bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of organisms for the co-evolution-based study of protein interactions
Authors: Herman Dorota , Ochoa David , Juan David , Lopez Daniel , Valencia Alfonso , Pazos Florencio 
Published: September 2011

Abstract

Background
The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature.

Results
We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions.

Conclusions
In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.
Overexpression of carbonic anhydrase and HIF-1α in Wilms tumours
Authors: Dungwa Josiah V , Hunt Linda P , Ramani Pramila 
Published: September 2011

Abstract

Background
Overexpression of carbonic anhydrase (CA IX) is associated with poor survival in several adult-type cancers but its expression is undocumented in Wilms tumour (WT), the most common tumour of the paediatric kidney.

Methods

CA9 expression was measured using polymerase chain reaction (PCR) in 13 WTs and matched-paired non-neoplastic kidneys (NKs). CA IX and hypoxia-inducible factor-1 α-subunit (HIF-1α) protein were quantified in 15 matched-paired WTs and NKs using enzyme-linked immunosorbent assays. CA IX and HIF-1α were localised by immunostaining tissue sections of 70 WTs (untreated WTs, n = 22; chemotherapy-treated WTs, n = 40; relapsed/metastatic WTs, n = 8). CA IX-positive untreated WTs (n = 14) were immunostained for vascular endothelial growth factor (VEGF), glucose transporter-1 (GLUT1) and CD31. Double staining for CA IX and CD31 was performed in WTs (n = 14).

Results

CA9 full length (FL) was significantly up-regulated in WTs compared to NKs (p = 0.009) by real-time PCR. Conventional PCR showed expression of alternative splice variant in all NKs and WTs but FL in WTs only. WTs showed a 2-fold increase in CA IX protein over NKs (p = 0.01). HIF-1α levels were up-regulated in WTs compared to NKs, although the difference was not statistically significant (p = 0.09). CA IX and HIF-1α immunolocalisation were observed in 63% and 93% of WTs, respectively. The median fraction of cells staining positively for CA IX and HIF-1α was 5% and 22%, respectively. There was no significant association between the expression of either CA IX or HIF-1α and clinicopathological variables in WTs resected following chemotherapy. VEGF and GLUT1 immunoreactivity was seen in 94% and 100% with the median fraction of 10% and 60% respectively. Co-expression and co-localisation of all four hypoxia markers was seen in 7/14 and 6/14 cases respectively. CA IX was seen in well vascularised areas as well as in the peri-necrotic areas.

Conclusions
Carbonic anhydrase 9 (mRNA and protein), and HIF-1α protein are overexpressed in a significant portion of WTs. No significant association was detected between the expression of either CA IX or HIF-1α and clinicopathological variables in WTs resected following chemotherapy. Cellular localisation studies in untreated WTs suggest that CA IX and HIF-1α are regulated by hypoxia and non-hypoxia mechanisms.
Metabolic engineering of the L-phenylalanine pathway in Escherichia coli for the production of S- or R-mandelic acid
Authors: Sun Zhoutong , Ning Yuanyuan , Liu Lixia , Liu Yingmiao , Sun Bingbing , Jiang Weihong , Yang Chen , Yang Sheng 
Published: September 2011

Abstract

Background
Mandelic acid (MA), an important component in pharmaceutical syntheses, is currently produced exclusively via petrochemical processes. Growing concerns over the environment and fossil energy costs have inspired a quest to develop alternative routes to MA using renewable resources. Herein we report the first direct route to optically pure MA from glucose via genetic modification of the L-phenylalanine pathway in E. coli.

Results
The introduction of hydroxymandelate synthase (HmaS) from Amycolatopsis orientalis into E. coli led to a yield of 0.092 g/L S-MA. By combined deletion of competing pathways, further optimization of S-MA production was achieved, and the yield reached 0.74 g/L within 24 h. To produce R-MA, hydroxymandelate oxidase (Hmo) from Streptomyces coelicolor and D-mandelate dehydrogenase (DMD) from Rhodotorula graminis were co-expressed in an S-MA-producing strain, and the resulting strain was capable of producing 0.68 g/L R-MA. Finally, phenylpyruvate feeding experiments suggest that HmaS is a potential bottleneck to further improvement in yields.

