bluuebunny/crossref_metadata_2025 huggingface dataset:
The Promise of a Personalized Genomic Approach to Pancreatic Cancer and Why Targeted Therapies Have Missed the Mark
Authors: Fisher William E.
Published: January 2011

Pancreatic cancer (PC) carries the highest mortality rate of any cancer type. Although minor advances in chemotherapy have been made, the mortality rate has remained the same over the last several decades. Clinical trials examining therapies targeting the epidermal growth factor (EGFR), vascular endothelial growth factor (VEGF), specific mutated proteins such as K‐ras, immunotherapy employing tumor‐associated antigens, and biologic therapy such as TNFerade (GenVec, Inc., Gaithersburg, MD) have all failed to substantially improve survival. Pancreatic cancer is likely a heterogeneous disease; therefore, a personalized genomic approach offers the possibility to tailor treatment to the unique characteristics of individual patients and their tumors. Rapid advances in sequencing technology are decreasing the time and cost of obtaining this information to a clinically useful level. However, many challenges remain to be faced in applying this technology in the field of PC. Even if patients with PC could be identified early in the course of the disease, localizing the disease and treating it in a minimally invasive fashion will remain problematic. Ethical issues including patient discrimination and access to care will be particularly important in PC. As the field advances, validation, education of clinicians, and determining the true value and source of funding will be difficult. Although the era of personalized genomic medicine has arrived, it will certainly take many years to begin to realize its potential. It is to be hoped that this new approach will result in a significant improvement in the survival curve for patients with PC.
Roles and Mechanisms of MicroRNAs in Pancreatic Cancer
Authors: Zhang Lidong , Jamaluddin Md Saha , Weakley Sarah M. , Yao Qizhi , Chen Changyi
Published: January 2011

Pancreatic cancer (PC) is an aggressive malignancy with poor survival. The discovery of microRNAs (miRNAs) has provided a new opportunity to study the disease. Thus far, altered expression of miRNAs has been reported in a wide range of malignancies, including PC, and some miRNAs are associated with PC cell proliferation, invasion, chemoresistance, and patient survival. This review summarizes recent advances with respect to the roles and mechanisms of miRNAs in PC and discusses potential clinical applications.
Greater than the Sum of their Parts: The benefits of Youth Violence Prevention Centers
Authors: Azrael Deborah , Hemenway David
Published: January 2011

Academic Centers for Excellence on Youth Violence Prevention (ACE), which support a broad range of activities over and above RO1‐type research projects, can add significantly to a community's capacity to respond to youth violence. We use the example of the Harvard Youth Violence Prevention Center to describe the types of research‐practice collaborations these centers can promote, as well as the ways in which these collaborations can foster adoption of program planning, development, implementation and evaluation practices consistent with evidence‐based approaches to youth violence prevention. Throughout, we describe the ways in which the existence of a center led, under the ACE format, to research, policy and practice opportunities that would not have existed in the absence of a center.
The Total Scaphoid Titanium Arthroplasty: A 15-Year Experience
Authors: Spingardi Ombretta , Rossello Mario Igor
Published: January 2011

Scaphoid nonunion followed by necrosis of bone segments is a common pathologic condition for the hand surgeon, and the difficulty of its management is well known. The total titanium scaphoid replacement, although not well-described in the literature, in our experience represents a reasonable choice in the treatment of this condition. Strict patient selection is necessary to achieve good clinical results. The titanium avoids the silicone synovitis, a well-described complication of silastic implants. Furthermore, this technique permits other surgical steps in case of failure.
The GAMY Project: young people’s attitudes to genetics in the South Wales valleys
Authors: Iredale Rachel , Madden Kim , Taverner Nicola , Yu Juping , McDonald Kevin
Published: January 2011

This paper explores young people’s attitudes to genetics. It describes a qualitative study involving a group of teenagers in a deprived South Wales valley town over a period of 18 months. The GAMY (Genetics and Merthyr Youth) Project involved a series of interactions with participants, including 2 interviews, 4 group days and 4 genetics tasks through which these young people learned about, and then reflected upon, issues relating to genetics and health. We have gathered data about the informed attitudes of teenagers to genetics based on deliberative learning and reflection over a long period of time, and as such this paper provides useful insights into the underlying values that are guiding young people’s views and the factors that are shaping their responses to new genetic technologies. Attitudes to genetics are complex and not easily generalisable. There were low levels of familiarity with, and knowledge of, genetics from the outset. Most young people did not have pre-existing attitudes towards genetics and had given little or no thought to the topic before the project began. However, levels of awareness and general genetic literacy increased as the project progressed. This study suggests that over time young people can develop an awareness of genetics that makes sense to them; they demonstrate that they can think creatively about genetics, and they are able to engage in considering genetic and other risk factors when thinking about health and disease.
The Economic Determinants of the Number of Minority Farmers in the Southeast Region of the United States, 1969–1997
Authors: Luster Tonshia , Barkley Andrew
Published: January 2011

