bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncertainty quantification for Markov state models of biomolecules constructed using rare event acceleration techniques
Authors: Bhattacharya Swati , Chatterjee Abhijit
Published: January 2019

Markov state models (MSMs) of biomolecular systems are often constructed using the molecular dynamics (MD) technique. Despite having very long MD trajectories, some states and pathways can be missing in the MD data, which may make the MSMs incomplete. Consequently, uncertainty quantification for the resulting MSM becomes important. Using deca-alanine as a prototype system, we demonstrate that rare-event acceleration techniques can be employed to greatly lower the MSM uncertainty with a high computational efficiency with the assumption that the rare-event acceleration technique is able to determine most pathways that are relevant to the dynamics. In particular, we explore applications of steered MD to construct MSMs. Upper and lower bounds for uncertainty in the resulting MSM are derived. Safeguards are built into our approach to handle scenarios where the rare-event acceleration technique is unable to discover some important pathways.
Two-path self-interference in PTCDA active waveguides maps the dispersion and refraction of a single waveguide mode
Authors: Schörner C. , Neuber C. , Hildner R.
Published: January 2019

Bound waveguide modes propagating along nanostructures are of high importance since they offer low-loss energy-/signal-transport for future integrated photonic circuits. Particularly, the dispersion relation of these modes is of fundamental interest for the understanding of light propagation in waveguides as well as of light-matter interactions. However, for a bound waveguide mode, it is experimentally very challenging to determine the dispersion relation. Here, we apply a two-path interference experiment on microstructured single-mode active organic waveguides that is able to directly visualize the dispersion of the waveguide mode in energy-momentum space. Furthermore, we are able to observe the refraction of this mode at a structure edge by detecting directional interference patterns in the back-focal plane.
Charge transport mechanism of high-resistive state in RRAM based on SiOx
Authors: Gismatulin A. A. , Kruchinin V. N. , Gritsenko V. A. , Prosvirin I. P. , Yen T.-J. , Chin A.
Published: January 2019

Nonstoichiometric silicon oxide SiOx is a promising material for developing a new generation of high-speed, reliable flash memory based on the resistive effect. It is necessary to understand the electron transport mechanism of the high-resistive state in SiOx to develop a resistive memory element. At present, it is generally accepted that the charge transport of the high-resistive state in the Resistive Random Access Memory (RRAM) is described by the Frenkel effect. In our work, the charge transport of the high-resistive state in RRAM based on SiOx is analyzed with two contact-limited and five volume-limited charge transport models. It is established that the Schottky effect model, thermally assisted tunneling, the Frenkel model of Coulomb trap ionization, the Makram-Ebeid and Lannoo model of multiphonon isolated trap ionization, and the Nasyrov-Gritsenko model of phonon-assisted tunneling between traps, quantitatively, do not describe the charge transport of the high-resistive state in the RRAM based on SiOx. The Shklovskii-Efros percolation model gives a consistent explanation for the charge transport of the high-resistive state in the RRAM based on SiOx at temperatures above room temperature.
Influence of wall shear stress and geometry on the lumen surface concentration of low density lipoprotein in a model abdominal aortic aneurysm
Authors: Choudhury Satyajit , Anupindi Kameswararao , Patnaik B. S. V.
Published: January 2019

In this work, the correlation between the wall shear stress (WSS) and the surface concentration variation of low density lipoprotein (LDL) on the walls of an idealized abdominal aortic aneurysm (AAA) is explored. It is observed that on the walls of AAA, the WSS has a significant effect on the LDL deposition pattern and a region of low WSS does not always correspond to a locally high concentration of LDL. The correlation between the WSS and the LDL deposition is found to be linked to the local fluid-flow pattern. This is explained by conducting an analysis on simplified geometries using steady inflow conditions that produced a fluid-flow pattern similar to that in the original AAA under physiologically relevant pulsatile inflow conditions. Furthermore, the influence of geometric parameters, such as the height, the width, and the shape of the aneurysm, on the surface concentration of LDL is studied. The width of the aneurysm is found to have a strong influence on the variation of the LDL surface concentration.
Adjoint approach to beam optics sensitivity based on Hamiltonian particle dynamics
Authors: Antonsen Thomas M. , Chernin David , Petillo John J.
Published: January 2019

We develop a sensitivity function for the design of electron optics using an adjoint approach based on a form of reciprocity implicit in Hamilton's equations of motion. The sensitivity function, which is computed with a small number of time-reversed runs of a beam optics code, allows for the determination of the effects on specific beam quality figures of merit of small, but arbitrary changes in electrode potentials, positions, and shapes and in magnet strengths and locations. The sensitivity function can thus be used in an optimization cycle of a focusing system's design and/or to predict the sensitivity of a particular design to manufacturing, assembly, and alignment errors.
Entanglement distillation by Hong-Ou-Mandel interference with orbital angular momentum states
Authors: Ndagano B. , Forbes A.
Published: January 2019

