bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal fluctuations in chemically cross-linked polymers of cyclodextrins
Authors: Rossi Barbara , Venuti Valentina , Paciaroni Alessandro , Mele Andrea , Longeville Stéphane , Natali Francesca , Crupi Vincenza , Majolino Domenico , Trotta Francesco
Published: January 2015

The thermal fluctuations and the relaxational dynamics in cyclodextrin based cross-linked polymers are explored by elastic and quasi-elastic neutron scattering.
On the formation of dendrimer/nucleolipids surface films for directed self-assembly
Authors: Arteta Marianna Yanez , Berti Debora , Montis Costanza , Campbell Richard A. , Eriksson Caroline , Clifton Luke A. , Skoda Maximilian W. A. , Soltwedel Olaf , Koutsioubas Alexandros , Baglioni Piero , Nylander Tommy
Published: January 2015

Molecular recognition of nucleic acids by dendrimers with non-covalently attached nucleolipids can be tuned by nucleolipid type and order of addition.
Morphology of latex and nanocomposite adsorbents prepared by freeze-casting
Authors: da Silva Lucimara Lopes , Galembeck Fernando
Published: January 2015

Freeze-cast monoliths prepared from a common amorphous latex in aqueous media presented unprecedented morphologies that contribute to dye sorption capacity.
A novel in situ preparation method for nanostructured α-Fe2O3 films from electrodeposited Fe films for efficient photoelectrocatalytic water splitting and the degradation of organic pollutants
Authors: Zeng Qingyi , Bai Jing , Li Jinhua , Xia Ligang , Huang Ke , Li Xuejin , Zhou Baoxue
Published: January 2015

Highly photoactive α-Fe2O3 films prepared from novel electrodeposited Fe films were reported for PEC water splitting and organic pollutant degradation.
A new printable and durable N,O-carboxymethyl chitosan–Ca2+–polyphosphate complex with morphogenetic activity
Authors: Müller Werner E. G. , Tolba Emad , Schröder Heinz C. , Neufurth Meik , Wang Shunfeng , Link Thorben , Al-Nawas Bilal , Wang Xiaohong
Published: January 2015

In the absence of Ca2+ the polymers N,O-carboxymethyl chitosan, together with Na-polyphosphate and alginate, form random-coiled structures. Addition of Ca2+ transforms these polymers to durable implants.
Smart electroconductive bioactive ceramics to promote in situ electrostimulation of bone
Authors: Mata Diogo , Oliveira Filipe J. , Neto Miguel A. , Belmonte Manuel , Bastos Alexandre C. , Lopes Maria A. , Gomes Pedro S. , Fernandes Maria H. , Silva Rui F.
Published: January 2015

Cell functions were controlledin situby an efficient mechanism of delivering electrical stimuli involving conductive biomaterials and non-invasive techniques.
Fluorescent ZnO for imaging and induction of DNA fragmentation and ROS-mediated apoptosis in cancer cells
Authors: Gupta Jagriti , Bhargava Parag , Bahadur D.
Published: January 2015

Systemic diagram shows the cell death mechanism through the generation of reactive oxygen species.
A SiO2 NP–DNA/silver nanocluster sandwich structure-enhanced fluorescence polarization biosensor for amplified detection of hepatitis B virus DNA
Authors: Chen Jia , Chen Qiao , Gao Cunji , Zhang Mingliang , Qin Bo , Qiu Hongdeng
Published: January 2015

A novel homogeneous biosensor based on the fluorescence polarization enhancement effect of the SiO2 NP–DNA/Ag nanocluster sandwich structure has been developed for sensitive and selective detection of hepatitis B virus DNA.
From macro to micro to nano: the development of a novel lysine based hydrogel platform and enzyme triggered self-assembly of macro hydrogel into nanogel
Authors: Wu De-Qun , Wu Jun , Qin Xiao-Hong , Chu Chih-Chang
Published: January 2015

Development of a novel lysine based hydrogel platform and the enzyme triggered self-assembly of macro hydrogel into nanogel.
Heteroleptic platinum(ii) NHC complexes with a C^C* cyclometalated ligand – synthesis, structure and photophysics
Authors: Tronnier Alexander , Heinemeyer Ute , Metz Stefan , Wagenblast Gerhard , Muenster Ingo , Strassner Thomas
Published: January 2015

Significant improvement of photophysical properties for blue emitting C^C* cyclometalated NHC complexes by changing the acac-ligands.
Exploiting the extended π-system of perylene bisimide for label-free single-molecule sensing
Authors: Al-Galiby Qusiy , Grace Iain , Sadeghi Hatef , Lambert Colin J.
Published: January 2015

We demonstrate the potential of perylene bisimide (PBI) for label-free sensing of organic molecules by investigating the change in electronic properties of five symmetric and asymmetric PBI derivatives, which share a common backbone, but are functionalised with various bay-area substituents.
Constant‐envelope dual QPSK‐like modulation and its generalised form for modern GNSS signals
Authors: Huang Xinming , Zhu Xiangwei , Ou Gang
Published: January 2015