The primary purpose of this research was to identify and quantify the determinants of the number of minority farmers in the Southeast region of the United States during the time period, 1969 to 1997. A second objective was to determine the potential impacts of globalization and international trade agreements on the number of minority farmers in the Southeast region of the United States. Regression results indicated that the number of minority farm owners was responsive to the returns to agricultural labor relative to nonfarm labor returns, as well as to cotton and rice prices. An increase in the cotton price was associated with a smaller rate of minority migration out of agriculture in the Southeast region of the United States. To the extent that globalization is likely to result in higher cotton export prices, international agricultural trade agreements are likely to result in decreased movement of minority farmers out of agriculture in the Southeast region of the United States. A third objective was to compare occupational migration rates out of agriculture of minorities with farmers of all races in the Southeast region. The data demonstrate that minority farm owners exhibited distinctly different migration patterns relative to all farm owners during 1969–1997.
A randomised double-blind placebo-controlled trial with Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis BB-12 for maintenance of remission in ulcerative colitis
Authors: Wildt Signe , Nordgaard Inge , Hansen Ulla , Brockmann Elke , Rumessen Jüri J.
Published: January 2011

Background and aims: To investigate the clinical effect of treatment with Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis BB-12 (Probio-Tec AB-25) to maintain remission in patients with ulcerative colitis.

Methods: Patients with left-sided ulcerative colitis in remission — including proctitis and at least one relapse within the last year were randomised (2:1) in a double-blind placebo-controlled study to Probio-Tec AB-25 or placebo for 52 weeks. The patients were evaluated clinically, endoscopically and histologically at entry and if relapsing. No other medication for ulcerative colitis than the study drug was allowed during the study. Primary endpoint was maintenance of clinical remission, secondary endpoints comparisons of days to relapse, and safety and tolerability of the study drug. The concentrations of the probiotic bacterial strains in stool were analysed in a subset of patients.

Results: Thirty-two patients were randomised. Twenty patients received Probio-Tec AB-25 and twelve patients received placebo. Five patients (25%) in the Probio-Tec AB-25 group and one patient (8%) in the placebo group maintained remission after 1 year of treatment (p = 0.37). The median time to relapse was 125.5 days (range 11–391 days) in the probiotic group and 104 days (range 28–369 days) in the placebo group respectively, (p = 0.683). Probio-Tec AB-25 was overall well tolerated.

Conclusions: In this small randomised placebo-controlled trial no significant clinical benefit of Probio-Tec AB-25 could be demonstrated in comparison with placebo for maintaining remission in patients with left-sided ulcerative colitis. A difference may be achieved in larger studies, but the clinical significance of this would be questionable. This study was registered in ClinicalTrial.gov (NCT00268164).
Preliminary findings from an Internet‐based dementia risk assessment
Authors: Brandt Jason , Rogerson Mark
Published: January 2011

Background

The identification of individuals who are at high risk of dementia may lead to earlier detection and diagnosis. In this study, we describe the development and preliminary validation of a very brief, Internet‐based risk assessment tool.

Methods

The Dementia Risk Assessment collected information on demographic, neurologic, and medical risk factors; perceived cognitive functioning; and emotional symptoms. Participants answered questions pertaining to themselves (“patient page”) or to a relative or friend (“proxy page”). Patients also completed a novel short‐delayed recognition memory test. Subjects received personalized feedback about their risk factors and were advised to seek clinical evaluation for concerning symptoms. By November 2009, 500 respondents completed the patient page.

Results

The 352 respondents aged 50 years or older (M = 62 years) included a high percentage of women (72%) and college graduates (67%). Among the respondents, only 10% complained of having severe memory problems, whereas 38% reported having a first‐degree relative who experienced severe memory loss. The prevalence of major neurologic risk factors was low. Although the delay interval for the recognition memory test averaged around 2 minutes, there was sufficient variability in performance. Individuals with scores ≤10th percentile were significantly older and more likely to be men, have hypertension, and report having severe memory problems.

Conclusions

History of major dementia risk factors can be ascertained through the Internet, and several of these factors are shown to be moderately predictive of performance on a brief test of episodic memory. These data provide preliminary validation of the Dementia Risk Assessment for identifying current cognitive impairment, and suggest its potential for assessing future dementia risk. Ongoing studies will further establish the validity of these findings against proxy reports of cognitive and functional decline, the results of more detailed cognitive assessments, and formal clinical diagnoses.
Effects of αs1-casein (CSN1S1) and κ-casein (CSN3) genotypes on milk coagulation properties in Murciano-Granadina goats
Authors: Caravaca Francisco , Ares José Luis , Carrizosa Juan , Urrutia Baltasar , Baena Francisca , Jordana Jordi , Badaoui Bouabid , Sànchez Armand , Angiolillo Antonella , Amills Marcel , Serradilla Juan Manuel
Published: January 2011

