bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Atrioventricular Region of the Teleost Heart. A Distinct Heart Segment
Authors: Icardo José M. , Colvee Elvira 
Published: December 2010

AbstractThis article reports the morphological characteristics of the atrioventricular (AV) region of the teleost heart. A total of 29 teleost species belonging to 19 families and 10 orders were analyzed. The study includes hearts with entirely trabeculated ventricles and hearts possessing a ventricular compacta. In all cases, the AV region is formed by a ring of compact myocardium surrounded by a connective tissue ring. The myocardium contains vessels in most species having entirely trabeculated ventricles, and in all species possessing a compacta. The ring of connective tissue is rich in collagen and elastin, partially isolating the AV muscle from the surrounding musculature. Continuity between the AV muscle and the atrial and ventricular musculature is always observed. The AV muscle supports the AV valves, which are formed by two leaflets, lack papillary muscles, show a collagenous fibrosa on the atrial side, and present a variable number of cells and a variable amount of extracellular material. Ventricular trabeculae attach to the AV muscle. These trabeculae may help to bear the stress generated by ventricular contraction and may constitute a preferential pathway for the conduction of electrical impulses. In all teleosts studied, the AV region can be recognized as a distinct morphological segment interposed between the atrium and the ventricle. The morphological characteristics of the AV segment appear to be species specific. Anat Rec, 2011. © 2010 Wiley‐Liss, Inc.
Differential Expression of Metallothionein in Gastrointestinal Stromal Tumors and Gastric Carcinomas
Authors: Soo Eliza Ting‐Li , NG Cheng‐Teng , Yip George Wai‐Cheong , Koo Chuay Yeng , Nga Min‐En , Tan Puay‐Hoon , Bay Boon‐Huat 
Published: December 2010

AbstractGastrointestinal stromal tumors (GISTs) are mesenchymal tumors that account for about 2% of gastric tumors. Metallothioneins (MTs) are multifunctional proteins associated with carcinogenesis and known to be coded by 10 functional MT genes. This study evaluated MT mRNA and protein expression in GISTs and compared the expression levels with gastric carcinomas. An immunohistochemical study of MT protein expression was performed in 15 GISTs (specifically located in the stomach) and 38 early stage gastric carcinomas. The percentage of cells stained and intensity of staining were determined. MT‐2A mRNA expression was investigated in 6 GISTs and 6 early stage gastric carcinoma patients. All GISTs displayed positive nuclear immunostaining, with most GISTs having predominantly mildly stained nuclei (93.3%). On the other hand, 37 out of 38 gastric carcinoma cases were positively stained for nuclear MT with 24 cases (63.2%) exhibiting predominantly mild nuclear staining, 7 cases (18.4%) moderate nuclear staining, and 6 cases (15.8%) strong nuclear staining. Nuclear MT expression was found to be significantly lower in GIST samples when compared with gastric carcinoma tissues based on the percentage stained and immunoreactive score. We then established that the MT‐2A gene transcript was the most abundant MT isoform in MKN28 gastric cancer cells and analyzed its expression in GIST and gastric carcinoma tissues. We found that GISTs had significantly lower MT‐2A mRNA levels than gastric carcinoma tissues. Lower MT‐2A gene expression and nuclear MT protein expression in GISTs when compared with gastric carcinomas may reflect their different underlying biology and divergent histogenesis. Anat Rec, 2011. © 2010 Wiley‐Liss, Inc.
“Anatomical” View of the Protein Composition and Protein Characteristics for Gloydius shedaoensis Snake Venom via Proteomics Approach
Authors: Liu Shuqing , Yang Fan , Zhang Qiaoqiao , Sun Ming‐Zhong , Gao Ying , Shao Shujuan 
Published: December 2010

AbstractThe bioactive protein components from snake venom complexes have been utilized for studies of enzymology, structural biology, and pharmacology. The Gloydius shedaoensis snake (GSS) is the only snake species found exclusively at the Chinese Shedao (snake) Island in Dalian. To investigate the protein components of Chinese GSS venom (GSSV), we initialized a proteomic assay for GSSV by the combination of sodium dodecyl sulfate‐polyacrylamide gel electrophoresis with high‐performance liquid chromatography (HPLC)‐nanoelectrospray ionization tandem mass spectrometry (nESI‐MS/MS). Thirty gel bands visualized by Coomassie blue staining were excised and digested by trypsin. The tryptic‐digested peptides were separated by HPLC and subsequently sequenced by nESI‐MS/MS. Twenty‐four types of proteins were identified by searching the mass spectrometry data against NCBInr database through TurboSequest Bioworks. The most abundant proteins are phospholipase A2, metalloproteinase, L‐amino acid oxidase (LAAO), serine protease/thrombin‐like enzyme. Except for 20 types of known snake venom proteins, the homolog peptides of hypothetical protein PFLC2230, LOC495267 protein, DEAD/DEAH box helicase‐like, and pancreatic trypsin 1 from other organisms are matched for GSSV protein components. Mass spectrometric data also indicated that (i) dimerization happens to PLA2s as monomer and dimer of PLA2s coexist in GSSV and (ii) truncation or hydrolysis might happen to LAAOs as three molecular‐weight‐ranged LAAO species are present in GSSV. The results provide an “anatomical” view of the protein composition and important information for protein characteristics of GSSV. Anat Rec, 2011. © 2010 Wiley‐Liss, Inc.
Pharmacokinetics of a combination of Δ9‐Tetrahydro‐cannabinol and celecoxib in a porcine model of hemorrhagic shock
Authors: Vaddady Pavan K. , Mehrotra Nitin , Zhang Xiaofeng , Yates Charles R. , Moore Bob M. , Meibohm Bernd 
Published: December 2010