Entanglement is an invaluable resource to various quantum communication, metrology, and computing processes. In particular, spatial entanglement has become topical, owing to its wider Hilbert space that allows photons to carry more information. However, spatial entanglement is susceptible to decay in the presence of external perturbations such as atmospheric turbulence. Here we show theoretically and experimentally that in a weak turbulence regime, maximally entangled states can be distilled through quantum interference. We generated entangled photons by spontaneous parametric down-conversion, with one photon in the entangled pairs being sent through a turbulent channel. We recombined the paths of the two photons at a beam-splitter in a Hong-Ou-Mandel interference setup and measured in coincidence, using spatial filters, the spatial correlations between photons in the output ports of the beam-splitter. We performed a state tomography and show that, from an ensemble of pure states with very low levels of entanglement, we distil entangled states with fidelities F ≥ 0.90 with respect to the singlet Bell state.
Newly discovered properties of a mixed metal oxide provide insight for catalytic applications
Authors: McCoy Berly
Published: January 2019

Scientists investigate the structural, geometric, and electronic properties of iron doping in cobalt oxide nanoislands.
Dietary calcium supplementation affects nutrient digestibility and antler-production performance during the antler-velvet growth period of male sika deer
Authors: Sun Weili , Zhao Haiping , Bao Kun , Li Chunyi , Li Guangyu
Published: January 2019

Effects of calcium (Ca) supplementation on nutrient digestibility, physiochemical characteristics and antler growth in farmed male sika deer were investigated. Eighteen sika deer (6 years old, 105.50 ± 5.05 kg) were assigned into the following three treatments where they had ad libitum access to water for 90 days: (1) control (C), basal diet containing 0.5% Ca; (2) Ca1.10, basal diet supplemented with 0.6% Ca; and (3) Ca1.70, basal diet supplemented with 1.2% Ca. The basal diet contained 0.50% Ca and 0.34% phosphorus (P). Each group consisted of the same ratio of Ca to P (provided as CaCO3 and CaHPO4). The results showed that the digestibility of dry matter (DM) and crude protein in the Ca1.70 group was lower than in the other two groups. The digestibilities of Ca, P and neutral detergent fibre in the Ca1.10 group were higher than those in the C group and Ca1.70 group (P < 0.05). Concentrations of Ca and P in faeces increased with an increasing supplementation level of Ca and the highest concentrations were observed in the Ca1.70 group (P < 0.05). There were no differences in the concentrations of parathyroid hormone, alkaline phosphatase and osteocalcin among the treatments. Testosterone and oestradiol concentrations of the Ca1.7 group were higher than those of the C and Ca1.10 groups (P < 0.05). Average daily gains of fresh antler weight and dry antler weight of the groups Ca1.10 and Ca1.70 were greater than those of the C (P < 0.05). Fresh and dry antler yields of the Ca1.10 group were higher than those of the other groups (P < 0.05). In conclusion, optimal level of Ca supplement was found to be total Ca concentration of 1.10–1.70%, on the basis of DM, which significantly increased feed digestibility and antler daily gain for the 6-year-old sika deer.
CSIRO and land research in Papua New Guinea 1950–2000: part 1: pre-Independence
Authors: Keig Gael , Hide Robin L. , Cuddy Susan M. , Buettikofer Heinz , Bellamy Jennifer A. , Bleeker Pieter , Freyne David , McAlpine John
Published: January 2019

During the period 1953–69, the Commonwealth Scientific and Industrial Research Organisation (CSIRO) conducted fourteen integrated land resource surveys in the Territory of Papua and New Guinea with the aim of identifying areas suitable for accelerated development. The resulting reconnaissance-level regional survey reports and maps provided extensive baseline information for national development planning. Related disciplinary publications expanded scientific knowledge of land resources and resource use in the wet tropics more generally. Substantial botanical collections carried out during the surveys contributed to building the Papua New Guinea (PNG) national collection at the Lae Herbarium and to the establishment of what is now the Australian National Herbarium.
Overlooked and undervalued: the neglected role of fauna and a global bias in ecological restoration assessments
Authors: Cross Sophie L. , Tomlinson Sean , Craig Michael D. , Dixon Kingsley W. , Bateman Philip W.
Published: January 2019

