bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production of hydroxycinnamoyl-shikimates and chlorogenic acid in Escherichia coli: production of hydroxycinnamic acid conjugates
Authors: Kim Bong-Gyu , Jung Woo Dam , Mok Hyejung , Ahn Joong-Hoon 
Published: February 2013

Abstract

Background
Hydroxycinnamates (HCs) are mainly produced in plants. Caffeic acid (CA), p-coumaric acid (PA), ferulic acid (FA) and sinapic acid (SA) are members of the HC family. The consumption of HC by human might prevent cardiovascular disease and some types of cancer. The solubility of HCs is increased through thioester conjugation to various compounds such as quinic acid, shikimic acid, malic acid, anthranilic acid, and glycerol. Although hydroxycinnamate conjugates can be obtained from diverse plant sources such as coffee, tomato, potato, apple, and sweet potato, some parts of the world have limited availability to these compounds. Thus, there is growing interest in producing HC conjugates as nutraceutical supplements.

Results
Hydroxycinnamoyl transferases (HCTs) including hydroxycinnamate-CoA shikimate transferase (HST) and hydroxycinnamate-CoA quinate transferase (HQT) were co-expressed with 4-coumarateCoA:ligase (4CL) in Escherichia coli cultured in media supplemented with HCs. Two hydroxycinnamoyl conjugates, p-coumaroyl shikimates and chlorogenic acid, were thereby synthesized. Total 29.1 mg/L of four different p-coumaroyl shikimates (3-p-coumaroyl shikimate, 4-p-coumaroyl shikimate, 3,4-di-p-coumaroyl shikimate, 3,5-di-p-coumaroyl shikimate, and 4,5-di-p-coumaroyl shikimate) was obtained and 16 mg/L of chlorogenic acid was synthesized in the wild type E. coli strain. To increase the concentration of endogenous acceptor substrates such as shikimate and quinate, the shikimate pathway in E. coli was engineered. A E. coli aroL and aroK gene were mutated and the resulting mutants were used for the production of p-coumaroyl shikimate. An E. coli aroD mutant was used for the production of chlorogenic acid. We also optimized the vector and cell concentration optimization.

Conclusions
To produce p-coumaroyl-shikimates and chlorogenic acid in E. coli, several E. coli mutants (an aroD mutant for chlorogenic acid production; an aroL, aroK, and aroKL mutant for p-coumaroyl-shikimates production) were made and each mutant was tested using an optimized construct. Using this strategy, we produced 235 mg/L of p-coumaroyl-shikimates and 450 mg/L of chlorogenic acid.
Depression pathogenesis and treatment: what can we learn from blood mRNA expression?
Authors: Hepgul Nilay , Cattaneo Annamaria , Zunszain Patricia A , Pariante Carmine M 
Published: February 2013

Abstract
Alterations in several biological systems, including the neuroendocrine and immune systems, have been consistently demonstrated in patients with major depressive disorder. These alterations have been predominantly studied using easily accessible systems such as blood and saliva. In recent years there has been an increasing body of evidence supporting the use of peripheral blood gene expression to investigate the pathogenesis of depression, and to identify relevant biomarkers. In this paper we review the current literature on gene expression alterations in depression, focusing in particular on three important and interlinked biological domains: inflammation, glucocorticoid receptor functionality and neuroplasticity. We also briefly review the few existing transcriptomics studies. Our review summarizes data showing that patients with major depressive disorder exhibit an altered pattern of expression in several genes belonging to these three biological domains when compared with healthy controls. In particular, we show evidence for a pattern of 'state-related' gene expression changes that are normalized either by remission or by antidepressant treatment. Taken together, these findings highlight the use of peripheral blood gene expression as a clinically relevant biomarker approach.
Pneumococcal ClpP modulates the maturation and activation of human dendritic cells: implications for pneumococcal infections
Authors: Cao Ju , Gong Yi , Dong ShanShan , Zhang Liping , Lai Xaiofei , Zhang Xuemei , Yin Yibing 
Published: February 2013