A new constant‐envelope modulation multiplexing two quadrature phase shift keying (QPSK)‐like global navigation satellite system (GNSS) signals and its generalised form with unbalanced power are presented. The modulations can be regarded as the extended form of generalised DualQPSK modulations and provide a solution to the Compass B1 band multiplexing problem.
Swarm‐inspired exploration of architecture and unrolling factors for nested‐loop‐based application in architectural synthesis
Authors: Mishra V.K. , Sengupta A.
Published: January 2015

A novel framework for automated design space exploration (DSE) of architecture and unrolling factor (UF) for perfectly nested loops in architectural synthesis (AS) is presented. The sub‐contributions are that it: (a) proposes a novel model for determining execution time based on architecture and UFs for nested loop without tiresomely unrolling completely; (b) proposes a novel methodology for exploration of architecture and loop UFs for a perfectly nested loop, based on swarm intelligence (SI); and (c) maintains a trade‐off between power and performance during exploration and also resolves orthogonal issues such as exploration speed and quality of result (QoR). Results of the proposed approach indicate an average improvement in QoR of >33% and reduction in runtime of >34% compared with recent approaches.
Compact stub‐loaded open‐loop BPF with enhanced stopband by introducing extra transmission zeros
Authors: Kumar Nagendra , Singh Yatendra Kumar
Published: January 2015

Open‐loop resonators (OLRs) are loaded with one or two stubs to design a compact bandpass filter (BPF) with a wide stopband by creating extra transmission zeros. By properly selecting the length of the stubs and their positions, extra transmission zeros are created in the stopband before the spurious passband, thus giving wide stopbands. Mathematical analyses are performed to show the effect of open stubs on the OLR. A two‐stub‐loaded BPF is designed and fabricated, which shows a harmonic suppression of up to 3.2fo by creating five transmission zeros and 44% size reduction as compared with a simple OLR‐based filter without stubs. Measured results are in good agreement with the theoretical analysis and simulation results.
Wide‐range harmonic lock detector with real‐time delay measurement of delay‐locked loop
Authors: Kim Sangseob , Hyoung Chang‐Hee , Park Kyoung‐Hwan
Published: January 2015

A new robust harmonic lock detector (HLD) suitable for a wide‐range delay‐locked loop (DLL) is presented. This detector is composed of some delay indicators measuring the total delay of the DLL in real time, and it can detect the harmonic lock for a wide frequency range close to 1–20 times higher than the minimum frequency. Owing to its seamless operation without any initialising process using external reset control, it can ensure reliable lock detection despite some unusual conditions, such as frequency change, electrical surge input or power‐ground fluctuation. The proposed HLD and the DLL were designed in 0.13 µm CMOS technology, and the simulation results showed the exact harmonic lock detection and reliable DLL locking properties over the whole frequency range from 25 to 500 MHz of the input clock.
Data analytics based neuro‐fuzzy controller for diesel‐photovoltaic hybrid AC microgrid
Authors: Sekhar P.C. , Mishra Sukumar , Sharma Rishi
Published: January 2015

The diesel‐photovoltaic (PV) based hybrid AC microgrid systems with conventional control philosophies deliver very good performance in the grid connected mode. However, once the microgrid is isolated from the main grid the same philosophies which control the PV at its maximum power can make the microgrid unstable. In this connection, this study proposes a novel neuro‐fuzzy controller to ensure the smooth transition of microgrid from grid connected mode to isolated mode, to retain the system stability even in isolated mode and to deliver the superior performance in grid connected mode as well. The considered artificial neural networks is trained with PMPP–Temp against VMPP characteristic, first of its kind. The fuzzy part of the controller derives the reference voltages subjected to the limits provided by the ANN. This study describes how well the data analytics can be utilised to retain the power system stability in emergencies. The proposed controller has been evaluated under different operating conditions and is exhibiting superior performance in achieving the desired control objectives. Results from the numerical simulations are confirmed from the experiments in real‐time environment.
Theoretical study of thorium monoxide for the electron electric dipole moment search: Electronic properties of H3Δ1 in ThO
Authors: Skripnikov L. V. , Titov A. V.
Published: January 2015

Recently, improved limits on the electron electric dipole moment, and dimensionless constant, kT,P, characterizing the strength of the T,P-odd pseudoscalar–scalar electron–nucleus neutral current interaction in the H3Δ1 state of ThO molecule were obtained by the ACME collaboration [J. Baron et al., Science 343, 269 (2014)]. The interpretation of the experiment in terms of these fundamental quantities is based on the results of theoretical study of appropriate ThO characteristics, the effective electric field acting on electron, Eeff, and a parameter of the T,P-odd pseudoscalar–scalar interaction, WT,P, given in Skripnikov et al. [J. Chem. Phys. 139, 221103 (2013)] by St. Petersburg group. To reduce the uncertainties of the given limits, we report improved calculations of the molecular state–specific quantities Eeff, 81.5 GV/cm, and WT,P, 112 kHz, with the uncertainty within 7% of the magnitudes. Thus, the values recommended to use for the upper limits of the quantities are 75.8 GV/cm and 104 kHz, correspondingly. The hyperfine structure constant, molecule-frame dipole moment of the H3Δ1 state, and the H3Δ1 → X1Σ+ transition energy which, in general, can serve as a measure of reliability of the obtained Eeff and WT,P values are also calculated. In addition, we report the first calculation of g-factor for the H3Δ1 state of ThO. The results are compared to the earlier experimental and theoretical studies, and a detailed analysis of uncertainties of the calculations is given.
Experimental evidence for an optical interference model for vibrational sum frequency generation on multilayer organic thin film systems. II. Consideration for higher order terms
Authors: O’Brien Daniel B. , Massari Aaron M.
Published: January 2015

