bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methionine sulfoxide and phosphonate containing double hydrophilic block copolypeptides and their mineralization of calcium carbonate
Authors: Captain Ilya , Deming Timothy J. 
Published: September 2016

ABSTRACTIn effort to address challenges in the efficient synthesis of highly functional block copolypeptides, we report use of a combination of functional monomer polymerization and postpolymerization modification to obtain new double hydrophilic block copolypeptides with desirable properties. We prepared copolymers that contain discrete hydrophilic, nonionic poly(l‐methionine sulfoxide) and Ca2+ ion binding poly(l‐phosphonohomoalanine) segments. The facile and selective postpolymerization conversion of inexpensive, readily prepared poly(l‐methionine) segments into nonionic, hydrophilic poly(l‐methionine sulfoxide) segments reduces the need for use of combinations of protecting groups. The complex copolypeptides prepared using this strategy were able to promote formation of CaCO3 microspheres with tunable polymorphism. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 3707–3712
Using MDECR‐PECVD to study the impact of ion bombardment energy on microstructural properties of μc‐Si:H thin film grown from an SiF4/H2 chemistry
Authors: Wang Junkang , Florea Ileana , Bulkin Pavel V. , Maurice Jean‐Luc , Johnson Erik V. 
Published: September 2016

AbstractThe matrix‐distributed electron cyclotron resonance plasma‐enhanced chemical vapor deposition (MDECR‐PECVD) technique has been shown to achieve high deposition rates for hydrogenated microcrystalline silicon (μc‐Si:H) thin film. Due to the fact that plasma is sustained by a microwave discharge, by biasing the substrate holder with additional power supply, one can achieve independent control over the plasma density and the maximum ion bombardment energy (IBE). In this work, we present studies of the impact of IBE on the microstructural properties of the μc‐Si:H film deposited by MDECR‐PECVD. Insufficient ion bombardment is found to be responsible for the substantial presence of nano‐porous regions within the material, resulting in significant post‐deposition oxidation. Good agreement between transmission electron microscopy (TEM) Fresnel contrast analysis and the results of infrared absorption and hydrogen effusion measurements for the deposited films suggest that moderate IBE is of vital importance to achieve high quality μc‐Si:H. In doing so, denser films with significantly decreased nano‐porous regions and better stability are obtained, which is of great interest to optimize the process parameters for solar cell applications. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Strength and weakness of rare earths based phosphors: Strategies to replace critical raw materials
Authors: Chiriu Daniele , Stagi Luigi , Carbonaro Carlo Maria , Ricci Pier Carlo 
Published: September 2016

AbstractRare earth based phosphors are largely the most applied luminescent materials in the present lightening devices. Their ubiquity in lighting system, like light emitting diodes or compact fluorescent lamps, is related to the optical high efficiency of the rare earth as luminescent ions but also to the relative easiness of growth technique as well high structural stability of rare earth based host matrices, like garnets, perovskites and oxyorthosilicatas. On the other hand, the need of new devices virtually free of any elements with high supply disruption, the ones classified by EU community and US government as critical raw materials, boosts the research for alternatives materials. In this paper, we focalize on the optical properties of the REE based phosphors with the intent to underline the performances the new materials should grant, thus addressing the possible direction for new material development. In particular the features related to the possibility of tuning the luminescence, the interaction among doping ions and with surface defects were analysed. Finally, a general model to predict the role of the REE in a host matrix is analysed. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Depicting electronic distributions from accurate computational first principles: On the relationship between the complex patterns of bonding interaction and the back‐donation phenomenon
Authors: Lobayan Rosana M. , Bochicchio Roberto C. , Pérez del Valle Carlos 
Published: September 2016

AbstractA detailed theoretical description of metal–ligand interactions in the case of the simple isoelectronic transition metal seriesand oneligand is presented. This task is performed in terms of the local and nonlocal topology‐based formalisms of the electronic density and its decomposition into paired and unpaired contributions. The analysis is mainly focused on the nature of the carbon–metal interactions under the traditional chemical back‐donation phenomena and the relationship with the existence of two‐electron three‐center (2e‐3c) complex patterns of bonding, that is, 2e‐3c atomic interactions. For these simple prototypical systems, which seem to be adequate examples to describe the topologic features of such electron distribution in terms of the density point of view, both phenomena, that is, the back‐donation and the 2e‐3c interactions, are mutually exclusive.
Automatic annotation and visualization tool for mass spectrometry based glycomics
Authors: Xu Guang , Liu Xin , Liu Qing Yan , Li Jianjun , Zhou Yanhong 
Published: September 2016

