bluuebunny/crossref_metadata_2025 huggingface dataset:
Visible-light-activated photoelectrochemical biosensor for the detection of the pesticide acetochlor in vegetables and fruit based on its inhibition of glucose oxidase
Authors: Jin Dangqin , Gong Aiqin , Zhou Hui
Published: March 2017

A new and sensitive photoelectrochemical (PEC) biosensor which is visible-light-activated was fabricated based on acetochlor’s ability to inhibit glucose oxidase (GOx) activity.
Fluorescence sensing of amine vapours based on ZnS-supramolecular organogel hybrid films
Authors: Xia Huiyun , Liu Guanyu , Zhao Chuan , Meng Xiaojuan , Li Fangfang , Wang Fengyan , Duan Li , Chen Huaxin
Published: March 2017

A selective fluorescent ZnS-supramolecular organogel hybrid film was constructed for sensing volatile organic monoamines and diamines vapour by adopting supramolecular gel films as substrates.
GLY67ARG substitution in RSPO4 disrupts the WNT signaling pathway due to an abnormal binding pattern with LGRs leading to anonychia
Authors: Raza Syed Irfan , Navid Abdul Khaliq , Noor Zainab , Shah Khadim , Dar Nasser Rashid , Ahmad Wasim , Rashid Sajid
Published: March 2017

R-Spondins regulate the WNT/β-catenin signaling pathway by interacting with leucine rich-repeat containing G-protein coupled receptors (LGR4–6).
Indolylbenzothiadiazoles with varying substituents on the indole ring: a systematic study on the self-recovering mechanochromic luminescence
Authors: Ito Suguru , Taguchi Tomohiro , Yamada Takeshi , Ubukata Takashi , Yamaguchi Yoshitaka , Asami Masatoshi
Published: March 2017

A series of mechanochromic fluorophores exhibited self-recovering mechanochromic luminescence properties with varying emission color and recovery times.
Greatly enhanced dielectric permittivity in La1.7Sr0.3NiO4/poly(vinylidene fluoride) nanocomposites that retained a low loss tangent
Authors: Meeporn Keerati , Thongbai Prasit , Yamwong Teerapon , Maensiri Santi
Published: March 2017

The effect of La1.7Sr0.3NiO4 nanoparticles (LSNO-NPs) on the dielectric properties of LSNO-NPs/polyvinylidene fluoride (LSNO-NPs/PVDF) composites is presented.
Graphene oxide and nanodiamond: same carboxylic groups, different complexation properties
Authors: Basiuk Vladimir A. , Rybak-Akimova Elena V. , Basiuk Elena V.
Published: March 2017

DFT calculations explain why carboxylic groups on graphene oxide and nanodiamond have different complexation properties toward Ni(ii) tetraazamacrocyclic cations.
New carbon allotropes with metallic conducting properties: a first-principles prediction
Authors: Fan Xinyu , Li Jiao , Chen Gang
Published: March 2017

Combining density functional theory computation and the global minimum structural search, we have found new α-, β-, and δ-phographene carbon allotropes.
Electroactive polymer/carbon nanotube hybrid materials for energy storage synthesized via a “grafting to” approach
Authors: Ernould Bruno , Bertrand Olivier , Minoia Andrea , Lazzaroni Roberto , Vlad Alexandru , Gohy Jean-François
Published: March 2017

Poly(2,2,6,6-tetramethylpiperidin-1-oxyl-4-yl methacrylate) has been grafted onto multi-walled carbon nanotubes to obtain conducting organic cathodes for Li-ion batteries.
Simultaneously improved electrical properties of crystalline YbAl3 thin films prepared by co-sputtering technique
Authors: Li Ran-Ran , He Dan-Qi , Mu Xin , Zhou Hong-Yu , Wei Ping , Zhu Wan-Ting , Nie Xiao-Lei , Zhao Wen-Yu , Zhang Qing-Jie
Published: March 2017

Crystalline and stoichiometric YbAl3 thin films with high electrical conductivity and high power factors were prepared by a co-sputtering technique and subsequent annealing treatment.
Enhancement in efficiency and optoelectronic quality of perovskite thin films annealed in MACl vapor
Authors: Khadka Dhruba B. , Shirai Yasuhiro , Yanagida Masatoshi , Masuda Takuya , Miyano Kenjiro
Published: March 2017

We analyzed and compared quantitatively the optoelectronic characteristics of perovskite PV devices with and without annealing the perovskite layer in a methyl ammonium chloride vapor atmosphere (MACl treatment).
Solution processing of air-stable molecular semiconducting iodosalts, Cs2SnI6−xBrx, for potential solar cell applications
Authors: Lee Byunghong , Krenselewski Anthony , Baik Sung Il , Seidman David N. , Chang Robert P. H.
Published: March 2017

An effort to develop a new class of air-stable tin-based molecular semiconducting iodosalts for solar cell application.
Silica-based nanoparticles for therapeutic protein delivery
Authors: Yu Meihua , Gu Zhengying , Ottewell Thomas , Yu Chengzhong
Published: March 2017

