bluuebunny/crossref_metadata_2025 huggingface dataset:
The advantages of three‐dimensional culture in a collagen hydrogel for stem cell differentiation
Authors: Naito Hiroshi , Yoshimura Mamiko , Mizuno Toshihide , Takasawa Shin , Tojo Takashi , Taniguchi Shigeki
Published: March 2013

We evaluated the advantages of three‐dimensional (3D) culture in a collagen hydrogel for stem cell differentiation, including the morphology of differentiated cells, differentiation efficiency of stem cells from aged rat and cells after passaging and freeze/thawing. Rat mesenchymal stem cells (MSCs) from young and aged rats, and MSCs after passaging and freeze/thawing were induced to differentiate into osteoblasts in 3D and 2D cultures, and histological studies were performed. Differentiation efficiency was evaluated by markers of osteoblastic differentiation including Runx2 and osterix gene expressions, osteocalcin secretion and calcium deposition. MSCs were stained positive for alkaline phosphatase in 3D and 2D cultures. However, the morphology of differentiated cells in 3D culture, which was different from that in 2D culture, was similar to that of osteoblasts in vivo. Markers of osteoblastic differentiation in MSCs from aged rats in 3D culture were higher than those in MSCs from young rats in 2D culture. Markers of osteoblastic differentiation in MSCs after passaging and freeze/thawing in 3D culture were higher than those in nonpassaged MSCs in 2D culture. These results indicate that 3D culture in a collagen hydrogel has advantages for the differentiation of MSCs into osteoblasts with a similar phenotype to that of in vivo, when using even MSCs from aged donors or after passaging and freeze/thawing. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 101A: 2838–2845, 2013.
In vivo effects of tailored laminin‐332 α3 conjugated scaffolds enhances wound healing: A histomorphometric analysis
Authors: Damodaran Gopinath , Tiong William H. C. , Collighan Russell , Griffin Martin , Navsaria Harshad , Pandit Abhay
Published: March 2013

Surface modification techniques have been used to develop biomimetic scaffolds by incorporating cell adhesion peptides. In our previous work, we have shown the tethering of laminin‐332 α3 chain to type I collagen scaffold using microbial transglutaminase (mTGase), promotes cell adhesion, migration, and proliferation. In this study, we evaluated the wound healing properties of tailored laminin‐332 α3 chain (peptide A: PPFLMLLKGSTR) tethered to a type I collagen scaffold using mTGase by incorporating transglutaminase substrate peptide sequences containing either glutamine (peptide B: PPFLMLLKGSTREAQQIVM) or lysine (peptide C: PPFLMLLKGSTRKKKKG) in rat full‐thickness wound model at two different time points (7 and 21 days). Histological evaluations were assessed for wound closure, epithelialization, angiogenesis, inflammatory, fibroblastic cellular infiltrations, and quantified using stereological methods (p < 0.05). Peptide A and B tethered to collagen scaffold using mTGase stimulated neovascularization, decreased the inflammatory cell infiltration and prominently enhanced the fibroblast proliferation which significantly accelerated the wound healing process. We conclude that surface modification by incorporating motif of laminin‐332 α3 chain (peptide A: PPFLMLLK GSTR) domain and transglutaminase substrate to the laminin‐332 α3 chain (peptide B: PPFLMLLKGSTREAQQIVM) using mTGase may be a potential candidate for tissue engineering applications and skin regeneration. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 101A:2788–2795, 2013.
Nano‐sized collagen I molecules enhanced the differentiation of rat mesenchymal stem cells into cardiomyocytes
Authors: Kang Pei‐Leun , Chen Chih‐Hao , Chen Shu Ying , Wu Yi‐Jhen , Lin Chia Yun , Lin Feng‐Huei , Kuo Shyh Ming
Published: March 2013

The aim of this study was to investigate the ability of nano‐sized collagen I molecules (nanoparticles or nanofibrils) and a 5‐azacytidine (5‐aza) treatment to enhance the differentiation of rat mesenchymal stem cells (MSCs) toward a cardiomyogenic phenotype in vitro. Second passaged MSCs were cocultured with nano‐sized collagen I molecules for 24 h and then treated with 10 μM 5‐aza for 24 h. The results demonstrated that the size of the cells increased significantly and acquired a flattened, triangular‐shaped morphology after treatment with nano‐sized collagen I molecules and 5‐aza. The cells are connecting with adjoining cells by forming myotube‐like structures. Additional treatment of the MSCs with nano‐sized collagen I fibrils significantly increased two transcription factors GATA‐4 (12.6‐fold increase) and Nkx2.5 (4.8‐fold increase) expressions compared with MSC groups treated only with 5‐aza at 3‐day culturing. Furthermore, MSCs pretreated with nano‐sized collagen fibrils significantly increased the expressions of cardiac genes of troponin I, β‐myosin heavy chain, and cardiac α‐actin compared with MSC groups treated only with 5‐aza (all, p < 0.01 or better). These results indicate that culturing MSCs with nano‐sized collagen I molecules, which may act as scaffolds or soluble protein ingredients, leads to alterations in gene expression and affects the differentiation fate induced with 5‐aza. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 101A: 2808–2816, 2013.
Gallai's Conjecture For Graphs of Girth at Least Four
Authors: Harding Peter , McGuinness Sean
Published: March 2013

In 1966, Gallai conjectured that for any simple, connected graph G having n vertices, there is a path‐decomposition of G having at most paths. In this article, we show that for any simple graph G having girth , there is a path‐decomposition of G having at most paths, where is the number of vertices of odd degree in G and is the number of nonisolated vertices of even degree in G.
Quetiapine for the treatment of delirium
Authors: Hawkins Stefanie B. , Bucklin Mason , Muzyk Andrew J.
Published: March 2013

BACKGROUND

Delirium is associated with high rates of morbidity and mortality in hospitalized medically ill patients. Haloperidol has historically been the agent of choice for the treatment of delirium, but recent studies have explored the efficacy of second‐generation antipsychotics such as quetiapine. The unique pharmacology of quetiapine may allow it to treat delirium and provide sedation without causing significant extrapyramidal side effects.