RationaleWith the development of glycomics, a large number of glycan structures have been determined by using mass spectrometry (MS)‐based techniques. However, most glycan MS data needs to be manually annotated which is time‐consuming, unreliable and inaccurate.MethodsHerein we report a tool for automatically annotating and browsing N‐glycan masses and isotopic distributions. We first constructed a training dataset using the Consortium for Functional Glycomics database, in conjunction with data preprocessing and filtering by composition matching. In addition, we improved a matching glycan isotope abundance algorithm through identifying potential overlap region and constructing an optimization model so that it can deconvolute the overlapped glycan isotopic clusters.ResultsIn the matching process, if them/zdifference of two detected ions was close to an integer from 1 to 5, them/zrange was considered as a potential overlapped region, from the lowerm/ztom/z + 5. It was found that there were more than 20 potential overlap regions in each group of data from CHO sample and human testing sample. Because the training dataset was imbalanced, we combined the Supporting Vector Machines (SVMs) algorithm with different sampling techniques, including Synthetic Minority Over‐sampling Technique (SMOTE), to classify all potential candidate compositions. The results demonstrated an average of 26.8% increase in annotation sensitivity through the SMOTE‐SVMs algorithm. The source code can be obtained fromhttps://sourceforge.net/projects/glycomaid/.ConclusionsWe have developed a new tool which facilities high‐throughput glycomics research and assists mass spectrometrists in the interpretation and annotation of glycan samples. Copyright © 2016 John Wiley & Sons, Ltd.
Sector‐based DNA information hiding method
Authors: Santoso Kevin , Lee Suk‐Hwan , Hwang Won‐Joo , Kwon Ki‐Ryong 
Published: September 2016

AbstractAs the next generation sequencing and deoxyribonucleic acid (DNA) synthesis technologies rapidly develop, DNA engineering became faster and cheaper with higher accuracy than before. External information such as secret messages or digital archives can be embedded into the DNA sequence by mutating its molecular sequence according to a certain algorithm. This study presents a sector‐based DNA steganography method using non‐coding regions of the DNA sequence as the host for carrying binary data. The aim of the sector‐based embedding is to have a high level of security, data capacity, and error handling while preserving the organism's life information. A sector consists of reference bases, segmented message bases, and parity bases. The parity bases can detect and handle mutation errors in each sector. The sector length controls the data capacity and security. Our in silico experiments verified that the bit‐per‐nucleotide of our method can be [1.2, 2.0] by controlling the sector length, which is 0.2 point higher than that of conventional methods. As many as 104 base mutations in the DNA sequence can be handled for perfect message retrieval. Furthermore, the probability for message detection without keys is lower than 1.3949 × 10−62, which is very low. Copyright © 2016 John Wiley & Sons, Ltd.
Exploiting spatial code proximity and order for improved source code retrieval for bug localization
Authors: Sisman Bunyamin , Akbar Shayan A. , Kak Avinash C. 
Published: September 2016

AbstractPractically all information retrieval based approaches developed to date for automatic bug localization are based on the bag‐of‐words assumption that ignores any positional and ordering relationships between the terms in a query. In this paper, we argue that bug reports are ill‐served by this assumption because such reports frequently contain various types of structural information whose terms must obey certain positional and ordering constraints. It therefore stands to reason that the quality of retrieval for bug localization would improve if these constraints could be taken into account when searching for the most relevant files. In this paper, we demonstrate that such is indeed the case. We show how the well‐known Markov Random Field based retrieval framework can be used for taking into account the term‐term proximity and ordering relationships in a query vis‐à‐vis the same relationships in the files of a source‐code library to greatly improve the quality of retrieval of the most relevant source files. We have carried out our experimental evaluations on popular large software projects using over 4000 bug reports. The results we present demonstrate unequivocally that the new proposed approach is far superior to the widely used bag‐of‐words based approaches. Copyright © 2016 John Wiley & Sons, Ltd.
Whisker Formation in Porosity in Al Alloys
Authors: Griffiths William David , Elsayed Ahmed , El-Sayed Mahmoud Ahmed 
Published: September 2016

Abstract
An examination of the fracture surfaces of tensile test bars from Al alloy castings held in the liquid state for up to 20 minutes revealed porosity which in some cases contained whisker-like features. Energy-dispersive X-ray analysis in a SEM suggested that these might be oxide whiskers forming in an oxide-related pore or double oxide film defect. Such entrainment defects (also known as bifilms) may entrap a small amount of the local atmosphere when they form and become incorporated into the liquid metal. This atmosphere may be predominantly air, which then subsequently reacts with the surrounding melt, firstly by reaction with oxygen and secondly by reaction with nitrogen. A CFD model of the heat distribution associated with the reactions between the interior atmosphere of a double oxide film defect and the surrounding liquid alloy suggested that highly localized increases in temperature, up to about 2000 K to 5000 K (1727 °C to 4727 °C), could occur, over a scale of a few hundred micrometers. Such localized increases in temperature might lead to the evaporation or disassociation of oxide within the pore, followed by condensation, to form the whisker structures observed. Hydrogen might also be expected to diffuse into the bifilm and may play a role in the chemical reactions associated with the development of the bifilm.
Stress and behavioral risk among young expectant couples
Authors: Divney Anna , Gordon Derrick , Magriples Urania , Kershaw Trace 
Published: September 2016