This review focuses on recent advances in silica-based nanoparticles (SiNPs) as therapeutic protein carriers for disease and cancer treatment.
The G2385R risk factor for Parkinson's disease enhances CHIP-dependent intracellular degradation of LRRK2
Authors: Rudenko Iakov N. , Kaganovich Alice , Langston Rebekah G. , Beilina Aleksandra , Ndukwe Kelechi , Kumaran Ravindran , Dillman Allissa A. , Chia Ruth , Cookson Mark R.
Published: March 2017

Autosomal dominant mutations in leucine-rich repeat kinase 2 (LRRK2) are associated with Parkinson's disease (PD). Most pathogenic LRRK2 mutations result in amino acid substitutions in the central ROC (Ras of complex proteins)–C-terminus of ROC–kinase triple domain and affect enzymatic functions of the protein. However, there are several variants in LRRK2, including the risk factor G2385R, that affect PD pathogenesis by unknown mechanisms. Previously, we have shown that G2385R LRRK2 has decreased kinase activity in vitro and altered affinity to LRRK2 interactors. Specifically, we found an increased binding to the chaperone Hsp90 (heat shock protein 90 kDa) that is known to stabilize LRRK2, suggesting that G2385R may have structural effects on LRRK2. In the present study, we further explored the effects of G2385R on LRRK2 in cells. We found that G2385R LRRK2 has lower steady-state intracellular protein levels compared with wild-type LRRK2 due to increased protein turnover of the mutant protein. Mechanistically, this is a consequence of a higher affinity of G2385R compared with the wild-type protein for two proteins involved in proteasomal degradation, Hsc70 and carboxyl-terminus of Hsc70-interacting protein (CHIP). Overexpression of CHIP decreased intracellular protein levels of both G2385R mutant and wild-type LRRK2, while short interfering RNA CHIP knockdown had the opposite effect. We suggest that the G2385R substitution tilts the equilibrium between refolding and proteasomal degradation toward intracellular degradation. The observation of lower steady-state protein levels may explain why G2385R is a risk factor rather than a penetrant variant for inherited PD.
Comments on ‘Finite‐time consensus of multi‐agent system via non‐linear event‐triggered control strategy’
Authors: Yu Shuanghe , Wang Yilin , Jin Lina
Published: March 2017

An event‐triggered protocol is recently developed to achieve finite‐time consensus in the commented paper. Although the Zeno behaviour is excluded by the lower‐bounded inter‐event time in Theorem 2, the misuse of Lemma 1 leads to the doubtful result in the proof. Through theoretical analysis and numerical simulation, this letter reveals that the Zeno behaviour is unavoidable under the protocol when approaching consensus in finite time. Furthermore, an alternative trigger function is presented to achieve practical consensus.
The XXL Survey
Authors: Butler Andrew , Huynh Minh , Delhaize Jacinta , Smolčić Vernesa , Kapińska Anna , Milaković Dinko , Novak Mladen , Baran Nikola , O'Brien Andrew , Chiappetti Lucio , Desai Shantanu , Fotopoulou Sotiria , Horellou Cathy , Lidman Chris , Pierre Marguerite
Published: March 2017

The 2.1 GHz radio source catalogue of the 25 deg2ultimate XMM extragalactic survey south (XXL-S) field, observed with the Australia Telescope Compact Array (ATCA), is presented. The final radio mosaic achieved a resolution of ~ 4.8″ and a median rms noise ofσ≈ 41μJy/beam. To date, this is the largest area radio survey to reach this flux density level. A total of 6350 radio components above 5σare included in the component catalogue, 26.4% of which are resolved. Of these components, 111 were merged together to create 48 multiple-component radio sources, resulting in a total of 6287 radio sources in the source catalogue, 25.9% of which were resolved. A survival analysis revealed that the median spectral index of the Sydney University Molonglo Sky Survey (SUMSS) 843 MHz sources in the field isα= −0.75, consistent with the values of − 0.7 to − 0.8 commonly used to characterise radio spectral energy distributions of active galactic nuclei. The 2.1 GHz and 1.4 GHz differential radio source counts are presented and compared to other 1.4 GHz radio surveys. The XXL-S source counts show good agreement with the other surveys.
Unilateral problems for thep-Laplace operator in perforated media involving large parameters
Authors: Gómez Delfina , Lobo Miguel , Pérez Eugenia , Podolskii Alexander V. , Shaposhnikova Tatiana A.
Published: March 2017

We address homogenization problems for variational inequalities issue from unilateral constraints for thep-Laplacian posed in perforated domains of ℝn, with n ≥ 3 andp ∈ [2,n]. εis a small parameter which measures the periodicity of the structure while aε≪εmeasures the size of the perforations. We impose constraints for solutions and their fluxes (associated with thep-Laplacian) on the boundary of the perforations. These constraints imply that the solution is positive and that the flux is bounded from above by a negative, nonlinear monotonic function of the solution multiplied by a parameter βεwhich may be very large, namely, βε → ∞asε→ 0. We first consider the case where p < nand the domains periodically perforated by tiny balls and we obtain homogenized problems depending on the relations between the different parameters of the problem:p,n,ε, aεandβε. Critical relations for parameters are obtained which mark important changes in the behavior of the solutions. Correctors which provide improved convergence are also computed. Then, we extend the results for p = nand the case of non periodically distributed isoperimetric perforations. We make it clear that in the averaged constants of the problem, the perimeter of the perforations appears for any shape.
Chemical Protein Synthesis through Selenocysteine Chemistry
Authors: Metanis Norman , Mousa Reem , Reddy Post
Published: March 2017

