bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raman spectroscopy in biomedicine – non‐invasive in vitro analysis of cells and extracellular matrix components in tissues
Authors: Brauchle Eva , Schenke‐Layland Katja 
Published: November 2012

AbstractRaman spectroscopy is an established laser‐based technology for the quality assurance of pharmaceutical products. Over the past few years, Raman spectroscopy has become a powerful diagnostic tool in the life sciences. Raman spectra allow assessment of the overall molecular constitution of biological samples, based on specific signals from proteins, nucleic acids, lipids, carbohydrates, and inorganic crystals. Measurements are non‐invasive and do not require sample processing, making Raman spectroscopy a reliable and robust method with numerous applications in biomedicine. Moreover, Raman spectroscopy allows the highly sensitive discrimination of bacteria. Rama spectra retain information on continuous metabolic processes and kinetics such as lipid storage and recombinant protein production. Raman spectra are specific for each cell type and provide additional information on cell viability, differentiation status, and tumorigenicity. In tissues, Raman spectroscopy can detect major extracellular matrix components and their secondary structures. Furthermore, the non‐invasive characterization of healthy and pathological tissues as well as quality control and process monitoring of in vitro‐engineered matrix is possible. This review provides comprehensive insight to the current progress in expanding the applicability of Raman spectroscopy for the characterization of living cells and tissues, and serves as a good reference point for those starting in the field.
Direct Methyl Formate Formation from Methanol over Supported Palladium Nanoparticles at Low Temperature
Authors: Wojcieszak Roberto , Gaigneaux Eric M. , Ruiz Patricio 
Published: November 2012

AbstractPalladium nanoparticles of different sizes and supported on TiO2 (2 wt. %) were synthesized by using the water‐in‐oil microemulsion method. The control of palladium nanoparticles was investigated in terms of the nature of organic surfactant and solvent. Attention was paid to the reduction of palladium ions in solution during synthesis. Materials were characterized by N2‐BET at low temperature, XRD, XPS, H2 chemisorption, and TEM and were tested in the gas phase oxidation of methanol. The results confirmed the effect of microemulsion composition on the size of palladium nanoparticles. The direct formation of methyl formate from methanol was observed. Supported palladium catalysts produced methyl formate at low temperature (<150 °C) with a very high selectivity, and, in some cases, a selectivity of approximately 100 %. At higher temperature, methyl formate is not formed at all and the total oxidation to CO2 occurs. A linear correlation between palladium particle size and methanol conversion was observed. Conversion and selectivity were correlated with the acidity of the catalysts. Very small particles were more active but less selective. A mechanism was proposed to explain the formation of methyl formate from methanol.
ChemInform Abstract: A New Environmentally Friendly Method for the Baeyer—Villiger Oxidation of Cyclobutanones Catalyzed by Thioureas Using H2O2 as an Oxidant.
Authors: Sasakura Niiha , Nakano Keiji , Ichikawa Yoshiyasu , Kotsuki Hiyoshizo 
Published: November 2012

AbstractThe present new oxidation method is only applicable to cyclobutanones.
ChemInform Abstract: Microwave‐Assisted Synthesis of 2‐Aminopyrimidines from Silica Gel‐Adsorbed Propargyl Alcohols and Guanidine.
Authors: Chen Qing‐Zhen , Ding Zong‐Cang , Ma Yan‐Li , Wang Zhen‐Dong , Zhan Zhuang‐Ping 
Published: November 2012

AbstractA diversity of propargyl alcohols undergoes a propargylation—cycloisomerization tandem reaction, offering a facile access to aminopyrimidines (III) and (V) under microwave‐assisted solvent‐free reaction condition.
ChemInform Abstract: Ph2PI as a Reduction/Phosphination Reagent: Providing Easy Access to Phosphine Oxides.
Authors: Wang Feijun , Qu Mingliang , Chen Feng , Xu Qin , Shi Min 
Published: November 2012

AbstractEfficient methods to prepare phosphorous compounds using Ph2PI, generated from the corresponding chloride, as multifunctional reagent are described.
ChemInform Abstract: Ph3P Catalyzed One‐Pot Synthesis of Heterocyclic Derivatives of Biological Active Curcumin.
Authors: Amiri Rahebeh , Padyab Parnia , Chalabian Firoozeh , Rajabi Nasir Ahmad 
Published: November 2012