Globally increasing rates of mine site discontinuations are resulting in the need for immediate implementation of effective conservation and management strategies. Surveying vegetation structure is a common method of assessing restoration success; however, responses of fauna to mine site restoration remain largely overlooked and understudied despite their importance within ecosystems as ecological engineers, pollinators, and restoration facilitators. Here we review the current state of the use of fauna in assessments of mine site restoration success globally, and address biases or shortcomings that indicate the assessment approach may undershoot closure and restoration success. We identified just 101 peer-reviewed publications or book chapters over a 49-year period that assess responses of fauna to mine site restoration globally. Most studies originate in Australia, with an emphasis on just one company. Assessments favour general species diversity and richness, with a particular focus on invertebrate responses to mine site restoration. Noteworthy issues included biases towards origin of study, study type, and target taxa. Further searches of the grey literature relating to fauna monitoring in mine site restoration, which was far more difficult to access, yielded six monitoring/guidance documents, three conference proceedings, two book chapters without empirical data, and a bulletin. As with peer-reviewed publications, grey literature focussed on invertebrate responses to restoration, or mentioned fauna only at the most basic level. We emphasise the need for global re-evaluation of regulatory standards to address these major limitations in assessing the capacity of the mining industry to comprehensively and representatively restore faunal communities after mining.
Influences of light and humidity on carbonyl sulfide-based estimates of photosynthesis
Authors: Kooijmans Linda M. J. , Sun Wu , Aalto Juho , Erkkilä Kukka-Maaria , Maseyk Kadmiel , Seibt Ulrike , Vesala Timo , Mammarella Ivan , Chen Huilin
Published: January 2019

Understanding climate controls on gross primary productivity (GPP) is crucial for accurate projections of the future land carbon cycle. Major uncertainties exist due to the challenge in separating GPP and respiration from observations of the carbon dioxide (CO
2
) flux. Carbonyl sulfide (COS) has a dominant vegetative sink, and plant COS uptake is used to infer GPP through the leaf relative uptake (LRU) ratio of COS to CO
2
fluxes. However, little is known about variations of LRU under changing environmental conditions and in different phenological stages. We present COS and CO
2
fluxes and LRU of Scots pine branches measured in a boreal forest in Finland during the spring recovery and summer. We find that the diurnal dynamics of COS uptake is mainly controlled by stomatal conductance, but the leaf internal conductance could significantly limit the COS uptake during the daytime and early in the season. LRU varies with light due to the differential light responses of COS and CO
2
uptake, and with vapor pressure deficit (VPD) in the peak growing season, indicating a humidity-induced stomatal control. Our COS-based GPP estimates show that it is essential to incorporate the variability of LRU with environmental variables for accurate estimation of GPP on ecosystem, regional, and global scales.
Human coronaviruses OC43 and HKU1 bind to 9-
O
-acetylated sialic acids via a conserved receptor-binding site in spike protein domain A
Authors: Hulswit Ruben J. G. , Lang Yifei , Bakkers Mark J. G. , Li Wentao , Li Zeshi , Schouten Arie , Ophorst Bram , van Kuppeveld Frank J. M. , Boons Geert-Jan , Bosch Berend-Jan , Huizinga Eric G. , de Groot Raoul J.
Published: January 2019

Human betacoronaviruses OC43 and HKU1 are endemic respiratory pathogens and, while related, originated from independent zoonotic introductions. OC43 is in fact a host-range variant of the species
Betacoronavirus-1
, and more closely related to bovine coronavirus (BCoV)—its presumptive ancestor—and porcine hemagglutinating encephalomyelitis virus (PHEV). The β1-coronaviruses (β1CoVs) and HKU1 employ glycan-based receptors carrying 9-
O
-acetylated sialic acid (9-
O
-Ac-Sia). Receptor binding is mediated by spike protein S, the main determinant of coronavirus host specificity. For BCoV, a crystal structure for the receptor-binding domain S1
A
is available and for HKU1 a cryoelectron microscopy structure of the complete S ectodomain. However, the location of the receptor-binding site (RBS), arguably the single-most important piece of information, is unknown. Here we solved the 3.0-Å crystal structure of PHEV S1
A
. We then took a comparative structural analysis approach to map the β1CoV S RBS, using the general design of 9-
O
-Ac-Sia-binding sites as blueprint, backed-up by automated ligand docking, structure-guided mutagenesis of OC43, BCoV, and PHEV S1
A
, and infectivity assays with BCoV-S–pseudotyped vesicular stomatitis viruses. The RBS is not exclusive to OC43 and related animal viruses, but is apparently conserved and functional also in HKU1 S1
A
. The binding affinity of the HKU1 S RBS toward short sialoglycans is significantly lower than that of OC43, which we attribute to differences in local architecture and accessibility, and which may be indicative for differences between the two viruses in receptor fine-specificity. Our findings challenge reports that would map the OC43 RBS elsewhere in S1
A
and that of HKU1 in domain S1
B
.
Dynamics of geologic CO
2
storage and plume motion revealed by seismic coda waves
Authors: Zhu Tieyuan , Ajo-Franklin Jonathan , Daley Thomas M. , Marone Chris
Published: January 2019