Methods for the preparation of small-to-medium-sized proteins by chemical protein synthesis have matured in recent years and proven valuable for protein science. Thanks to the many recent discoveries and developments in the field, proteins up to 300 amino acids can now be prepared in the lab in a matter of days. This technology gives the scientists the flexibility to substitute any atom in the protein sequence; hence synthesis is not constrained to the 20 canonical amino acids. In this Synpacts article we briefly highlight the recent studies on selenocysteine chemistry in the field of chemical protein synthesis.

1 Introduction

2 Selenocysteine in Nature and in Folding Studies

3 Selenocysteine in Protein Synthesis

4 Selenocysteine in Natural Selenoproteins

5 Outlook
Variations in Infant CYP2B6 Genotype Associated with the Need for Pharmacological Treatment for Neonatal Abstinence Syndrome in Infants of Methadone-Maintained Opioid-Dependent Mothers
Authors: McLaughlin Poppy , Gillis Cheryl , Osselton Michael , Mactier Helen
Published: March 2017

Background Neonatal abstinence syndrome (NAS) in infants of methadone-maintained opioid-dependent (MMOD) mothers cannot be predicted in individual cases. We investigated whether variation in infant genotype is associated with severity of NAS.

Methods This is a pilot observational cohort study of 21 MMOD mothers and their newborns. Infant buccal swabs were obtained soon after delivery, together with a maternal blood sample for the determination of maternal plasma methadone concentration. Genomic variation in five opioid-related genes (ABCB1, COMT, CYP2B6, CYP2D6, and OPRM1) was ascertained from infant buccal swabs and related to need for pharmacological treatment of NAS.

Results Out of 21 infants, 11 (52%) required treatment for NAS. Mothers of treated infants tended to have been prescribed higher doses of methadone, but plasma methadone concentrations did not differ between mothers of treated or untreated babies. Treated and untreated babies did not differ in terms of method of feeding. Treated infants were more likely to carry the normal (homozygous) allele at 516 and 785 regions of CYP2B6 gene (p = 0.015 and 0.023, respectively). There were no differences in any other genes between infants who did or did not require treatment for NAS.

Conclusion Genomic variation in CYP2B6 may explain, at least in part, severity of NAS.
Redefinition of Atypical Parkinsonian Syndromes
Authors: Respondek G. , Levin J. , Höglinger G.
Published: March 2017

The definition of atypical parkinsonian syndromes is undergoing a change. The umbrella concept of atypical parkinsonian syndromes includes diseases with different underlying pathologies. These are, on the one hand, multiple system atrophy (MSA) and dementia with Lewy bodies (DLB), both of which are characterized by intracellular aggregates of the protein alpha-synuclein, and on the other hand, corticobasal degeneration (CBD) and progressive supranuclear palsy (PSP), which are characterized by aggregates of the protein tau. The current syndrome-based classification of these diseases no longer meets current requirements since 1) numerous clinico-pathological studies have shown that the clinical syndromes do not always coincide with the molecular-pathological diagnosis, 2) a clinical parkinsonian syndrome is sometimes not even present in patients with a pathological diagnosis of an atypical parkinsonian syndrome, and 3) current therapeutic trials that intervene in the molecular disease mechanisms require no symptom-oriented, but a pathogenetically oriented diagnosis. The early and correct prediction of the underlying molecular pathology as a prerequisite for a causative therapy therefore presents a challenge that the old disease concept is no longer capable of meeting.
Cardiac Arrhythmia following Stroke
Authors: Kallmünzer Bernd , Schwab Stefan
Published: March 2017

One in 4 patients with acute stroke suffers from clinically relevant cardiac arrhythmia that may complicate the clinical course by hemodynamic instability, limit the success of rehabilitative care and increase the risk of stroke recurrence. A structured analysis of the continuous ECG recordings at the stroke unit can double the detection rate of paroxysmal atrial fibrillation compared to conventional monitoring. In case of suspected cardiac arrhythmia, ambulatory long-term heart rhythm monitoring is available for patients with stroke of unknown cause. Apart from the emergency management of arrhythmia, different aspects of the antithrombotic treatment for secondary prevention are of major therapeutic relevance and represent clinical challenges for the neurologist.
A Shakespeare of one’s own: female users of playbooks from the seventeenth to the mid-eighteenth century
Authors: Sae Kitamura
Published: March 2017