The effects of the caprine αs1-casein (CSN1S1) polymorphisms on milk quality and cheese yield have been widely studied in French and Italian goat breeds. Much less is known about the consequences of κ-casein (CSN3) genotype on the technological and coagulation properties of goat milk. In the current study, we have performed an association analysis between polymorphisms at the goat CSN1S1 and CSN3 genes and milk coagulation (rennet coagulation time, curdling rate and curd firmness) and technological (time to cutting of curd and cheese yield) properties. In this analysis, we have included 193 records from 74 Murciano-Granadina goats (with genotypes constituted by different combinations of alleles B, E and F of the gene CSN1S1 and alleles A and B of the gene CSN3) distributed in three herds, which were collected bimonthly during a whole lactation. Data analysis, using a linear mixed model for repeated observations, revealed significant associations between CSN1S1 genotypes and the rate of the curdling process. In this way, milk from EE goats had a significantly higher curdling rate than milk from BB individuals (P<0·05). Contrary to previous experiments performed in French breeds, cheese yield was not significantly different in BB, EE and EF goats. Moreover, we have shown that CSN3 genotype has a significant effect on the rennet coagulation time (BB>AB, P<0·05) but not on cheese yield. No interaction between the CSN1S1 and CSN3 genotypes was observed.
Effect of flaxseed lignans added to milk or fed to cows on oxidative degradation of dairy beverages enriched with polyunsaturated fatty acids
Authors: Matumoto-Pintro Paula T , Petit Hélène V , Giroux Hélène J , Côrtes Cristiano , Gagnon Nathalie , Britten Michel
Published: January 2011

Nutritional value is a priority in new product development. Using vegetable or marine oils, rich in polyunsaturated fatty acids, in dairy beverage formulations is an option to provide the consumers with healthier products. However, these formulations are prone to oxidation, which is responsible for rapid flavour degradation and the development of potentially toxic reaction products during storage. Flaxseed lignans, secoisolariciresinol diglucoside (SDG), and its mammalian metabolites have antioxidant activity and could be used in beverage formulations to prevent oxidation. Commercially available SDG extract was added to the formulation of dairy beverages enriched with flaxseed oil. As an alternative approach, dairy beverages were produced from milk naturally rich in SDG metabolites obtained through the alteration of cow diet. Resistance to oxidation was determined from the kinetics of hexanal and propanal production during heat and light exposure treatments. Increasing SDG concentration in dairy beverage slightly reduced redox potential but had no effect on oxygen consumption during oxidation treatments. The presence of SDG in dairy beverage significantly improved resistance to heat- and light-induced oxidation. However, purified enterolactone, a mammalian metabolite from SDG, prevented oxidation at much lower concentrations. The use of milk from dairy cow fed flaxseed meal did not improve resistance to oxidation in dairy beverage. Enterolactone concentration in milk was increased by the experimental diet but it remained too low to observe any significant effect on dairy beverage oxidation.
A melanocortin 1 receptor (MC1R) gene polymorphism is useful for authentication of Massese sheep dairy products
Authors: Fontanesi Luca , Beretti Francesca , Dall'Olio Stefania , Portolano Baldassare , Matassino Donato , Russo Vincenzo
Published: January 2011

Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set up a DNA based protocol for authentication of Massese dairy products, we further investigated the presence and distribution of one of these SNPs (c.-31G>A) in 143 Massese sheep and in another 13 sheep breeds (for a total of 351 animals). The Massese breed was fixed for allele c.-31A, whereas in all other breeds allele c.-31 G was the most frequent or with frequency of 0·50. At the same nucleotide position the cattleMC1Rgene carries the G nucleotide. Using these data we developed a method to detect adulterating milk (from other sheep breeds or from cow) in Massese dairy products based on the analysis of the c.-31G>A SNP. We first tested the sensitivity of the protocol and then applied it to analyse DNA extracted from ricotta and Pecorino cheese obtained with only Massese milk or obtained with unrestricted sheep and cattle milk. To our knowledge, this system represents the first one that can be used for breed authentication of a sheep production and that, at the same time, can reveal frauds derived from the admixture of milk of an unreported species.
The economic costs of extreme weather events: a hydrometeorological CGE analysis for Malawi
Authors: PAUW KARL , THURLOW JAMES , BACHU MURTHY , VAN SEVENTER DIRK ERNST
Published: January 2011