AbstractHemorrhagic shock involves loss of a substantial portion of circulating blood volume leading to diminished cardiac output and oxygen delivery to peripheral tissues. In situations where an immediate resuscitation cannot be provided, pharmacotherapy with a novel combination of Δ9‐tetrahydro‐cannabinol (THC) and celecoxib (CEL) is currently investigated as an alternative strategy to prevent organ damage. In the present study, 28 Yorkshire × Landrace pigs were used to study the pharmacokinetics of THC and CEL in an established porcine model of hemorrhagic shock. Pigs in hemorrhagic shock received 0.5, 1 or 4 mg/kg THC and 2 mg/kg CEL, while normotensive pigs received 1 mg/kg THC and 2 mg/kg CEL by intravenous injection. THC and CEL plasma concentrations were simultaneously determined by LC‐MS/MS. Pharmacokinetic parameters and their between animal variability were obtained using standard non‐compartmental analysis as well as a compartmental analysis using nonlinear mixed effects modeling. The concentration–time profiles of THC and CEL followed a multi‐exponential decline and their pharmacokinetics were similar in hemorrhagic shock and normotensive conditions, despite the substantial change in hemodynamics in the animals with shock. This interesting finding might be due to the pharmacologic effect of the THC/CEL combination, which is intended to maintain adequate perfusion of vital organs in shock. Overall, this study established THC and CEL pharmacokinetics in a porcine shock model and provides the basis for dose selection in further studies of THC and CEL in this indication. Copyright © 2010 John Wiley & Sons, Ltd.
Exposure assessment in front of a multi‐band base station antenna
Authors: Kos Bor , Valič Blaž , Kotnik Tadej , Gajšek Peter 
Published: December 2010

AbstractThis study investigates occupational exposure to electromagnetic fields in front of a multi‐band base station antenna for mobile communications at 900, 1800, and 2100 MHz. Finite‐difference time‐domain method was used to first validate the antenna model against measurement results published in the literature and then investigate the specific absorption rate (SAR) in two heterogeneous, anatomically correct human models (Virtual Family male and female) at distances from 10 to 1000 mm. Special attention was given to simultaneous exposure to fields of three different frequencies, their interaction and the additivity of SAR resulting from each frequency. The results show that the highest frequency—2100 MHz—results in the highest spatial‐peak SAR averaged over 10 g of tissue, while the whole‐body SAR is similar at all three frequencies. At distances >200 mm from the antenna, the whole‐body SAR is a more limiting factor for compliance to exposure guidelines, while at shorter distances the spatial‐peak SAR may be more limiting. For the evaluation of combined exposure, a simple summation of spatial‐peak SAR maxima at each frequency gives a good estimation for combined exposure, which was also found to depend on the distribution of transmitting power between the different frequency bands. Bioelectromagnetics 32:234–242, 2011. © 2010 Wiley‐Liss, Inc.
Integrating DNA barcode data and taxonomic practice: Determination, discovery, and description
Authors: Goldstein Paul Z. , DeSalle Rob 
Published: December 2010

AbstractDNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.
Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress
Authors: Ruenwai Rawisara , Neiss Andrea , Laoteng Kobkul , Vongsangnak Wanwipa , Dalfard Arastoo Badoei , Cheevadhanarak Supapon , Petranovic Dina , Nielsen Jens 
Published: December 2010