The aim of this article is to understand women’s intellectual activities involving Shakespeare’s playbooks by analysing their various book-related activities, such as annotating, editing, signing and attaching ex libris to books. Although researchers have increasingly recognized women’s participation in the canonization of Shakespeare, ex libris and book users’ signatures, unlike other resources, have not been systematically studied in relation to gender. Discreet observations and evaluations, typified by reading, are rarely appreciated as a participatory or creative process. However, it is hoped that this study focusing on women’s use of Shakespeare’s playbooks will give a voice to these seemingly quiet interpreters. For primary sources, more than 800 pre-1769 copies of Shakespeare’s playbooks held in major libraries throughout the world, including the British Library and Folger Shakespeare Library, were consulted. This research shows that women were actively involved in book-related activities; for example, they exchanged Shakespeare’s playbooks as gifts and preserved rare copies as family treasures. Some female readers even annotated Shakespeare’s works earlier than believed, approximately 40 years before the publication of Harriet Bowdler’s The Family Shakespeare in 1807. This article is published as part of a collection to commemorate the 400th anniversary of Shakespeare’s death.
Efficient noble metal nanocatalysts supported on HfC(001) for O2 dissociation
Authors: Wang Shiyan , Zhang Xilin , Zhang Yanxing , Mao Jianjun , Yang Zongxian
Published: March 2017

The adsorption and dissociation of O2 on the M4 (M=Au, Pd, Pt) clusters supported on HfC(001) (Hafnium Carbide) are investigated using ab initio density functional theory calculations. The geometric and electronic structures are analyzed in detail. It is found that the dissociation barriers of O2 on Au4/HfC(001) (0.26 eV), Pd4/HfC(001) (0.49 eV) and Pt4/HfC(001) (0.09 eV) are much smaller than those on the clean surfaces of HfC(001) (1.60 eV), Au(111) (1.37 eV), Pd(111) (1.0 and 0.91 eV) and Pt(111) (0.27–0.7 eV), respectively. The low dissociation barriers imply that the Pt4/HfC(001) exhibits the highest catalytic activity for O2 dissociation, and the Au4/HfC(001) and Pd4/HfC(001) may also be possible substitutes with lower cost for the current Pt/C catalyst for O2 dissociation. The present study is conductive to designing new efficient noble metal catalyst using HfC support for efficiently promoting O2 dissociation.
The attachment of α-synuclein to a fiber: A coarse-grain approach
Authors: Ilie Ioana M. , den Otter Wouter K. , Briels Wim J.
Published: March 2017

We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson’s disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet. Flexible linkers between the particles enable sampling of the tertiary structure. This novel model is applied here to study the growth of an amyloid fibril, by calculating the free energy profile of a protein attaching to the end of a fibril. The simulation results suggest that the attaching protein readily becomes trapped in a mis-folded state, thereby inhibiting further growth of the fibril until the protein has readjusted to conform to the fibril structure, in line with experimental findings and previous simulations on small fragments of other proteins.
Scanning tunneling microscopy study of thin PTCDI films on Ag/Si(111)-√3 × √3
Authors: Emanuelsson C. , Zhang H. M. , Moons E. , Johansson L. S. O.
Published: March 2017

3,4,9,10-perylene tetracarboxylic diimide molecules were evaporated onto a Ag/Si(111)-√3 × √3 surface and studied by scanning tunneling microscopy/spectroscopy and low energy electron diffraction (LEED). The growth mode was characterized as layer-by-layer growth with a single molecular unit cell in a short range order. The growth of the first two monolayers involves a molecule/substrate superstructure and a molecule/molecule superstructure. At higher coverages, the molecules in each layer were found to align so that unit cells are on top of each other. The experimentally obtained LEED pattern is described as a combination of patterns from the molecular unit cell and the molecule/substrate superstructure. The electronic structure was found to be strongly dependent on the film thickness for the first few layers: Several extra states are found at low coverages compared to higher coverages resulting in a very small pseudo gap of 0.9 eV for the first layer, which widens up to 4.0 eV for thicker films.
Localization crossover and phase coherent electron transport in a-InGaZnO4 thin films
Authors: Mukherjee Joynarayan , Ramachandra Rao M. S.
Published: March 2017

Electrical and magnetotransport properties have been studied on pulsed laser deposition grown amorphous InGaZnO4 thin films exhibiting different disorder. A crossover from strong to weak localization was observed as disorder (quantified by a parameter kfl) decreases. The sample with kfl value 0.04 showed strong localization behavior whereas for the sample with kfl > 1, electron transport is governed by weak localization. The samples with kfl > 1 showed negative magnetoresistance (MR) because of the suppression of weak localization. From the MR study, we estimated the phase coherence length which scales with temperature as T−3∕4. The maximum phase coherence length was found to be 130 nm at 5 K for the sample with kfl = 1.71 and this can significantly influence the spintronic research in amorphous semiconductors.
Heterodyne technique in photoinduced force microscopy with photothermal effect
Authors: Yamanishi J. , Naitoh Y. , Li Y. J. , Sugawara Y.
Published: March 2017