Extreme weather events such as droughts and floods have potentially damaging implications for developing countries. Previous studies have estimated economic losses during hypothetical or single historical events, and have relied on historical production data rather than explicitly modeling climate. However, effective mitigation strategies require knowledge of the full distribution of weather events and their isolated effects on economic outcomes. We combine stochastic hydrometeorological crop-loss models with a regionalized computable general equilibrium model to estimate losses for the full distribution of possible weather events in Malawi. Results indicate that, based on repeated sampling from historical events, at least 1.7 per cent of Malawi's gross domestic product (GDP) is lost each year due to the combined effects of droughts and floods. Smaller-scale farmers in the southern region of the country are worst affected. However, poverty among urban and nonfarm households also increases due to national food shortages and higher domestic prices.
Agricultural Extension and the Campaign to Assimilate the Native Americans of Wisconsin, 1914–1932
Authors: Firkus Angela
Published: January 2011

Congress founded the Agricultural Extension Service (AES) in the Smith-Lever Act of 1914 to disseminate agricultural research to individual farmers. In some states the AES also worked to encourage Native Americans to adopt sedentary intensive agriculture and all aspects of assimilation connected with that occupation. J. F. Wojta, AES administrator in Wisconsin from 1914 to 1940, took a deep interest in Indian farmers and used the power and resources of his office to instruct Native Americans. Ho-Chunks, Menominees, Ojibwes, and Oneidas in Wisconsin adopted or rejected these social, economic, and political assimilation efforts during the Progressive Era according to their own circumstances and goals. The experience of Wisconsin tribes with the state's agricultural extension programs illustrates different ways that Native peoples tried to benefit from modern government services while maintaining their own culture and kinship ties.
Birth of a Quotation: Woodrow Wilson and “Like Writing History with Lightning”
Authors: Benbow Mark E.
Published: January 2011

In February 1915, upon viewingThe Birth of a Nationat a special White House screening, President Woodrow Wilson reportedly remarked, “It's like writing history with lightning. My only regret is that it is all so terribly true.” This line has appeared in numerous books and articles over the past seventy years. This article examines the history of this alleged quotation and the sources where it has appeared. The article weighs the evidence that Wilson effusively praised in these words one of the most racist major movies in American history.
The role of fungi in mediating ecosystem responses to global change
Authors: Treseder Kathleen
Published: January 2011

Background/Question/Methods

In this synthesis of published studies, we address two global change scenarios (global warming and anthropogenic N deposition) in which fungi can form feedbacks on carbon cycling that are counterintuitive to prevailing predictions and models. In each case, a consideration of fungal ecology, physiology, or evolutionary constraints could lead to changes in the sign or magnitude of carbon storage within soils, compared to current predictions. In the case of global warming, the majority of global carbon models that address this issue are parameterized so that decomposition rates increase in response to warming, and that this increase is sustained in the long-term. Indeed, the majority of field studies have confirmed this response, at least within the first years after onset of warming. Nevertheless, longer-term studies have reported reductions in the warming effect over time. One mechanism for this decline is thermal adaptation of fungal communities, in which mass-specific respiration rates decrease following long-term exposure to warming, possibly owing to changes in efficiencies of enzymes. In addition, evolutionary trade-offs could reduce the ability of warming-adapted strains to use particular carbon substrates or to tolerate drier conditions that often coincide with warming. In respect to N deposition, recent coupled C-N models either (1) allow inorganic N availability to increase decomposition rates overall, or (2) do not include a direct effect of N availability on decomposition. However, meta-analyses indicate that microbes typically become less abundant following N enrichment, with corresponding reductions in respiration rates. In addition, turnover rates of recalcitrant material can decrease. These declines in microbial abundance and activity could result from sensitivity of microbial taxa (particularly white rot fungi) to toxins produced via “browning” of organic compounds by nitrogenous compounds. Moreover, mycorrhizal fungi decrease under N enrichment owing to reduction in investments by host plants. Any decomposition of soil organic matter by mycorrhizal fungi could likewise be reduced.

Results/Conclusions

Microbial ecologists can support the efforts of modelers by examining and quantifying relevant microbial mechanisms that provide feedbacks on global change, especially if these feedbacks are counter-intuitive. For large-scale models, global syntheses of empirical data would be especially valuable in determining the extent of these feedbacks.*The audio track for talks in this symposium may be obtained at the following web address:**https://sites.google.com/site/esa2010symposium13audiocontent/esa2010-symposium13-audio-content*
Patterns in soil ammonia-oxidizer response to global change
Authors: Docherty Kathryn , Bohannan Brendan , Niboyet Audrey , LeRoux Xavier
Published: January 2011

Background/Question/Methods

The Domains Archaea and Bacteria contain the vast majority of Earth’s biodiversity and biomass, and their members play critical, often exclusive, roles in many biogeochemical cycles and ecosystem services. Human-induced global change, particularly with respect to increased nitrogen deposition, has the potential to drastically alter how soil nitrifying communities perform their biogeochemical function. Additionally, multi-factor global change can alter how microbial communities interact with each other and with the associated plant communities. This study, performed in the context of the long-term Jasper Ridge Global Change Experiment (JRGCE) in a California grassland ecosystem, examines how ammonia-oxidizing Archaea and Bacteria (AOA and AOB, respectively) respond to multi-factor global change. Manipulations at the JRGCE include simultaneous increases in CO2, warming, precipitation and nitrogen deposition. Past studies have utilized DNA-fingerprinting methods to assess ammonia-oxidizer response to multi-factor global change. This study compares how seed bank (DNA-based) versus metabolically active (RNA-based) ammonia-oxidizing communities respond to global change manipulations over several seasons. We have employed ultra-deep 454-pyrosequencing techniques to examine these communities using the ammonia monooxygenase (amoA) functional gene marker. Effects of global change have been examined at several phylogenetic levels and linked this community information to gross rates of nitrification using 15N stable isotopic methods. Ammonia-oxidizer and plant communities have been compared using multivariate statistical methods.