ABSTRACTFew studies have explored stress and coping among adolescents who are expecting a baby. In particular, young men's experiences during pregnancy have largely been ignored, despite the fact that a young man's experiences and behaviors carry implications for his own, his partner's and his child's health. This study examined the association between maternal and paternal experiences of stress during pregnancy with one's own and one's partner's health behaviors and depressive symptoms among 294 young expectant couples in the U.S. Multilevel modeling showed that one's own experiences of stress were associated with more unhealthy behaviors and more depressive symptoms among both expectant mothers and fathers. Paternal experiences of stress were predictive of more maternal conduct problems, while maternal experiences of stress were predictive of more paternal depressive symptoms and less paternal substance use. These findings highlight the importance of social relationships in affecting health behaviors and mental health among expectant adolescents.
Combining seasonal yield, silage dry matter yield, quality and persistency in an economic index to assist perennial ryegrass variety selection
Authors: O'DONOVAN M. , MCHUGH N. , MCEVOY M. , GROGAN D. , SHALLOO L. 
Published: September 2016

SUMMARYA total economic merit index (Pasture Profit Index, PPI) for perennial ryegrass variety selection was developed to rank perennial ryegrass varieties (Lolium perenneL.) based on their economic potential for grass-based ruminant production systems. The key traits of importance identified were: spring, mid-season (April 11–August 10) and autumn dry matter (DM) yield, first and second cut silage DM yield, grass quality April to July (inclusive) and sward persistency. Variety persistency was quantified by determining the ground score (GS) change across years, which was associated with a yield threshold which triggered sward replacement. Each one-unit decline in GS was associated with a 1683 kg loss in DM yield. Data generated in the Irish recommended list trials for value for cultivation and use were analysed to quantify the relative performance of each variety for each of the aforementioned traits. A previously developed methodology to generate economic values was used with updated price assumptions to develop economic values, which were applied to the analysed performance data of individual varieties. These data were used to estimate the total economic merit of each variety. Thirty-nine varieties were ranked on total economic merit with the highest performing variety (Cv111) generating €213 per ha/year compared withCv201, which was the lowest ranking variety generating −€31 per ha/year. Use of the PPI provides information to end users in relation to the economic merit of one variety over another, facilitating a more informed decision-making process at farm level.
Nutrient composition, rate of fermentation andin vitrorumen methane output from tropical feedstuffs
Authors: BHATTA R. , SARAVANAN M. , BARUAH L. , MALIK P. K. , SAMPATH K. T. 
Published: September 2016

SUMMARYIn vitrorumen methane output (IRMO) of over 200 feed/feed mix samples representing approximately 74 feed types was investigated in a series of completely randomized experiments. The samples comprised dry fodder, grass, tree leaves, cultivated grasses, cereal by-products, cereal grains, oilseed/meals, compound feeds and total mixed rations (TMRs) from the tropical regions. These samples were subjected to threein vitrogas production tests at 39 °C in 100 ml Heberle syringes. The first incubation was conducted with 200 mg dry matter (DM) substrate for 96 h to determine half-time gas production (t1/2, h) value of each sample. The second and third incubations were carried out simultaneously. The second incubation was done with 200 mg DM substrate untilt1/2time to determine IRMO and third with 500 mg DM to estimatein vitrodry matter digestibility (IVDMD) of each samples, respectively. The IRMO was expressed as ml/100 mg digestible substrate. Crude protein content (g/kg DM) was lowest in dry fodder samples and highest in oilseed meals, whereas it was similar in local grass and tree leaves. The IVDMD values ranged from 0·48 to 0·87; the lowest digestibility was recorded in tree leaves. The potential gas production (PGP, ml/200 mg DM) ranged from 9·76 to 61·3. The PGP from grasses and compound feeds was similar, whereas it was lowest in tree leaves. The rate constant (mg/h) was maximum in compound feed followed by oilseed meal. The rate constant was similar among other group of feedstuffs. Thet1/2time ranged from 9·8 to 19·4 h. The highestt1/2time was recorded in local grass samples followed by dry fodder and cultivated grasses. However, they were similar among tree leaves, cereal grains, by-products and compound feeds. The methane % in the total gas varied from 9·79 (tree leaves) to 20·2 (local grasses). Among straw, IRMO varied from 3·88 (Zea maysfodder) to 12·0 (Sorghum vulgare) and it was lower in fruit tree leaves than cultivated grasses. Among protein and energy sources, IRMO was higher in cereal by-products as compared with cereal grains, oil meals and compound feed. The IRMO was similar among TMR, irrespective of the composition of the concentrate mixture. Nevertheless, it varied with the amount of concentrate in the TMR. This is the first exhaustive data on IRMO from the tropical region. Because of the substantial amount of dietary gross energy lost in methane, knowledge of the methane output from these feed ingredients will help in formulating low methane emitting diets for ruminants. Incorporation of tropical tree leaves in the diets and feeding TMR are potential strategies to reduce enteric methane emission in ruminants.
Upscaling of integrated photoelectrochemical water-splitting devices to large areas
Authors: Turan Bugra , Becker Jan-Philipp , Urbain Félix , Finger Friedhelm , Rau Uwe , Haas Stefan 
Published: September 2016