The generalized optical interference model for interfacial contributions to vibrational sum frequency generation (VSFG) spectroscopic signals from organic thin film systems is extended to include a description of optical interferences contained in the thin film bulk response. This is based on electric quadrupolar interactions with the input fields and includes a discussion on possible contribution from the electric quadrupolar polarization. VSFG data from the first of this two part report are analyzed and include effects from higher order responses, for both bulk and higher order interfacial terms. The results indicate that although it is capable of capturing many of the data features, the electric dipole treatment is likely not a complete description of the VSFG intensity data from this system. An analysis based on the signs of the resulting response amplitudes is used to deduce the relative magnitude of the electric dipole and higher order interfacial terms. It is found that the buried interface is closer to satisfying the electric dipole approximation, consistent with smaller field gradients due to closer index matching between the organic thin film and substrate relative to air. The procedure outlined in this work allows for the difficult task of deducing a physical picture of average molecular orientation at the buried interface of a multilayer organic thin film system while including higher order effects.
Carbon and nitrogen metabolism in arbuscular mycorrhizal maize plants under low-temperature stress
Authors: Zhu Xian-Can , Song Feng-Bin , Liu Fu-Lai , Liu Sheng-Qun , Tian Chun-Jie
Published: January 2015

Effects of the arbuscular mycorrhizal (AM) fungus Glomus tortuosum on carbon (C) and nitrogen (N) metabolism of Zea mays L. grown under low-temperature stress was investigated. Maize plants inoculated or not inoculated with AM fungus were grown in a growth chamber at 25°C for 4 weeks and subsequently subjected to two temperature treatments (15°C, low temperature; 25°C, ambient control) for 2 weeks. Low-temperature stress significantly decreased AM colonisation, plant height and biomass. Total N content and activities of glutamate oxaloacetate transaminase and glutamate pyruvate transaminase of AM plants were higher than those of non-AM plants. AM plants had a higher net photosynthetic rate (Pn) than non-AM plants, although low temperature inhibited the Pn. Compared with non-AM plants, AM plants exhibited higher leaf soluble sugars, reducing sugars, root sucrose and fructose contents, and sucrose phosphate synthase and amylase activities at low temperature. Moreover, low-temperature stress increased the C : N ratio in the leaves of maize plants, and AM colonisation decreased the root C : N ratio. These results suggested a difference in the C and N metabolism of maize plants at ambient and low temperature regimes. AM symbiosis modulated C metabolic enzymes, thereby inducing an accumulation of soluble sugars, which may have contributed to an increased tolerance to low temperature, and therefore higher Pn in maize plants.
Causes of natural variation in fitness: Evidence from studies of
Drosophila
populations
Authors: Charlesworth Brian
Published: January 2015

Significance

The extent and causes of genetic variation have been debated for 60 y. This paper synthesizes evidence from studies of DNA sequence variability in
Drosophila
and from experiments on the quantitative genetics of fitness components. Two major conclusions emerge. First, a class of mutations with relatively large fitness effects contributes importantly to both the overall effect of new mutations on fitness components and to standing variation. These mutations are not detected in analyses of sequence variability. Second, a large fraction of variability in fitness components must be maintained by selection rather than reflecting deleterious variants introduced by mutation. These results imply that both approaches to the study of natural variation are needed to obtain a complete understanding of its causes.
Emerging vector-borne diseases and the potential to prevent them spreading.
Authors: Sánchez-Vizcaíno J. M. , Martínez-Avilés M. , Sánchez-Matamoros A. , Rodríguez-Prieto V.
Published: January 2015

Europe has experienced an increasing number of emerging vector-borne diseases and the recrudescence or re-emergence of others. Global warming offers suitable conditions for arthropod proliferation, some of which can be competent vectors of such diseases. With the increased risk of introduction of potentially infected animals because of shortened travelling times to any part of the world, vector-borne diseases are likely to emerge if the conditions for competent vector proliferation and suitable hosts are found at the destination. Vector-borne diseases are generally complex to deal with, so cooperation and collaboration of the different sectors implied, and with neighbouring countries, are fundamental to coordinate control and prevention actions. Among these, surveillance to detect these infections early is crucial, since susceptible hosts are frequently asymptomatic or mildly symptomatic. However, when conditions are suitable, the impact of these diseases can be very severe. The combination of epidemiological and diagnostic tools to identify locations, time and populations where an outbreak is expected to occur, and how to detect it as soon as possible, are fundamental for an effective surveillance. Another area of cooperation is the preparedness, through vaccine banks, against the different known strains, profound knowledge of immunity to vector-borne pathogens, and the development of diagnostic tests that can differentiate vaccinated from infected individuals. In this paper we review bluetongue, African horse sickness, West Nile fever and Rift Valley fever, and we focus on Europe's experience in tackling the emergence of these pathogens.
The horn of conflict
Authors: Markakis John
Published: January 2015