Results/Conclusions

Our results show that both AOB and AOA communities are highly influenced by nitrogen deposition in both their abundance and community structure. These changes are linked to increased nitrification rate in the elevated nitrogen deposition plots. Our results further show that the relationship between the AOB and plant communities fundamentally changes under long-term nitrogen deposition manipulation. This positive feedback loop may enhance the rate of change in ammonia-oxidizer communities, which may further elevate nitrification rates. This study provides strong evidence that incorporating microbial community and abundance information into global change predictions is crucial for understanding how ecosystem-level nutrient cycling rates may change.*The audio track for talks in this symposium may be obtained at the following web address:**https://sites.google.com/site/esa2010symposium13audiocontent/esa2010-symposium13-audio-content*
Targeted Assembly of Short Sequence Reads
Authors: Warren Rene , Holt Robert
Published: January 2011

As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants, by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled strin-gently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming ge-nomic mutations, polymorphism, fusion and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.
Comparative theoretical investigation on the isomerization energies of long-chain perfluoroalkanes: A case study with perfluorooctanoic acid congeners
Authors: Rayne Sierra , Forest Kaya
Published: January 2011

The gas and solution phase relative thermodynamic stabilities of the 39 linear and branched perfluorooctanoic acid (PFOA) congeners in both their acid and anionic forms were calculated at various levels of density functional (B3LYP, wB97XD, and M062X functionals with the 6-311++G(d,p) basis set) and second order Moller-Plesset perturbation (MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p)) theory using the SMD implicit solvation model. The B3LYP functional does not accurately model the expected trends in thermodynamic stability of PFOA isomers with linear versus branched perfluoroalkyl chains. Calculations obtained with the M062X and MP2 model chemistries suggest these theoretical methods may be more appropriate for relative thermodynamic stability studies on various perfluoroalkyl compounds.
PECAn: workflow management for data assimilation and forecasting
Authors: LeBauer David , Wang Dan , Feng Xiaohui , Dietze Michael
Published: January 2011

Background/Question/Methods

Ecosystem models use physiological traits and environmental data to model land-air carbon exchange. Such models can integrate heterogeneous ecological and environmental data, but rarely account for the contribution of each input to the overall uncertainty in model output. Quantifying uncertainty in each model input and propagating uncertainty through model ensembles directly estimates overall uncertainty in model output. Identification of data that would most effectively constrain uncertainty can also be directly inferred by processing output. Real-time data assimilation and forecasting benefits from a method that is transparent, scalable, and adaptable. A tool that manages these steps while tracking the provenance of data inputs, model parameters, output, and post-processing would facilitate evaluation, reproducibility, and adaptation of the workflow.

Results/Conclusions

We present such a workflow management tool, the Predictive Ecophysiological Carbon flux Analyzer (PECAn). PECAn is an open source utility that encapsulates 1) acquisition of meteorological inputs, 2) synthesis of physiological trait data as the posterior distribution of a Bayesian meta-analysis, 3) sampling trait meta-analysis posterior distributions to parameterize ensembles of an ecophysiological model, Ecosystem Demography, version 2 (ED2), 4) probabilistic forecasts,5) postprocessing to constrain forecasts and model parameters with field, meterological, eddy flux, and spectral data, and 6) provenance tracking. This system provides a detailed analysis of the past and present ecosystem functioning that seamlessly transitions into forecasts. We demonstrate an application of PECAn to an intensively monitored and data-rich plot of a perennial biofuel crop, switchgrass (Panicum virgatum). This particular context will be used to highlight PECAn's general utility to support model-data integration, ecological research, and decision support.
Large low field magnetoresistance in La0.67Sr0.33MnO3 nanowire devices
Authors: Jugdersuren Battogtokh , Kang Sungmu , DiPietro Robert S. , Heiman Don , McKeown David , Pegg Ian. L. , Philip John
Published: January 2011