PURPOSE

To evaluate the efficacy of quetiapine for the treatment of delirium.

DATA SOURCES

A search was conducted in MEDLINE and Embase (January 1960–December 2012) using keywords “quetiapine,” “second‐generation antipsychotic,” “atypical antipsychotic,” “delirium,” and “agitation.”

STUDY SELECTION AND DATA EXTRACTION

The search was limited to English‐language articles and trials with treatment of delirium as the primary end point. Eight trials met this inclusion criterion.

DATA SYNTHESIS

Two randomized controlled trials, 5 open‐label studies, and 1 retrospective cohort study evaluating quetiapine for the treatment of delirium were reviewed. One randomized controlled trial showed no differences in total mean delirium scores, but found the rate of delirium improvement was significantly shorter with quetiapine. The second randomized controlled trial showed the time to first resolution of delirium was shorter with quetiapine compared to placebo. Results of the open‐label and retrospective cohort trials have also shown significant resolution of delirium from baseline and equal efficacy with quetiapine compared to amisulpride and haloperidol.

CONCLUSIONS

Quetiapine appears to be an effective and safe agent for the treatment of delirium in both general medicine and intensive care unit patients. The trials summarized suggest that quetiapine resolves symptoms of delirium more quickly than placebo and has equal efficacy compared to haloperidol and the atypical antipsychotic amisulpride. Further study is needed. Journal of Hospital Medicine 2013;8:215–220. © 2013 Society of Hospital Medicine
Deregulation of glutamate dehydrogenase in human neurologic disorders
Authors: Plaitakis Andreas , Zaganas Ioannis , Spanaki Cleanthe
Published: March 2013

Mammalian glutamate dehydrogenase is an allosterically regulated enzyme that is central to glutamate metabolism. It contributes to important cellular processes, including Krebs cycle anaplerotic mechanisms, energy production, and ammonia homeostasis. In addition to this housekeeping hGDH1, humans have acquired through duplication an hGDH2 isoenzyme expressed in neural tissues with distinct regulatory properties. There is increasing evidence that deregulation of human GDHs leads to human disorders. Thus, in hGDH1, regulatory mutations that attenuate GTP inhibition can result in the hyperinsulinism/hyperammonemia syndrome, which is often associated with epileptic seizures, mental retardation, and generalized dystonia. Also, transgenic overexpression of GLUD1 in neurons has resulted in age‐dependent degeneration of the CA1 behippocampal region, associated with upregulation of α‐synuclein and other proteins linked to major human movement disorders. With regard to hGDH2, a rare T1492G variation in the GLUD2 gene, resulting in substitution of Ala for Ser445 in the regulatory domain of hGDH2, interacts significantly with Parkinson's disease (PD) onset. In two independent Greek and one North American PD cohorts, Ser445Ala hemizygous males, but not heterozygous females, developed PD 6–13 years earlier than subjects with other genotypes. The Ala445‐hGDH2 variant displays increased catalytic activity that is amenable to inhibition by estrogens. Enhanced glutamate oxidation by Ala445‐hGDH2 is thought to accelerate nigral cell degeneration in hemizygous males, and inhibition of the overactive variant by estrogens may protect heterozygous females. Hence, deregulation of hGDH1 and hGDH2 may play a role in degenerative processes, so these observations identify novel targets for therapeutic intervention in human disorders. © 2013 Wiley Periodicals, Inc.
In vivo imaging of paraCEST agents using frequency labeled exchange transfer MRI
Authors: Lin Chien‐Yuan , Yadav Nirbhay N. , Ratnakar James , Sherry A. Dean , van Zijl Peter C. M.
Published: March 2013

Purpose

A main obstacle to in vivo applications of paramagnetic chemical exchange saturation transfer (paraCEST) is interference from endogenous tissue magnetization transfer contrast (MTC). The suitability of excitation‐based frequency labeled exchange transfer (FLEX) to separate out such MTC effects in vivo was tested.

Methods

The FLEX sequence measures modulation of the water signal based on the chemical shift evolution of solute proton magnetization as a function of evolution time. Time‐domain analysis of this water signal allows identification of different solute components and provides a mechanism to separate out the rapidly decaying MTC components with short effective transverse relaxation time (
) values.

Results

FLEX imaging of paraCEST agents was possible in vitro in phantoms and in vivo in mouse kidneys and bladder. The results demonstrated that FLEX is capable of separating out the MTC signal from tissues in vivo while providing a quantitative exchange rate for the rapidly exchanging paraCEST water protons by fitting the FLEX time‐domain signal to FLEX theory.