Abstract
Pneumococcal ClpP regulates DCs by acting as a novel TLR4 ligand during pneumococcal infections.
DCs are essential for host immune response to pathogens. Pneumococcal diseases still remain to be a major global-health issue, and HSP100/ClpP is a ubiquitously present virulence determinant for Streptococcus pneumoniae. Here, we show that ClpP expression facilitates the uptake and phagocytosis of pneumococci by human DCs, and it could increase apoptosis of DCs infected with pneumococci. Furthermore, pneumococcal ClpP is required for optimal production of inflammatory cytokines and chemokines and an efficient activation of adaptive immune response in DCs. Complementary, purified rClpP protein recognizes TLR4 and functionally activates human DCs by augmenting the expression of surface molecules and the production of inflammatory cytokines and chemokines dependent on MAPKs and NF-κB signaling pathways. Besides, ClpP-treated DCs induce T cell proliferation and contribute to Th1 immune response. This study describes a novel role of ClpP in the interaction of DCs with pneumococci that could provide new insight for the progression of pneumococcal diseases and has important implications for designing pneumococcal protein vaccines.
A fast interpretation of self-potential data using the depth from extreme points method
Authors: Fedi Maurizio , Abbas Mahmoud Ahmed 
Published: February 2013

We used a fast method to interpret self-potential data: the depth from extreme points (DEXP) method. This is an imaging method transforming self-potential data, or their derivatives, into a quantity proportional to the source distribution. It is based on upward continuing of the field to a number of altitudes and then multiplying the continued data with a scaling law of those altitudes. The scaling law is in the form of a power law of the altitudes, with an exponent equal to half of the structural index, a source parameter related to the type of source. The method is autoconsistent because the structural index is basically determined by analyzing the scaling function, which is defined as the derivative of the logarithm of the self-potential (or of its [Formula: see text]th derivative) with respect to the logarithm of the altitudes. So, the DEXP method does not need a priori information on the self-potential sources and yields effective information about their depth and shape/typology. Important features of the DEXP method are its high-resolution power and stability, resulting from the combined effect of a stable operator (upward continuation) and a high-order differentiation operator. We tested how to estimate the depth to the source in two ways: (1) at the positions of the extreme points in the DEXP transformed map and (2) at the intersection of the lines of the absolute values of the potential or of its derivative (geometrical method). The method was demonstrated using synthetic data of isolated sources and using a multisource model. The method is particularly suited to handle noisy data, because it is stable even using high-order derivatives of the self-potential. We discussed some real data sets: Malachite Mine, Colorado (USA), the Sariyer area (Turkey), and the Bender area (India). The estimated depths and structural indices agree well with the known information.
Clinicopathologic Findings Predictive of Relapse in Children With Stage III Favorable-Histology Wilms Tumor
Authors: Ehrlich Peter F. , Anderson James R. , Ritchey Michael L. , Dome Jeffrey S. , Green Daniel M. , Grundy Paul E. , Perlman Elizabeth J. , Kalapurakal John A. , Breslow Norman E. , Shamberger Robert C. 
Published: February 2013

PurposeStage III designation in NWTS-5 (National Wilms Tumor Study–5) was determined by four pathologic criteria: positive lymph nodes (LNs), peritoneal implants, residual disease, and tumor rupture. The objective of this study was to determine the prognostic significance of each of the stage III criteria.Patients and MethodsChildren with stage III Wilms tumor (WT) treated in NWTS-5 were assessed for event-free (EFS) and overall survival (OS). Sites of relapse and molecular status of tumors are reported. EFS and OS are reported 8 years after diagnosis.ResultsThere were 569 patients with local stage III favorable-histology (FH) WT in this analysis, of whom 109 had overall stage IV disease. LN involvement alone was the most frequent criterion for stage III designation (38%), followed by microscopic residual disease alone (20%), microscopic residual disease and LN involvement (14%), and spill or soilage alone (9%). The 8-year EFS and OS estimates for all patients with local stage III FHWT were 82% and 91%, respectively. Multivariate analysis demonstrated that both LN involvement (relative risk, 1.89; P = .005) and microscopic residual disease (relative risk, 1.87; P = .007) were predictive of EFS, and OS results were similar. There was no apparent difference in pattern of relapse according to stage III subtype. The rate of loss of heterozygosity was higher (6%) for those with positive LNs than for those without (2%; P = .05).ConclusionLN involvement and microscopic residual are the stage III criteria highly predictive of EFS and OS for patients with stage III FHWT. It is possible that in future studies, patients with different stage III criteria may receive different therapies.
Identification of a 24-Gene Prognostic Signature That Improves the European LeukemiaNet Risk Classification of Acute Myeloid Leukemia: An International Collaborative Study
Authors: Li Zejuan , Herold Tobias , He Chunjiang , Valk Peter J.M. , Chen Ping , Jurinovic Vindi , Mansmann Ulrich , Radmacher Michael D. , Maharry Kati S. , Sun Miao , Yang Xinan , Huang Hao , Jiang Xi , Sauerland Maria-Cristina , Büchner Thomas , Hiddemann Wolfgang , Elkahloun Abdel , Neilly Mary Beth , Zhang Yanming , Larson Richard A. , Le Beau Michelle M. , Caligiuri Michael A. , Döhner Konstanze , Bullinger Lars , Liu Paul P. , Delwel Ruud , Marcucci Guido , Lowenberg Bob , Bloomfield Clara D. , Rowley Janet D. , Bohlander Stefan K. , Chen Jianjun 
Published: February 2013