Nearly twenty years ago, the editorial of ROAPE's first special issue (No. 30, 1984) on the Horn of Africa opened with the sombre comment: ‘Manifold, violent social conflict is the hallmark of contemporary history in the Horn of Africa.’ Civil wars were raging then in Sudan, Ethiopia and Somalia. The latter two states had fought their second war a few years earlier, and relations between them were extremely hostile. Each was patronised and armed by one of the rival superpowers that were running a cold war sideshow in this corner of African. Not unrelated to conflict, a biblical famine was ravaging the region for the second time within a decade. The editorial of the second ROAPE special issue (No. 70, 1996) on this region observed that some things there had changed for the better. One major conflict had ended when Eritrea gained its independence from Ethiopia, and both states now had a young, battle-tested and sophisticated leadership avowedly committed to peace and development. Foreign power interference had subsided with the end of the cold war, and a continent-wide wave of democratisation was seen lapping at the borders of the Horn. Interstate relations in the region had improved greatly, ambitious schemes of regional cooperation were envisaged, and demobilisation of armies and guerilla forces was in progress. Added to the expected peace dividend, foreign investment was anticipated to boost development now that socialism, previously the vogue in the region, had given way to the free market. The editorial also noted some things had changed for the worse. Conflict had caused the collapse of the Somali Republic – a first for Africa – and had spread to Djibouti and to parts of northern Sudan. The latter now claimed the dubious distinction of hosting Africa's oldest conflict.
TPLF: reform or decline?
Authors: Tadesse Medhane , Young John
Published: January 2015

Founded and led by the Tigray People's Liberation Front (TPLF), the Ethiopian Peoples Revolutionary Democratic Front (EPRDF) came to power in 1991, after a sixteen-year armed struggle against the military regime that had ruled Ethiopia since 1974. While not formally a marxist-leninist party, the TPLF nonetheless was devoted to these ideals and they figured prominently in the structure and functioning of the organisation. While the TPLF's base represented the peasantry of Tigray, its leadership was dominated by young, radical intellectuals. Itself representing an ethnic group of relatively modest size, the TPLF formed a coalition of ethnically based organisations, the EPRDF, in 1989, to give itself Ethiopia-wide political scope and legitimacy. Once it came to power, the Front faced serious problems of adjustment, but managed to overcome them thanks to the coherence of its programme, the commitment of its cadres, and the cohesiveness of its leadership. In the face of dramatically changed international circumstances, the EPRDF moderated its policies, abandoning marxism and embracing the free market. It weathered an insurrection by the Oromo Liberation Front (OLF) in 1992-93, contained Islamist incursions from Sudan and Somalia, won the war against Eritrea (1998-2000), achieved a measure of economic progress, and took large steps towards state decentralisation and smaller ones towards democratisation.
Eritrea: transition to dictatorship, 1991-2003
Authors: Hedru Debessay
Published: January 2015

Eritrea's image in the early 1990s as a peaceful and well-ordered state was coloured by the euphoria of independence following a military victory over the formidable army of Ethiopia. Against all odds, the country seceded in 1991 and attained international recognition in 1993. Emphasis on self-reliance reliance and hard work made it easy to overlook the ingrained authoritarianism and basic intolerance of the Eritrean Peoples Liberation Front (EPLF) leadership. Eritreans and foreign observers believed the promise made by the victorious guerilla leadership that Eritrea would learn the lessons of post-colonial African history and would not repeat its mistakes. The EPLF, renamed the Popular Front for Democracy and Justice (PFDJ) in February 1994, reiterated this promise so frequently and eloquently that even the most cynical of persons was inclined to hope Eritrea would be spared the nightmare of dictatorship.
THE AKARI 2.5–5.0 μm SPECTRAL ATLAS OF TYPE-1 ACTIVE
GALACTIC NUCLEI: BLACK HOLE MASS ESTIMATOR, LINE RATIO, AND HOT DUST
TEMPERATURE
Authors: Kim Dohyeong , Im Myungshin , Kim Ji Hoon , Jun Hyunsung David , Woo Jong-Hak , Lee Hyung Mok , Lee Myung Gyoon , Nakagawa Takao , Matsuhara Hideo , Wada Takehiko , Oyabu Shinki , Takagi Toshinobu , Ohyama Youichi , Lee Seong-Kook
Published: January 2015

We present 2.5–5.0 μm spectra of 83 nearby
(0.002 < z < 0.48) and bright (K <
14 mag) type-1 active galactic nuclei (AGNs) taken with the Infrared Camera on
board AKARI. The 2.5–5.0 μm spectral region contains emission
lines such as Brβ (2.63 μm), Brα (4.05 μm), and polycyclic aromatic hydrocarbons
(3.3 μm), which can be used for studying the black hole (BH) masses and star
formation activity in the host galaxies of AGNs. The spectral region also
suffers less dust extinction than in the ultra violet (UV) or optical
wavelengths, which may provide an unobscured view of dusty AGNs. Our sample is
selected from bright quasar surveys of Palomar-Green and SNUQSO, and AGNs with
reverberation-mapped BH masses from Peterson et al. Using 11 AGNs with reliable
detection of Brackett lines, we derive the Brackett-line-based BH mass
estimators. We also find that the observed Brackett line ratios can be explained
with the commonly adopted physical conditions of the broad line region.
Moreover, we fit the hot and warm dust components of the dust torus by adding
photometric data of SDSS, 2MASS, WISE, and ISO
to the AKARI spectra, finding hot and warm dust temperatures of
∼1100 K and ∼220 K, respectively, rather than the commonly cited hot dust
temperature of 1500 K.
On syzygies of linear sections
Authors: Park Euisung
Published: January 2015