Conclusions

The first in vivo FLEX images of a paraCEST agent were acquired, which allowed separation of the tissue MTC components. These results show that FLEX imaging has potential for imaging the distribution of functional paraCEST agents in biological tissues. Magn Reson Med 71:286–293, 2014. © 2013 Wiley Periodicals, Inc.
Myelin water mapping by spatially regularized longitudinal relaxographic imaging at high magnetic fields
Authors: Labadie Christian , Lee Jing‐Huei , Rooney William D. , Jarchow Silvia , Aubert‐Frécon Monique , Springer Charles S. , Möller Harald E.
Published: March 2013

Purpose

Magnetic resonance T1‐weighted images are routinely used for human brain segmentation, brain parcellation, and clinical diagnosis of demyelinating diseases. Myelin is thought to influence the longitudinal relaxation commonly described by a mono‐exponential recovery, although reports of bi‐exponential longitudinal relaxation have been published. The purpose of this work was to investigate if a myelin water T1 contribution could be separated in geometrically sampled Look‐Locker trains of low flip angle gradient echoes.

Methods

T1 relaxograms from normal human brain were computed by a spatially regularized inverse Laplace transform after estimating the apparent inversion efficiency.

Results

With sufficiently long inversion‐time sampling (ca. 5 × T1 of cerebrospinal fluid), the T1 relaxogram revealed a short‐T1 peak (106–225 ms). The apparent fraction of this water component increased in human brain white matter from 8.3% at 3 T, to 11.3% at 4 T and 15.0% at 7 T. The T2* of the short‐T1 peak at 3 T was shorter, 27.9 ± 13.0 ms, than that of the long‐T1 peak, 51.3 ± 5.6 ms.

Conclusion

The short‐T1 fraction is interpreted as the water resident in myelin. Its detection is facilitated by longer T1 of axoplasmic water at higher magnetic field. Magn Reson Med 71:375–387, 2014. © 2013 Wiley Periodicals, Inc.
Multiband accelerated spin‐echo echo planar imaging with reduced peak RF power using time‐shifted RF pulses
Authors: Auerbach Edward J. , Xu Junqian , Yacoub Essa , Moeller Steen , Uğurbil Kâmil
Published: March 2013

Purpose:

To evaluate an alternative method for generating multibanded radiofrequency (RF) pulses for use in multiband slice‐accelerated imaging with slice‐GRAPPA unaliasing, substantially reducing the required peak power without bandwidth compromises. This allows much higher accelerations for spin‐echo methods such as SE‐fMRI and diffusion‐weighted MRI where multibanded slice acceleration has been limited by available peak power.

Theory and Methods:

Multibanded “time‐shifted” RF pulses were generated by inserting temporal shifts between the applications of RF energy for individual bands, avoiding worst‐case constructive interferences. Slice profiles and images in phantoms and human subjects were acquired at 3 T.

Results:

For typical sinc pulses, time‐shifted multibanded RF pulses were generated with little increase in required peak power compared to single‐banded pulses. Slice profile quality was improved by allowing for higher pulse bandwidths, and image quality was improved by allowing for optimum flip angles to be achieved.

Conclusion:

A simple approach has been demonstrated that significantly alleviates the restrictions imposed on achievable slice acceleration factors in multiband spin‐echo imaging due to the power requirements of multibanded RF pulses. This solution will allow for increased accelerations in diffusion‐weighted MRI applications where data acquisition times are normally very long and the ability to accelerate is extremely valuable. Magn Reson Med 69:1261–1267, 2013 Wiley Periodicals, Inc.
Supplier certification and quality investment in supply chains
Authors: Chen Ying‐Ju , Deng Mingcherng
Published: March 2013

Global sourcing has made quality management a more challenging task, and supplier certification has emerged as a solution to overcome suppliers' informational advantage about their product quality. This article analyzes the impact of certification standards on the supplier's investment in quality, when a buyer outsources the production process. Based on our results, deterministic certification may lead to under‐investment in quality improvement technology for efficient suppliers, thereby leading to potential supply chain inefficiency. The introduction of noisy certification may alleviate this under‐investment problem, when the cost of information asymmetry is high. While allowing noisy certification always empowers the buyer to offer a menu to screen among heterogeneous suppliers, the buyer may optimally choose only a limited number of certification standards. Our analysis provides a clear‐cut prediction of the types of certifiers the buyer should use for heterogeneous suppliers, and we identify the conditions under which the supplier benefits from noisy certification. © 2013 Wiley Periodicals, Inc. Naval Research Logistics, 2013
The graph association problem: Mathematical models and a lagrangian heuristic
Authors: Tauer Gregory , Nagi Rakesh , Sudit Moises
Published: March 2013

Graph association is the problem of merging many graphs that collectively describe a set of possibly repetitive entities and relationships into a single graph that contains unique entities and relationships. As a form of data association, graph association can be used to identify when two sensors are observing the same object so information from both sensors can be combined and analyzed in a meaningful and consistent way. Graph association between two graphs is related to the problem of graph matching, and between multiple graphs it is related to the common labeling of a graph set (also known as multiple graph matching) problem. This article contribution is to formulate graph association as a binary linear program and introduce a heuristic for solving multiple graph association using a Lagrangian relaxation approach to address issues with between‐graph transitivity requirements. The algorithms are tested on a representative dataset. The developed model formulation was found to accurately solve the graph association problem. Furthermore, the Lagrangian heuristic was found to solve the developed model within 3% of optimal on many problem instances, and found better solutions to large problems than is possible by directly using CPLEX. © 2013 Wiley Periodicals, Inc. Naval Research Logistics, 2013
Efficient generation of densely packed convex polyhedra for 3D discrete and finite‐discrete element methods
Authors: Buechler S.R. , Johnson S.M.
Published: March 2013