Significance

The sequestration of CO
2
into geological formations as a strategy for reducing atmospheric greenhouse gases requires accurate monitoring of CO
2
plume for safe long-term storage. However, imaging CO
2
plume migration in the subsurface is a challenging problem for existing seismic monitoring methods. Here, we present an approach for CO
2
monitoring based on seismic coda waves and apply it to the 3-d period of CO
2
injection in a pilot experiment. We find that velocity reduction is nonlinearly correlated with the cumulative CO
2
mass inside the reservoir, and that coda waves can effectively monitor the spatiotemporal evolution of CO
2
plumes in the subsurface. Our findings suggest approaches for using seismic data in long-term monitoring of subsurface CO
2
plume evolution.
Genetically modified hematopoietic stem/progenitor cells that produce IL-10–secreting regulatory T cells
Authors: Ng Sze-Ling , Leno-Duran Ester , Samanta Dibyendu , Almo Steven C. , Strominger Jack L.
Published: January 2019

Significance

Amino acid copolymers that are used in the treatment of experimental autoimmune encephalomyelitis (EAE) in mice or multiple sclerosis (MS) in humans result in the induction of immunosuppressive IL-10–secreting regulatory T cells. The TCRs of these T cells have previously been isolated and sequenced. Introduction of these TCR into a retroviral vector was used to transduce murine hematopoietic stem/progenitor cells (HSC/HPC). These genetically modified HSC/HPC were then transplanted to create retrogenic mice. Splenocytes or T cells of these retrogenic mice produced high levels of IL-10 on appropriate stimulation, and strongly suggests that the TCR itself encodes information for IL-10 secretion. Moreover, these retrogenic mice were resistant to induction of EAE, suggesting an approach to therapy for progressive MS using genetically modified HSC/HPC for transplantation.
Dynamics of frequency-swept nuclear spin optical pumping in powdered diamond at low magnetic fields
Authors: Zangara Pablo R. , Dhomkar Siddharth , Ajoy Ashok , Liu Kristina , Nazaryan Raffi , Pagliero Daniela , Suter Dieter , Reimer Jeffrey A. , Pines Alexander , Meriles Carlos A.
Published: January 2019

Significance

We articulate theory and experimental observations to understand the dynamic polarization of
13
C spins in nitrogen vacancy (NV)-hosting diamond particles. The explored powder geometry is ideally suited to hyperpolarize fluids, as its inherently large surface-to-volume ratio is much greater than that possible in systems based on single crystals. Given the low-field magnets and low-intensity microwave and light sources we use, our technique promises to serve as a platform for low-cost, portable spin polarizers operating under ambient conditions. Alternatively, the diamond particles themselves could be exploited as background-free contrast agents for magnetic resonance imaging, a modality that builds on the biocompatibility of diamond and thus is complementary to the use of NV-hosting diamond particles as in vivo, fluorescent labels and drug delivery agents.
The impact of income, land, and wealth inequality on agricultural expansion in Latin America
Authors: Ceddia M. Graziano
Published: January 2019

Agricultural expansion remains the most prominent proximate cause of tropical deforestation in Latin America, a region characterized by deforestation rates substantially above the world average and extremely high inequality. This paper deploys several multivariate statistical models to test whether different aspects of inequality, within a context of increasing agricultural productivity, promote agricultural expansion (Jevons paradox) or contraction (land-sparing) in 10 Latin American countries over 1990–2010. Here I show the existence of distinct patterns between the instantaneous and the overall (i.e., accounting for temporal lags) effect of increasing agricultural productivity, conditional on the degree of income, land, and wealth inequality. In a context of perfect equality, the instantaneous effect of increases in agricultural productivity is to promote agricultural expansion (Jevons paradox). When temporal lags are accounted for, agricultural productivity appears to be mainly land-sparing. Increases in the level of inequality, in all its forms, promote agricultural expansion, thus eroding the land-sparing effects of increasing productivity. The results also suggest that the instantaneous impact of inequality is larger than the overall effect (accounting for temporal lags) and that the effects of income inequality are stronger than those of land and wealth inequality, respectively. Reaping the benefits of increasing agricultural productivity, and achieving sustainable agricultural intensification in Latin America, requires policy interventions that specifically address inequality.
Realizing the potential of dielectric elastomer artificial muscles
Authors: Duduta Mihai , Hajiesmaili Ehsan , Zhao Huichan , Wood Robert J. , Clarke David R.
Published: January 2019

Significance

To build new robots that can safely interact with people, while completing complex tasks, we need artificial muscles. Ideally, these devices would be completely soft, as strong as natural muscles, and powered by electricity for easy integration with the rest of the robot. We found a materials solution that relies on an established technology, a dielectric elastomer soft capacitor, which deforms when an electric field is applied. By using a unique combination of nanoscale conductive particles and soft elastomers, we can apply high electric fields and reach contraction forces on par with natural muscles. Potential uses include novel surgical tools, prosthetics and artificial limbs, haptic devices, and more capable soft robots for exploration.
Actuation of magnetoelastic membranes in precessing magnetic fields
Authors: Brisbois Chase Austyn , Tasinkevych Mykola , Vázquez-Montejo Pablo , Olvera de la Cruz Monica
Published: January 2019