In this paper, we study how the minimal free resolution of a closed subscheme

X
⊂

P

r

X \subset \mathbb {P}^r

relates to that of a linear section

X
∩
Λ
⊂
Λ
=

P

s

X \cap \Lambda \subset \Lambda = \mathbb {P}^s

(
0
>
s
>
r
)

(0 > s >r)

. Our main result implies that the shape of the final non-zero row of the Betti diagram of

X
X

is preserved under taking the zero-dimensional and one-dimensional linear sections.
LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors
Authors: Druet Tom , Georges Michel
Published: January 2015

Summary: Many applications in genetics require haplotype reconstruction. We present a phasing program designed for large half-sibs families (as observed in plant and animals) that is robust to genotyping and map errors. We demonstrate that it is more efficient than previous versions and other programs, particularly in the presence of genotyping errors.

Availability and implementation: The software LINKPHASE3 is included in the PHASEBOOK package and can be freely downloaded from www.giga.ulg.ac.be/jcms/prod_381171/software. The package is written in FORTRAN and contains source codes. A manual is provided with the package.

Contact:  tom.druet@ulg.ac.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Combining tree-based and dynamical systems for the inference of gene regulatory networks
Authors: Huynh-Thu Vân Anh , Sanguinetti Guido
Published: January 2015

Motivation: Reconstructing the topology of gene regulatory networks (GRNs) from time series of gene expression data remains an important open problem in computational systems biology. Existing GRN inference algorithms face one of two limitations: model-free methods are scalable but suffer from a lack of interpretability and cannot in general be used for out of sample predictions. On the other hand, model-based methods focus on identifying a dynamical model of the system. These are clearly interpretable and can be used for predictions; however, they rely on strong assumptions and are typically very demanding computationally.

Results: Here, we propose a new hybrid approach for GRN inference, called Jump3, exploiting time series of expression data. Jump3 is based on a formal on/off model of gene expression but uses a non-parametric procedure based on decision trees (called ‘jump trees’) to reconstruct the GRN topology, allowing the inference of networks of hundreds of genes. We show the good performance of Jump3 on in silico and synthetic networks and applied the approach to identify regulatory interactions activated in the presence of interferon gamma.

Availability and implementation: Our MATLAB implementation of Jump3 is available at http://homepages.inf.ed.ac.uk/vhuynht/software.html.

Contact:  vhuynht@inf.ed.ac.uk or G.Sanguinetti@ed.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification
Authors: Borozan Ivan , Watt Stuart , Ferretti Vincent
Published: January 2015

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized.

Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences.

Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html.

Contact:  ivan.borozan@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Using isoelectric point to determine the pH for initial protein crystallization trials
Authors: Kirkwood Jobie , Hargreaves David , O’Keefe Simon , Wilson Julie
Published: January 2015

Motivation: The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate.

Results: Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes.

Availability and implementation: Data used to generate models are available as Supplementary Material.

Contact:  julie.wilson@york.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
NKT cells can help mediate the protective effects of 1,25-dihydroxyvitamin D3 in experimental autoimmune encephalomyelitis in mice
Authors: Waddell Amanda , Zhao Jun , Cantorna Margherita T.
Published: January 2015

Active vitamin D [1,25-dihydroxyvitamin D3 (1,25D3)] blocks the development of experimental autoimmune diseases. However, the molecular and immunobiological mechanisms underlying 1,25D3’s anti-inflammatory properties are not fully understood. We employed a murine model of experimental autoimmune encephalomyelitis (EAE) in order to determine the role of NKT cells in 1,25D3-mediated protection from EAE. Wild-type (WT) mice or mice lacking all NKT cells (CD1d−/−) or invariant NKT cells (Jα18−/−) were fed control or 1,25D3-supplemented diets. All mice fed with the control diet developed severe EAE. 1,25D3 treatment of WT mice protected them from developing EAE. CD1d−/− and Jα18−/− mice treated with 1,25D3 were not protected to the same extent as WT mice. Myelin oligodendrocyte glycoprotein-specific IL-17 and IFN-γ production was significantly reduced in 1,25D3 WT mice compared with WT but was not decreased in 1,25D3 CD1d−/− mice compared with CD1d−/− mice. IL-4−/− mice were utilized to determine how IL-4 deficiency affects susceptibility to EAE. IL-4−/− mice were not protected from developing EAE by α-galactosylceramide (α-GalCer) or 1,25D3 treatment. Furthermore, 1,25D3 treatment of splenocytes in vitro decreased α-GalCer-induced IL-17 and increased IL-4, IL-5 and IL-10 production. 1,25D3 alters the cytokine profile of invariant NKT cells in vitro. These studies demonstrate that NKT cells are important mediators of 1,25D3-induced protection from EAE in mice and NKT cell-derived IL-4 may be an important factor in providing this protection.
Trends in Hospitalizations With Primary Varicella and Herpes Zoster During the Prevaricella and Initial Postvaricella and Herpes Zoster Vaccine Eras, Connecticut, 1994–2012
Authors: Humes Elizabeth A. , Weinberger Daniel M. , Kudish Kathy S. , Hadler James L.
Published: January 2015