Conclusions
We have constructed E. coli strains that successfully accomplished the production of S- and R-MA directly from glucose. Our work provides the first example of the completely fermentative production of S- and R-MA from renewable feedstock.
Tuning the electronic transport properties of graphene through functionalisation with fluorine
Authors: Withers Freddie , Russo Saverio , Dubois Marc , Craciun Monica F 
Published: September 2011

Abstract
We demonstrate the possibility to tune the electronic transport properties of graphene mono-layers and multi-layers by functionalisation with fluorine. For mono-layer samples, with increasing the fluorine content, we observe a transition from electronic transport through Mott variable range hopping (VRH) in two dimensions to Efros-Shklovskii VRH. Multi-layer fluorinated graphene with high concentration of fluorine show two-dimensional Mott VRH transport, whereas CF0.28 multi-layer flakes exhibit thermally activated transport through near neighbour hopping. Our experimental findings demonstrate that the ability to control the degree of functionalisation of graphene is instrumental to engineer different electronic properties in graphene materials.
Ethnozoology in Brazil: current status and perspectives
Authors: Alves Rômulo RN , Souto Wedson MS 
Published: September 2011

AbstractAncient connections between animals and human are seen in cultures throughout the world in multiple forms of interaction with the local fauna that form the core of Ethnozoology. Historically, ethnozoological publications grew out of studies undertaken in academic areas such as zoology, human ecology, sociology and anthropology - reflecting the interdisciplinary character of this discipline. The rich fauna and cultural diversity found in Brazil, with many different species of animals being used for an extremely wide diversity of purposes by Amerindian societies (as well as the descendents of the original European colonists and African slaves), presents an excellent backdrop for examining the relationships that exist between humans and other animals. This work presents a historical view of ethnozoological research in Brazil and examines its evolution, tendencies, and future perspectives. In summary, literature researches indicated that ethnozoology experienced significant advances in recent years in Brazil, although from a qualitative point of view improvement is still needed in terms of methodological procedures, taxonomic precision, and the use of quantitative techniques. A wide range of methodologies and theories are available in different areas of learning that can be put to good use in ethnozoological approaches if the right questions are asked. The challenges to studying ethnozoology in Brazil are not insignificant, and the tendencies described in the present study may aid in defining research strategies that will maintain the quantitative growth observed in the recent years but likewise foster needed qualitative improvements.
The presence of a lipoma in the Eustachian tube: a case report
Authors: Liu Zhuofu , Wang Dehui , Liu Quan 
Published: September 2011

Abstract

Introduction
The incidence of lipoma in the Eustachian tube is very rare, and to the best of our knowledge, has not been reported in the literature. Tumors that form in the cartilaginous portion of the Eustachian tube can be successfully removed by an endoscopic approach.

Case presentation
We report an incidentally-detected lipoma of the Eustachian tube in a 34-year-old Asian woman with a six-year history of persistent otitis media in her right ear. Our patient underwent surgery five years ago for the possibility of a choanal polyp, but her ear symptoms continued to be problematic following the surgery. Our patient was examined at our hospital, and computed tomography revealed a well-defined, hypodense, non-enhancing lesion involving the right Eustachian tube, measuring 1.6 × 2.4 cm. The mass was excised using an endoscopic approach, and was found to originate from the cartilaginous portion of the Eustachian tube. The tumor was sent for histopathologic evaluation. The postoperative course went smoothly, and our patient recovered during follow-up over the next five months.

