bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
Authors: Pan Keyao , Kim Do-Nyun , Zhang Fei , Adendorff Matthew R. , Yan Hao , Bathe Mark 
Published: December 2014

AbstractDNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science.
Observing classical nucleation theory at work by monitoring phase transitions with molecular precision
Authors: Sleutel Mike , Lutsko Jim , Van Driessche Alexander E.S. , Durán-Olivencia Miguel A. , Maes Dominique 
Published: December 2014

AbstractIt is widely accepted that many phase transitions do not follow nucleation pathways as envisaged by the classical nucleation theory. Many substances can traverse intermediate states before arriving at the stable phase. The apparent ubiquity of multi-step nucleation has made the inverse question relevant: does multistep nucleation always dominate single-step pathways? Here we provide an explicit example of the classical nucleation mechanism for a system known to exhibit the characteristics of multi-step nucleation. Molecular resolution atomic force microscopy imaging of the two-dimensional nucleation of the protein glucose isomerase demonstrates that the interior of subcritical clusters is in the same state as the crystalline bulk phase. Our data show that despite having all the characteristics typically associated with rich phase behaviour, glucose isomerase 2D crystals are formed classically. These observations illustrate the resurfacing importance of the classical nucleation theory by re-validating some of the key assumptions that have been recently questioned.
Investigation of the sympathetic tripping problem in power systems with large penetrations of distributed generation
Authors: Jennett Kyle I. , Booth Campbell D. , Coffele Federico , Roscoe Andrew J. 
Published: December 2014

This study contains an investigation into sympathetic tripping – the undesirable disconnection of distributed generators (DGs) (in accordance with the recently‐introduced G83/2 under voltage protection) when a network fault occurs in the vicinity of the DG and is not cleared quickly enough by the network protection (i.e. before the DG's under voltage protection operates). An evaluation of the severity of and proposal of solutions to the problem of sympathetic tripping on a typical UK distribution power network is presented. An inverter model (as the majority of DGs will be inverter‐interfaced) that characterises the fault response of the inverter and its associated protection functions has been developed for use in simulation through exhaustive laboratory testing of a commercially‐available 3 kW inverter for DG application; the observed responses have been modelled and incorporated in a power system simulation package. It is shown, when using presently‐adopted DG interface and network protection settings, that the risk of sympathetic tripping is high in several future scenarios. To mitigate this risk, the impact of modifying network protection settings is evaluated. This study has two key findings – determination of the conditions at which the risk of sympathetic tripping is high and evaluation of a technique to mitigate this risk.
Ni-based nanoalloys: Towards thermally stable highly magnetic materials
Authors: Palagin Dennis , Doye Jonathan P. K. 
Published: December 2014

Molecular dynamics simulations and density functional theory calculations have been used to demonstrate the possibility of preserving high spin states of the magnetic cores within Ni-based core-shell bimetallic nanoalloys over a wide range of temperatures. We show that, unlike the case of Ni–Al clusters, Ni–Ag clusters preserve high spin states (up to 8 μB in case of Ni13Ag32 cluster) due to small hybridization between the electronic levels of two species. Intriguingly, such clusters are also able to maintain geometrical and electronic integrity of their cores at temperatures up to 1000 K (e.g., for Ni7Ag27 cluster). Furthermore, we also show the possibility of creating ordered arrays of such magnetic clusters on a suitable support by soft-landing pre-formed clusters on the surface, without introducing much disturbance in geometrical and electronic structure of the cluster. We illustrate this approach with the example of Ni13Ag38 clusters adsorbed on the Si(111)–(7×7) surface, which, having two distinctive halves to the unit cell, acts as a selective template for cluster deposition.
Bimodal regulation of ICR1 levels generates self-organizing auxin distribution
Authors: Hazak Ora , Obolski Uri , Prat Tomáš , Friml Jiří , Hadany Lilach , Yalovsky Shaul 
Published: December 2014

