bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraseasonal to interannual variability of the Atlantic meridional overturning circulation from eddy‐resolving simulations and observations
Authors: Xu Xiaobiao , Chassignet Eric P. , Johns William E. , Schmitz William J. , Metzger E. Joseph 
Published: July 2014

AbstractResults from two 1/12° eddy‐resolving simulations, together with data‐based transport estimates at 26.5°N and 41°N, are used to investigate the temporal variability of the Atlantic meridional overturning circulation (AMOC) during 2004–2012. There is a good agreement between the model and the observation for all components of the AMOC at 26.5°N, whereas the agreement at 41°N is primarily due to the Ekman transport. We found that (1) both observations and model results exhibit higher AMOC variability on seasonal and shorter time scales than on interannual and longer time scales; (2) on intraseasonal and interannual time scales, the AMOC variability is often coherent over a wide latitudinal range, but lacks an overall consistent coherent pattern over the entire North Atlantic; and (3) on seasonal time scales, the AMOC variability exhibits two distinct coherent regimes north and south of 20°N, due to different wind stress variability in the tropics and subtropics. The high AMOC variability south of 20°N in the tropical Atlantic comes primarily from the Ekman transport of the near‐surface water, and is modulated to some extent by the transport of the Antarctic Intermediate water below the thermocline. These results highlight the importance of the surface wind in driving the AMOC variability.
Aerosol radiative forcing from the 2010 Eyjafjallajökull volcanic eruptions
Authors: Flanner M. G. , Gardner A. S. , Eckhardt S. , Stohl A. , Perket J. 
Published: July 2014

AbstractAlthough the 2010 volcanic eruptions of Eyjafjallajökull did not exert a large climate forcing, several features of their emissions favored weaker aerosol cooling or stronger warming than commonly attributed to volcanic events. These features include a high ratio of fine ash to SO2, occurrence near reflective surfaces exposed to strong insolation, and the production of very little stratospheric sulfate. We derive plausible ranges of optical properties and top‐of‐atmosphere direct radiative forcing for aerosol emissions from these events and find that shortwave cooling from sulfate was largely offset by warming from ash deposition to cryospheric surfaces and longwave warming from atmospheric ash and sulfate. Shortwave forcing from atmospheric ash was slightly negative in the global mean under central estimates of optical properties, though this forcing term was uniquely sensitive to the simulated distribution of clouds. The forcing components sum to near climate‐neutral global mean 2010 instantaneous (−1.9 mWm−2) and effective (−0.5 mWm−2) radiative forcing, where the latter is elevated by high efficacy of snow‐deposited ash. Ranges in net instantaneous (−7.3 to +2.8 mWm−2) and effective (−7.2 to +4.9 mWm−2) forcing derived from sensitivity studies are dominated by uncertainty in ash shortwave absorptivity. Forcing from airborne ash decayed quickly, while sulfate forcing persisted for several weeks and ash deposits continued to darken snow and sea ice surfaces for months following the eruption. Despite small global forcing, monthly averaged net forcing exceeded 1 Wm−2 in some regions. These findings indicate that ash can be an important component of climate forcing from high‐latitude volcanic eruptions and in some circumstances may exceed sulfate forcing.
Synthesis, Characterization, and Thermal Properties of Organic–Inorganic Hybrids Based on Gelatin and Organomodified Silicones
Authors: Wojciechowska Patrycja , Pietras Przemysław , Maciejewski Hieronim 
Published: July 2014

ABSTRACTThe synthesis of organic–inorganic hybrids is an interesting approach as it offers the possibility of combining the advantages of organic polymer (elasticity, formability) and inorganic material (hardness, strength, high chemical resistance, and thermal stability). Gelatin–siloxane hybrid materials were prepared in the reaction of gelatin and organomodified silicones containing epoxy‐ and both epoxy‐ as well as fluoroalkyl groups. The hybrids obtained were characterized using Fourier transform infrared spectroscopy, proton nuclear magnetic resonance (1H NMR) spectroscopy, and scanning electron microscopic analysis. Thermal properties of the samples were evaluated by means of thermogravimetric analysis and differential scanning calorimetric measurements, showing the influence of type and amount of organosilicon compound on thermal properties of the hybrid materials. The samples obtained with siloxane containing fluoroalkyl groups as well as with mixed siloxanes revealed higher thermal stability than unmodified gelatin. Glass transition temperatures of the hybrids occurred at lower values than for gelatin, exhibiting the plasticizing effect of the applied siloxanes. Enthalpy values of the hybrids decreased, indicating the changes in the helical structure of gelatin caused by the introduction of siloxane.
Evaluation of a community‐based participatory farmworker eye health intervention in the “black dirt” region of New York State
Authors: Earle‐Richardson Giulia , Wyckoff Lynae , Carrasquillo Marilyn , Scribani Melissa , Jenkins Paul , May John 
Published: July 2014