Background.  The introductions of the varicella vaccine in 1995 and herpes zoster (HZ) vaccine in 2006 have an ongoing potential to modify the epidemiology of both diseases. Analysis of data on hospitalizations can be conducted to examine trends in the occurrence of severe disease over time and to assess the possible impact of vaccination on the incidence of hospitalization.

Methods.  Statewide hospital discharge data 1994–2012 in Connecticut were used to ide.jpegy individuals discharged with a diagnosis of varicella and the initial admissions of persons with a discharge diagnosis of HZ in the first or second diagnostic position. Trends in overall age-standardized and age group-specific hospitalization rates for preselected time intervals before and after the introduction of vaccines were examined using Poisson regression models or Mantel–Haenszel χ2 tests.

Results.  Beginning in 2001, 5 years after the introduction of varicella vaccine, HZ hospitalization rates decreased significantly in individuals <15 years at an average rate of 19.4% per year through 2012. Among individuals ≥60 years, HZ hospitalization rates increased by 5.1% per year from 2001 to 2006 but decreased by 4.2% per year from 2007 to 2012. Primary varicella hospitalization rates declined 82.9% from the prevaccine era (1994–1995) to the 1-dose era (2001–2005) (P < .001). Rates further decreased significantly in the 2-dose era (2010–2012) among 5 to 9 year olds (100% decrease).

Conclusions.  Varicella vaccine seems to have had an impact on both varicella and HZ hospitalizations, and introduction of the HZ vaccine may be having an impact on HZ hospitalizations.
Screening for Schistosoma mansoni and Strongyloides stercoralis Infection Among Brazilian Immigrants in the United States
Authors: Rapoport Alison B. , McCormick Danny , Cohen Pieter A.
Published: January 2015

The prevalence of schistosomiasis and strongyloidiasis among Brazilian immigrants in the United States is unknown. We performed a retrospective chart review of serologic screening of asymptomatic Brazilian immigrants during routine physicals. Of 208 eligible patients, 189 were screened: 27.7% (n = 52) had elevated Schistosoma antibodies and 5.8% (n = 11) had elevated Strongyloides stercoralis antibodies.
Cost-effectiveness of TNF inhibitors vs synthetic disease-modifying antirheumatic drugs in patients with rheumatoid arthritis: a Markov model study based on two longitudinal observational studies
Authors: Kvamme Maria K. , Lie Elisabeth , Uhlig Till , Moger Tron A. , Kvien Tore K. , Kristiansen Ivar S.
Published: January 2015

Objective. The objective of this study was to estimate the additional costs and health benefits of adding a TNF inhibitor (TNFi) (adalimumab, certolizumab, etanercept, golimumab, infliximab) to a synthetic DMARD (sDMARD), e.g. MTX, in patients with RA.

Methods. We developed the Norwegian RA model as a Markov model simulating 10 years of treatment with either TNFi plus sDMARDs (TNFi strategy) or sDMARDs alone (synthetic strategy). Patients in both strategies started in one of seven health states, based on the Short Form-6 Dimensions (SF-6D). The patients could move to better or worse health states according to transition probabilities. In the TNFi strategy, patients could stay on TNFi (including switch of TNFi), or switch to non-TNFi-biologics (abatacept, rituximab, tocilizumab), sDMARDs or no DMARD. In the synthetic strategy, patients remained on sDMARDs. Data from two observational studies were used for the assessment of resource use and utilities in the health states. Health benefits were evaluated using the EuroQol-5 Dimensions (EQ-5D) and SF-6D.

Results. The Norwegian RA model predicted that 10-year discounted health care costs totalled €124 942 (€475 266 including production losses) for the TNFi strategy and €65 584 (€436 517) for the synthetic strategy. The cost per additionally gained quality-adjusted life-year of adding a TNFi was €92 557 (€60 227 including production losses) using SF-6D and €61 285 (€39 841) using EQ-5D. Including health care costs only, the probability that TNFi treatment was cost-effective was 90% when using EQ-5D, assuming a Norwegian willingness-to-pay level of €67 300.