AbstractPhotoelectrochemical water splitting promises both sustainable energy generation and energy storage in the form of hydrogen. However, the realization of this vision requires laboratory experiments to be engineered into a large-scale technology. Up to now only few concepts for scalable devices have been proposed or realized. Here we introduce and realize a concept which, by design, is scalable to large areas and is compatible with multiple thin-film photovoltaic technologies. The scalability is achieved by continuous repetition of a base unit created by laser processing. The concept allows for independent optimization of photovoltaic and electrochemical part. We demonstrate a fully integrated, wireless device with stable and bias-free operation for 40 h. Furthermore, the concept is scaled to a device area of 64 cm2 comprising 13 base units exhibiting a solar-to-hydrogen efficiency of 3.9%. The concept and its successful realization may be an important contribution towards the large-scale application of artificial photosynthesis.
High cell-surface density of HER2 deforms cell membranes
Authors: Chung Inhee , Reichelt Mike , Shao Lily , Akita Robert W. , Koeppen Hartmut , Rangell Linda , Schaefer Gabriele , Mellman Ira , Sliwkowski Mark X. 
Published: September 2016

AbstractBreast cancers (BC) with HER2 overexpression (referred to as HER2 positive) progress more aggressively than those with normal expression. Targeted therapies against HER2 can successfully delay the progression of HER2-positive BC, but details of how this overexpression drives the disease are not fully understood. Using single-molecule biophysical approaches, we discovered a new effect of HER2 overexpression on disease-relevant cell biological changes in these BC. We found HER2 overexpression causes deformation of the cell membranes, and this in turn disrupts epithelial features by perturbing cell–substrate and cell–cell contacts. This membrane deformation does not require receptor signalling activities, but results from the high levels of HER2 on the cell surface. Our finding suggests that early-stage morphological alterations of HER2-positive BC cells during cancer progression can occur in a physical and signalling-independent manner.
DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses
Authors: Wicker Thomas , Yu Yeisoo , Haberer Georg , Mayer Klaus F. X. , Marri Pradeep Reddy , Rounsley Steve , Chen Mingsheng , Zuccolo Andrea , Panaud Olivier , Wing Rod A. , Roffler Stefan 
Published: September 2016

AbstractDNA (class 2) transposons are mobile genetic elements which move within their ‘host’ genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind.
Functional Magnetic Resonance Imaging of Electrical and Optogenetic Deep Brain Stimulation at the Rat Nucleus Accumbens
Authors: Albaugh Daniel L. , Salzwedel Andrew , Van Den Berge Nathalie , Gao Wei , Stuber Garret D. , Shih Yen-Yu Ian 
Published: September 2016

AbstractDeep brain stimulation of the nucleus accumbens (NAc-DBS) is an emerging therapy for diverse, refractory neuropsychiatric diseases. Although DBS therapy is broadly hypothesized to work through large-scale neural modulation, little is known regarding the neural circuits and networks affected by NAc-DBS. Using a healthy, sedated rat model of NAc-DBS, we employed both evoked- and functional connectivity (fc) MRI to examine the functional circuit and network changes achieved by electrical NAc stimulation. Optogenetic-fMRI experiments were also undertaken to evaluate the circuit modulation profile achieved by selective stimulation of NAc neurons. NAc-DBS directly modulated neural activity within prefrontal cortex and a large number of subcortical limbic areas (e.g., amygdala, lateral hypothalamus) and influenced functional connectivity among sensorimotor, executive and limbic networks. The pattern and extent of circuit modulation measured by evoked-fMRI was relatively insensitive to DBS frequency. Optogenetic stimulation of NAc cell bodies induced a positive fMRI signal in the NAc, but no other detectable downstream responses, indicating that therapeutic NAc-DBS might exert its effect through antidromic stimulation. Our study provides a comprehensive mapping of circuit and network-level neuromodulation by NAc-DBS, which should facilitate our developing understanding of its therapeutic mechanisms of action.