AbstractReaction of curcumin (I) with electron‐deficient acetylenes provides access towards curcumin derivatives containing coumarin (III), (IV) or benzofuran moieties (VI), (VII).
Super‐resolution in magnetic resonance imaging: A review
Authors: Van Reeth Eric , Tham Ivan W. K. , Tan Cher Heng , Poh Chueh Loo 
Published: November 2012

AbstractFor the last 15 years, super‐resolution (SR) algorithms have successfully been applied to magnetic resonance imaging (MRI) data to increase the spatial resolution of scans after acquisition has been performed, thus facilitating the doctors' diagnosis. The variety of application and techniques has grown ever since, especially in the MRI modality, showing the interest of the community to such postacquisition processing. This article presents a review of the general principle of SR as well as how this principle has been adapted to MRI data. The main algorithms and the principal acquisition protocols are detailed for both static and moving subjects. The presented strategies are discussed and compared according to the data specificities. Later, different ways of measuring the resolution enhancement and quantify the benefit of SR are detailed. Finally, unexplored perspectives on the application of SR to MRI data are discussed. © 2012 Wiley Periodicals, Inc. Concepts Magn Reson Part A 40A: 306–325, 2012.
Oxygen Migration Pathways in NO‐bound Truncated Hemoglobin
Authors: Cazade Pierre‐André , Meuwly Markus 
Published: November 2012

AbstractAtomistic simulations of dioxygen (O2) dynamics and migration in nitric oxide‐bound truncated Hemoglobin N (trHbN) of Mycobacterium tuberculosis are reported. From more than 100 ns of simulations the connectivity network involving the metastable states for localization of the O2 ligand is built and analyzed. It is found that channel I is the primary entrance point for O2 whereas channel II is predominantly an exit path although access to the protein active site is also possible. For O2 a new site compared to nitric oxide, from which reaction with the heme group can occur, was found. As this site is close to the heme iron, it could play an important role in the dioxygenation mechanism as O2 can remain there for hundreds of picoseconds after which it can eventually leave the protein, while NO is localized in Xe2. The present study supports recent experimental work which proposed that O2 docks in alternative pockets than Xe close to the reactive site. Similar to other proteins, a phenylalanine residue (Phe62) plays the role of a gate along the access route in channel I. The most highly connected site is the Xe3 pocket which is a “hub” and free energy barriers between the different metastable states are ≈1.5 kcal mol−1 which allows facile O2 migration within the protein.
Uniformity, Structure, and Photocatalytic Activity of TiO2 Films Deposited by Atmospheric‐Pressure Linear Cold Plasma
Authors: Di Lan‐Bo , Shi Chuan , Li Xiao‐Song , Liu Jing‐Lin , Zhu Ai‐Min 
Published: November 2012

AbstractAtmospheric‐pressure (AP) linear cold plasma CVD is employed to deposit TiO2 photocatalytic films uniformly on a moving substrate. The in‐plane and in‐depth uniformities of the as‐deposited TiO2 films are investigated by scanning electron microscopy (SEM) and UV‐vis spectroscopy. The chemical binding states and compositions of the as‐deposited TiO2 films are characterized by X‐ray photoelectron spectroscopy (XPS). Raman, X‐ray diffraction (XRD), and Fourier transform infrared (FTIR) spectra prove the structures of the as‐deposited and calcined TiO2 films are mainly hydro‐oxygenated amorphous (a‐TiOx:OH), and exclusively anatase, respectively. The photocatalytic activity of the as‐deposited and calcined TiO2 films is evaluated in a continuous flow reactor for HCHO removal with simulated air. The activity of the as‐deposited TiO2 films increases with film thickness, leveling off at about 780 nm. The activity of the as‐deposited TiO2 film is lower than that of the calcined one.
Evaluation of Different Electrochemical Transducers Based on Polystyrene Sulfonate – Carbon Composites with Nickel Catalyst for Rapid Detection of Fragrance Allergens
Authors: Cantalapiedra Alberto , Gismera Ma Jesús , da Silva Ma Pilar , Procopio Jesús R. , Sevilla Teresa 
Published: November 2012