BackgroundEye irritation is a constant hazard for migrant and seasonal farmworkers, but there are few studies of the problem or how to address it. Researchers evaluated the effect of a community‐based participatory eye health intervention on farmworker eye symptoms in the Hudson Valley, NY.MethodsA randomized pre‐post intervention with 2, 4‐week follow‐up periods was implemented with a sample of 97 farmworkers. Five eye symptoms were measured, along with utilization of protective eyewear and eye drops.ResultsLeading baseline eye symptoms were redness (49%), blurred vision (43%), itching (43%), and eye pain (29%). Significant reductions in eye pain (P = 0.009), and non‐significant reductions in redness were observed for the intervention group while controls experienced increases in both.ConclusionsThe intervention was effective in significantly reducing eye pain, and to a lesser extent, redness. Future eyewear promotion programs should offer a range of eye wear, tailor offerings to local climate and tasks, evaluate eyewear durability, and include eye drops. Am. J. Ind. Med. 57:1053–1063, 2014. © 2014 Wiley Periodicals, Inc.
Health and disease: Exploring the relation between parasitic infections, child nutrition status, and markets
Authors: Tanner Susan ,   TAPS Bolivia Study Team
Published: July 2014

ABSTRACTResearch in bioarchaeology and among living people provides insight into the biological and biocultural consequences of subsistence, political, and economic transitions. Central to this effort is examining infectious disease, such as diarrheal disease, respiratory infections, and parasitic infections because they are an important source of nutritional and energetic stress in both past and current groups. Although infection may not always result in overt disease, frequent exposure results in biological stress with a negative effect on child growth and, by extension, health. The goal of this article is to examine the association between a common class of infectious disease, soil‐transmitted helminth worms, and nutritional status among youth living in communities that vary with respect to their distance from a commercial center. In 2007, anthropometric measurements and parasitological surveys were collected for 338 2–14‐year‐old children and adolescents living in lowland Bolivia as part of the Tsimane' Amazonian Panel Study. Associations between the presence of helminth infections and markers of both short‐ and long‐term nutritional status were overall weak. Youth living in communities distant from the commercial center were more likely to be positive for multiple parasite species than youth in near communities, but youth in mid‐distance communities had lower infection rates. This article demonstrates the challenge of identifying associations between nutritional and disease stress when individual and household factors are nested in a larger context of socioeconomic and environmental change. Increased collaboration between bioarchaeology and human biology should continue to examine the connections between stress and disease across time. Am J Phys Anthropol 155:221–228, 2014. © 2014 Wiley Periodicals, Inc.
Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture)
Authors: Warshel Arieh 
Published: July 2014

AbstractA detailed understanding of the action of biological molecules is a pre‐requisite for rational advances in health sciences and related fields. Here, the challenge is to move from available structural information to a clear understanding of the underlying function of the system. In light of the complexity of macromolecular complexes, it is essential to use computer simulations to describe how the molecular forces are related to a given function. However, using a full and reliable quantum mechanical representation of large molecular systems has been practically impossible. The solution to this (and related) problems has emerged from the realization that large systems can be spatially divided into a region where the quantum mechanical description is essential (e.g. a region where bonds are being broken), with the remainder of the system being represented on a simpler level by empirical force fields. This idea has been particularly effective in the development of the combined quantum mechanics/molecular mechanics (QM/MM) models. Here, the coupling between the electrostatic effects of the quantum and classical subsystems has been a key to the advances in describing the functions of enzymes and other biological molecules. The same idea of representing complex systems in different resolutions in both time and length scales has been found to be very useful in modeling the action of complex systems. In such cases, starting with coarse grained (CG) representations that were originally found to be very useful in simulating protein folding, and augmenting them with a focus on electrostatic energies, has led to models that are particularly effective in probing the action of molecular machines. The same multiscale idea is likely to play a major role in modeling of even more complex systems, including cells and collections of cells.
N‐Heterocyclic Carbene Coordinated Neutral and Cationic Heavier Cyclopropylidenes
Authors: Jana Anukul , Omlor Isabell , Huch Volker , Rzepa Henry S. , Scheschkewitz David 
Published: July 2014