The heterodyne technique is used to detect short-range forces. Using the heterodyne technique, we demonstrate photoinduced force microscopy (PiFM) imaging and z-spectroscopy without the artifact of photothermal vibration. The rejection ratio was at least 99.975% under a high-scattering condition. In addition, the heterodyne technique employs the optimal amplitude at the first resonance frequency of the cantilever to detect the photoinduced force sensitively. According to our calculation, the optimal ratio of the amplitude to the distance between the dipole of the tip and that of the sample is 0.4448. The heterodyne technique can be employed to perform PiFM without the artifact by using the optimal amplitude.
Martensitic transformation and phase diagram in ternary Co-V-Ga Heusler alloys
Authors: Xu Xiao , Nagashima Akihide , Nagasako Makoto , Omori Toshihiro , Kanomata Takeshi , Kainuma Ryosuke
Published: March 2017

We report the martensitic transformation behavior in Co-V-Ga Heusler alloys. Thermoanalysis and thermomagnetization measurements were conducted to observe the martensitic transformation. By using a transmission electron microscope and an in situ X-ray diffractometer, martensitic transformation was found to occur from the L21 Heusler parent phase to the D022 martensite phase. Phase diagrams were determined for two pseudo-binary sections where martensitic transformation was detected. Magnetic properties, including the Curie temperatures and spontaneous magnetization of the parent phase, were also investigated. The magnetic properties showing behaviors different from those of NiMn-based alloys were found.
Intrinsic flux pinning mechanisms in different thickness MgB2 films
Authors: Yang C. , Ni Z. M. , Guo X. , Hu H. , Wang Y. , Zhang Y. , Feng Q. R. , Gan Z. Z.
Published: March 2017

MgB2 films in four thickness (60 nm, 200nm, 600nm and 1μm) have been fabricated by hybrid physical–chemical vapor deposition technique (HPCVD). By measuring the magnetization hysteresis loops and the resistivity, we have obtained the transport and magnetic properties of the four films. After that, the pinning mechanisms in them were discussed. Comparing the pinning behaviors in these ultrathin films, thin films and thick films, it was found that there exist different pinning types in MgB2 films of different thickness. In combination with the study of the surface morphology, cross-section and XRD results, we concluded that MgB2 films had different growth modes in different growth stages. For thin films, films grew along c axis, and grain boundaries acted as surface pinning. While for thick films, films grew along c axis at first, and then changed to a-b axis growth. As a result, the a-b axis grains acted as strong volume pinning.
SPECTROSCOPIC STUDIES OF EXCHANGE INTERACTIONS IN
POLYNUCLEAR TRANSITION METAL COMPLEXES II. [(NH3)5Cr(OH)Cr(NH3)5] Cl5,3H20.
Authors: Ferguson J , Gudel H.U , Puza M
Published: March 2017

Single crystals of phydroxo-bis[pentaamminechromium(III)] chloride monohydrate
have been prepared. The spectroscopic properties of these crystals have been
measured and two crystal forms have been characterized. The first form is obtained
from solutions at 2�C and it changes to the second, stable form, at room temperature.
The latter is tetragonal, space group D44-P41212 with a = 16.28 %L, c = 14.84 A, and
Z = 8. The spectroscopic properties require two inequivalent sets of dimer units in the
unit cell and this result is consistent with the X-ray data. The spectroscopic properties
of the first form require four inequivalent sets of dimers and the ground state energy
levels of each of these are described by the isotropic Hamiltonian
H = JSa . Sb - j(Sa. Sb)2
with the following values: set 1, J = 30.4+/- 0.2, j = 0.32+/-0. 10; set 2, J = 30.4
+/-0.2, j = 0.221 0.10; set 3, J = 31.4 +/-0.2, j = 0-18+/- 0.10; set 4, J = 31-4+/- 0.4,
j = 0.0+/- 0.20. High-resolution luminescence excitation spectroscopy shows that
sets 1 and 2 are not strongly coupled to sets 3 and 4. The small differences between
sets 1 and 2 and between sets 3 and 4 suggest that these differences arise from structural
disorder within the two inequivalent sets of the room temperature stable form.
Previous differences in the interpretation of the earlier magnetic and
Microorganism profile, fermentation quality and rumen digestibility in vitro of maize-stalk silages produced at different maturity stages
Authors: Zhang Miao , Wang Yanping , Tan Zhongfang , Li Zongwei , Li Ya , Lv Haoxin , Zhang Bei , Jin Qingsheng
Published: March 2017