Conclusion. TNFi treatment for RA is cost-effective when accounting for production losses. Excluding production losses, TNFi treatment is cost-effective using EQ-5D, but not SF-6D.
HIGHLY METHYL ESTERIFIED SEEDS Is a Pectin Methyl Esterase Involved in Embryo Development
Authors: Levesque-Tremblay Gabriel , Müller Kerstin , Mansfield Shawn D. , Haughn George W.
Published: January 2015

Homogalacturonan pectin domains are synthesized in a highly methyl-esterified form that later can be differentially demethyl esterified by pectin methyl esterase (PME) to strengthen or loosen plant cell walls that contain pectin, including seed coat mucilage, a specialized secondary cell wall of seed coat epidermal cells. As a means to identify the active PMEs in seed coat mucilage, we identified seven PMEs expressed during seed coat development. One of these, HIGHLY METHYL ESTERIFIED SEEDS (HMS), is abundant during mucilage secretion, peaking at 7 d postanthesis in both the seed coat and the embryo. We have determined that this gene is required for normal levels of PME activity and homogalacturonan methyl esterification in the seed. The hms-1 mutant displays altered embryo morphology and mucilage extrusion, both of which are a consequence of defects in embryo development. A significant decrease in the size of cells in the embryo suggests that the changes in embryo morphology are a consequence of lack of cell expansion. Progeny from a cross between hms-1 and the previously characterized PME inhibitor5 overexpression line suggest that HMS acts independently from other cell wall-modifying enzymes in the embryo. We propose that HMS is required for cell wall loosening in the embryo to facilitate cell expansion during the accumulation of storage reserves and that its role in the seed coat is masked by redundancy.
Computing stoichiometric molecular composition from crystal structures
Authors: Gražulis Saulius , Merkys Andrius , Vaitkus Antanas , Okulič-Kazarinas Mykolas
Published: January 2015

Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases.
Determining the Bravais lattice using a single electron backscatter diffraction pattern
Authors: Li Lili , Han Ming
Published: January 2015

Theab initioderivation of the Bravais lattice from the Kikuchi bands detected from a single electron backscatter diffraction (EBSD) pattern is successfully performed. The as-measured band widths and azimuths always suffer from gnomonic distortions which need to be corrected. A primitive reciprocal cell is first reconstructed by means of the corrected data and the cell parameters are then refined by least-squares analysis of hugely over-determined equations. This allows one to further derive a Niggli reduced cell from the primitive cell. The algorithm presented is not related to any crystal symmetry information and is therefore applicable to all crystal systems. The feasibility of the determination of the Bravais lattice type and parameters from a single EBSD pattern is demonstrated using a mineral sample without anya prioriinformation about its crystal structure. The novel application developed in the present work opens the way to the determination of the Bravais lattice of crystalline materials using scanning electron microscopy combined with the EBSD technique.
Towards multi-order hard X-ray imaging with multilayer zone plates
Authors: Osterhoff Markus , Eberl Christian , Döring Florian , Wilke Robin N. , Wallentin Jesper , Krebs Hans-Ulrich , Sprung Michael , Salditt Tim
Published: January 2015

This article describes holographic imaging experiments using a hard X-ray multilayer zone plate (MZP) with an outermost zone width of 10 nm at a photon energy of 18 keV. An order-sorting aperture (OSA) is omitted and emulated during data analysis by a `software OSA'. Scanning transmission X-ray microscopy usually carried out in the focal plane is generalized to the holographic regime. The MZP focus is characterized by a three-plane phase-retrieval algorithm to an FWHM of 10 nm.
Design study of a Laue lens for nuclear medicine
Authors: Paternò Gianfranco , Bellucci Valerio , Camattari Riccardo , Guidi Vincenzo
Published: January 2015

A Laue lens is an ensemble of crystals capable of focusing, through diffraction in transmission geometry, a fraction of the photons emitted by an X- or γ-ray source onto a small area of a detector. The present study facilitates a thorough understanding of the effect of each system parameter on the efficiency, the resolution and the field of view of the lens. In this way, the structure and the size of the crystals can be set to achieve a compact lens capable of providing a high-resolution image of the radioactivity distribution lying inside a restricted region of a patient's body. As an application, a Laue lens optimized at 140.5 keV, the γ-line emitted by99mTc, has been designed. The lens is composed of ten rings of Ge crystals with curved diffracting planes and focuses the photons onto a detector 50 cm apart from the source with 1.16 × 10−5efficiency and 0.2 mm resolution. The combination of these two important figures of merit makes the proposed device better performing than pinhole single photon emission computed tomography, which is the technique employed for top-resolution images in nuclear medicine. Finally, the imaging capability of the designed lens has been tested through simulations performed with a custom-made Monte Carlo code.
Use of radial symmetry for the calculation of cylindrical absorption coefficients and optimal capillary loadings
Authors: Khalifah Peter
Published: January 2015

The problem of numerically evaluating absorption correction factors for cylindrical samples has been revisited using a treatment that fully takes advantage of the sample symmetry. It is shown that the path lengths for all points within the sample at all possible diffraction angles can be trivially determined once the angle-dependent distance distribution for a single line of points is calculated. This provides advantages both in computational efficiency and in gaining an intuitive understanding of the effects of absorption on the diffraction data. A matrix of absorption coefficients calculated for μRproducts between 0 and 20 for diffraction angles θDof 0–90° were used to examine the influence of (1) capillary diameter and (2) sample density on the overall scattered intensity as a function of diffraction angle, where μ is the linear absorption coefficient for the sample andRis the capillary radius. On the basis of this analysis, the optimal sample loading for a capillary experiment to maximize diffraction at angles of 0–50° is in general expected to be achieved when the maximum radius capillary compatible with the beam is used and when the sample density is adjusted to be 3/(4μR) of its original density.
A structural study of 4-aminoantipyrine and six of its Schiff base derivatives
Authors: Mnguni Malitsatsi J. , Lemmerer Andreas
Published: January 2015