Large low field magnetoresistance (LFMR) of about 28% is observed in La0.67Sr0.33MnO3 nanowires with 80 nm in diameter at T=300 K. A gradual decrease in the LFMR has been found with increase in wire diameter. The LFMR drops to zero for wires above 280 nm in diameter. The nanowires are grown by means of electrospinning process and exhibit distorted orthorhombic crystal structure. The large LFMR is considered as a grain boundary effect as observed in several perovskite systems. The large LFMR observed in these manganites with reduced dimensions may be useful for room temperature device applications.
Dominant folding pathways of a peptide chain from ab initio quantum-mechanical simulations
Authors: a Beccara Silvio , Faccioli Pietro , Sega Marcello , Pederiva Francesco , Garberoglio Giovanni , Orland Henri
Published: January 2011

Using the dominant reaction pathways method, we perform an ab initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of these systems, without resorting to an empirical representation of the molecular force field. It also allows to study rare transitions involving rearrangements in the electronic structure. By comparing the results of the ab initio simulation with those obtained by employing a standard force field, we discuss its capability to describe the nonequilibrium dynamics of conformational transitions.
Alternating current impedance spectroscopy measurement under high pressure
Authors: He Chunyuan , Liu Bingguo , Li Ming , Gao Chunxiao
Published: January 2011

A microcircuit was designed and fabricated on a diamond anvil cell for alternating current impedance spectroscopy measurement under high pressure. Sputtered molybdenum film on a diamond anvil was used as an electrode, maintained the contact between the sample and the electrode stable, and reduced the electrode effect on the impedance measurement. By the empty cell and short circuit tests, the parasitic capacitive impedance from the sample chamber wall was observed to be larger than 105 Ω at a frequency lower than 1.0 MHz and could be ignored for samples with higher conductivity. The wire inductance was only 1.0 μH and just appeared at frequency higher than 20 kHz, which could be subtracted from measured impedance for the samples with higher impedance than several hundred ohms. Using this apparatus, the impedances of the II–VI group cadmium sulfide were measured. The pressure dependence of the grain interior conductance of CdS crystal was obtained, which reflected that the phase transitions of CdS under high pressure are the same as the single crystal measurement results.
Poration of lipid bilayers by shock-induced nanobubble collapse
Authors: Choubey Amit , Vedadi Mohammad , Nomura Ken-ichi , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya
Published: January 2011

We investigate molecular mechanisms of poration in lipid bilayers due to shock-induced collapse of nanobubbles. Our multimillion-atom molecular dynamics simulations reveal dynamics of nanobubble shrinkage and collapse, leading to the formation and penetration of nanojets into lipid bilayers. The nanojet impact generates shear flow of water on bilayer leaflets and pressure gradients across them, which transiently enhance the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined.
Temperature and electric field dependence of the dielectric property and domain evolution in [001]-oriented 0.34Pb(In1/2Nb1/2)O3–0.25Pb(Mg1/3Nb2/3)O3–0.41PbTiO3 single crystal
Authors: Chen Y. , Lam K. H. , Zhou D. , Gao X. S. , Dai J. Y. , Luo H. S. , Chan H. L. W.
Published: January 2011

Ferroelectric domain structure and evolution, as well as phase transition, of [001]-oriented 34Pb(In1/2Nb1/2)O3–0.25Pb(Mg1/3Nb2/3)O3–0.41PbTiO3 single crystal has been studied through temperature and frequency-dependent relative permittivity characterization. Under dc bias, the transition temperature from rhombohedral-to-tetragonal phases becomes lower and the transition temperature from macrodomain to microdomain structures increases. Phase transition from rhombohedral to tetragonal is confirmed by temperature-dependent x-ray diffraction. These results are also well supported by direct domain observation by means of piezoresponse force microscopy under dc bias at different temperatures, as well as polarization-electric field hysteresis loop measurement.
Distorted wurtzite unit cells: Determination of lattice parameters of nonpolar a-plane AlGaN and estimation of solid phase Al content
Authors: Laskar Masihhur R. , Ganguli Tapas , Rahman A. A. , Mukherjee Amlan , Hatui Nirupam , Gokhale M. R. , Bhattacharya Arnab
Published: January 2011

Unlike c-plane nitrides, “nonpolar” nitrides, e.g., those grown in the a-plane or m-plane orientation encounter anisotropic in-plane strain due to the anisotropy in the lattice and thermal mismatch with the substrate or buffer layer. Such anisotropic strain results in a distortion of the wurtzite unit cell and creates difficulty in accurate determination of lattice parameters and solid phase group-III content (xsolid) in ternary alloys. In this paper we show that the lattice distortion is orthorhombic, and outline a relatively simple procedure for measurement of lattice parameters of nonpolar group III-nitrides epilayers from high resolution x-ray diffraction measurements. We derive an approximate expression for xsolid taking into account the anisotropic strain. We illustrate this using data for a-plane AlGaN, where we measure the lattice parameters and estimate the solid phase Al content, and also show that this method is applicable for m-plane structures as well.
The Weitzenböck connection and time reparameterization in nonholonomic mechanics
Authors: Fernandez O. E. , Bloch A. M.
Published: January 2011