AbstractNovel electrochemical transducers have been prepared in a polystyrene sulfonate (PSS) matrix introducing carbon nanopowder (CnP) as conductive filler and nickel as catalyst. Composite materials were incorporated on commercial screen‐printed devices. Higher catalytic activities were obtained for composites prepared in 2.6 % PSS containing 2 % CnP in which nickel was incorporated as NiO particles synthesized by a microemulsion procedure (PSS‐NiO‐ME‐CnP sensor) or by immersion of the devices in a Ni(II) solution (PSS‐Ni‐CnP sensor). The PSS‐Ni‐CnP sensor was employed in geraniol analysis with a LOD of 12 mg L−1 and RSD<1.5 %.
Activation of serum/glucocorticoid‐induced kinase 1 (SGK1) is important to maintain skeletal muscle homeostasis and prevent atrophy
Authors: Andres‐Mateos Eva , Brinkmeier Heinrich , Burks Tyesha N. , Mejias Rebeca , Files Daniel C. , Steinberger Martin , Soleimani Arshia , Marx Ruth , Simmers Jessica L. , Lin Benjamin , Finanger Hedderick Erika , Marr Tom G. , Lin Brian M. , Hourdé Christophe , Leinwand Leslie A. , Kuhl Dietmar , Föller Michael , Vogelsang Silke , Hernandez‐Diaz Ivan , Vaughan Dana K. , Alvarez de la Rosa Diego , Lang Florian , Cohn Ronald D. 
Published: November 2012

AbstractMaintaining skeletal muscle mass is essential for general health and prevention of disease progression in various neuromuscular conditions. Currently, no treatments are available to prevent progressive loss of muscle mass in any of these conditions. Hibernating mammals are protected from muscle atrophy despite prolonged periods of immobilization and starvation. Here, we describe a mechanism underlying muscle preservation and translate it to non‐hibernating mammals. Although Akt has an established role in skeletal muscle homeostasis, we find that serum‐ and glucocorticoid‐inducible kinase 1 (SGK1) regulates muscle mass maintenance via downregulation of proteolysis and autophagy as well as increased protein synthesis during hibernation. We demonstrate that SGK1 is critical for the maintenance of skeletal muscle homeostasis and function in non‐hibernating mammals in normal and atrophic conditions such as starvation and immobilization. Our results identify a novel therapeutic target to combat loss of skeletal muscle mass associated with muscle degeneration and atrophy.
Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving‐vessel ADCP measurements
Authors: Parsons D. R. , Jackson P. R. , Czuba J. A. , Engel F. L. , Rhoads B. L. , Oberg K. A. , Best J. L. , Mueller D. S. , Johnson K. K. , Riley J. D. 
Published: November 2012

ABSTRACTThe use of acoustic Doppler current profilers (ADCP) for discharge measurements and three‐dimensional flow mapping has increased rapidly in recent years and has been primarily driven by advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross‐section vector and contouring), and analysis of a range of ADCP‐derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open‐source code along with this publication. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
Simulating Realistic Genomic Data With Rare Variants
Authors: Xu Yaji , Wu Yinghua , Song Chi , Zhang Heping 
Published: November 2012

AbstractIncreasing evidence suggests that rare and generally deleterious genetic variants might have a strong impact on disease risks of not only Mendelian disease, but also many common diseases. However, identifying such rare variants remains challenging, and novel statistical methods and bioinformatic software must be developed. Hence, we have to extensively evaluate various methods under reasonable genetic models. Although there are abundant genomic data, they are not most helpful for the evaluation of the methods because the disease mechanism is unknown. Thus, it is imperative that we simulate genomic data that mimic the real data containing rare variants and that enable us to impose a known disease penetrance model. Although resampling simulation methods have shown their advantages in computational efficiency and in preserving important properties such as linkage disequilibrium (LD) and allele frequency, they still have limitations as we demonstrated. We propose an algorithm that combines a regression‐based imputation with resampling to simulate genetic data with both rare and common variants. Logistic regression model was employed to fit the relationship between a rare variant and its nearby common variants in the 1000 Genomes Project data and then applied to the real data to fill in one rare variant at a time using the fitted logistic model based on common variants. Individuals then were simulated using the real data with imputed rare variants. We compared our method with existing simulators and demonstrated that our method performed well in retaining the real sample properties, such as LD and minor allele frequency, qualitatively.
Synthesis and Structure Revision of Goupiolone A: A Benzotropolone Natural Product
Authors: Fukui Nobuaki , Ohmori Ken , Suzuki Keisuke 
Published: November 2012

AbstractGoupiolone A, a benzotropolone natural product, has been synthesized by assembling a benzocyclobutene derivative and a silyl‐substituted cyclopropane unit, followed by thermal ring enlargement. The synthetic sample did not correspond to the reported data. On the basis of biogenetic considerations, an alternative structure with a catechol moiety was proposed, and the synthesis established it as the correct structure.
Asymmetric Proline‐Catalyzed Addition of Aldehydes to 3H‐Indol‐3‐ones: Enantioselective Synthesis of 2,3‐Dihydro‐1H‐indol‐3‐ones with Quaternary Stereogenic Centers
Authors: Rueping Magnus , Rasappan Ramesh , Raja Sadiya 
Published: November 2012