Significance
In nature, patterns form by self-organizing mechanisms that involve distribution of components called morphogens. In many cases, the molecular mechanisms that underlie morphogen distribution in living organisms are not well-known. In plants, a small molecule called auxin serves as a morphogen that regulates diverse developmental processes. The ability of cells to transport or accumulate auxin defines its distribution. Here, we present experimental data and theoretical modeling showing that auxin concentrations regulate the levels of a protein called INTERACTOR of CONSTITUTIVELY active ROP (RHO of Plants) 1 (ICR1), which is required for auxin transport. ICR1 expression is induced by auxin, but when auxin levels exceed a critical concentration, ICR1 is rapidly degraded, leading to auxin accumulation. Thus, auxin self-regulates its distribution by bimodal regulation of ICR1.
Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation
Authors: Rivera-Cancel Giomar , Ko Wen-huang , Tomchick Diana R. , Correa Fernando , Gardner Kevin H. 
Published: December 2014

Significance
All organisms regulate biological processes in response to changes in their environment. Bacteria often achieve this control via two-component signal transduction pathways, which use histidine kinases to perceive environmental signals and relay this information to downstream effectors. Despite substantial efforts, key aspects of the mechanisms by which histidine kinases are activated by these signals remain poorly understood. In this paper, we present structural and functional data that shed light on the signaling strategy used by a monomeric histidine kinase. Our results demonstrate the versatility of histidine kinases by expanding the prevailing view that they must form dimers to function, while also highlighting conserved aspects of their signaling strategies.
Constitutively active Notch4 receptor elicits brain arteriovenous malformations through enlargement of capillary-like vessels
Authors: Murphy Patrick A. , Kim Tyson N. , Huang Lawrence , Nielsen Corinne M. , Lawton Michael T. , Adams Ralf H. , Schaffer Chris B. , Wang Rong A. 
Published: December 2014

SignificanceBrain arteriovenous malformations are focal lesions of enlarged, tangled vessels that shunt blood from arteries directly to veins. They can cause ischemia, hemorrhage, disability, and death, particularly in young people, accounting for 50% of childhood stroke. The molecular etiology of the disease remains poorly understood, hindering the development of therapeutic treatments. Here, we report that, in an animal model, the lesion arises from the enlargement of capillary-like vessels. Notch signaling in the endothelium of microvasculature and veins is critical for the disease initiation by increasing cell areas but not proliferation. Blood flow mediates disease progression by a positive feedback of increasing flow and vessel diameter. Our data shed light on the mechanism underlying the pathogenesis of this devastating disease.
Flagellated bacterial motility in polymer solutions
Authors: Martinez Vincent A. , Schwarz-Linek Jana , Reufer Mathias , Wilson Laurence G. , Morozov Alexander N. , Poon Wilson C. K. 
Published: December 2014

SignificanceThe way microorganisms swim in concentrated polymer solutions has important biomedical implications, i.e., how pathogens invade the mucosal lining of mammal guts. Physicists are also fascinated by self-propulsion in such complex non-Newtonian fluids. The current standard model of how bacteria propelled by rotary helical flagella swim through concentrated polymer solutions postulates bacteria-sized pores, allowing them relative easy passage. Our experiments using high-throughput methods overturn this standard model. Instead, we show that the peculiarities of flagellated bacteria locomotion in concentrated polymer solutions are due to the fast-rotating flagellum, giving rise to a lower local viscosity in its vicinity. The bacterial flagellum is therefore a nano-rheometer for probing flows at the molecular level.
Molecular basis of a shattering resistance boosting global dissemination of soybean
Authors: Funatsuki Hideyuki , Suzuki Masaya , Hirose Aya , Inaba Hiroki , Yamada Tetsuya , Hajika Makita , Komatsu Kunihiko , Katayama Takeshi , Sayama Takashi , Ishimoto Masao , Fujino Kaien 
Published: December 2014

SignificancePod dehiscence is a critical step in the seed dispersal (shattering) of legume and crucifer crops and can cause significant yield losses. Upon drying, pod walls are dehisced by two factors: the reduction of pod-wall binding strength and the generation of dehiscing forces. Although the previously reported shattering-resistant mutants maintained binding strength, here, we show a gene regulating the dehiscing force. The gene,Pdh1, encodes a dirigent family protein, known to be involved in lignification, which increases dehiscing forces by promoting torsion of dried pod walls. The loss-of-functionpdh1gene has been widely used as a shattering-resistance gene in soybean breeding. This knowledge could be useful in improving other legume and crucifer crops, as well as soybean breeding.
Microtubule nucleation remote from centrosomes may explain how asters span large cells
Authors: Ishihara Keisuke , Nguyen Phuong A. , Groen Aaron C. , Field Christine M. , Mitchison Timothy J. 
Published: December 2014