Significance

Understanding the properties of elastic membranes with superparamagnetic particles advances the design of autonomous, soft robots. Magnetic fields readily penetrate most materials and can be used remotely to induce rapid and precise changes in membrane shape. Here, we compare analytical and numerical models to molecular dynamics simulations to explain how rapidly precessing biaxial magnetic fields can be used to control the forces on magnetoelastic membranes. These forces are closely linked to its actuating behavior and its potential applications in micromechanics.
The structure of the catalytic domain of the ATP synthase from
Mycobacterium smegmatis
is a target for developing antitubercular drugs
Authors: Zhang Alice Tianbu , Montgomery Martin G. , Leslie Andrew G. W. , Cook Gregory M. , Walker John E.
Published: January 2019

The crystal structure of the F
1
-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from
Mycobacterium smegmatis
which hydrolyzes ATP very poorly. The structure of the α
3
β
3
-component of the catalytic domain is similar to those in active F
1
-ATPases in
Escherichia coli
and
Geobacillus stearothermophilus
. However, its ε-subunit differs from those in these two active bacterial F
1
-ATPases as an ATP molecule is not bound to the two α-helices forming its C-terminal domain, probably because they are shorter than those in active enzymes and they lack an amino acid that contributes to the ATP binding site in active enzymes. In
E. coli
and
G. stearothermophilus
, the α-helices adopt an “up” state where the α-helices enter the α
3
β
3
-domain and prevent the rotor from turning. The mycobacterial F
1
-ATPase is most similar to the F
1
-ATPase from
Caldalkalibacillus thermarum
, which also hydrolyzes ATP poorly. The β
E
-subunits in both enzymes are in the usual “open” conformation but appear to be occupied uniquely by the combination of an adenosine 5′-diphosphate molecule with no magnesium ion plus phosphate. This occupation is consistent with the finding that their rotors have been arrested at the same point in their rotary catalytic cycles. These bound hydrolytic products are probably the basis of the inhibition of ATP hydrolysis. It can be envisaged that specific as yet unidentified small molecules might bind to the F
1
domain in
Mycobacterium tuberculosis
, prevent ATP synthesis, and inhibit the growth of the pathogen.
Canonical Wnt is inhibited by targeting one-carbon metabolism through methotrexate or methionine deprivation
Authors: Albrecht Lauren V. , Bui Maggie H. , De Robertis Edward M.
Published: January 2019

Significance

Metabolism, one of the most conserved features across all domains of life, is interwoven with cellular signaling networks and the posttranslational modification state of proteins. Methionine is an essential amino acid in one-carbon metabolism that serves as the substrate for S-adenosylmethionine, the universal methyl donor for cellular methylation. Here we report that the use of methionine-depleted medium inhibits Wnt-induced endolysosomal formation and canonical Wnt/β-catenin signaling. Use of methotrexate, a folate cycle inhibitor used in cancer chemotherapy, prevented PRMT1 and GSK3 vesicular sequestration, decreased Wnt-driven endolysosomal activity, and reduced canonical Wnt β-catenin luciferase signaling. In sum, these results imply a role for one-carbon metabolism in the regulation of Wnt signaling and endolysosomal biology.
Instant messaging, digital writing and spelling production quality in French
Authors: Simoës-Perlant Aurélie , Lanchantin Tonia , Gunnarsson-Largy Cecilia , Largy Pierre
Published: January 2019

The increased use of digital writing led to the appearance of written content that may differ from the standards
of spelling. Writing instant messages leads to the production of two different types of written forms that differ from standard
spelling: (a) those that can be confused with misspellings and (b) those that cannot. We showed that the production of the second
type of modifications has no effect on spelling production. Our research protocol allowed comparing two corpora (written in 1974
and 2012). These results showed that when a modification has no orthographic equivalent, its use cannot damage the quality of
spelling production. When it does, the effect on spelling may be negative.
Re-using the names of newborns: symbolic reincarnation in an age of infant mortality
Authors: Bush Stephen J.
Published: January 2019

The naming of a newborn for a deceased relative is a means by which a meaningful connection can be maintained with the dead. This study analyses the birth, marriage and death records of England and Wales to highlight a historic naming custom–that should a child die shortly after birth, their name could often be re-used for a later sibling.This re-use of names in response to child bereavement is considered in the context of historic and cross-cultural naming customs offering pragmatic responses to infant mortality, such as apotropaic (protective) naming, and within the theoretical framework of ‘continuing bonds’, whereby namesakes can facilitate a post-mortem social life for the deceased. By considering the intricate relationship between one’s name and one’s personhood, the re-use of a name in full, shortly after death, could be interpreted as the symbolic reincarnation of an individual, rather than simply as a commemorative act.
A Dictionary of Organizational Behaviour
Authors: Jeanes Emma
Published: January 2019

Over 300 entries

This accessible dictionary provides authoritative definitions of terms in the field of organizational behaviour. Coverage spans ethics, stress and well-being, teamwork, leadership, and management knowledge. Including entries on key terms such as actor-network theory, iron cage, organizational space, and work–life balance, the dictionary encapsulates the different perspectives and concepts that make up organizational behaviour in one easy-to-use resource.