This study aimed to investigate the microorganism profile, fermentation quality and rumen digestibility in vitro of maize-stalk silage at different maturity stages. Maize-stalk samples were harvested at the stages milk-ripe, dough, fully ripe, and fully ripe exposed to air for 3 or 10 days. Silage pH, ammonia-N and chemical composition were measured. Thirteen representative lactic acid bacteria (LAB) strains isolated from the raw materials were categorised into five profile clusters: Leuconostoc citreum (23.1%), Weissella paramesenteroides (15.4%), Lactococcus garvieae (23.1%), Enterococcus faecalis (7.7%), and Lactobacillus paraplantarum (30.8%). The total LAB numbers in silages with raw materials reaped at the stages milk-ripe, dough, fully ripe, and fully ripe exposed to air for 3 or 10 days, respectively, were approximately 8, 6, 10, 3.5 and 10 log CFU g–1. The dominant LAB types of maize-stalk silage at different stages were all different. The epiphytic pathogens Escherichia coli, aerobic bacteria, filamentous fungi and Saccharomycetes were found in silages of all stages. There were significant differences (P < 0.001) in crude protein, ether extract, dry matter, acid detergent fibre and organic matter of silage at different stages; however, no significant difference (P > 0.05) was observed in dry matter digestibility after 24 h of fermentation in vitro, with NH3-N varying from 0.7 ± 0.1 to 1.7 ± 0.3 mg L–1.
Hacking nature: genetic tools for reprograming enzymes
Authors: Hartley Carol J , Wilding Matthew , Scott Colin
Published: March 2017

Enzymes have many modern industrial applications, from biomass decomposition in the production of biofuels to highly stereospecific biotransformations in pharmaceutical manufacture. The capacity to find or engineer enzymes with activities pertinent to specific applications has been essential for the growth of a multibillion dollar enzyme industry. Over the course of the past 50–60 years our capacity to address this issue has become increasingly sophisticated, supported by innumerable advances, from early discoveries such as the co-linearity of DNA and protein sequence1 to modern computational technologies for enzyme design. The design of enzyme function is an exciting nexus of fundamental biochemical understanding and applied engineering. Herein, we will cover some of the methods used in discovery and design, including some ‘next generation’ tools.
Spatial patterns of road mortality of medium–large mammals in Mato Grosso do Sul, Brazil
Authors: Ascensão Fernando , Desbiez Arnaud L. J. , Medici Emília P. , Bager Alex
Published: March 2017

Context Brazil has one of the richest biodiversity and one of the most extensive road networks in the world. Several negative impacts emerge from this interaction, including wildlife–vehicle collisions (WVC), which may represent a significant source of non-natural mortality in several species. The understanding of the main drivers of WVC is, therefore, crucial to improve the safe coexistence between human needs (transportation of goods and people) and animal populations. Aims We aimed to (1) evaluate the relative influence of land-cover patterns on the distribution of WVC, (2) assess whether WVCs are clustered forming hotspots of mortality, and, if so, (3) evaluate the benefits of mitigating only hotspot sections. Methods We collected WVC data involving medium–large mammals (4–260kg) along three road transects (920km), fortnightly over 1 year (n=1006 records). We used boosted regression trees to relate the WVC locations with a set of environmental variables including a roadkill index, reflecting overall habitat suitability and landscape connectivity, while accounting for spatial autocorrelation effects. We identified hotspots of mortality using Ripley’s K statistic and testing whether data follow a random Poisson distribution correcting for Type I error. Key results We found a strong association between WVC probability and roadkill index for all focal species. Distance to riparian areas, tree cover, terrain ruggedness and distance to urban areas were also important predictors, although to a lesser extent. We detected 21 hotspots of mortality, yet with little spatial overlapping as only four road sections (2%) were classified as hotspot for more than one species. Conclusions Our results supported that WVC mainly occur in road sections traversing areas with more abundant and diverse mammal communities. Hotspots of mortality may provide important information to prioritise road sections for mitigation, but this should be used in complement with roadkill indexes accounting for overall mortality. Implications The results support focusing on hotspots and habitat quality and landscape connectivity for a better assessment of road mortality. At the local scale, a larger number and improved road passages with exclusionary fencing of appropriate mesh size in riparian areas may provide safe crossings for many species and constitute a promising mitigation measure.
Development of the discourse marker kulentey (‘but, by the way’) in Korean
Authors: Sohn Sung-Ock S.
Published: March 2017

This study examines the diachronic and synchronic development of the discourse marker kulentey (‘but, by the way’). Etymologically, having derived from the sequence of the deictic predicate and the clause-final suffix –nuntey (‘but, in the circumstance that’), kulentey is frequently used as a turn-initiator in spoken discourse. While each source form of kulentey is attested in the earliest text written in Korean (fifteenth century), the form itself is found only in early-twentieth-century texts. The development of kulentey at peripheries shows unique features in terms of discourse functions and prosody. There exists a functional asymmetry between the left and the right peripheral kulentey. Prosodically, LP kulentey forms a salient disjuncture, while the RP kulentey is integrated into the preceding element. Using both written and spoken corpora, this study investigates the emergence and development of kulentey at peripheries, and its interaction with prosody.
Robustness and Independent Evidence
Authors: Stegenga Jacob , Menon Tarun
Published: March 2017

