle of Ralstonia eutropha H16
Authors: Schwartz Edward , Voigt Birgit , Zühlke Daniela , Pohlmann Anne , Lenz Oliver , Albrecht Dirk , Schwarze Alexander , Kohlmann Yvonne , Krause Cornelia , Hecker Michael , Friedrich Bärbel
Published: October 2009

Ralstonia eutropha H16 is an H2‐oxidizing, facultative chemolithoautotroph. Using 2‐DE in conjunction with peptide mass spectrometry we have cataloged the soluble proteins of this bacterium during growth on different substrates: (i) H2 and CO2, (ii) succinate and (iii) glycerol. The first and second conditions represent purely lithoautotrophic and purely organoheterotrophic nutrition, respectively. The third growth regime permits formation of the H2‐oxidizing and CO2‐fixing systems concomitant to utilization of an organic substrate, thus enabling mixotrophic growth. The latter type of nutrition is probably the relevant one with respect to the situation faced by the organism in its natural habitats, i.e. soil and mud. Aside from the hydrogenase and Calvin‐cycle enzymes, the protein inventories of the H2‐CO2‐ and succinate‐grown cells did not reveal major qualitative differences. The protein complement of the glycerol‐grown cells resembled that of the lithoautotrophic cells. Phosphoenolpyruvate (PEP) carboxykinase was present under all three growth conditions, whereas PEP carboxylase was not detectable, supporting earlier findings that PEP carboxykinase is alone responsible for the anaplerotic production of oxaloacetate from PEP. The elevated levels of oxidative stress proteins in the glycerol‐grown cells point to a significant challenge by ROS under these conditions. The results reported here are in agreement with earlier physiological and enzymological studies indicating that R. eutropha H16 has a heterotrophic core metabolism onto which the functions of lithoautotrophy have been grafted.
Quantitative prediction of protein–protein binding affinity with a potential of mean force considering volume correction
Authors: Su Yu , Zhou Ao , Xia Xuefeng , Li Wen , Sun Zhirong
Published: October 2009

Quantitative prediction of protein–protein binding affinity is essential for understanding protein–protein interactions. In this article, an atomic level potential of mean force (PMF) considering volume correction is presented for the prediction of protein–protein binding affinity. The potential is obtained by statistically analyzing X‐ray structures of protein–protein complexes in the Protein Data Bank. This approach circumvents the complicated steps of the volume correction process and is very easy to implement in practice. It can obtain more reasonable pair potential compared with traditional PMF and shows a classic picture of nonbonded atom pair interaction as Lennard‐Jones potential. To evaluate the prediction ability for protein–protein binding affinity, six test sets are examined. Sets 1–5 were used as test set in five published studies, respectively, and set 6 was the union set of sets 1–5, with a total of 86 protein–protein complexes. The correlation coefficient (R) and standard deviation (SD) of fitting predicted affinity to experimental data were calculated to compare the performance of ours with that in literature. Our predictions on sets 1–5 were as good as the best prediction reported in the published studies, and for union set 6, R = 0.76, SD = 2.24 kcal/mol. Furthermore, we found that the volume correction can significantly improve the prediction ability. This approach can also promote the research on docking and protein structure prediction.
Folding and assembly kinetics of procaspase‐3
Authors: Milam Sara L. , Clark A. Clay
Published: October 2009

Caspases are vital to apoptosis and exist in the cell as inactive zymogens. Dimerization is central to procaspase activation because the active sites are comprised of loops from both monomers. Although initiator procaspases are stable monomers until activated on cell death scaffolds, the effector caspases, such as procaspase‐3, are stable dimers. The activation mechanisms are reasonably well understood in terms of polypeptide chain cleavage and subsequent active site rearrangements in the dimer, but the mechanisms that govern dimer assembly are not known. To further understand procaspase dimerization, we examined the folding and assembly of procaspase‐3 by fluorescence emission, circular dichroism, differential quenching by acrylamide, anisotropy, and enzyme activity assays. Single‐mixing stopped‐flow refolding studies showed a complex burst phase in which multiple monomeric species form rapidly. At longer times, the monomer folds through several intermediates, some of which appear to be off‐pathway or misfolded, before eventually forming a dimerization‐competent species. Enzyme activity studies demonstrated a slow rate of dimerization (∼70 M−1 s−1). In addition, single‐mixing stopped‐flow unfolding studies revealed a complex unfolding process with a slow rate of dimer dissociation. Interestingly, multiple dimeric species were observed in the burst phase for unfolding, suggesting that the native ensemble consists of at least two major conformations. Collectively, these results demonstrate complex folding and unfolding behavior for procaspase‐3 and suggest that slow dimerization results from the lack of stabilizing native contacts in the initial encounter complex.
Revealing the dimer dissociation and existence of a folded monomer of the mature HIV‐2 protease
Authors: Louis John M. , Ishima Rieko , Aniana Annie , Sayer Jane M.
Published: October 2009