For granular mechanics studies, efficiently creating a realistic consolidated pack is a challenging task. To achieve this, particle shapes are traditionally restricted to simple shapes (disks, ellipses, spheres, ellipsoids) or constructed from a library, loosely populated, and subsequently settled under gravity. These methods suffer from both a lack of physicality in terms of the particle shapes and impractically long sample preparation times. To address these shortcomings, we introduce a method to generate and pack polyhedra within arbitrary boundaries through a tetrahedral element erosion process. This approach yields tightly packed systems of convex hulls for traditional discrete element calculations and internal tetrahedral meshing of the individual bodies for use in finite‐discrete element or finite element calculations. To demonstrate the method, we present its application to packing sphere‐like and ellipsoid‐like particles for simple and complex bounding volumes. Copyright © 2013 John Wiley & Sons, Ltd.
Feasibility of reduced‐intensity allogeneic stem cell transplantation with imatinib in children with philadelphia chromosome‐positive acute lymphoblastic leukemia
Authors: Yamada Kayo , Yasui Masahiro , Kondo Osamu , Sato Maho , Sawada Akihisa , Kawa Keisei , Inoue Masami
Published: March 2013

Philadelphia chromosome‐positive acute lymphoblastic leukemia (Ph + ALL) in children is one of the highest‐risk ALL groups. Improved outcome in combination with imatinib has been reported. However, intensive chemotherapy or myeloablative conditioning followed by hematopoietic stem cell transplantation (HSCT) can be associated with significant adverse late effects. We report a case series of five children with Ph + ALL underwent reduced‐intensity allogeneic HSCT (RIST) after induction and consolidation in chemotherapy combined with imatinib. Four of the five patients remain first complete remission for a median of 3.1 years after RIST. These results are preliminary, but suggest the feasibility and effectiveness of RIST with imatinib. Pediatr Blood Cancer 2013;60:E60–E62. © 2013 Wiley Periodicals, Inc.
Timing of Factor VIIa in Liver Transplantation Impacts Cost and Clinical Outcomes
Authors: Scheffert Jenna L. , Taber David J. , Pilch Nicole A. , McGillicuddy John W. , Baliga Prabhakar K. , Chavin Kenneth D.
Published: March 2013

Study Objective

To investigate the clinical and economic outcomes associated with the use of recombinant factor VIIa (rFVIIa) in perioperative liver transplantation (LT).

Design

Retrospective review.

Setting

Academic medical center.

Patients

A total of 63 adults who underwent LT between January 2000 and September 2008 and received rFVIIa prior to or during the procedure. Using a propensity‐scoring method, these patients were matched in a 1:2 ratio with 120 controls.

Measurements and Main Results

Of the 473 patients who received any LT during the study period, 63 (13%) received rFVIIa and were matched with propensity score matched controls at a ratio of approximately 1:2. Of those who received rFVIIa, 27 (43%) received preemptive administration and 14 (22%) received intraoperative administration. (The remaining 22 patients received rFVIIa outside of a 12‐hour window of time before or after surgery.) Clinical outcomes were similar between the preemptive and the control groups, although patients in the control group had a shorter length of stay in the intensive care unit (ICU) and incurred fewer expenses. Compared with both the preemptive and the control groups, patients who received rFVIIa intraoperatively required more blood products, longer stays in the ICU, and incurred higher costs. They also had poorer graft survival and decreased overall survival rates at 30 days and 1 year.

Conclusion

Intraoperative administration of rFVIIa in LT was associated with higher blood product use, lower graft and patient survival rates, longer ICU stays, and higher overall costs compared with preemptive administration. The use of preemptive rFVIIa in select high‐risk LT patients may prevent the development of poor clinical outcomes and may be more cost effective compared with intraoperative administration.
Do healthcare professionals discuss the emotional impact of cancer with patients?
Authors: Bonito Allison , Horowitz Nina , McCorkle Ruth , Chagpar Anees B.
Published: March 2013

Background

It is known that cancer may affect patients' emotions and their relationships with other people and that those with strong emotional support may enjoy improved outcomes. We sought to determine the frequency with which healthcare professionals discuss the impact of cancer on patients' emotions and relationships with others.

Methods

Data regarding healthcare professionals' discussions of the emotional impact of cancer and relevant covariates were obtained from the 2010 National Health Interview Survey. Statistical analyses were performed using sudaan software (Research Triangle Institute, Raleigh, NC, USA).

Results

Of the 2074 people with a prior diagnosis of cancer surveyed, 701 (33.8%) claimed that a doctor, nurse, or other healthcare professional had discussed with them ‘how cancer could affect their emotions or relationships with others’. Of these, 586 (84.5%) reported that they were ‘very satisfied’ with how well their emotional and social needs were met; 73.4% of those who had not had this discussion reported being very satisfied. Patients with leukemia/lymphoma, younger patients, African Americans, and those with a lower degree of education were most likely to report having discussions about emotional issues. Gender was not correlated with these discussions (30.6% in men vs. 33.3% in women). On multivariate analysis, age, race, and cancer type remained independent significant predictors of having a discussion regarding the emotional impact of cancer.