Significance
How the cell cytoplasm is spatially organized is of fundamental interest. In ordinary animal cells the cytoplasm is organized by a radial array of microtubules, called an aster. Aster microtubules are nucleated by the centrosome and elongate to the periphery. We investigated how asters grow in an extremely large cell, the frog egg, using microscopy of an extract system. Asters were initially nucleated at centrosomes, but then additional microtubules nucleated far from the centrosome, apparently stimulated by preexisting microtubules. The resulting growth process allows asters to scale to the size of huge egg cells while maintaining a high density of microtubules at the periphery. Microtubule-stimulated microtubule nucleation might be a general principle for organizing large cells.
HIGH-RESOLUTION H-BAND SPECTROSCOPY OF Be STARS WITH SDSS-III/APOGEE.
I. NEW Be STARS, LINE IDENTIFICATIONS, AND LINE PROFILES
Authors: Chojnowski S. Drew , Whelan David G. , Wisniewski John P. , Majewski Steven R. , Hall Matthew , Shetrone Matthew , Beaton Rachael , Burton Adam , Damke Guillermo , Eikenberry Steve , Hasselquist Sten , Holtzman Jon A. , Mészáros Szabolcs , Nidever David , Schneider Donald P. , Wilson John , Zasowski Gail , Bizyaev Dmitry , Brewington Howard , Brinkmann J. , Ebelke Garrett , Frinchaboy Peter M. , Kinemuchi Karen , Malanushenko Elena , Malanushenko Viktor , Marchante Moses , Oravetz Daniel , Pan Kaike , Simmons Audrey 
Published: December 2014

ABSTRACT
The Apache Point Observatory Galactic Evolution Experiment (APOGEE) has amassed
the largest ever collection of multi-epoch, high-resolution
(R∼22,500), H-band spectra for B-type
emission line (Be) stars. These stars were targeted by APOGEE as telluric
standard stars and subsequently identified via visual inspection as Be stars
based on H i Brackett series emission or shell absorption in addition
to otherwise smooth continua and occasionally non-hydrogen emission features.
The 128/238 APOGEE Be stars for which emission had never previously been
reported serve to increase the total number of known Be stars by ∼6%.
Because the H band is relatively unexplored compared to other
wavelength regimes, we focus here on identification of the
H-band lines and analysis of the emission peak velocity
separations (

) and emission peak intensity ratios (V/R) of the usually
double-peaked H i and non-hydrogen emission lines. H i Br11
emission is found to preferentially form in the circumstellar disks at an
average distance of ∼2.2 stellar radii. Increasing

toward the weaker Br12–Br20 lines suggests these lines
are formed interior to Br11. By contrast, the observed IR Fe ii
emission lines present evidence of having significantly larger formation radii;
distinctive phase lags between IR Fe ii and H i Brackett
emission lines further supports that these species arise from different radii in
Be disks. Several emission lines have been identified for the first time
including C i 16895, a prominent feature in the spectra for almost a
fifth of the sample and, as inferred from relatively large

compared to the Br11–Br20, a tracer of the inner regions
of Be disks. Emission lines at 15760 Å and 16781 Å remain
unidentified, but usually appear along with and always have similar line profile
morphology to Fe ii 16878. Unlike the typical metallic lines observed
for Be stars in the optical, the H-band metallic lines, such as
Fe ii 16878, never exhibit any evidence of shell absorption, even when
the H i lines are clearly shell-dominated. The first known example of a
quasi-triple-peaked Br11 line profile is reported for HD 253659, one of several
stars exhibiting intra- and/or extra-species V/R and radial velocity variation
within individual spectra. Br11 profiles are presented for all discussed stars,
as are full APOGEE spectra for a portion of the sample.
A CLOSER LOOK AT THE FLUCTUATIONS IN THE BRIGHTNESS OF SN 2009IP DURING ITS LATE 2012 ERUPTION
Authors: Martin J. C. , Hambsch F.-J. , Margutti R. , Tan T. G. , Curtis I. , Soderberg A. 
Published: December 2014