We show that the torsion of the Weitzenböck connection is responsible for the fictitious pseudogyroscopic force experienced by a general mechanical system in a noncoordinate moving frame. In particular, we show that for the class of mechanical systems subjected to nonintegrable constraints known as non-abelian nonholonomic Chaplygin systems, the constraint reaction force directly depends on this torsion. For these Chaplygin systems, we show how this torsional force can in some cases be removed by an appropriate choice of frame depending on a multiplier f(q), linking these results to the process of Chaplygin Hamiltonization through time reparameterization. Lastly, we show that the cyclic symmetries of f in some cases lead to the existence of momentum conservation laws for the original nonholonomic system and illustrate the results through several examples.
Combined x-ray photoelectron spectroscopy and scanning electron microscopy studies of the LiBH4–MgH2 reactive hydride composite with and without a Ti-based additive
Authors: Deprez E. , Muñoz-Márquez M. A. , Jimenez de Haro M. C. , Palomares F. J. , Soria F. , Dornheim M. , Bormann R. , Fernández A.
Published: January 2011

A detailed electronic and microstructural characterization is reported for the LiBH4–MgH2 reactive hydride composite system with and without titanium isopropoxide as additive. Surface characterization by x-ray photoelectron spectroscopy combined to a morphological study by scanning electron microscopy as well as elemental map composition analysis by energy dispersive x-ray emission are presented in this paper for the first time for all sorption steps. Although sorption reactions are not complete at the surface due to the unavoidable superficial oxidation, it has been shown that the presence of the additive is favoring the heterogeneous nucleation of the MgB2 phase. Ti-based phases appear in all the samples for the three sorption steps well dispersed and uniformly distributed in the material. Li-based phases are highly dispersed at the surface while the Mg-based ones appear, either partially covered by the Li-based phases, or forming bigger grains. Ball milling is promoting mixing of phases and a good dispersion of the additive what favors grain refinement and heterogeneous reactions at the interfaces.
Regarding the validity of the time-dependent Kohn–Sham approach for electron-nuclear dynamics via trajectory surface hopping
Authors: Fischer Sean A. , Habenicht Bradley F. , Madrid Angeline B. , Duncan Walter R. , Prezhdo Oleg V.
Published: January 2011

The implementation of fewest-switches surface-hopping (FSSH) within time-dependent Kohn–Sham (TDKS) theory [Phys. Rev. Lett. 95, 163001 (2005)] has allowed us to study successfully excited state dynamics involving many electronic states in a variety of molecular and nanoscale systems, including chromophore–semiconductor interfaces, semiconductor and metallic quantum dots, carbon nanotubes and graphene nanoribbons, etc. At the same time, a concern has been raised that the KS orbital basis used in the calculation provides only approximate potential energy surfaces [J. Chem. Phys. 125, 014110 (2006)]. While this approximation does exist in our method, we show here that FSSH-TDKS is a viable option for computationally efficient calculations in large systems with straightforward excited state dynamics. We demonstrate that the potential energy surfaces and nonadiabatic transition probabilities obtained within the TDKS and linear response (LR) time-dependent density functional theories (TDDFT) agree semiquantitatively for three different systems, including an organic chromophore ligating a transition metal, a quantum dot, and a small molecule. Further, in the latter case the FSSH-TDKS procedure generates results that are in line with FSSH implemented within LR-TDDFT. The FSSH-TDKS approach is successful for several reasons. First, single-particle KS excitations often give a good representation of LR excitations. In this regard, DFT compares favorably with the Hartree–Fock theory, for which LR excitations are typically combinations of multiple single-particle excitations. Second, the majority of the FSSH-TDKS applications have been performed with large systems involving simple excitations types. Excitation of a single electron in such systems creates a relatively small perturbation to the total electron density summed over all electrons, and it has a small effect on the nuclear dynamics compared, for instance, with thermal nuclear fluctuations. In such cases an additional, classical-path approximation can be made. Third, typical observables measured in time-resolved experiments involve averaging over many initial conditions. Such averaging tends to cancel out random errors that may be encountered in individual simulated trajectories. Finally, if the flow of energy between electronic and nuclear subsystems is insignificant, the ad hoc FSSH procedure is not required, and a straightforward mean-field, Ehrenfest approach is sufficient. Then, the KS representation provides rigorously a convenient and efficient basis for numerically solving the TDDFT equations of motion.
Structural and optical properties of europium doped zirconia single crystals fibers grown by laser floating zone
Authors: Soares M. R. N. , Nico C. , Peres M. , Ferreira N. , Fernandes A. J. S. , Monteiro T. , Costa F. M.
Published: January 2011