Purification and in vitro protein‐folding schemes were developed to produce monodisperse samples of the mature wild‐type HIV‐2 protease (PR2), enabling a comprehensive set of biochemical and biophysical studies to assess the dissociation of the dimeric protease. An E37K substitution in PR2 significantly retards autoproteolytic cleavage during expression. Furthermore, it permits convenient measurement of the dimer dissociation of PR2E37K (elevated Kd ∼20 nM) by enzyme kinetics. Differential scanning calorimetry reveals a Tm of 60.5 for PR2 as compared with 65.7°C for HIV‐1 protease (PR1). Consistent with weaker binding of the clinical inhibitor darunavir (DRV) to PR2, the Tm of PR2 increases by 14.8°C in the presence of DRV as compared with 22.4°C for PR1. Dimer interface mutations, such as a T26A substitution in the active site (PR2T26A) or a deletion of the C‐terminal residues 96–99 (PR21–95), drastically increase the Kd (>105‐fold). PR2T26A and PR21–95 consist predominantly of folded monomers, as determined by nuclear magnetic resonance (NMR) and size‐exclusion chromatography coupled with multiangle light scattering and refractive index measurements (SMR), whereas wild‐type PR2 and its active‐site mutant PR2D25N are folded dimers. Addition of twofold excess active‐site inhibitor promotes dimerization of PR2T26A but not of PR21–95, indicating that subunit interactions involving the C‐terminal residues are crucial for dimer formation. Use of SMR and NMR with PR2 facilitates probing for potential inhibitors that restrict protein folding and/or dimerization and, thus, may provide insights for the future design of inhibitors to circumvent drug resistance.
Efficacy and attractiveness of zinc phosphide bait in common voles (Microtus arvalis)
Authors: Jacob Jens , Budde Mechthild , Leukers Angela
Published: October 2009

BACKGROUND: Minimising the concentration of active ingredient in rodenticide bait is desirable economically and for the protection of the agroecosystem. This study aimed to identify a zinc phosphide concentration that balances palatability and efficacy for common vole (Microtus arvalis Pall.) management and to compare the attractiveness of two bait carriers.

RESULTS: Bait uptake of voles was reduced by 87–98% compared with plain bait when bait contained 0.4–3.2% zinc phosphide. There was an almost 50% decrease in the uptake of zinc phosphide when the zinc phosphide concentration of bait was doubled. Red dye used in commercially available bait decreased bait consumption by 10%. Daily consumption of zinc phosphide bait on days 2 to 5 was half the consumption on the first day of exposure. In bait choice tests, wheat kernels were preferred initially, but within 12 h similar amounts of wheat‐based pellets and wheat kernels were eaten.

CONCLUSIONS: According to the results from the laboratory trial, a zinc phosphide concentration of 2.1% seemed to balance uptake/efficacy best and may be most appropriate for the management of common vole populations. This concentration is substantially lower than the concentration used in many registered products. A reduced concentration of active ingredient and the use of pellet bait instead of wheat which is highly attractive for birds may have advantages for agroecosystem health when applying zinc phosphide for rodent control. © Jens Jacob, Mechthild Budde and Angela Leukers, employees of the Federal Research Centre for Cultivated Plants, Germany. Printed with permission.
QSAR modeling of photosynthesis‐inhibiting nostoclide derivatives
Authors: Teixeira Róbson Ricardo , Pinheiro Patrícia F , Barbosa Luiz Cláudio de Almeida , Carneiro José Walkimar de M , Forlani Giuseppe
Published: October 2009

BACKGROUND: A statistical model, built using the CODESSA software package, was developed to describe the relationship between the structure of nostoclide derivatives and their ability to interfere with the electron transport chain in the Hill reaction.

RESULTS: A QSAR treatment was carried out on a series of compounds designed using the naturally occurring toxin nostoclides to correlate molecular descriptors with their in vitro biological activity (the ability to interfere with light‐driven reduction of ferricyanide by isolated spinach chloroplast thylakoid membranes). The treatment using the CODESSA software package resulted in a three‐parameter model with n = 19, R2 = 0.83, F = 23.8 and R2cv = 0.72. In the proposed model, the Image of Onsager Kirkwood solvation energy, which gives a measure of the polarity of a given compound, is the most important descriptor. The model was internally validated.