AbstractCyclopropylidene is a transient intermediate of the allene–propyne–cyclopropene isomerization. The incorporation of heavier Group 14 elements into the cyclopropylidene scaffold has to date been restricted to the formal replacement of the carbenic carbon atom by a base‐coordinated silicon(II) center. Herein we report the synthesis and characterization of NHC‐coordinated heavier cyclopropylidenes (Si2GeR3X, and Si3R3Br; X=Cl, Mes; R=Tip=2,4,6‐iPr3C6H2) in which the three‐membered ring is exclusively formed by silicon and germanium. In case of the chloro‐substituted Si2Ge‐cyclopropylidene, a stable heavier cycloprop‐1‐yl‐2‐ylidene cation is obtained by NHC‐induced chloride dissociation.
Copper‐Promoted Site‐Selective Acyloxylation of Unactivated C(sp3)H Bonds
Authors: Wu Xuesong , Zhao Yan , Ge Haibo 
Published: July 2014

AbstractThe site‐selective acyloxylation of aliphatic amides was achieved via a copper‐promoted C(sp3)H bond functionalization process directed by a bidentate ligand. The reaction showed a great preference for activating CH bonds of β‐methyl groups over those of γ‐methyl and unactivated methylene groups.
A functional high‐content miRNA screen identifies miR‐30 family to boost recombinant protein production in CHO cells
Authors: Fischer Simon , Buck Theresa , Wagner Andreas , Ehrhart Carolin , Giancaterino Julia , Mang Samuel , Schad Matthias , Mathias Sven , Aschrafi Armaz , Handrick René , Otte Kerstin 
Published: July 2014

AbstractThe steady improvement of mammalian cell factories for the production of biopharmaceuticals is a key challenge for the biotechnology community. Recently, small regulatory microRNAs (miRNAs) were identified as novel targets for optimizing Chinese hamster ovary (CHO) production cells as they do not add any translational burden to the cell while being capable of regulating entire physiological pathways. The aim of the present study was to elucidate miRNA function in a recombinant CHO‐SEAP cell line by means of a genome‐wide high‐content miRNA screen. This screen revealed that out of the 1, 139 miRNAs examined, 21% of the miRNAs enhanced cell‐specific SEAP productivity mainly resulting in elevated volumetric yields, while cell proliferation was accelerated by 5% of the miRNAs. Conversely, cell death was diminished by 13% (apoptosis) or 4% (necrosis) of all transfected miRNAs. Besides these large number of identified target miRNAs, the outcome of our studies suggest that the entire miR‐30 family substantially improves bioprocess performance of CHO cells. Stable miR‐30 over expressing cells outperformed parental cells by increasing SEAP productivity or maximum cell density of approximately twofold. Our results highlight the application of miRNAs as powerful tools for CHO cell engineering, identified the miR‐30 family as a critical component of cell proliferation, and support the notion that miRNAs are powerful determinants of cell viability.
Rapid identification of metal‐binding peptoid oligomers by on‐resin X‐ray fluorescence screening
Authors: Nalband Danielle M. , Warner Benjamin P. , Zahler Nathan H. , Kirshenbaum Kent 
Published: July 2014

ABSTRACTN‐Substituted glycine peptoid oligomers have recently attracted attention for their metal binding capabilities. Due to their efficient synthesis on solid phase, peptoids are well suited for generation of compound libraries, followed by screening for molecular recognition and other diverse functional attributes. Ideally, peptoids could be simultaneously screened for binding to a number of metal species. Here, we demonstrate the use of bench‐top X‐ray fluorescence (XRF) instrumentation to screen rapidly, on solid support, a library of peptoid oligomers incorporating metal‐binding functionalities. A subset of the peptoid sequences exhibited significant metal binding capabilities, including a peptoid pentamer and a nonamer that were shown to selectively bind nickel. The binding capabilities were validated by colorimetric assay and by depletion of Ni2+ ion concentration from solution, establishing bench‐top XRF as a rapid, practicable high‐throughput screening technique for peptoid oligomers. This protocol will facilitate discovery of metallopeptoids with unique material properties. © 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 407–415, 2014.
Cosolvent, ions, and temperature effects on the structural properties of cecropin A‐Magainin 2 hybrid peptide in solutions
Authors: Sarukhanyan Edita , Milano Giuseppe , Roccatano Danilo 
Published: July 2014