Six derivatives of 4-amino-1,5-dimethyl-2-phenyl-2,3-dihydro-1H-pyrazol-3-one (4-aminoantipyrine), C11H13N3O, (I), have been synthesized and structurally characterized to investigate the changes in the observed hydrogen-bonding motifs compared to the original 4-aminoantipyrine. The derivatives were synthesized from the reactions of 4-aminoantipyrine with various aldehyde-, ketone- and ester-containing molecules, producing (Z)-methyl 3-[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]but-2-enoate, C16H19N3O3, (II), (Z)-ethyl 3-[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]but-2-enoate, C17H21N3O3, (III), ethyl 2-[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]cyclohex-1-enecarboxylate, C20H25N3O3, (IV), (Z)-ethyl 3-[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]-3-phenylacrylate, C22H23N3O3, (V), 2-cyano-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)acetamide, C14H14N4O2, (VI), and (E)-methyl 4-{[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]methyl}benzoate, C20H19N3O3, (VII). The asymmetric units of all these compounds have one molecule on a general position. The hydrogen bonding in (I) forms chains of moleculesviaintermolecular N—H...O hydrogen bonds around a crystallographic sixfold screw axis. In contrast, the formation of enamines for all derived compounds except (VII) favours the formation of a six-membered intramolecular N—H...O hydrogen-bonded ring in (II)–(V) and an intermolecular N—H...O hydrogen bond in (VI), whereas there is an intramolecular C—H...O hydrogen bond in the structure of imine (VII). All the reported compounds, except for (II), feature π–π interactions, while C—H...π interactions are observed in (II), C—H...O interactions are observed in (I), (III), (V) and (VI), and a C—O...π interaction is observed in (II).
The three-component cocrystal 1,3,5-trifluoro-2,4,6-triiodobenzene–pyridineN-oxide–water (1/2/1) built up by halogen bonds, hydrogen bonds and π–π interactions
Authors: Raffo Pablo A. , Cukiernik Fabio D. , Baggio Ricardo F.
Published: January 2015

The title three-component cocrystal, C6F3I3·2C5H5NO·H2O, has been prepared as a strong candidate for multiple I...O interactions. Its crystal structure is compared with its 1:1 close relative, C6F3I3·C5H5NO [Aakeröyet al.(2014a).CrystEngComm,16, 28–31]. The 1,3,5-trifluoro-2,4,6-triiodobenzene and water species both have crystallographic twofold axial symmetry. The main synthon in both structures is the π–π stacking of benzene rings, complemented by a number of O—H...O, C—F...π and, fundamentally, C—I...O interactions. As expected, the latter are among the strongest and more directional interactions of the sort reported in the literature, confirming that pyridineN-oxide is an eager acceptor. On the other hand, the structure presents only two of these contacts per 1,3,5-trifluoro-2,4,6-triiodobenzene molecule instead of the expected three. Possible reasons for this limitation are analyzed.
Synthesis and crystal structure of 2-amino-3-hydroxypyridinium dioxido(pyridine-2,6-dicarboxylato-κ3O2,N,O6)vanadate(V) and its conversion to nanostructured V2O5
Authors: Hejrani-Dalir Ali , Tabatabaee Masumeh , Sheibani Ali
Published: January 2015

2-Amino-3-hydroxypyridinium dioxido(pyridine-2,6-dicarboxylato-κ3O2,N,O6)vanadate(V), (C5H7N2O)[V(C7H3NO4)O2] or [H(amino-3-OH-py)][VO2(dipic)], (I), was prepared by the reaction of VCl3with dipicolinic acid (dipicH2) and 2-amino-3-hydroxypyridine (amino-3-OH-py) in water. The compound was characterized by elemental analysis, IR spectroscopy and X-ray structure analysis, and consists of an anionic [VO2(dipic)]−complex and an H(amino-3-OH-py)+counter-cation. The VVion is five-coordinated by oneO,N,O′-tridentate dipic dianionic ligand and by two oxide ligands. Thermal decomposition of (I) in the presence of polyethylene glycol led to the formation of nanoparticles of V2O5. Powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM) were used to characterize the structure and morphology of the synthesized powder.
A two-dimensional zinc(II) coordination polymer createdvia in situligand synthesis involving C—N bond formation
Authors: Cai Hua , Guo Ying , Li Jian-Gang
Published: January 2015

The novel ZnIIcoordination polymer poly[{μ4-2-[3-(pyridin-2-yl)-1H-pyrazol-3-yl]butanedioato}zinc(II)], [Zn(C12H9N3O4)]n, has been synthesized hydrothermally and structurally characterized. The results demonstrate that the complex shows two-dimensional neutral wave-like layers. The complex was prepared by the conjugate addition reaction of 2-(1H-pyrazol-3-yl)pyridine tocis-fumaric acid in the presence of Zn(OAc)2·2H2O (OAc is acetate) at 413 K.