ABSTRACT
The supernova (SN) impostor SN 2009ip has re-brightened several times since its initial discovery in 2009 August. During its last outburst in late 2012 September, it reached a peak brightness of m
v
∼13.5 (M
v
brighter than −18), causing some to speculate that it had undergone a terminal core-collapse SN. Relatively high-cadence multi-wavelength photometry of the post-peak decline revealed bumps in brightness infrequently observed in other SNe IIn. These bumps occurred synchronously in all ultraviolet (UV) and optical bands with amplitudes of 0.1–0.4 mag at intervals of 10–30 days. Episodic continuum brightening and dimming in the UV and optical with these characteristics is not easily explained within the context of models that have been proposed for the late September 2012 outburst of SN 2009ip. We also present evidence that the post-peak fluctuations in brightness occur at regular intervals and raise more questions about their origin.
Some new results on differential inclusions for differential forms
Authors: Bandyopadhyay Saugata , Dacorogna Bernard , Kneuss Olivier 
Published: December 2014

In this article we study some necessary and sufficient conditions for the existence of solutions in

W

0

1
,
∞

(
Ω
;

Λ

k

)

W_{0}^{1,\infty }(\Omega ;\Lambda ^{k})

of the differential inclusion
\[

d
ω
∈
E

a.e. in
Ω

d\omega \in E\quad \text {a.e. in }\Omega

\]
where

E
⊂

Λ

k
+
1

E\subset \Lambda ^{k+1}

is a prescribed set.
Elevated Diastolic But Not Systolic Blood Pressure Increases Mortality Risk in Hypertensive But Not Normotensive Patients With Acute Ischemic Stroke
Authors: Tziomalos Konstantinos , Giampatzis Vasilios , Bouziana Stella D. , Spanou Marianna , Papadopoulou Maria , Kostaki Stavroula , Dourliou Vasiliki , Papagianni Marianthi , Savopoulos Christos , Hatzitolios Apostolos I. 
Published: December 2014

BACKGROUND
The relationship between blood pressure (BP) at admission for acute ischemic stroke and outcome is controversial. We aimed to assess whether only systolic BP (SBP), only diastolic BP (DBP), both or neither predict outcome and whether these associations differ between patients with and without a history of hypertension.

METHODS
We prospectively studied all patients who were admitted with acute ischemic stroke (n = 415; 39.5% males, age 78.8±6.6 years). The severity of stroke was assessed at admission with the National Institutes of Health Stroke Scale (NIHSS). The outcome was evaluated with dependency at discharge (modified Rankin scale between 2 and 5) and in-hospital mortality.

RESULTS
In the total study population, independent predictors of dependency at discharge were age, history of prior ischemic stroke, and NIHSS score at admission. Independent predictors of in-hospital mortality were DBP at admission and NIHSS score at admission. In patients with a history of hypertension (n = 343), independent predictors of dependency at discharge were age and NIHSS score at admission whereas independent predictors of in-hospital mortality were DBP at admission and NIHSS score at admission. In patients without a history of hypertension (n = 72), the only independent predictor of dependency at discharge and in-hospital mortality was the NIHSS score at admission.

CONCLUSIONS
Higher DBP at admission predict in-hospital mortality in patients with acute ischemic stroke whereas SBP in the acute phase is not associated with short-term outcome. The relationship between DBP at admission and outcome appears to be more prominent in hypertensive patients.
Economic incentives to target species and fish size: prices and fine-scale product attributes in Norwegian fisheries
Authors: Asche Frank , Chen Yanyou , Smith Martin D. 
Published: December 2014