Purpose To identify a robust prognostic gene expression signature as an independent predictor of survival of patients with acute myeloid leukemia (AML) and use it to improve established risk classification. Patients and Methods Four independent sets totaling 499 patients with AML carrying various cytogenetic and molecular abnormalities were used as training sets. Two independent patient sets composed of 825 patients were used as validation sets. Notably, patients from different sets were treated with different protocols, and their gene expression profiles were derived using different microarray platforms. Cox regression and Kaplan-Meier methods were used for survival analyses. Results A prognostic signature composed of 24 genes was derived from a meta-analysis of Cox regression values of each gene across the four training sets. In multivariable models, a higher sum value of the 24-gene signature was an independent predictor of shorter overall (OS) and event-free survival (EFS) in both training and validation sets (P < .01). Moreover, this signature could substantially improve the European LeukemiaNet (ELN) risk classification of AML, and patients in three new risk groups classified by the integrated risk classification showed significantly (P < .001) distinct OS and EFS. Conclusion Despite different treatment protocols applied to patients and use of different microarray platforms for expression profiling, a common prognostic gene signature was identified as an independent predictor of survival of patients with AML. The integrated risk classification incorporating this gene signature provides a better framework for risk stratification and outcome prediction than the ELN classification.
Phase II Randomized Study of Trastuzumab Emtansine Versus Trastuzumab Plus Docetaxel in Patients With Human Epidermal Growth Factor Receptor 2–Positive Metastatic Breast Cancer
Authors: Hurvitz Sara A. , Dirix Luc , Kocsis Judit , Bianchi Giulia V. , Lu Janice , Vinholes Jeferson , Guardino Ellie , Song Chunyan , Tong Barbara , Ng Vivian , Chu Yu-Waye , Perez Edith A. 
Published: February 2013

Purpose Trastuzumab emtansine (T-DM1), an antibody-drug conjugate composed of the cytotoxic agent DM1 conjugated to trastuzumab via a stable thioether linker, has shown clinical activity in single-arm studies enrolling patients with human epidermal growth factor receptor 2 (HER2) –positive metastatic breast cancer (MBC) whose disease had progressed on HER2-targeted therapy in the metastatic setting. Patients and Methods Patients (N = 137) with HER2-positive MBC or recurrent locally advanced breast cancer were randomly assigned to trastuzumab plus docetaxel (HT; n = 70) or T-DM1 (n = 67) as first-line treatment until disease progression or unacceptable toxicity. Primary end points were investigator-assessed progression-free survival (PFS) and safety. Key secondary end points included overall survival (OS), objective response rate (ORR), duration of objective response, clinical benefit rate, and quality of life. Results Median PFS was 9.2 months with HT and 14.2 months with T-DM1 (hazard ratio, 0.59; 95% CI, 0.36 to 0.97); median follow-up was approximately 14 months in both arms. ORR was 58.0% (95% CI, 45.5% to 69.2%) with HT and 64.2% (95% CI, 51.8% to 74.8%) with T-DM1. T-DM1 had a favorable safety profile versus HT, with fewer grade ≥ 3 adverse events (AEs; 46.4% v 90.9%), AEs leading to treatment discontinuations (7.2% v 40.9%), and serious AEs (20.3% v 25.8%). Preliminary OS results were similar between treatment arms; median follow-up was approximately 23 months in both arms. Conclusion In this randomized phase II study, first-line treatment with T-DM1 for patients with HER2-positive MBC provided a significant improvement in PFS, with a favorable safety profile, versus HT.
Solvent-Free Diels–Alder Reaction in a Closed Batch System
Authors: Sun Daolai , Sato Fumiya , Yamada Yasuhiro , Sato Satoshi 
Published: February 2013