AbstractDue to their health benefits there is much interest in developing microbial processes for efficient production of polyunsaturated fatty acids (PUFAs). In this study we co‐expressed Mucor rouxii Δ12‐ and Δ6‐desaturase genes in Saccharomyces cerevisiae, which resulted in a yeast strain that accumulated linoleic acid and γ‐linolenic acid in the different lipid species. Additionally, the strain contained higher levels of phospholipids and lower levels of ergosterol than the reference strain. Integrated analysis of the transcriptome revealed decreased expression of genes involved in ergosterol biosynthesis, but more unexpectedly it also pointed towards attenuated activity of the ubiquitin‐proteasome system and a reduced oxidative stress response. In vitro and in vivo measurements showed reduced levels of all three proteasomal activities and also increased levels of reactive oxidative species in the PUFA‐producing strain. Overall our results clearly show that PUFAs in yeast can be detrimental for several key cellular pathways, such as the oxidative stress response and proteasomal activity, suggesting that the membrane composition is of vital importance for these processes.
β‐peptoid “Foldamers”—Why the additional methylene unit?
Authors: Olsen Christian A. 
Published: December 2010

AbstractThe field of peptoid (i.e., N‐alkylglycine) research has been thriving since the first publications on this molecular design appeared in 1992. A highly efficient and modular synthetic platform, which is compatible with automation and ready generation of combinatorial libraries, was published the same year. This has enabled the investigation of numerous compounds with this architecture, and ligands with a wide variety of interesting biological targets have thus been discovered. Furthermore, detailed biophysical and structural studies focusing on the investigation of the conformational space adopted and three‐dimensional folding of these peptidemimics have been undertaken. The same is true for β‐peptides (i.e., oligomers composed of β‐amino acids). Since the first publication describing peptide mimics combining these two structural modifications [the N‐alkyl‐β‐alanines (β‐peptoids)] in 1998, on the other hand, the application of this backbone construct has appeared much more sparsely in the literature. The present perspective article will provide an overview of the data obtained for β‐peptoid‐containing peptide mimics as well as a discussion of the future challenges associated with this type of backbone modification. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 561–566, 2011.
Nonadditivity in the alpha‐helix to coil transition
Authors: Wood Gregory G. , Clinkenbeard Drew A. , Jacobs Donald J. 
Published: December 2010

AbstractThe Lifson‐Roig Model (LRM) and all its variants describe the α‐helix to coil transition in terms of additive component‐free energies within a free energy decomposition scheme, and these contributions are interpreted through sequence‐context dependent nucleation and propagation parameters. Although this phenomenological approach is able to adequately fit experimental data on helix content and heat capacity, the number of required parameters increases dramatically with additional sequence variation. Moreover, due to nonadditive competing microscopic effects that are difficult to disentangle within a LRM, large uncertainties within the parameters emerge. We offer an alternative view that removes the need for sequence‐context parameterization by focusing on individual microsopic interactions within a free energy decomposition and explicitly account for nonadditivity in conformational entropy through network rigidity using a Distance Constraint Model (DCM). We apply a LRM and a DCM to previously published experimental heat capacity and helix content data for a series of heterogeneous polypeptides. Both models describe the experimental data well, and the parameters from both models are consistent with prior work. However, the number of DCM parameters is independent of sequence‐variability, the parameter values exhibit better transferability, and the helix nucleation is predicted by the DCM explicitly through the nonadditive nature of conformational entropy. The importance of these results is that the DCM offers a system‐independent approach for modeling stability within polypeptides and proteins, where the demonstrated accuracy for the α‐helix to coil transition over a series of heterogeneous polypeptides described here is one case in point. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 240–253, 2011.
Peptoid origins
Authors: Zuckermann Ronald N. 
Published: December 2010

AbstractPeptoid oligomers were initially developed as part of a larger basic research effort to accelerate the drug‐discovery process in the biotech/biopharma industry. Their ease of synthesis, stability, and structural similarity to polypeptides made them ideal candidates for the combinatorial discovery of novel peptidomimetic drug candidates. Diverse libraries of short peptoid oligomers provided one of the first demonstrations in the mid‐1990s that high‐affinity ligands to pharmaceutically relevant receptors could be discovered from combinatorial libraries of synthetic compounds. The solid‐phase submonomer method of peptoid synthesis was so efficient and general that it soon became possible to explore the properties of longer polypeptoid chains in a variety of areas beyond drug discovery (e.g., diagnostics, drug delivery, and materials science). Exploration into protein‐mimetic materials soon followed, with the fundamental goal of folding a non‐natural sequence‐specific heteropolymer into defined secondary or tertiary structures. This effort first yielded the peptoid helix and much later the peptoid sheet, both of which are secondary‐structure mimetics that are close relatives to their natural counterparts. These crucial discoveries have brought us closer to building proteinlike structure and function from a non‐natural polymer and have provided great insight into the rules governing polymer and protein folding. The accessibility of peptoid synthesis to chemists and nonchemists alike, along with a lack of information‐rich non‐natural polymers available to study, has led to a rapid growth in the field of peptoid science by many new investigators. This work provides an overview of the initial discovery and early developments in the peptoid field. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 545–555, 2011.
Peptoid conformational free energy landscapes from implicit‐solvent molecular simulations in AMBER
Authors: Voelz Vincent A. , Dill Ken A. , Chorny Ilya 
Published: December 2010