With additional features including a guide to further reading and recommended websites, it will be an invaluable resource for students, lecturers, and business professionals, and serve as a useful supplement to the dictionaries of Business and Management, Human Resource Management, Marketing, and Psychology.
Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions
Authors: Ribeiro Judemir , Ríos-Vera Carlos , Melo Francisco , Schüller Andreas
Published: January 2019

Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visualization. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein–DNA complexes. SASA-based approximations underestimated protein–DNA contact surfaces on average by 40%. This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development.

Availability and implementation

A web server, stand-alone binaries for Linux, MacOS and Windows and C++ source code are freely available from http://schuellerlab.org/dr_sasa/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Aligning optical maps to de Bruijn graphs
Authors: Mukherjee Kingshuk , Alipanahi Bahar , Kahveci Tamer , Salmela Leena , Boucher Christina
Published: January 2019

Motivation

Optical maps are high-resolution restriction maps (Rmaps) that give a unique numeric representation to a genome. Used in concert with sequence reads, they provide a useful tool for genome assembly and for discovering structural variations and rearrangements. Although they have been a regular feature of modern genome assembly projects, optical maps have been mainly used in post-processing step and not in the genome assembly process itself. Several methods have been proposed for pairwise alignment of single molecule optical maps—called Rmaps, or for aligning optical maps to assembled reads. However, the problem of aligning an Rmap to a graph representing the sequence data of the same genome has not been studied before. Such an alignment provides a mapping between two sets of data: optical maps and sequence data which will facilitate the usage of optical maps in the sequence assembly step itself.

Results

We define the problem of aligning an Rmap to a de Bruijn graph and present the first algorithm for solving this problem which is based on a seed-and-extend approach. We demonstrate that our method is capable of aligning 73% of Rmaps generated from the Escherichia coli genome to the de Bruijn graph constructed from short reads generated from the same genome. We validate the alignments and show that our method achieves an accuracy of 99.6%. We also show that our method scales to larger genomes. In particular, we show that 76% of Rmaps can be aligned to the de Bruijn graph in the case of human data.

Availability and implementation

The software for aligning optical maps to de Bruijn graph, omGraph is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/omGraph.

Supplementary information

Supplementary data are available at Bioinformatics online.
P860 Evaluation of the probiotic features of two different multi-strain probiotic preparations from two different manufacturers
Authors: Colombo S , Sagheddu V , Elli M , Mora D
Published: January 2019

Background

The aim of this work was to compare the probiotic adhesion features and immunomodulatory properties of 2 probiotic products characterised by the same bacterial content but manufactured in different places (Italy and USA).

Methods

The multi-strain probiotic products under investigation were composed by a mixture of 8 different strains. The two products were manufactured in Italy (VSL#3 - Lot 710061 expiry date 10/2019) and in US (Vivomixx - Lot 1708702 expiry date 31/03/2019). The cell viability in each lot was assessed by flow cytometry. The adhesive abilities of probiotics were evaluated on three different eukaryotic intestinal cell lines (Caco-2, HT-29 and mucus-producing HT29-MTX).

For the evaluation of immune-modulatory activity, human Dendritic Cells (hDCs) obtained from blood mononuclear cells were exposed for 6 days to cytokines cocktail (IL-4 20 ng/ml + GM-CSF 50 ng/ml) and then to both probiotic mixtures for 2 h with MOI 1:10. A positive inflammatory condition was obtained by incubating washed hDCs in fresh medium containing Salmonella sp. for additional two h. Finally, hDCs were then cultured for 23 h in complete medium with antibiotics for the final analysis of soluble and surface molecules with ELISA or cytofluorimetric analysis method, respectively.

Results

The two products showed a comparable amount of live cells, 2.2 1011 (FU/g) and 2.4 1011 (FU/g), respectively, for the VSL#3 and Vivomixx. The two tested products showed similar adhesive capacity to the 3 cell lines considered, with adhesion values in the range 67–71%. No significant differences were observed in the percentage of adhesiveness expressed by the two mixtures according to the type of cell line considered. Regarding the immune-modulatory ability of the two tested products, results showed that they have the same behaviours. The exposure of the probiotic mixtures to hDCs resulted in a meaningful reduction of the expression of IL-12 following Salmonella induction. We observed that both products slightly increase the proportion of HLA-DR+/CD11+ and CD80+/CD11+ hDCs. Moreover, both mixtures significantly reduce Salmonella-induced HLA-DR+/CD11+ and CD80+/CD11+ hDCs. Both probiotic products did not significantly induce TNF-α production by hDCs at basal condition, and they did not result in further TNF-α production if compared with that induced by Salmonella sp. alone even if the response of the two products was almost identical.