Conclusion

Only a third of cancer patients discussed the emotional impact of a cancer diagnosis with their healthcare professional. Age, race, and type of malignancy affect the likelihood of having these discussions. Copyright © 2013 John Wiley & Sons, Ltd.
Combustion Mechanism of Triaminoguanidine Nitrate
Authors: Serushkin Valery V. , Sinditskii Valery P. , Egorshev Viacheslav Yu. , Filatov Sergey A.
Published: March 2013

The combustion behavior of triaminoguanidine nitrate (TAGN) was investigated over a wide pressure range and a detailed combustion mechanism has been proposed. Temperature profiles in the TAGN combustion wave were measured with thin tungsten‐rhenium microthermocouples. It was shown that the surface temperature in combustion of TAGN as well as for other onium salts is controlled by the process of dissociation. The burning rate of TAGN is governed by processes in the condensed phase.
Development and Performance of Boron Carbide‐Based Smoke Compositions
Authors: Shaw Anthony P. , Poret Jay C. , Gilbert Robert A. , Domanico Joseph A. , Black Ernest L.
Published: March 2013

Pyrotechnic smoke compositions for visual obscuration containing boron carbide, potassium nitrate, potassium chloride, and various lubricants are described. Only the waxy lubricants stearic acid and calcium stearate slowed the burning rate into a range suitable for end‐burning smoke grenades. For compositions pressed into steel cans, the addition of just 2 wt‐% calcium stearate was shown to reduce the burning rate from 0.50 cm s−1to 0.09 cm s−1. In this system, potassium chloride serves as a diluent that reduces incandesence but also increases slag formation. Compositions containing potassium chloride in the 25–30 wt‐% range exhibited both acceptably low incandescense and slag formation upon burning, while also producing copious amounts of white smoke. These experimental compositions were loaded into full‐size grenade cans; field and smoke chamber testing revealed that they outperform the US Army’s in‐service M83 TA grenade both qualitatively and quantitatively. The photopic mass‐based figures of merit for experimental grenades KCl‐25, KCl‐30, and a production‐run M83 TA grenade were 2.51, 2.19, and 1.44 m2 g−1, respectively.
Modifying Aluminum Reactivity with Poly(Carbon Monofluoride) via Mechanical Activation
Authors: Sippel Travis. R. , Son Steven F. , Groven Lori J.
Published: March 2013

Modification of the reactivity of micrometer‐sized aluminum through inclusion of low levels of poly(carbon monofluoride) (PMF) using mechanical activation (MA) is reported. Resulting composite particle combustion enthalpy, average particle size, and specific surface area depend on MA intensity, duration, and inclusion level, and range from 18.9 to 28.5 kJ g−1, 23.0 to 67.5 μm, and 5.3 to 34.8 m2 g−1, respectively. Differential scanning calorimetry experiments in O2/Ar indicate that MA reduces the exotherm onset from 555 to 480 °C (70/30 wt‐%). Particles are sensitive to electrostatic discharge stimulus (11.5–47.5 mJ) but not to impact (>213 cm) or friction (>360 N) and some low energy MA particles are ignitable by optical flash. With their altered reactivity and high combustion enthalpy, these nanofeatured, micrometer‐sized particles may have use as replacements for aluminum in energetic applications.
A simple probabilistic model of multibody interactions in proteins
Authors: Johansson Kristoffer Enøe , Hamelryck Thomas
Published: March 2013

Protein structure prediction methods typically use statistical potentials, which rely on statistics derived from a database of know protein structures. In the vast majority of cases, these potentials involve pairwise distances or contacts between amino acids or atoms. Although some potentials beyond pairwise interactions have been described, the formulation of a general multibody potential is seen as intractable due to the perceived limited amount of data. In this article, we show that it is possible to formulate a probabilistic model of higher order interactions in proteins, without arbitrarily limiting the number of contacts. The success of this approach is based on replacing a naive table‐based approach with a simple hierarchical model involving suitable probability distributions and conditional independence assumptions. The model captures the joint probability distribution of an amino acid and its neighbors, local structure and solvent exposure. We show that this model can be used to approximate the conditional probability distribution of an amino acid sequence given a structure using a pseudo‐likelihood approach. We verify the model by decoy recognition and site‐specific amino acid predictions. Our coarse‐grained model is compared to state‐of‐art methods that use full atomic detail. This article illustrates how the use of simple probabilistic models can lead to new opportunities in the treatment of nonlocal interactions in knowledge‐based protein structure prediction and design. Proteins 2013; 81:1340–1350. © 2013 Wiley Periodicals, Inc.
Pilot testing of fire sprinkler system in extremely corrosive industrial duct environments
Authors: Su Paul , Doerr William W. , Harrington J.C. , Fuller David B. , Barna Jon M.
Published: March 2013

Due to the extremely corrosive environments inside many exhaust ducts fabricated from combustible materials, the mechanical integrity of fire sprinkler system components is often prematurely compromised, leaving the system unable to protect against fires originating within these ducts [FM Global Loss Prevention Data Sheet, 7–78, Industrial Exhaust System, 2011; Understanding the Hazard, Fire in Industrial Exhaust Systems, FM Global, Johnston, RI, 2006]. Pilot testing of a new fire sprinkler system was conducted to protect the fiber‐reinforced plastic duct at a nitric/hydrofluoric (HF/HNO3) mixed acid pickling operation. Based on previous laboratory and field tests [Su and Doerr, Process Saf Prog 29 (2010) 70–78], this fire sprinkler system was composed of corrosion resistant sprinkler nozzles, a linear heat detector, flexible mounting connections, sprinkler piping, and controls. Pilot testing results have led to development and recommendation of a new fire protection system capable of protecting combustible exhaust ducts from fire in extremely corrosive environments. © 2013 American Institute of Chemical Engineers Process Saf Prog 32: 277–282, 2013
Methanol synthesis on ZnO from molecular dynamics
Authors: Frenzel Johannes , Kiss Janos , Nair Nisanth N. , Meyer Bernd , Marx Dominik
Published: March 2013