CONCLUSIONS: The results obtained in this study indicate that polarity, as expressed by the dipole moment, is the most relevant molecular property determining efficiency of photosynthetic inhibitory activity. Copyright © 2009 Society of Chemical Industry
Non‐local electron‐positron correlation effects for SiC
Authors: Rubaszek Anna
Published: October 2009

In the present work we study the influence of the electron‐positron (e‐p) interaction on the resulting e‐p momentum density and positron lifetime for a perfect SiC of 3C cubic structure. Results obtained within the independent particle model (IPM) and the local density approximation (LDA) are compared with their counterparts calculated beyond the local approach, within the weighted density approximation (WDA) (Rubaszek et al., Phys. Rev. B 58, 11285 (1998); Rubaszek et al., Phys. Rev. B 61, 10100 (2000) [1]). It is shown that the positron annihilation characteristics, calculated within various approximations to the e‐p correlation functions, are very sensitive to the approach. Non‐locality of the e‐p interaction is of vital importance for core electrons and has less influence on the valence electrons contribution to the e‐p momentum density and positron lifetime. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron annihilation lifetime data and actual porosity of polymers
Authors: Shantarovich Victor , Gustov Vadim , Polyakova Aleksandra , Belousova Eleonora , Filimonov Mikhail , Yampolskii Yurii
Published: October 2009

Application of the three‐component LT9.0 analyses and discrete four‐component PATFIT analysis to PAL distribution in some porous polymers, such as PIM‐1, AF2400, AF1600, PTMSP, give practically the same good fitting. In the conditions of this uncertainty, some additional experiments (thermomechanical tests, NMR on the protons of the absorbed water, thermo‐stimulated luminescence TSL, low temperature gas sorption BET, mathematic molecular‐dynamic simulation) give some arguments in favour of non‐Gaussian distribution of elementary free volumes EFV in some porous polymers and their possible heterogeneity. Furthermore, a comparison of PAL and TSL data confirm the idea on the interconnection between the rigidity of the polymer chains and effective size of the EFV. This interconnection is illustrated by the correlation of the o ‐Ps lifetime and intensity of the high‐temperature peak in the TSL glow curve. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrogen sorption kinetics in Nb doped Mg: role of Nb clustering and open volume defects formation
Authors: Toniutti L. , Checchetto R. , Mengucci P. , Miotello A. , Brusa R. S.
Published: October 2009

Mg and Nb‐doped Mg films were grown by rf magnetron sputtering and their structure was studied as a function of the hydrogen sorption‐desorption cycles. The Nb doping improves the H desorption kinetics: anyway the characteristic desorption time increases in the first eight cycles until the desorption kinetics attain a stationary condition. The as grown Mg films are found to be rich of vacancies, while in the as grown Nb doped Mg films small vacancy clusters are present. After eight cycles the dispersed Nb agglomerates forming clusters of few nanometers. The evolution, under H cycling, of the detected vacancies and vacancy clusters is found to be very different in the Mg and in the Nb‐doped Mg films. The results are discussed and correlated to the desorption kinetics of the two systems. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positronium formation in a liquid phase: Influence of intratrack reactions and temperature
Authors: Stepanov Sergey V. , Byakov Vsevolod M. , Duplâtre Gilles , Zvezhinskiy Dmitriy S. , Lomachuk Yuri V.
Published: October 2009

This work clarifies some discrepancies between conventional models, used in positron annihilation lifetime (PAL) spectroscopy, and experimental data. The importance of taking into account Ps interactions with primary intratrack radiolytic products is demonstrated, for example, for PAL data in water. We examine the applicability of a nonhomogeneous chemical kinetics approach and of a well‐known expression for the reaction rate constants to describe intratrack processes, and show that the prescribed diffusion approximation (PDA) is a reasonable model for this. Moreover, we have derived an analytical expression for the time‐dependent reaction rate coefficient, which previously entered PDA as an external parameter. Preliminary fittings of the PAL spectra in H2O over a wide temperature range indicate that Ps reactions in intratrack processes are diffusion controlled (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron source based on the 48V isotope dedicated to positron lifetime spectroscopy
Authors: Dryzek Jerzy
Published: October 2009

In the paper we consider application of the 48V isotope as a source in the positron lifetime spectroscopy. The isotope was produced in the 48Ti(p,n)48V reaction using 15 MeV proton beam. As a target the natural titanium thin plate was used. The measurements using the typical positron lifetime spectrometer have shown the usefulness of the source obtained for this application. Due to its properties, the source may be used for measurements of positron annihilation characteristics in high temperature or aggressive environments. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron annihilation study of ion‐exchanged forms of Nafion® membrane
Authors: Mohamed Hamdy F. M. , Kobayashi Y. , Kuroda C. S. , Ohira A.
Published: October 2009