Conclusions

Investigative activities described in this work demonstrated a comparable adhesive performances and interesting immunomodulatory activity against inflammation induced by Salmonella sp. for both VSL#3 and Vivomixx showing same behaviours irrespective of the manufacturer.
Changes in Physiological Functioning in Loblolly Pine Trees Undergoing Bark Beetle Simulated Mortality
Authors: Hornslein Nicole J , Siegert Courtney M , Renninger Heidi J
Published: January 2019

The southeastern United States contains extensive loblolly pine (Pinus taeda L.) plantations at risk from bark beetle damage that can change ecosystem biogeochemical cycling. Functional changes in tree physiology have the potential to occur before visual evidence of mortality making them difficult to incorporate into ecosystem models. Therefore, we girdled loblolly pines to simulate bark beetle damage and measured physiological processes including sapflow rates, photosynthesis, litterfall, and needle nitrogen concentrations to determine the physiological changes occurring in trees undergoing mortality. We found that the girdling treatment took 5 months to significantly reduce sapflow rates but visual crown mortality occurred more than one year after girdling. Girdled pines had approximately 2.5 times lower water use than control pines and exhibited greater susceptibility to atmospheric water stress. Girdled and control pines had similar needle nitrogen concentrations and photosynthetic rates measured during the mortality year. However, more litterfall with higher nitrogen concentrations occurred in the mortality year than in the previous year, resulting in redistribution of carbon and nitrogen in the ecosystem. Overall, these data allow for better quantification of the effects of background disturbance levels and individual tree mortality on water, carbon, and nitrogen cycling within a loblolly pine ecosystem.
Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden
Authors: Liu Huan , Wei Jinpu , Yang Ting , Mu Weixue , Song Bo , Yang Tuo , Fu Yuan , Wang Xuebing , Hu Guohai , Li Wangsheng , Zhou Hongcheng , Chang Yue , Chen Xiaoli , Chen Hongyun , Cheng Le , He Xuefei , Cai Hechen , Cai Xianchu , Wang Mei , Li Yang , Sahu Sunil Kumar , Yang Jinlong , Wang Yu , Mu Ranchang , Liu Jie , Zhao Jianming , Huang Ziheng , Xu Xun , Liu Xin
Published: January 2019

Background

Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank.

Results

The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications.

Conclusions

The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for “planetary-scale” projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project.
Capacity building and personal empowerment: participatory food costing in Nova Scotia, Canada
Authors: Monteith Hiliary , Anderson Barbara , Williams Patricia L
Published: January 2019

Food insecurity impacts millions of people globally. It has been recognized as a priority and a human right by the United Nations where empowerment of women is identified as a significant goal in addressing food insecurity. In the Maritime Province of Nova Scotia (NS), Canada, more than one in five children live in food insecure households. Since 2002, participatory action research (PAR) has been an integral component of food costing in NS with an aim to support capacity building for food security. Building on earlier research that examined short-term outcomes, and recognizing a lack of research examining outcomes of PAR processes, this study aimed to explore the medium-term individual capacity building processes and outcomes of women involved in Participatory Food Costing (PFC). Findings revealed that capacities were built with respect to interrelated themes of ‘awareness, participation, personal development, readiness to change, political impact, influence on others, self-esteem, project growth and project continuity’. In addition, the involvement of these women in PFC resulted in both personal empowerment and food security-related policy change. Involving vulnerable populations through PAR is valuable in influencing health-related policy.
Chain-like ground states in three dimensions
Authors: Lazzaroni Giuliano , Stefanelli Ulisse
Published: January 2019

We investigate the minimization of configurational energies of Brenner type. These include two- and three-body interaction terms, which favor the alignment of first neighbors. In particular, such configurational energies arise in connection with the molecular-mechanical modeling of covalent$sp$-bonding in carbon. Ground states in three dimensions are characterized and the stability of chains and rings is discussed. The interaction energy is then augmented with terms corresponding to weaker interactions favoring the stratification of configurations. This gives rise to stratified structures, which are reminiscent of nanoscrolls and multi-wall nanotubes. Optimal stratified configurations are identified and their geometry is discussed.
Bold diagrammatic Monte Carlo in the lens of stochastic iterative methods
Authors: Li Yingzhou , Lu Jianfeng
Published: January 2019