This paper reviews our efforts to simulate methanol synthesis from CO and H2 on defective ZnO surfaces using advanced molecular dynamics techniques. This apparently simple chemical reaction occurring on a seemingly well‐defined surface appears to be astonishingly complex. First of all, the preferred oxidation state of F centers at the polar oxygen terminated surface is found to be dictated by the chemical composition and the thermodynamic properties of the gas phase in contact with ${\rm ZnO}(000\overline {1} )$. Secondly, reaction intermediates and pathways along the catalytic cycle taking place at or close to these defects are found to depend in a sensitive way on their oxidation state. Thirdly, it is seen that the gas phase close to the catalytic surface might be transiently involved in some of the reaction steps in a non‐trivial manner. Last but not least, the scenario is found to be greatly enriched upon involving copper clusters on polar ZnO surfaces in view of utmost strong metal‐support interactions (SMSIs), which are directly related to the polar nature of ${\rm ZnO}(000\overline {1} )$. Taken together, an unexpectedly rich picture is unveiled by the molecular dynamics approach to computational heterogeneous catalysis when applied to methanol synthesis on bare ZnO.
Colloidal deposition as method to study the influence of the support on the activity of gold catalysts in CO‐oxidation
Authors: Schüth Ferdi
Published: March 2013

The strong influence of the support properties on the activity of gold catalysts has been observed in many publications. The most studied reaction in this respect seems to be CO‐oxidation, for which gold catalysts have outstanding activity. However, since in most studies the support properties are also important in influencing the nature of the gold particles deposited on them by co‐precipitation or deposition–precipitation, it is difficult to study the support effect alone. We have in a series of studies used colloidal impregnation of preformed gold particles approximately 3 nm in size on different supports in order to decouple the gold particle formation from the deposition process, in order to isolate the support effect. Even for such similarly prepared catalysts very strong differences between different supports were observed. The analysis of the data, also in the light of literature data, suggests that there is no unique factor explaining the high activity of gold catalysts, but rather a combination of effects, which act in different proportion for different catalysts.
Properties of manganite/ruthenate superlattices with ultrathin layers
Authors: Ziese Michael , Vrejoiu Ionela
Published: March 2013

The properties of manganite/ruthenate superlattices are reviewed with a specific focus on the manganite/ruthenate interface. La0.7Sr0.3MnO3/SrRuO3 and Pr0.7Ca0.3MnO3/SrRuO3 superlattices grow with a high crystalline perfection as illustrated in the figure to the right: at the interface the individual cation species can be clearly identified, interdiffusion is marginal. The superlattices show magnetization processes with an intricate interplay between magnetocrystalline anisotropy, size of the layer magnetization, spin confinement and interfacial antiferromagnetic interlayer coupling. There is further an unprecedented Curie temperature stabilization at room temperature values of the La0.7Sr0.3MnO3 layers in the superlattices down to layer thicknesses of one unit cell. The magnetotransport properties, especially the Hall effect, indicate the existence of a quasi‐two‐dimensional hole gas at the La0.7Sr0.3MnO3/SrRuO3 interface; this is further supported by an analysis of cation displacements as determined from scanning transmission electron microscopy. The manganite/ruthenate interface might be considered as a model system for the study of interfacial reconstruction and charge transfer in a highly correlated ferromagnetic system.

magnified image

HAADF‐STEM micrograph of two La0.7Sr0.3MnO3/SrRuO3 interfaces in a superlattice with four unit cell thick La0.7Sr0.3MnO3 and eight unit cell thick SrRuO3 layers. The spheres indicate the cations as determined from the Z‐contrast.

(© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inhibition of TNF‐α‐Induced MUC5AC Mucin Gene Expression and Production by Wogonin Through the Inactivation of NF‐κB Signaling in Airway Epithelial Cells
Authors: Sikder Md. Asaduzzaman , Lee Hyun Jae , Mia Md. Zakaria , Park Su Hyun , Ryu Jiho , Kim Jang‐Hyun , Min Sang Yeon , Hong Jang‐Hee , Seok Jeong Ho , Lee Choong Jae
Published: March 2013

In this study, we investigated whether wogonin significantly affects MUC5AC mucin gene expression and production in human airway epithelial cells. Confluent NCI‐H292 cells were pretreated with wogonin for 30 min and then stimulated with tumor necrosis factor‐α (TNF‐α) for 24 h or the indicated periods. The MUC5AC mucin gene expression and mucin protein production were measured by RT‐PCR and ELISA, respectively. We found that incubation of NCI‐H292 cells with wogonin significantly inhibited mucin production and down‐regulated MUC5AC gene expression induced by TNF‐α in a dose‐dependent fashion. To elucidate the action mechanism of wogonin, effect of wogonin on TNF‐α‐induced NF‐κB signaling pathway was investigated by western blot analysis. Wogonin inhibited NF‐κB activation induced by TNF‐α. Inhibition of IKK by wogonin led to the suppression of IκB phosphorylation and degradation, p65 nuclear translocation and NF‐κB‐regulated gene expression. This, in turn, led to the down‐regulation of MUC5AC protein production in NCI‐H292 cells. Wogonin also inhibited the gene products involved in cell survival (Bcl‐2) and proliferation (cyclooxygenase‐2). These results suggest that wogonin inhibits the NF‐κB signaling pathway, which may explain its role in the inhibition of MUC5AC mucin gene expression and production. Copyright © 2013 John Wiley & Sons, Ltd.
The layer‐by‐layer stoichiometry of La0.7Sr0.3MnO3/SrTiO3 thin films and interfaces
Authors: Song F. , Monsen Å. F. , Li Z. S. , Wells J. W. , Wahlström E.
Published: March 2013