Conclusion
Lipoma of the Eustachian tube is very rare compared with other tumors. Improved radiologic modalities aid the diagnosis of this benign tumor. Endoscopic removal of the tumor is possible and has helped in early recovery.
Lymphocyte-Depleted Classical Hodgkin's Lymphoma: A Comprehensive Analysis From the German Hodgkin Study Group
Authors: Klimm Beate , Franklin Jeremy , Stein Harald , Eichenauer Dennis A. , Haverkamp Heinz , Diehl Volker , Fuchs Michael , Borchmann Peter , Engert Andreas 
Published: September 2011

Purpose To investigate the clinical characteristics and treatment outcome of patients with lymphocyte-depleted classical Hodgkin's lymphoma (LDCHL) compared with other histologic subtypes of Hodgkin's lymphoma (HL). Patients and Methods From a total of 12,155 evaluable patients with biopsy-proven HL treated within the German Hodgkin Study Group trials HD4 to HD15, 10,019 patients underwent central expert pathology review. Eighty-four patients with LDCHL (< 1%) were identified and confirmed. The median follow-up time was 67 months. Results Patients with LDCHL, compared with patients with other histologic subtypes, presented more often with advanced disease (74% v 42%, respectively; P < .001) and “B” symptoms (76% v 41%, respectively; P < .001). Other risk factors were also more frequent in patients with LDCHL. Complete remission or unconfirmed complete remission was achieved in 82% of patients with LDCHL compared with 93% of patients with other HL subtypes (P < .001), and more patients with LDCHL had progressive disease. At 5 years, progression-free survival (PFS) and overall survival (OS) were significantly lower in patients with LDCHL compared with patients with other HL subtypes (PFS, 71% v 85%, respectively; P < .001; OS, 83% v 92%, respectively; P = .0018). However, when analyzing the subgroup of patients who underwent treatment with intensified or dose-dense bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone, patients with LDCHL (n = 39) had similar outcomes when compared with patients with other subtypes of HL (n = 3,564; P = .61). Conclusion LDCHL has a different pattern from other HL subtypes with more clinical risk factors at initial diagnosis and significantly poorer prognosis. Patients with LDCHL should be treated with modern dose-intense treatment strategies.
High-sensitivity troponin assays in the evaluation of patients with acute chest pain in the emergency department
Authors: Christ Michael , Bertsch Thomas , Popp Steffen , Bahrmann Philipp , Heppner Hans-Jürgen , Müller Christian 
Published: September 2011

AbstractEvaluating patients with acute chest pain presenting to the emergency department remains an ongoing challenge. The spectrum of etiologies in acute chest pain ranges from minor disease entities to life-threatening diseases, such as pulmonary embolism, acute aortic dissection or acute myocardial infarction (MI). The diagnosis of acute MI is usually made integrating the triad of patient history and clinical presentation, readings of 12-lead ECG and measurement of cardiac troponins (cTn). Introduction of high-sensitivity cTn assays substantially increases sensitivity to identify patients with acute MI even at the time of presentation to the emergency department at the cost of specificity. However, the proportion of patients presenting with cTn positive, non-vascular cardiac chest pain triples with the implementation of new sensitive cTn assays increasing the difficulty for the emergency physician to identify those patients who are at need for invasive diagnostics. The main objectives of this mini-review are 1) to discuss elements of disposition decision made by the emergency physician for the evaluation of chest pain patients, 2) to summarize recent advances in assay technology and relate these findings into the clinical context, and 3) to discuss possible consequences for the clinical work and suggest an algorithm for the clinical evaluation of chest pain patients in the emergency department.
Refiner bleaching in a peroxide-based ATMP process compared with conventional bleaching
Authors: Gorski Dmitri , Johansson Lars , Engstrand Per 
Published: September 2011

AbstractThe aim of this study was to compare refiner bleaching with conventional laboratory bleaching by means of hydrogen peroxide and magnesium hydroxide. Refiner bleaching in this study was a part of the ATMP (advanced thermo mechanical pulping) process, in which bleaching chemicals are added to the first stage refiner. Unbleached reference pulp which underwent similar mechanical treatment as refiner bleached pulp was used for laboratory bleaching. Bleaching efficiency was found to be almost equal for pilot scale refiner bleaching and conventional laboratory bleaching. A brightness increase of 10 ISO% was reached with addition of 26 kg t-1hydrogen peroxide leading to a final brightness of 66 ISO% using both methods. Slightly more COD (52 kg t-1compared with 46 kg t-1) was generated in refiner bleaching compared with conventional laboratory bleaching to equal brightness with the same chemicals added.
Robust Inversion of Time-domain Electromagnetic Data: Application to Unexploded Ordnance Discrimination
Authors: Beran Laurens , Billings Stephen , Oldenburg Doug 
Published: September 2011