This work aims at understanding of bold diagrammatic Monte Carlo (BDMC) methods for stochastic summation of Feynman diagrams from the angle of stochastic iterative methods. The convergence enhancement trick of the BDMC is investigated from the analysis of condition number and convergence of the stochastic iterative methods. Numerical experiments are carried out for model systems to compare the BDMC with related stochastic iterative approaches.
Emerging roles of metabolites of ω3 and ω6 essential fatty acids in the control of intestinal inflammation
Authors: Nagatake Takahiro , Kunisawa Jun
Published: January 2019

The gastrointestinal tract is continuously exposed to the external environment, which contains numerous non-self antigens, including food materials and commensal micro-organisms. For the maintenance of mucosal homeostasis, the intestinal epithelial layer and mucosal immune system simultaneously provide the first line of defense against pathogens and are tightly regulated to prevent their induction of inflammatory responses to non-pathogenic antigens. Defects in mucosal homeostasis lead to the development of inflammatory and associated intestinal diseases, such as Crohn’s disease, ulcerative colitis, food allergy and colorectal cancer. The recent discovery of novel dietary ω3 and ω6 lipid-derived metabolites—such as resolvin, protectin, maresin, 17,18-epoxy-eicosatetraenoic acid and microbe-dependent 10-hydroxy-cis-12-octadecenoic acid—and their potent biologic effects on the regulation of inflammation have initiated a new era of nutritional immunology. In this review, we update our understanding of the role of lipid metabolites in intestinal inflammation.
The Danish unique personal identifier and the Danish Civil Registration System as a tool for research and quality improvement
Authors: Mainz Jan , Hess Mikkel Hagen , Johnsen Søren Paaske
Published: January 2019

All countries want to improve the health of their populations and to improve the quality of care and patient safety. Consequently, there is an ongoing need to assess and document population health, the quality of care and patient safety using valid and reliable data. This requires the ability to monitor the same individuals over time as they receive prevention, diagnostics, treatments, care and rehabilitation and experience improvements or deteriorations in their health or healthcare. This is, however, a challenge for most healthcare systems. A prerequisite to such data is the unique personal identifier. This perspective on quality paper describes the experience with the unique personal identifier in Denmark, based on the Danish Civil Registration System (DCRS) as a tool for research in epidemiology, health services research, quality improvement and patient safety. DCRS has been celebrating its 50 years anniversary.
Historical Population Size Change and Differentiation of Relict Populations of the Endangered Giant Kangaroo Rat
Authors: Statham Mark J , Bean William T , Alexander Nathan , Westphal Michael F , Sacks Benjamin N
Published: January 2019

From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species’ range, including 1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and 2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This keystone species underwent a ~97% range reduction over the past century, resulting in a current range that is highly fragmented, with 2 dominant northern and southern populations occurring 150 km apart. We sequenced >800 bp of mitochondrial DNA and genotyped 17 nuclear microsatellites in >275 D. ingens to assess the evolutionary relationship of these populations as well as the genetic structure within the northern metapopulation. A Bayesian Skyline Plot indicated that the species experienced a demographic expansion toward the end of the Pleistocene, with a recent population decline. Northern and southern D. ingens split 1857–13 443 years ago, prior to the massive conversion of the San Joaquin Valley to irrigated agriculture. We recommend that the northern and southern populations of D. ingens be re-classified as distinct population segments under the United States Endangered Species Act. We also observed population structure and asymmetrical migration within northern D. ingens where the Tumey Hills acted as a source contributing gene flow to all peripheral populations. This emphasized the importance of this location in the conservation of the metapopulation as a whole.
What We Know (And Don’t Know) About the Bereavement Experiences of Same-Sex Spouses
Authors: Donnelly Rachel , Reczek Corinne , Umberson Debra
Published: January 2019

The death of a spouse is an involuntary form of relationship dissolution with deleterious health consequences for the surviving partner. Yet, to date, researchers have not examined widowhood experiences of individuals in same-sex marriages. Past research shows that spousal caregiving during illness and end-of-life planning shapes the bereavement experience for different-sex couples. Thus this chapter reviews literature on midlife caregiving, illness experiences, and end-of-life planning to provide clues about how bereavement experiences might unfold for spouses in same-sex marriages. We further provide an empirical analysis of caregiving and illness using dyadic survey data collected from same- and different-sex spouses. Our results show that same-sex married couples report receiving the most care from spouses during past health events and have the most confidence in their spouse to provide adequate care in the future. Evidence on caregiving and end-of-life experiences points to future directions for research on bereaved same-sex spouses.
Ethics and Research with Children
Authors: Kodish Eric , Nelson Robert M.
Published: January 2019

This brief introductory chapter highlights the central tension between the need to protect children from research risk with the imperative to conduct pediatric research. After reviewing several policy shifts that help to provide historical context, the authors discuss the case-based method that is employed in the remainder of the book. The value and perils of using cases are explored. The chapter subsequently provides some suggestions for how the book might best be used inside and out of the classroom and concludes with a discussion of the ultimate aspiration for this second edition of Ethics and Research with Children: A Case-Based Approach.