By using a combination of synchrotron photoemission and a finite element model, the layer‐by‐layer stoichiometry of pulsed laser deposited La0.7Sr0.3MnO3 (LSMO) thin films is extracted. For 3‐ and 5‐unit‐cell films, the LSMO stoichiometry at the LSMO/SrTiO3 interface has been studied, and it is found that the Sr surface segregation is reversed at the lower interface such that it becomes La rich and Sr depleted. Mn is depleted throughout the entire layer, consistent with reports of a magnetically ‘dead’ layer and the formation of a Ruddlesden–Popper phase. The depth‐averaged Mn concentration is less than 50% of the expected value, suggesting that interface mixing or segregation into the bulk is important, whereas the depth‐averaged La and Sr concentrations are close to the expected values. Copyright © 2013 John Wiley & Sons, Ltd.
Aligned Carbon Nanotubes for High‐Efficiency Schottky Solar Cells
Authors: Di Jiangtao , Yong Zhenzhong , Zheng Xinhe , Sun Baoquan , Li Qingwen
Published: March 2013

The development of low‐cost and high‐efficiency silicon Schottky solar cells has drawn considerable interest in recent years. A facial approach for the fabrication of carbon nanotube–silicon (CNT–Si) Schottky solar cells by using aligned double‐walled CNTs drawn from a CNT array is demonstrated. The aligned CNTs help to form high CNT–Si junction density and provide efficient charge‐transport paths. The power conversion efficiency (PCE) reaches 10.5%, which is higher than that of solar cells fabricated using pristine and random CNT networks. Furthermore, the cell fabrication is scalable, and the solar cells fabricated in one batch show very small PCE fluctuations.
Model‐driven physical‐design automation for FPGAs: fast prototyping and legacy reuse
Authors: Teodorov Ciprian , Lagadec Loïc
Published: March 2013

The current integrated circuit technologies are approaching their physical limits in terms of scaling and power consumption, in this context, the electronic design automation (EDA) industry is pushed towards solving ever more challenging problems in terms of performance, scalability and adaptability. Meeting these constraints needs innovation at both the algorithmic and the methodological level. Amongst academic EDA tools, Madeo toolkit has been targeting field‐programmable gate array (FPGA) design‐automation at the logic and the physical level since the late 1990s. As many other long‐living software, despite embedding valuable legacy, Madeo exhibits unwanted characteristics that penalize evolution and render the automation problems even more difficult. This study presents a methodological approach to physical‐design automation relying on model‐driven engineering, which is illustrated through the incremental redesign of the Madeo framework. A benefit of this approach is the emergence of a common vocabulary to describe the EDA domain in an FPGA scope. A second advantage is the isolation of the optimization algorithms from the structural domain models. However, the main asset is the possibility to re‐inject into the newly designed toolkit most of the legacy code. The redesigned framework is compared with and scored against initial code‐base, and demonstrates a regression‐free remodeling of the environment with net improvements in terms of size and complexity metrics. As a consequence, the evolution capability is back on stage, and the domain‐space exploration widens to the algorithmic axis. Copyright © 2013 John Wiley & Sons, Ltd.
Automatic reaction mapping and reaction center detection
Authors: Chen William Lingran , Chen David Z. , Taylor Keith T.
Published: March 2013

A reaction center is the part of a chemical reaction that undergoes changes, the heart of the chemical reaction. The reaction atom–atom mapping indicates which reactant atom becomes which product atom during the reaction. Automatic reaction mapping and reaction center detection are of great importance in many applications, such as developing chemical and biochemical reaction databases and studying reaction mechanisms. Traditional reaction mapping algorithms are either based on extended‐connectivity or maximum common substructure (MCS) algorithms. With the development of several biochemical reaction databases (such as KEGG database) and increasing interest in studying metabolic pathways in recent years, several novel reaction mapping algorithms have been developed to serve the new needs. Most of the new algorithms are optimization based, designed to find optimal mappings with the minimum number of broken and formed bonds. Some algorithms also incorporate the chemical knowledge into the searching process in the form of bond weights. Some new algorithms showed better accuracy and performance than the MCS‐based method.WIREs Comput Mol Sci2013, 3:560–593. doi: 10.1002/wcms.1140

This article is categorized under:

Computer and Information Science > Chemoinformatics
Flavor violating Higgs decays
Authors: Harnik Roni , Kopp Joachim , Zupan Jure
Published: March 2013

Abstract

We study a class of nonstandard interactions of the newly discovered 125 GeV Higgs-like resonance that are especially interesting probes of new physics: flavor violating Higgs couplings to leptons and quarks. These interaction can arise in many frameworks of new physics at the electroweak scale such as two Higgs doublet models, extra dimensions, or models of compositeness. We rederive constraints on flavor violating Higgs couplings using data on rare decays, electric and magnetic dipole moments, and meson oscillations. We confirm that flavor violating Higgs boson decays to leptons can be sizeable with, e.g., h → τμ and h → τe branching ratios of
$ \mathcal{O} $
(10%) perfectly allowed by low energy constraints. We estimate the current LHC limits on h → τμ and h → τe decays by recasting existing searches for the SM Higgs in the ττ channel and find that these bounds are already stronger than those from rare tau decays. We also show that these limits can be improved significantly with dedicated searches and we outline a possible search strategy. Flavor violating Higgs decays therefore present an opportunity for discovery of new physics which in some cases may be easier to access experimentally than flavor conserving deviations from the Standard Model Higgs framework.
Un-twisting the NHEK with spectral flows
Authors: Bena Iosif , Guica Monica , Song Wei
Published: March 2013