ABSTRACTAntimicrobial peptides are promising alternative to traditional antibiotics and antitumor drugs for the battle against new antibiotic resistant bacteria strains and cancer maladies. The study of their structural and dynamics properties at physiological conditions can help to understand their stability, delivery mechanisms, and activity in the human body. In this article, we have used molecular dynamics simulations to study the effects of solvent environment, temperature, ions concentration, and peptide concentration on the structural properties of the antimicrobial hybrid peptide Cecropin A–Magainin 2. In TFE/water mixtures, the structure of the peptide retained α‐helix contents and an average hinge angle in close agreement with the experimental NMR and CD measurements reported in literature. Compared to the TFE/water mixture, the peptide simulated at the same ionic concentration lost most of its α‐helix structure. The increase of peptide concentration at both 300 and 310 K resulted in the peptide aggregation. The peptides in the complex retained the initial N‐ter α‐helix segment during all the simulation. The α‐helix stabilization is further enhanced in the high salt concentration simulations. The peptide aggregation was not observed in TFE/water mixture simulations and, the peptide aggregate, obtained from the water simulation, simulated in the same conditions did dissolve within few tens of nanoseconds. The results of this study provide insights at molecular level on the structural and dynamics properties of the CA‐MA peptide at physiological and membrane mimic conditions that can help to better understand its delivery and interaction with biological interfaces. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 1–14, 2015.
Fumaric acid production by Torulopsis glabrata: Engineering the urea cycle and the purine nucleotide cycle
Authors: Chen Xiulai , Wu Jing , Song Wei , Zhang Limei , Wang Hongjiang , Liu Liming 
Published: July 2014

ABSTRACTA multi‐vitamin auxotrophic Torulopsis glabrata strain, a pyruvate producer, was further engineered to produce fumaric acid. Using the genome‐scale metabolic model iNX804 of T. glabrata, four fumaric acid biosynthetic pathways, involving the four cytosolic enzymes, argininosuccinate lyase (ASL), adenylosuccinate lyase (ADSL), fumarylacetoacetase (FAA), and fumarase (FUM1), were found. Athough single overexpression of each of the four enzymes in the cytosol improved fumaric acid production, the highest fumaric acid titer (5.62 g L−1) was obtained with strain T.G‐ASL(H)‐ADSL(L) by controlling the strength of ASL at a high level and ADSL at a low level. In order to further improve the production of fumaric acid, the SpMAE1 gene encoding the C4‐dicarboxylic acids transporter was overexpressed in strain T.G‐ASL(H)‐ADSL(L)‐SpMAE1 and the final fumaric acid titer increased to 8.83 g L−1. This study provides a novel strategy for fumaric acid biosynthesis by utilizing the urea cycle and the purine nucleotide cycle to enhance the bridge between carbon metabolism and nitrogen metabolism. Biotechnol. Bioeng. 2015;112: 156–167. © 2014 Wiley Periodicals, Inc.
Biosynthesis of rare ketoses through constructing a recombination pathway in an engineered Corynebacterium glutamicum
Authors: Yang Jiangang , Zhu Yueming , Li Jitao , Men Yan , Sun Yuanxia , Ma Yanhe 
Published: July 2014