Robustness arguments hold that hypotheses are more likely to be true when they are confirmed by diverse kinds of evidence. Robustness arguments require the confirming evidence to be independent. We identify two kinds of independence appealed to in robustness arguments: ontic independence (OI)—when the multiple lines of evidence depend on different materials, assumptions, or theories—and probabilistic independence. Many assume that OI is sufficient for a robustness argument to be warranted. However, we argue that, as typically construed, OI is not a sufficient independence condition for warranting robustness arguments. We show that OI evidence can collectively confirm a hypothesis to a lower degree than individual lines of evidence, contrary to the standard assumption undergirding usual robustness arguments. We employ Bayesian networks to represent the ideal empirical scenario for a robustness argument and a variety of ways in which empirical scenarios can fall short of this ideal.
Inequalities and monotonicity results for zeros of modified Bessel functions of purely imaginary order
Authors: Laforgia Andrea
Published: March 2017

Let

x
k

(
v
)

{x_k}\left ( v \right )

and

x
k
′

(
v
)

{x’_k}\left ( v \right )

denote the

k
k

th positive zeros, in decreasing order, of the modified Bessel function

K

i
v

(
x
)

{K_{iv}}\left ( x \right )

of purely imaginary order and of its derivative

K

i
v

′

(
x
)

=

d

d
x

K

i
v

(
x
)

{K’_{iv}}\left ( x \right ) = {\textstyle {d \over {dx}}}{K_{iv}}\left ( x \right )

, respectively. We show that for

k
=
1
,
2
,
.
.
.

k = 1,2,...

and

0
>
v
>
∞
,

x
k

(
v
)

>

x
k
′

(
v
)

>
v

0 > v > \infty ,{x_k}\left ( v \right ) > {x’_k}\left ( v \right ) > v

and

x
k

(
v
)

/

x

k
+
1

(
v
)

{x_k}\left ( v \right )/{x_{k + 1}}\left ( v \right )

and

x
k

(
v
)

−

x

k
+
1

(
v
)

{x_k}\left ( v \right ) - {x_{k + 1}}\left ( v \right )

decrease as

k
k

increases. Some related results are mentioned for the zeros of

K

i
v

′

(
x
)

{K’_{iv}}\left ( x \right )

and the chain of inequalities
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartAbsoluteValue upper K Subscript i v Baseline left-parenthesis x prime Subscript 1 Baseline left-parenthesis v right-parenthesis right-parenthesis EndAbsoluteValue greater-than StartAbsoluteValue upper K Subscript i v Baseline left-parenthesis x prime Subscript 2 Baseline left-parenthesis v right-parenthesis right-parenthesis EndAbsoluteValue greater-than dot dot dot greater-than StartAbsoluteValue upper K Subscript i v Baseline left-parenthesis x prime Subscript n Baseline left-parenthesis v right-parenthesis right-parenthesis EndAbsoluteValue greater-than StartAbsoluteValue upper K Subscript i v Baseline left-parenthesis x prime Subscript n plus 1 Baseline left-parenthesis v right-parenthesis right-parenthesis EndAbsoluteValue greater-than dot dot dot">

|

K

i
v

(

x
′

1

(
v
)

)

|

>

|

K

i
v

(

x
′

2

(
v
)

)

|

>
⋅
⋅
⋅
>

|

K

i
v

(

x
′

n

(
v
)

)

|

>

|

K

i
v

(

x
′

n
+
1

(
v
)

)

|

>
⋅
⋅
⋅

\left | {{K_{iv}}\left ( {{{x’}_1}\left ( v \right )} \right )} \right | > \left | {{K_{iv}}\left ( {{{x’}_2}\left ( v \right )} \right )} \right | > \cdot \cdot \cdot > \left | {{K_{iv}}\left ( {{{x’}_n}\left ( v \right )} \right )} \right | > \left | {{K_{iv}}\left ( {{{x’}_{n + 1}}\left ( v \right )} \right )} \right | > \cdot \cdot \cdot

is established.
ViPTree: the viral proteomic tree server
Authors: Nishimura Yosuke , Yoshida Takashi , Kuronishi Megumi , Uehara Hideya , Ogata Hiroyuki , Goto Susumu
Published: March 2017

ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. ViPTree also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes.

Availability and Implementation

ViPTree is freely available at: http://www.genome.jp/viptree.

Supplementary information

Supplementary data are available at Bioinformatics online.
CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets
Authors: Flobak Åsmund , Vazquez Miguel , Lægreid Astrid , Valencia Alfonso
Published: March 2017

Motivation

Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required.

Results

CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships.

Availability and Implementation

CImbinator is written in Ruby and R. It uses the R package drc for advanced drug response modeling. CImbinator is available at http://cimbinator.bioinfo.cnio.es, the source-code is open and available at https://github.com/Rbbt-Workflows/combination_index. A Docker image is also available at https://hub.docker.com/r/mikisvaz/rbbt-ci_mbinator/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Effector Gene Suites in Some Soil Isolates of Fusarium oxysporum Are Not Sufficient Predictors of Vascular Wilt in Tomato
Authors: Jelinski Nicolas A. , Broz Karen , Jonkers Wilfried , Ma Li-Jun , Kistler H. Corby
Published: March 2017