Abstract

We show that the six-dimensional uplift of the five-dimensional Near-Horizon-Extremal-Kerr (NHEK) spacetime can be obtained from anAdS3×S3solution by a sequence of supergravity — but not string theory — dualities. We present three ways of viewing these pseudo-dualities: as a series of transformations in the STU model, as a combination of Melvin twists and T-dualities and, finally, as a sequence of two generalized spectral flows and a coordinate transformation. We then use these to find an infinite family of asymptotically flat embeddings of NHEK spacetimes in string theory, parameterized by the arbitrary values of the moduli at infinity. Our construction reveals the existence of non-perturbative deformations of asymptotically-NHEK spacetimes, which correspond to the bubbling of nontrivial cycles wrapped by flux, and paves the way for finding a microscopic field theory dual to NHEK which involves Melvin twists of the D1-D5 gauge theory. Our analysis also clarifies the meaning of the generalized spectral flow solution-generating techniques that have been recently employed in the literature.
Total Tumor Volume Is a Better Marker of Tumor Burden in Hepatocellular Carcinoma Defined by the Milan Criteria
Authors: Lee Yun‐Hsuan , Hsia Cheng‐Yuan , Hsu Chia‐Yang , Huang Yi‐Hsiang , Lin Han‐Chieh , Huo Teh‐Ia
Published: March 2013

Background

The Milan criteria are used to define small hepatocellular carcinoma (HCC) and to select patients for curative treatments. Total tumor volume (TTV) is an alternative parameter for tumor burden. We aimed to evaluate whether TTV is a feasible prognostic marker in HCC patients with upper boundary TTV of 65.5 cm3, which is equivalent to a single 5 cm tumor nodule defined by the Milan criteria.

Methods

A total of 774 HCC patients with TTV <65.5 cm3 receiving surgical resection, liver transplantation, or radiofrequency ablation (RFA) as the primary treatment were retrospectively analyzed.

Results

Of these patients, 50 (6.5 %) did not fulfill the Milan criteria. Patients beyond the Milan criteria more often had larger tumor size and TTV, as well as more tumor nodules (p values all <0.01). There was no significant survival difference between patients within and beyond the Milan criteria (p = 0.205). Patients with TTV >15 cm3 had a significantly poorer survival than patients with TTV <15 cm3 (p = 0.007). There was no survival difference between patients receiving surgical treatments versus RFA (p = 0.932). In the Cox proportional hazards model, TTV >15 cm3 [risk ratio (RR): 1.474, p = 0.005], serum bilirubin ≥1.5 mg/dL (RR: 1.663, p = 0.003), serum sodium <135 mmol/L (RR: 2.016, p = 0.01), and α‐fetoprotein (AFP) ≥100 ng/mL (RR: 1.37, p = 0.033) were independent predictors of poor prognosis.

Conclusions

Total tumor volume, is an independent and better prognostic marker than the Milan criteria to indicate tumor burden in HCC patients who had tumor volume defined by the Milan criteria and underwent curative therapies.
Preoperative Carcinoembryonic Antigen Level Predicts Prognosis in Patients with Pseudomyxoma Peritonei Treated with Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy
Authors: Canbay Emel , Ishibashi Haruaki , Sako Shouzou , Mizumoto Akiyoshi , Hirano Masamitsu , Ichinose Masumi , Takao Nobuyuki , Yonemura Yutaka
Published: March 2013

Background

Even though management of pseudomyxoma peritonei (PMP) was improved with cytoreductive surgery (CRS) and hyperthermic chemotherapy (HIPEC), several aspects of PMP still need to be optimized, including patient selection for surgery and prognostic factors. We assessed the role of preoperative carcinoembryonic antigen (CEA) levels in PMP patients treated with CRS and HIPEC.

Methods

A total of 449 PMP patients with documented preoperative CEA levels referred to our center between 2005 and 2011 underwent CRS and HIPEC. The association between CEA levels and characteristics of patients with PMP was assessed withχ2test, linear correlation, and logistic regression analyses. Survival analysis was performed with Cox proportional hazard model.

Results

Median age was 55 (range 19–84) years. There were 245 (54.5 %) females and 204 (45.5 %) males. Preoperative CEA levels were elevated in 328 (73 %, sensitivity) patients with PMP. Preoperative CEA levels were also related to peritoneal cancer index (P< 0.0001), cytoreductive surgery scores (P< 0.0001), progress free survival (P< 0.001) and overall survival (P< 0.001) in patients with PMP.

Conclusions

Our results indicated that preoperative CEA levels are useful in predicting the extent of disease and surgical success as well as progress‐free and overall survival in patients with PMP treated with cytoreductive surgery and HIPEC.
Micellization Studies of Dicationic Gemini Surfactants (m‐2‐m Type) in the Presence of Various Counter‐ and Co‐Ions
Authors: Aslam Jeenat , Siddiqui Umme Salma , Ansari Wajid Husain , Kabir‐ud‐Din
Published: March 2013

Salts have the ability to influence the water activity and self‐association of ionic micelles. In the present case, gemini surfactants; ethanediyl‐α,ω‐bis(dimethyl alkyl ammonium bromide) (referred to as m‐2‐m, m = 10, 12, 14) are synthesized and their micellization study in aqueous medium in presence of monovalent inorganic (NaBr, NaNO3, NaCl, KCl, LiCl) and organic salts (NaTos, NaBenz, NaSal) at 303 K is systematically investigated by conductometric and tensiometric methods. All the salts have the tendency to lower the critical micelle concentration of the surfactants. The effect of inorganic salts on the micellization properties has been found to obey the Hofmeister series. Organic salts reduce the CMC more effectively as compared to inorganic salts. The theoretical models of Rubingh and Rosen have been used to compare the results and obtain the interaction parameters, minimum area per molecule, surface excess, mixed micelle composition, activity coefficients and free energies of micellization/adsorption.