ABSTRACTRare sugars have various known biological functions and potential for applications in pharmaceutical, cosmetics, and food industries. Here we designed and constructed a recombination pathway in Corynebacterium glutamicum, in which dihydroxyacetone phosphate (DHAP), an intermediate of the glycolytic pathway, and a variety of aldehydes were condensed to synthesize rare ketoses sequentially by rhamnulose‐1‐phosphate aldolase (RhaD) and fructose‐1‐phosphatase (YqaB) obtained from Escherichia coli. A wild‐type strain harboring this artificial pathway had the ability to produce D‐sorbose and D‐psicose using D‐glyceraldehyde and glucose as the substrates. The tpi gene, encoding triose phosphate isomerase was further deleted, and the concentration of DHAP increased to nearly 20‐fold relative to that of the wild‐type. After additional optimization of expression levels from rhaD and yqaB genes and of the fermentation conditions, the engineered strain SY6(pVRTY) exhibited preferable performance for rare ketoses production. Its yield increased to 0.59 mol/mol D‐glyceraldehyde from 0.33 mol/mol D‐glyceraldehyde and productivity to 2.35 g/L h from 0.58 g/L h. Moreover, this strain accumulated 19.5 g/L of D‐sorbose and 13.4 g/L of D‐psicose using a fed‐batch culture mode under the optimal conditions. In addition, it was verified that the strain SY6(pVRTY) meanwhile had the ability to synthesize C4, C5, C6, and C7 rare ketoses when a range of representative achiral and homochiral aldehydes were applied as the substrates. Therefore, the platform strain exhibited the potential for microbial production of rare ketoses and deoxysugars. Biotechnol. Bioeng. 2015;112: 168–180. © 2014 Wiley Periodicals, Inc.
Modeling of plant in vitro cultures: Overview and estimation of biotechnological processes
Authors: Maschke Rüdiger W. , Geipel Katja , Bley Thomas 
Published: July 2014

ABSTRACTPlant cell and tissue cultivations are of growing interest for the production of structurally complex and expensive plant‐derived products, especially in pharmaceutical production. Problems with up‐scaling, low yields, and high‐priced process conditions result in an increased demand for models to provide comprehension, simulation, and optimization of production processes. In the last 25 years, many models have evolved in plant biotechnology; the majority of them are specialized models for a few selected products or nutritional conditions. In this article we review, delineate, and discuss the concepts and characteristics of the most commonly used models. Therefore, the authors focus on models for plant suspension and submerged hairy root cultures. The article includes a short overview of modeling and mathematics and integrated parameters, as well as the application scope for each model. The review is meant to help researchers better understand and utilize the numerous models published for plant cultures, and to select the most suitable model for their purposes. Biotechnol. Bioeng. 2015;112: 1–12. © 2014 Wiley Periodicals, Inc.
Contribution of transcription factor, SP1, to the promotion of HB‐EGF expression in defense mechanism against the treatment of irinotecan in ovarian clear cell carcinoma
Authors: Miyata Kohei , Yotsumoto Fusanori , Nam Sung Ouk , Odawara Takashi , Manabe Sadao , Ishikawa Toyokazu , Itamochi Hiroaki , Kigawa Junzo , Takada Shuji , Asahara Hiroshi , Kuroki Masahide , Miyamoto Shingo 
Published: July 2014

AbstractOvarian clear cell carcinoma (OCCC) is a worst histological subtype than other ovarian malignant tumor. Heparin‐binding epidermal growth factor‐like growth factor (HB‐EGF) is a promising target for ovarian cancer therapy. The aims of this study were to validate the efficacy of HB‐EGF–targeted therapy for OCCC and to identify the transcription factor that contributed to the induction of HB‐EGF by SN38 treatment in OCCC cells. HB‐EGF was highly expressed in OCCC cells, and an increase of HB‐EGF was induced by SN38 which had only antitumor effect among conventional anticancer agents on OCCC. A specific inhibitor of HB‐EGF, a cross‐reacting material 197 (CRM197), led to a synergistic increase in the number of apoptotic OCCC cells with the treatment of SN38. The luciferase assay with 5′‐deletion promoter constructs identified a GC‐rich element between −125 and −178 (the distal transcription start site was denoted +1) as a cis‐regulatory region, and the treatment of SN38 induced luciferase activity in this region. An in silico and chromatin immunoprecipitation analysis estimated that SP1 bound to the cis‐regulatory region of HB‐EGF in OCCC cells. Real‐time PCR and cell viability assays showed that the transfection of a small interfering RNA targeting SP1 suppressed the expression of HB‐EGF induced by SN38, resulting in the enhanced sensitivity of SN38. Taken together, these results indicate that induction of HB‐EGF expression contributed to defense mechanism against treatment of SN38 through the transcriptional activity of SP1 in OCCC cells.