Abstract
Solvent-free Diels–Alder reactions were carried out by heating a mixture of a volatile diene, such as 1,3-butadiene, isoprene, or 2,3-dimethyl-1,3-butadiene, and a dienophile, such as methyl vinyl ketone, methyl acrylate, or maleic anhydride, in a closed batch reactor. High yields of Diels–Alder products were obtained without using solvents and catalysts within a short reaction time in most of the reactions. In particular, several reactions of dienophiles with 1,3-butadiene, which is known as a diene with low reactivity because of its gaseous form, also proceeded with high yields of Diels–Alder products in the closed batch reactor under conditions pressured by the reactant vapor. Solvent-free reactions provided high yields compared to reactions in solvent since the reaction heat directly resulted in increasing the reaction temperature and pressure. Energy in the exothermic reaction was used effectively in the closed batch system under solvent-free conditions.
Preanalytical Aspects and Sample Quality Assessment in Metabolomics Studies of Human Blood
Authors: Yin Peiyuan , Peter Andreas , Franken Holger , Zhao Xinjie , Neukamm Sabine S , Rosenbaum Lars , Lucio Marianna , Zell Andreas , Häring Hans-Ulrich , Xu Guowang , Lehmann Rainer 
Published: February 2013

BACKGROUND
Metabolomics is a powerful tool that is increasingly used in clinical research. Although excellent sample quality is essential, it can easily be compromised by undetected preanalytical errors. We set out to identify critical preanalytical steps and biomarkers that reflect preanalytical inaccuracies.

METHODS
We systematically investigated the effects of preanalytical variables (blood collection tubes, hemolysis, temperature and time before further processing, and number of freeze–thaw cycles) on metabolomics studies of clinical blood and plasma samples using a nontargeted LC-MS approach.

RESULTS
Serum and heparinate blood collection tubes led to chemical noise in the mass spectra. Distinct, significant changes of 64 features in the EDTA-plasma metabolome were detected when blood was exposed to room temperature for 2, 4, 8, and 24 h. The resulting pattern was characterized by increases in hypoxanthine and sphingosine 1-phosphate (800% and 380%, respectively, at 2 h). In contrast, the plasma metabolome was stable for up to 4 h when EDTA blood samples were immediately placed in iced water. Hemolysis also caused numerous changes in the metabolic profile. Unexpectedly, up to 4 freeze–thaw cycles only slightly changed the EDTA-plasma metabolome, but increased the individual variability.

CONCLUSIONS
Nontargeted metabolomics investigations led to the following recommendations for the preanalytical phase: test the blood collection tubes, avoid hemolysis, place whole blood immediately in ice water, use EDTA plasma, and preferably use nonrefrozen biobank samples. To exclude outliers due to preanalytical errors, inspect the biomarker signal intensities reflecting systematic as well as accidental and preanalytical inaccuracies before processing the bioinformatics data.
A comparison of Paley–Wiener theorems for real reductive Lie groups
Authors: van den Ban Erik P. , Souaifi Sofiane 
Published: February 2013

Abstract

In this paper we make a detailed comparison between the Paley–Wiener theorems of
J. Arthur and P. Delorme for a real reductive Lie group G. We prove that these theorems are equivalent from an a priori point of view.
We also give an alternative formulation of the theorems in terms of the Hecke algebra
of bi-K-finite distributions supported on K, a maximal compact subgroup of G. Our techniques
involve derivatives of holomorphic families of continuous representations and Harish-Chandra modules.
The formate/nitrite transporter family of anion channels
Authors: Lü Wei , Du Juan , Schwarzer Nikola J. , Wacker Tobias , Andrade Susana L.A. , Einsle Oliver 
Published: February 2013