AbstractThe proline‐catalyzed addition of various aliphatic aldehydes to sterically hindered 2‐aryl‐substituted 3H‐indol‐3‐ones affords 2,2‐disubstituted 2,3‐dihydro‐1H‐indol‐3‐one derivatives with excellent enantioselectivities. In addition, the synthesis of a chiral derivative, (S)‐2‐(2‐bromophenyl)‐2,3‐dihydro‐2‐(2‐hydroxyethyl)‐1H‐indol‐3‐one, which can be used as an intermediate for the preparation of the natural product hinckdentine A was accomplished with a high level of enantioselectivity.
EphrinB2/EphB4 inhibition in the osteoblast lineage modifies the anabolic response to parathyroid hormone
Authors: Takyar Farzin M , Tonna Stephen , Ho Patricia WM , Crimeen-Irwin Blessing , Baker Emma K , Martin T John , Sims Natalie A 
Published: November 2012

Abstract
Previous reports indicate that ephrinB2 expression by osteoblasts is stimulated by parathyroid hormone (PTH) and its related protein (PTHrP) and that ephrinB2/EphB4 signaling between osteoblasts and osteoclasts stimulates osteoblast differentiation while inhibiting osteoclast differentiation. To determine the role of the ephrinB2/EphB4 interaction in the skeleton, we used a specific inhibitor, soluble EphB4 (sEphB4), in vitro and in vivo. sEphB4 treatment of cultured osteoblasts specifically inhibited EphB4 and ephrinB2 phosphorylation and reduced mRNA levels of late markers of osteoblast/osteocyte differentiation (osteocalcin, dentin matrix protein-1 [DMP-1], sclerostin, matrix-extracellular phosphoglycoprotein [MEPE]), while substantially increasing RANKL. sEphB4 treatment in vivo in the presence and absence of PTH increased osteoblast formation and mRNA levels of early osteoblast markers (Runx2, alkaline phosphatase, Collagen 1α1, and PTH receptor [PTHR1]), but despite a substantial increase in osteoblast numbers, there was no significant change in bone formation rate or in late markers of osteoblast/osteocyte differentiation. Rather, in the presence of PTH, sEphB4 treatment significantly increased osteoclast formation, an effect that prevented the anabolic effect of PTH, causing instead a decrease in trabecular number. This enhancement of osteoclastogenesis by sEphB4 was reproduced in vitro but only in the presence of osteoblasts. These data indicate that ephrinB2/EphB4 signaling within the osteoblast lineage is required for late stages of osteoblast differentiation and, further, restricts the ability of osteoblasts to support osteoclast formation, at least in part by limiting RANKL production. This indicates a key role for the ephrinB2/EphB4 interaction within the osteoblast lineage in osteoblast differentiation and support of osteoclastogenesis. © 2013 American Society for Bone and Mineral Research.
Lower fracture risk in older men with higher sclerostin concentration: A prospective analysis from the MINOS study
Authors: Szulc Pawel , Bertholon Cindy , Borel Olivier , Marchand Francois , Chapurlat Roland 
Published: November 2012

Abstract
Sclerostin is synthesized by osteocytes and inhibits bone formation. We measured serum sclerostin levels in 710 men aged 50 years and older. Bone mineral density (BMD) was measured at the lumbar spine, hip, and distal forearm. Serum sclerostin increased with age (unadjusted r = 0.30, p &lt; 0.001). After adjustment for age, weight, and bioavailable 17β-estradiol, serum sclerostin correlated positively with BMD (r = 0.24 to 0.35, p &lt; 0.001) and negatively with the levels of bone turnover markers (r = − 0.09 to − 0.23, p &lt; 0.05 to 0.001). During a 10-year follow-up, 75 men sustained fragility fractures. Fracture risk was lower in the two upper quintiles of sclerostin combined versus three lower quintiles combined (6.1 versus 13.5%, p &lt; 0.01). We compared fracture risk in the two highest quintiles combined versus three lower quintiles combined using the Cox model adjusted for age, weight, leisure physical activity, BMD, bone width (tubular bones), prevalent fracture, prevalent falls, ischemic heart disease, and severe abdominal aortic calcification. Men with higher sclerostin concentration had lower fracture risk (adjusted for hip BMD, hazard ratio [HR] = 0.55, 95% confidence interval [CI] 0.31 to 0.96, p &lt; 0.05). The results were similar in 47 men with major fragility fractures (adjusted for lumbar spine BMD: HR = 0.39, 95% CI 0.17 to 0.90, p &lt; 0.05). Men who had higher sclerostin and higher BMD (two highest quintiles) had lower risk of fracture compared with men who had lower BMD and lower sclerostin levels (three lower quintiles) (HR = 0.24, 95% CI 0.10 to 0.62, p &lt; 0.005). Circulating sclerostin was not associated with mortality rate or the incidence of major cardiovascular events. Thus, in older men, higher serum sclerostin levels are associated with lower risk of fracture, higher BMD, and lower bone turnover rate. © 2013 American Society for Bone and Mineral Research.
Dicer‐Processed Small RNAs: Rules and Exceptions
Authors: Langenberger David , Çakir M. Volkan , Hoffmann Steve , Stadler Peter F. 
Published: November 2012