Positron annihilation lifetime and oxygen permeability in ion‐exchanged forms (H+‐, Na+‐, K+‐, Cu2+‐, Ni2+‐, and Fe3+‐forms) of Nafion® membranes for polymer electrolyte fuel cells (PEFC's) have been investigated as a function of temperature. Exchange of H+ with Cu2+, Ni2+, or Fe3+ in Nafion® decreases both the o ‐Ps lifetime and its intensity, being interpreted as the result of inhibition and quenching of Ps. For the H+‐, Na+‐, and K+‐forms good correlations were observed between the logarithm of the O2 permeability and o ‐Ps lifetime (free volume size) at different temperatures indicating the important role played by the free volume in O2 permeation. Considerable downward deviation of the correlations for the Na+‐ and K+‐forms from the H+‐form revealed the importance of polymer stiffening in O2 permeation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron annihilation studies on 9Cr reduced activation ferritic/martensitic steels
Authors: Ragunanthan V. , Babu S. Hari , Chirayath Varghese Anto , Rajaraman R. , Amarendra G. , Saroja S. , Sundar C. S. , Alamo Ana , Raj Baldev
Published: October 2009

Positron annihilation, microstructural and hardness studies were carried out in a 9Cr reduced activation ferrtic ‐ martensitic steel (9%Cr‐1%W‐0.1%C) subjected to isochronal annealing in the temperature range of 300 to 1273 K. The measured lifetime in the ‘as‐received’ (normalized and tempered) condition was 147 ps, which exhibited considerable reduction around 670 K, indicating the annealing out of small vacancy‐defects in the matrix or matrix‐precipitate interfaces. The observed positron lifetime exhibited a broad maximum between 670 K and 1070 K, indicating the existence of second annealing stage. Between 1070 K and 1270 K, a sharp maxium is exhibited in lifetime as third annealing stage. Doppler S‐parameter has also exhibited similar annealing stages. Ab‐intio positron lifetime calculations for various defect‐impurity cluster configurations in ferritic‐matrix based Fe system are reported to understand the experimental results. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quenched‐in vacancies in Fe‐Al alloys
Authors: Melikhova Oksana , Cizek Jakub , Prochazka Ivan , Kuriplach Jan , Lukac Frantisek , Cieslar Miroslav , Brauer Gerhard , Anwand Wolfgang
Published: October 2009

Quenched‐in vacancies in Fe3Al‐based intermetallics were studied in this work. A stoichiometric Fe3Al alloy was compared with non‐stoichiometric specimens either with a deficiency or with an excess in Al content. Vacancies in specimens quenched from the disordered A2 phase were investigated by three independent techniques of positron annihilation spectroscopy: positron lifetime (LT) studies, slow positron implantation spectroscopy (SPIS) with a continuous slow positron beam, and coincidence Doppler broadening (CDB). It was found that the combination of LT and SPIS enables to determine reliably even very high concentrations of vacancies. Infor‐mation about the local chemical environment of quenched‐in vacancies was obtained from CDB measurements. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrogen‐induced defects in Pd films
Authors: Cizek Jakub , Prochazka Ivan , Melikhova Oksana , Vlach Martin , Zaludova Nada , Brauer Gerhard , Anwand Wolfgang , Egger Werner , Sperr Peter , Hugenschmidt Christoph , Gemma Ryota , Pundt Astrid , Kirchheim Reiner
Published: October 2009

Hydrogen absorbed in crystalline solids causes a lattice expansion and the formation of hydride phases. Contrary to free standing bulk samples, thin films are fixed at substrates, which prevent their in‐plane expansion. This makes hydrogen‐induced expansion of thin films highly anisotropic and leads to the formation of high stresses in hydrogen loaded thin films. As a consequence, lattice defects may be created in thin films loaded with hydrogen. This work reports about defects created by hydrogen loading in epitaxial Pd films deposited on Al2O3 substrates by cold cathode beam sputtering. Hydrogen‐induced defects are characterized by positron annihilation spectroscopy performed with variable energy slow positron beams. Extended studies of defect depth profile and its development with increasing concentration of hydrogen are performed by measurement of Doppler broadening of annihilation profile using a continuous positron beam. Selected states are investigated also by positron lifetime spectroscopy on an intense pulsed positron beam. Firstly, the microstructure of virgin films is characterized. Subsequently, the hydrogen concentration in the films is increased step‐by‐step by electrochemical charging. The development of the film microstructure and the evolution of defects are investigated. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron annihilation studies of defects in Si1‐xGex/SOI heterostructures
Authors: Calloni A. , Ferragut R. , Moia F. , Dupasquier A. , Isella G. , Marongiu D. , Norga G. , Fedorov A. , Chrastina D.
Published: October 2009

The strain of a SiGe alloy epitaxially grown on Si can be released by heating at 750°C. However the strain relaxation is accompanied by the generation of threading dislocations and associated point defects. The attempted remedy is to let SiGe grow on a very thin Si substrate on top of a SOI heterostructure, with the purpose of concentrating the defects at the Si‐SiO2 interface of the SOI substrate. A slow positron beam was used to investigate the effectiveness of the remedy. The positron diffusion length in SiGe decreases after the thermal treatment. This result shows the generation of lattice defects still occurs in the SiGe layer, in spite of the deposition on SOI. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)