Abstract
The formate/nitrite transporter (FNT) family of integral membrane proteins comprises pentameric channels for monovalent anions that exhibit a broad specificity for small anions such as chloride, the physiological cargo molecules formate, nitrite, and hydrosulfide, and also larger organic acids. Three-dimensional structures are available for the three known subtypes, FocA, NirC, and HSC, which reveal remarkable evolutionary optimizations for the respective physiological context of the channels. FNT channels share a conserved translocation pathway in each protomer, with a central hydrophobic cavity that is separated from both sides of the membrane by a narrow constriction. A single protonable residue, a histidine, plays a key role by transiently protonating the transported anion to allow an uncharged species to pass the hydrophobic barrier. Further selectivity is reached through variations in the electrostatic surface potential of the proteins, priming the formate channel FocA for anion export, whereas NirC and HSC should work bidirectionally. Electrophysiological studies have shown that a broad variety of monovalent anions can be transported, and in the case of FocA, these match exactly the products of mixed-acid fermentation, the predominant metabolic pathway for most enterobacterial species.
Variational inequalities and higher order convergence rates for Tikhonov regularisation on Banach spaces
Authors: Grasmair Markus 
Published: February 2013

Abstract.
In this paper we derive higher order convergence rates in terms of the Bregman distance
for Tikhonov like convex regularisation for linear operator equations
on Banach spaces. The approach is based on the idea of variational inequalities,
which are, however, not imposed on the original Tikhonov functional,
but rather on a dual functional. Because of that, the approach is not limited to convergence
rates of lower order, but yields the same range of rates
that is well known for quadratic regularisation on Hilbert spaces.
TGV for diffusion tensors: A comparison of fidelity functions
Authors: Valkonen Tuomo , Bredies Kristian , Knoll Florian 
Published: February 2013

Abstract.
We study the total generalised variation regularisation
of symmetric tensor fields from medical applications,
namely diffusion tensor regularisation. We study the effect
of the pointwise positivity constraint on the tensor field,
as well as the difference between direct denoising of the
tensor field first solved from the Stejskal–Tanner equation,
as was done in our earlier work, and of incorporating this
equation into the fidelity function. Our results indicate
that the latter novel approach provides improved computational
results.
An H1
-Kaczmarz reconstructor for atmospheric tomography
Authors: Eslitzbichler Markus , Pechstein Clemens , Ramlau Ronny 
Published: February 2013

Abstract.
Atmospheric tomography is a prerequisite step before wavefront perturbations can
be corrected in Multi Conjucate Adaptive Optics (MCAO) systems. Recently, the
use of a Landweber–Kaczmarz iteration has been proposed to solve the tomography
problem. However, due to the geometric partitioning of the update steps in this
method, discontinuities in the solution appear that are physically implausible. We investigate augmenting the Landweber–Kaczmarz iteration with a smoothing step
based on solving an elliptic partial differential equation to alleviate these
discontinuities.
Calibration of Seal Coat Application Rate Design
Authors: Lee Jusang , Ahn Hyung Jun , Shields Todd , Harris Dwayne , Li Shuo 
Published: February 2013

Abstract
This paper presents seal coat performance evaluations of various emulsion and aggregate application rates using three different evaluation methods: International Roughness Index (IRI), friction test, and visual evaluation. Then, considering the seal coat failure criteria, correction factors for seal coat application equipment are introduced. This study confirms the lack of relevance between seal coat application and IRI values because of the thickness of a seal coat. In addition, friction improvements caused by seal coat applications were confirmed within the range of seal coat rates applied. Overall, IRI, friction, and visual inspection did not reveal distinct differences in seal coat performance in terms of application rates in the testing range. Accordingly, seal coats with rates based on the McLeod method showed acceptable performance. The aggregate application rate should be high enough to protect the seal coat from immediate failure during construction but low enough to avoid unacceptable levels of accumulated fines content. Furthermore, immediate failure occurring locally during construction because of incorrect application rate (e.g., insufficient aggregate rate) can cause total failure of a seal coat road because of a chain reaction. However, discrepancies between designed rates and applied rates were observed in the study even after the seal coat equipment was calibrated prior to operation. The equipment factor for aggregate can compensate for rate discrepancies between the target and actual application rates. It was found that the designed emulsion application rate does not need to be corrected for the emulsion distributor because the emulsion rate discrepancy has an insignificant impact on a seal coat’s performance.