AbstractCanonical microRNAs are excised from their hairpin‐shaped precursors by Dicer. In order to find possible exceptions to this rule and to identify additional substrates for Dicer processing we re‐evaluate the small RNA sequencing data of the Dicer knockdown experiment in MCF‐7 cells orignally published by Friedländer et al. [Friedländer et al., 2012, Nucleic Acids Res 40:37–52]. While the well‐known non‐Dicer mir‐451 is not sufficiently expressed in these experiments, there are several additional Dicer‐independent microRNAs, among them the important tumor supressor mir‐663a. We recover previously described examples of non‐miRNA Dicer substrates such as tRNA‐Gln and several snoRNAs. Interestingly, sdRNAs derived from box C/D snoRNAs are Dicer‐independent, while those derived from box H/ACA snoRNAs are often Dicer dependent. Several pol‐III transcripts, in particular the vault RNAs and the great ape specific snaRs are processed by Dicer, while the small RNAs originating from Y RNAs seem to be Dicer independent. J. Exp. Zool. (Mol. Dev. Evol.) 320B:35–46, 2013. © 2012 Wiley Periodicals, Inc.
Mitochondrial membrane protein associated neurodegenration: A novel variant of neurodegeneration with brain iron accumulation
Authors: Schulte Eva C. , Claussen Malte C. , Jochim Angela , Haack Tobias , Hartig Monika , Hempel Maja , Prokisch Holger , Haun‐Jünger Ursula , Winkelmann Juliane , Hemmer Bernhard , Förschler Annette , Ilg Rüdiger 
Published: November 2012

BackgroundRecently, mutations in an open‐reading frame on chromosome 19 (C19orf12) were identified as a novel genetic factor in neurodegeneration with brain iron accumulation (NBIA). Because of the mitochondrial localization of the derived protein, this variant is referred to as mitochondrial membrane protein‐associated neurodegeneration with brain iron accumulation (MPAN).Methods/ResultsWe describe the clinical phenotype and MRI of 3 newly identified individuals with MPAN due to either previously reported or novel homozygous or compound heterozygous genetic alterations in C19orf12.ConclusionsMPAN is characterized by a juvenile‐onset, slowly progressive phenotype with predominant lower limb spasticity, generalized dystonia, and cognitive impairment. Typical additional features include axonal motor neuropathy and atrophy of the optic nerve. MRI showed iron deposition in the globus pallidus and substantia nigra without the eye‐of‐the‐tiger sign, which is typical for PKAN, the most frequent form of NBIA. © 2012 Movement Disorder Society
Is Quantum Tunneling Relevant in Free‐Radical Polymerization?
Authors: Cuccato Danilo , Dossi Marco , Polino Daniela , Cavallotti Carlo , Moscatelli Davide 
Published: November 2012

AbstractQuantum tunneling in hydrogen transfer reactions active in FRP is investigated theoretically. Three systems are examined: polyethylene, polystyrene, and poly(vinyl chloride). Kinetic parameters of backbiting reactions are evaluated adopting quantum chemistry. Tunneling corrections are estimated adopting the one‐dimensional Eckart model, which provides a reasonable accuracy along with a limited computational effort. The relevance of quantum tunneling in the investigated systems is highlighted, with focus on the temperature dependence of the tunneling correction in the typical polymerization conditions of the investigated monomers. Obtained results clearly show that tunneling plays an important role in the kinetics estimation of hydrogen abstractions in FRP. magnified image