We invert time-domain electromagnetic data for the purpose of discriminating between buried unexploded ordnance (UXO) and non-hazardous metallic clutter. The observed secondary magnetic field radiated by a conductor is forward modeled as a linear combination of decaying, orthogonal dipoles. We show via a perturbation analysis that errors in the measurement of sensor position propagate to non-normal errors on the observed data. A least squares (L2) inversion assumes normal errors on the data, so non-normal errors have the potential to bias dipole parameter estimates. In contrast, robust norms are designed to downweight the effect of outlying (noisy) data and so can provide useful parameter estimates when there is a non-normal component to the noise. When positional errors are modeled as independent Gaussian perturbations, we find that weighted least squares and robust inversions have comparable performance. Both inversion techniques estimate data uncertainties from observed data, and this has the effect of making the least squares inversion robust to outliers. However, when simulated errors are correlated, robust inversion with a bisquare norm provides a marked improvement over L2 inversion. Application of robust inversion to real data sets from Camp Sibert, Alabama produced an incremental improvement to the initial L2 inversion, identifying outlying ordnance items and improving discrimination performance.
Genotypic tropism of antiretroviral‐treated patients with drug resistant HIV‐1
Authors: Parczewski Milosz , Leszczyszyn‐Pynka Magdalena , Urbanska Anna , Bander Dorota , Boron‐Kaczmarska Anna 
Published: September 2011

AbstractCCR5 inhibitors remain an attractive antiretroviral treatment option for HIV‐infected patients; however, tropism testing should be utilized prior their introduction. This study analyzed genotypic HIV‐1 tropisms in patients with evidence of genotypic drug resistance to antiretroviral therapies in Northwest Poland. V3 loop sequences were analyzed from plasma samples obtained from patients presenting with virologic treatment failure while on combined antiretroviral treatment and with evidence of genotypic drug resistance. Genotypic X4 and R5 tropisms were identified using the geno2pheno algorithm with a false positive rate threshold set at 10%. Clinical data for all patients examined was collected, in addition to determining the CCR5 Δ32 genotype and calculating the genotypic susceptibility score (GSS). Virologic treatment failure and the presence of drug resistant mutations were observed in 37/450 (8.4%) patients on cART (combination antiretroviral therapy) with successful tropism analysis carried out on 35 (95%) cases. In 22 (62.9%) and 13 (37.1%) cases the R5 and X4 tropisms were predicted, respectively. An association between viral X4 tropism and the M41L (P = 0.04) resistance mutation and R5 tropism and the K103N (P = 0.07) resistance mutation were observed. GSS values were lower in the group with NRTI (P = 0.01) and NNRTI resistance (P = 0.048). In the majority of the drug resistant patients, R5 tropic viruses were found. As genotypic tropism testing is easy to carry out and interpret, its use in clinical practice would be highly useful in determining the use of appropriate drug therapies. J. Med. Virol. 83:1869–1875, 2011. © 2011 Wiley‐Liss, Inc.
Adherence, therapeutic intensity, and the number of dispensed drugs
Authors: Hovstadius Bo , Petersson Göran 
Published: September 2011

ABSTRACTPurposeTo estimate non‐adherence in relation to the therapeutic intensity (TI) and the number of dispensed drugs per individual and study whether the TI can be used as an estimator of non‐adherence with an increasing number of drugs.MethodsThe study comprised an individual‐based register of all dispensed outpatient prescriptions in Sweden in 2006, including 6.2 million individuals. The applied definition of drug was the chemical entity or substance comprising the fifth level in the World Health Organisation's Anatomic, Therapeutic, Chemical classification. The defined daily dosage per individual during 12 months was applied as an indicator of the TI.ResultsWe found a positive linear relation between the TI and the increasing number of dispensed drugs per individual, both for men and women. We found a slightly diminishing TI with an increasing number of drugs only for the age groups above 70 years, at a level above 13 drugs per individual.ConclusionsThe linear relationship between the TI and the increasing number of dispensed drugs per individual provides poor support for using decreasing TI as an estimator of non‐adherence. The low rate of cost‐related non‐adherence in Sweden might contribute to explaining the linear relationship. Copyright © 2011 John Wiley & Sons, Ltd.
Starch re‐crystallization kinetics as a function of various cations
Authors: Beck Margit , Jekle Mario , Becker Thomas 
Published: September 2011