AbstractTo test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798–16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis–trans isomerization barriers. Compared to (Nrch)5 and cyclo‐octasarcosyl, the free energy of N‐(2‐nitro‐3‐hydroxyl phenyl)glycine–N‐(phenyl)glycine has the most “foldable” free energy landscape, due to deep trans‐amide minima dictated by N‐aryl sidechains. For peptoids with (S)‐N(1‐phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n → π* interactions. For these residues, an empirical φ‐angle biasing potential can “rescue” the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit–solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first‐principles design of sequences with specific folding properties. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 639–650, 2011.
Temperature‐dependent higher order structures of the (Pro‐Pro‐Gly)10‐modified dendrimer
Authors: Suehiro Tomoyuki , Tada Tomoko , Waku Tomonori , Tanaka Naoki , Hongo Chizuru , Yamamoto Shinya , Nakahira Atsushi , Kojima Chie 
Published: December 2010

AbstractCollagen is the most abundant protein in mammals and is widely used as a biomaterial for tissue engineering and drug delivery. We previously reported that dendrimers and linear polymers, modified with collagen model peptides (Pro‐Pro‐Gly)5, form a collagen‐like triple‐helical structure; however, its triple helicity needs improvement. In this study, a collagen‐mimic dendrimer modified with the longer collagen model peptides, (Pro‐Pro‐Gly)10, was synthesized and named PPG10‐den. Circular dichroism analysis shows that the efficiency of the triple helix formation in PPG10‐den was much improved over the original. The X‐ray diffraction analysis suggests that the higher order structure was similar to the collagen triple helix. The thermal stability of the triple helix in PPG10‐den was higher than in the PPG10 peptide itself and our previous collagen‐mimic polymers using (Pro‐Pro‐Gly)5. Interestingly, PPG10‐den also assembled at low temperatures. Self‐assembled structures with spherical and rod‐like shapes were observed by transmission electron microscopy. Furthermore, a hydrogel of PPG10‐den was successfully prepared which exhibited the sol‐gel transition around 45°C. Therefore, the collagen‐mimic dendrimer is a potential temperature‐dependent biomaterial. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 270–277, 2011.
Pretreatment of rat bone marrow mesenchymal stem cells with a combination of hypergravity and 5‐azacytidine enhances therapeutic efficacy for myocardial infarction
Authors: Ling Shu‐Kuan , Wang Rui , Dai Zhong‐Quan , Nie Jie‐Lin , Wang Hong‐Hui , Tan Ying‐Jun , Cao Hong‐Qing , Huang Zeng‐Ming , Wan Yu‐Min , Li Ying‐Hui 
Published: December 2010

AbstractBackground and Purpose: The in vivo cardiac differentiation and functional effects of unmodified adult bone marrow mesenchymal stem cells (BMSCs) after myocardial infarction (MI) is controversial. Our previous results suggested that hypergravity promoted the cardiomyogenic differentiation of BMSCs, and thus we postulated that ex vivo pretreatment of BMSCs using hypergravity and 5‐azacytidine (5‐Aza) would lead to cardiomyogenic differentiation and result in superior biological and functional effects on cardiac regeneration of infarcted myocardium. Methods: We used a rat MI model generated by ligation of the coronary artery. Homogeneous rat BMSCs were isolated, culture expanded, and differentiated into a cardiac lineage by adding hypergravity (2G) for 3 days and 5‐Aza (50 lmol/L, 24 h). Rats underwent BMSCs (labeled with DAPI) injection after the infarction and were randomized into five groups. Group A rats received the control medium, Group B rats received unmodified BMSCs, Group C rats received BMSCs treated with hypergravity, Group D rats received BMSCs treated with 5‐Aza, and Group E rats received BMSCs treated with 5‐Aza and hypergravity (n = 6). Results: After hypergravity and 5‐Aza treatment, BMSCs showed positive for the early muscle and cardiac markers GATA‐4, MEF‐2, and Nkx2‐5 with RT‐PCR. We also found that hypergravity could enhance the activities of MEF‐2 via promoting the nuclear export of HDAC5. The frozen section showed that the implanted BMSCs labeled with DAPI survived and angiogenesis was identified at the implantation site. In Groups B, C, D, and E rats, pre‐treated BMSCs colocalized with α‐actinin, and Group E rats showed a significantly larger increase in left ventricular function. Conclusions: The biological ex vivo cardiomyogenic differentiation of adult BMSCs with hypergravity and 5‐Aza prior to their transplantation is feasible and appears to improve their in vivo cardiac differentiation as well as the functional recovery in a rat model of the infarcted myocardium. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011