Abstract
Improved fisheries management provides fishers with more opportunities to maximize harvest value by accounting for valuable attributes of the harvest such as species, harvest timing, fish size, product form, and landing location. Harvest values can also vary by vessel and gear type. Moreover, the extent of targeting can influence the ecosystem in which the fishers operate and provide important management challenges. We utilize a unique dataset containing daily vessel-level fish landings in one region of Norway in 2010 to investigate the value of an array of attributes, including species, product form, product condition, timing, fish size, vessel type, gear type, and landing location for cod and other whitefish species, as well as king crab. We also investigate to what extent landed value differs across different communities, firms, and plants. The results indicate substantial variation for all attributes, highlighting opportunities for fishers as well as potential management challenges. For whitefish, the species landed accounts for three-quarters of the variation in prices. For cod in particular, the fish size accounts for nearly all variation in prices. In these fisheries, market conditions justify management focus on the biological composition of the catch.
Deriving optimal fishing effort for managing Australia's Moreton Bay multispecies trawl fishery with aggregated effort data
Authors: Wang Na , Wang You-Gan , Courtney Anthony J. , O'Neill Michael F. 
Published: December 2014

Abstract
Deriving an estimate of optimal fishing effort or even an approximate estimate is very valuable for managing fisheries with multiple target species. The most challenging task associated with this is allocating effort to individual species when only the total effort is recorded. Spatial information on the distribution of each species within a fishery can be used to justify the allocations, but often such information is not available. To determine the long-term overall effort required to achieve maximum sustainable yield (MSY) and maximum economic yield (MEY), we consider three methods for allocating effort: (i) optimal allocation, which optimally allocates effort among target species; (ii) fixed proportions, which chooses proportions based on past catch data; and (iii) economic allocation, which splits effort based on the expected catch value of each species. Determining the overall fishing effort required to achieve these management objectives is a maximizing problem subject to constraints due to economic and social considerations. We illustrated the approaches using a case study of the Moreton Bay Prawn Trawl Fishery in Queensland (Australia). The results were consistent across the three methods. Importantly, our analysis demonstrated the optimal total effort was very sensitive to daily fishing costs—the effort ranged from 9500–11 500 to 6000–7000, 4000 and 2500 boat-days, using daily cost estimates of $0, $500, $750, and $950, respectively. The zero daily cost corresponds to the MSY, while a daily cost of $750 most closely represents the actual present fishing cost. Given the recent debate on which costs should be factored into the analyses for deriving MEY, our findings highlight the importance of including an appropriate cost function for practical management advice. The approaches developed here could be applied to other multispecies fisheries where only aggregated fishing effort data are recorded, as the literature on this type of modelling is sparse.
Pathogenicity of pan-drug-resistant Serratia marcescens harbouring blaNDM-1
Authors: Gruber Teresa M. , Göttig Stephan , Mark Laura , Christ Sara , Kempf Volkhard A. J. , Wichelhaus Thomas A. , Hamprecht Axel 
Published: December 2014

Abstract

Objectives
To characterize a pan-drug-resistant Serratia marcescens clinical isolate carrying the New Delhi metallo-β-lactamase (NDM)-1.

Methods
The presence of β-lactamase genes was examined by PCR and sequencing. Antibiotic susceptibility was determined by antibiotic gradient test. Transformation assays, transconjugation assays, PFGE and PCR-based replicon typing were used for plasmid analysis. Horizontal gene transfer was evaluated by liquid mating using Escherichia coli J53 as a recipient. Pathogenicity of NDM-1 expressing S. marcescens was analysed using the Galleria mellonella infection model.

Results
S. marcescens isolate SM1890 was non-susceptible to all tested antibiotics, with minocycline retaining intermediate activity. blaNDM-1 was located on a 140 kb IncA/C-type plasmid which was transferable to E. coli and Klebsiella pneumoniae by conjugation. The LD50 of the NDM-positive, SM1890 isolate was higher than that of other, NDM-1 negative, S. marcescens strains.

Conclusions
The presence of a blaNDM-1-harbouring IncA/C plasmid resulted in marked resistance to β-lactam antibiotics, but had no significant effect on virulence of isogenic strains. Because of the intrinsic resistance of S. marcescens to colistin and reduced susceptibility to tigecycline, treatment options for infections by NDM-1-positive isolates are extremely limited in this species.