Seventy-four Fusarium oxysporum soil isolates were assayed for known effector genes present in an F. oxysporum f. sp. lycopersici race 3 tomato wilt strain (FOL MN-25) obtained from the same fields in Manatee County, Florida. Based on the presence or absence of these genes, four haplotypes were defined, two of which represented 96% of the surveyed isolates. These two most common effector haplotypes contained either all or none of the assayed race 3 effector genes. We hypothesized that soil isolates with all surveyed effector genes, similar to FOL MN-25, would be pathogenic toward tomato, whereas isolates lacking all effectors would be nonpathogenic. However, inoculation experiments revealed that presence of the effector genes alone was not sufficient to ensure pathogenicity on tomato. Interestingly, a nonpathogenic isolate containing the full suite of unmutated effector genes (FOS 4-4) appears to have undergone a chromosomal rearrangement yet remains vegetatively compatible with FOL MN-25. These observations confirm the highly dynamic nature of the F. oxysporum genome and support the conclusion that pathogenesis among free-living populations of F. oxysporum is a complex process. Therefore, the presence of effector genes alone may not be an accurate predictor of pathogenicity among soil isolates of F. oxysporum.
Passive leg raising for assessment of volume responsiveness: a review
Authors: Mesquida Jaume , Gruartmoner Guillem , Ferrer Ricard
Published: March 2017

Purpose of review

To evaluate the existing evidence on the passive leg raising (PLR) test for fluid responsiveness prediction.

Recent findings

It has been well established that either insufficient or excessive fluid administration derives in worse outcomes in critically ill patients, highlighting that a more accurate assessment of fluid management is required. Accordingly, several cardiovascular indices have been tested to improve our ability to predict patients’ response to fluid loading at the bedside, the so-called functional hemodynamic monitoring. The standardized PLR is a relatively novel maneuver that, over the past 10 years, has repeatedly demonstrated high sensitivity and specificity for fluid responsiveness prediction.

The current review underlines that PLR is an easy-to-perform and reliable method to assess fluid responsiveness. Its excellent performance is maintained even in many situations in which other dynamic predictive indices are not consistent and represents a valid alternative to the fluid challenge to avoid unnecessary volume administration.
A new (multi-reference configuration interaction) potential energy surface for H
2
CO and preliminary studies of roaming
Authors: Wang Xiaohong , Houston Paul L. , Bowman Joel M.
Published: March 2017

We report a new global potential energy surface (PES) for H
2
CO, based on precise fitting of roughly 67 000 MRCI/cc-pVTZ energies. This PES describes the global minimum, the
cis
- and
trans
-HCOH isomers, and barriers relevant to isomerization, formation of the molecular (H
2
+CO) and radical (H+HCO) products, and the loose so-called roaming transition-state saddle point. The key features of the PES are reviewed and compared with a previous PES, denoted by PES04, based on five local fits that are ‘stitched’ together by switching functions (Zhang
et al.
2004
J. Phys. Chem. A
108
, 8980–8986 (
doi:10.1021/jp048339l
)). Preliminary quasi-classical trajectory calculations are performed at the total energy of 36 233 cm
−1
(103 kcal mol
−1
), relative to the H
2
CO global minimum, using the new PES, with a particular focus on roaming dynamics. When compared with the results from PES04, the new PES findings show similar rotational distributions, somewhat more roaming and substantially higher H
2
vibrational excitation.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies
Authors: Simon A. , Rapacioli M. , Rouaut G. , Trinquier G. , Gadéa F. X.
Published: March 2017

We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC–DFTB) level of theory. The SCC–DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene

, pyrene

and coronene

at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and
C
2
H
2
(recognized as the ethyne molecule) were identified as major dissociation channels. The H/C
2
H
2
ratio was found to increase with PAH size and to decrease with energy. For

, which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Insights into the deactivation of 5-bromouracil after ultraviolet excitation
Authors: Peccati Francesca , Mai Sebastian , González Leticia
Published: March 2017

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright
ππ
* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C–Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the
1
n
O
π
* and
3
ππ
* states.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching
Authors: Glowacki David R. , Rodgers W. J. , Shannon Robin , Robertson Struan H. , Harvey Jeremy N.
Published: March 2017

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level
ab initio
electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH
3
does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Development of optical choppers for time-resolved measurements at soft X-ray synchrotron radiation beamlines
Authors: Osawa Hitoshi , Ohkochi Takuo , Fujisawa Masami , Kimura Shigeru , Kinoshita Toyohiko
Published: March 2017

Two types of optical choppers for time-resolved measurements at synchrotron radiation soft X-ray beamlines have been developed. One type uses an air-spindle-type rotation mechanism with a two-stage differential pumping system to maintain the ultra-high vacuum of the X-ray beamline, and the other uses a magnetic bearing. Both can be installed at the soft X-ray beamlines at SPring-8, greatly improving the accessibility of pump-and-probe spectroscopy. The combination of X-ray chopper and pump-and-probe photoemission electron microscope at SPring-8 provides drastic improvements in signal-to-noise ratio and resolution compared with techniques using high-voltage gating of channel plate detectors. The choppers have the capability to be used not only at synchrotron radiation facilities but also at other types of soft X-ray and VUV beamlines.