Yttria stabilized zirconia single crystal fibers doped with europium ions were developed envisaging optical applications. The laser floating zone technique was used in order to grow millimetric high quality single crystal fibers. The as-grown fibers are completely transparent and inclusion free, exhibiting a cubic structure. Under ultraviolet (UV) excitation, a broad emission band appears at 551 nm. The europium doped fibers are translucent with a tetragonal structure and exhibit an intense red emission at room temperature under UV excitation. The fingerprint transition lines between the D50 and F7J(0–4) multiplets of the Eu3+ ions are observed with the main emission line at ∼606 nm due to D50→F72 transition. Photoluminescence excitation and wavelength dependent the photoluminescence spectra confirm the existence of different Eu3+ optical centers.
Modeling the interactions of phthalocyanines in water: From the Cu(II)-tetrasulphonate to the metal-free phthalocyanine
Authors: Martín Elisa I. , Martínez Jose M. , Marcos Enrique Sánchez
Published: January 2011

A quantum and statistical study on the effects of the ions Cu2+ and SO3− in the solvent structure around the metal-free phthalocyanine (H2Pc) is presented. We developed an ab initio interaction potential for the system CuPc–H2O based on quantum chemical calculations and studied its transferability to the H2Pc–H2O and [CuPc(SO3)4]4−–H2O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H2Pc, and [CuPc(SO3)4]4− in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu2+ cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO3− anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye–Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.
Cathodoluminescent properties and surface characterization of bluish-white LiAl5O8:Tb phosphor
Authors: Pitale Shreyas S. , Kumar Vinay , Nagpure I. M. , Ntwaeaborwa O. M. , Coetsee E. , Swart H. C.
Published: January 2011

Cathodoluminescence (CL) characteristics and electron-beam induced surface chemical changes in nanocrystalline Tb3+ doped LiAl5O8 powder phosphors are presented. Bluish-white CL with a maximum at ∼543 nm was observed when the powders were irradiated with a 2 keV electron beam. The emissions in the green and the blue regions arise from the magnetic dipole D54-F7J (J=6–0) and D53-F7J transitions of the Tb3+ ion. The appearance of the line emissions in the blue region are discussed in terms of Tb oxidation states and their corresponding interconversion. Auger electron spectroscopy and x-ray photoelectron spectroscopy (XPS) were used to probe the chemical changes on the surface of the LiAl5O8 phosphor under electron bombardment. The XPS data suggest that the Tb ions exist both in trivalent and tetravalent oxidation states which could be the reason for the observed green as well as blue CL emissions. A thermodynamically stable Al2O3 layer formed on the surface as a result of the electron stimulated surface chemical reactions is possibly contributing to the CL stability of the LiAl5O8:Tb phosphor. The time stability of the phosphor under prolonged electron beam exposure suggests that it can be used in information displays.
Fluxoid-based digitized mechanical torque in subfemtonewton-meter range
Authors: Choi Jae-Hyuk , Lee Soon-Gul
Published: January 2011

A technique is proposed that realizes fluxoid-based mechanical torque in the subfemtonewton-meter range. By exploiting the fluxoid quantization of a superconductor ring, one can generate discrete torque steps in constant interval. The interval of the torque steps is estimated be 0.40 fN m for a 50-nm-thick Nb-film ring of diameter 21 μm with a hole of diameter 7 μm under field 0.02 T applied parallel to the ring plane. Working principles and numerical estimation are discussed by using a model system composed of a microbridge torsion lever loaded with a superconducting quantum interference device.
Near infrared light driven organic p-i-n solar cells incorporating phthalocyanine J-aggregate
Authors: Hiramoto Masahiro , Kitada Keitaro , Iketaki Kai , Kaji Toshihiko
Published: January 2011

Organic p-i-n solar cells having near infrared (NIR) sensitivity to 1050 nm were fabricated using a codeposited i-interlayer consisting of lead phthalocyanine (PbPc) and fullerene (C60). The external quantum efficiency and conversion efficiency for NIR light reached 43% (860 nm) and 2.3%, respectively. The codeposited i-interlayer was shown to have three separate nanostructural components each making a contribution to the operation of the cell. These were electron transport through amorphous C60, hole transport through the H-aggregates of PbPc, and carrier generation by NIR light at the J-aggregate sites of PbPc.
Organic solar cells with a multicharge separation structure consisting of a thin rubrene fluorescent dye for open circuit voltage enhancement
Authors: Huang Jiang , Yu Junsheng , Wang Wan , Jiang Yadong
Published: January 2011

Organic solar cells were fabricated by inserting a thin rubrene fluorescent dye between pentacene and fullerene heterojunction with a multicharge separation (MCS) structure, which was adopted to inherently further improve maximum open circuit voltage and power conversion efficiency. The morphology of organic films showed that a more surface roughness of pentacene film could be beneficial for an effective MCS interface, exciton dissociation, and charge carrier transportation. Moreover, a slight improvement of short-circuit current density when adding a 1 or 2 nm rubrene layer was also analyzed in detail based on external quantum efficiency spectra and optical transfer matrix theory.