AbstractStarch retrogradation is the main cause of quality deterioration in starch‐containing foods during storage. The current work investigates the effect of different cations on the retrogradation of corn starch and the potential of reducing starch retrogradation with the aim of preparing products with an extended shelf life. To gelatinize the starch, starch–water suspensions containing various chloride salts (LiCl, NaCl, KCl, MgCl2, CaCl2, and NH4Cl) were heated in a DSC, stored up to 504 h at 8°C, and reheated again. Analysis of gelatinization behavior for each salt type indicates a relationship to the aW‐value of the starch–water system. The degree of re‐crystallization was calculated using the Avrami equation, and indicates that the starch re‐crystallization rate (k) is significantly (p < 0.01) reduced with the addition of a cation, unlike the reference (starch–water systems without salt). Further, bivalent cations such as Ca2+, Mg2+ decreased the starch re‐crystallization rate (k) more than univalent cations (Li+, NH, Na+, and K+). This result may be based on the theory that high cations with higher charge densities show greater hydration, and, therefore, lower aW‐values, than cations with lower charge densities. The results illustrate important results for predicting starch quality change when using sodium replacements.
Antibiofilm Effects of Azithromycin and Erythromycin on Porphyromonas gingivalis
Authors: Maezono H. , Noiri Y. , Asahi Y. , Yamaguchi M. , Yamamoto R. , Izutani N. , Azakami H. , Ebisu S. 
Published: September 2011

ABSTRACT

Antibiotic resistance of biofilm-grown bacteria contributes to chronic infections, such as marginal and periapical periodontitis, which are strongly associated with
Porphyromonas gingivalis
. Concurrent azithromycin (AZM) administration and mechanical debridement improve the clinical parameters of periodontal tissue
in situ
. We examined the
in vitro
efficacy of AZM against
P. gingivalis
biofilms. The susceptibilities of adherent
P. gingivalis
strains 381, HW24D1, 6/26, and W83 to AZM, erythromycin (ERY), ampicillin (AMP), ofloxacin (OFX), and gentamicin (GEN) were investigated using a static model. The optical densities of adherent
P. gingivalis
cells were significantly decreased by using AZM and ERY at sub-MIC levels compared with those of the controls in all the strains tested, except for the effect of ERY on strain W83. AMP and OFX inhibited
P. gingivalis
adherent cells at levels over their MICs, and GEN showed no inhibition in the static model. The effects of AZM and ERY against biofilm cells were investigated using a flow cell model. The ATP levels of
P. gingivalis
biofilms were significantly decreased by AZM at concentrations below the sub-MICs; however, ERY was not effective for inhibition of
P. gingivalis
biofilm cells at their sub-MICs. Furthermore, decreased density of
P. gingivalis
biofilms was observed three-dimensionally with sub-MIC AZM, using confocal laser scanning microscopy. These findings suggest that AZM is effective against
P. gingivalis
biofilms at sub-MIC levels and could have future clinical application for oral biofilm infections, such as chronic marginal and periapical periodontitis.
Draft Genome Sequence of Lactobacillus malefermentans KCTC 3548
Authors: Kim Dong-Wook , Choi Sang-Haeng , Kang Aram , Nam Seong-Hyeuk , Kim Dae-Soo , Kim Ryong Nam , Kim Aeri , Park Hong-Seog 
Published: September 2011

ABSTRACT

We announce the draft genome sequence of the type strain
Lactobacillus malefermentans
KCTC 3548 (2,003,922 bp, with a G+C content of 41.1%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of beer; the genome consists of 172 large contigs (>100 bp in size). All of the contigs were assembled by using Newbler Assembler 2.3 (454 Life Science).