bluuebunny/crossref_metadata_2025 huggingface dataset:
Extension of Kirkwood-Buff theory to the canonical ensemble
Authors: Rogers David M.
Published: February 2018

Kirkwood-Buff (KB) integrals are notoriously difficult to converge from a canonical simulation because they require estimating the grand-canonical radial distribution. The same essential difficulty is encountered when attempting to estimate the direct correlation function of Ornstein-Zernike theory by inverting the pair correlation functions. We present a new theory that applies to the entire, finite, simulation volume, so that no cutoff issues arise at all. The theory gives the direct correlation function for closed systems, while smoothness of the direct correlation function in reciprocal space allows calculating canonical KB integrals via a well-posed extrapolation to the origin. The present analysis method represents an improvement over previous work because it makes use of the entire simulation volume and its convergence can be accelerated using known properties of the direct correlation function. Using known interaction energy functions can make this extrapolation near perfect accuracy in the low-density case. Because finite size effects are stronger in the canonical than in the grand-canonical ensemble, we state ensemble correction formulas for the chemical potential and the KB coefficients. The new theory is illustrated with both analytical and simulation results on the 1D Ising model and a supercritical Lennard-Jones fluid. For the latter, the finite-size corrections are shown to be small.
Drag reduction induced by superhydrophobic surfaces in turbulent pipe flow
Authors: Costantini Roberta , Mollicone Jean-Paul , Battista Francesco
Published: February 2018

The drag reduction induced by superhydrophobic surfaces is investigated in a turbulent pipe flow. Wetted superhydrophobic surfaces are shown to trap gas bubbles in their asperities. This stops the liquid from coming in direct contact with the wall in that location, allowing the flow to slip over the air bubbles. We consider a well-defined texture with streamwise grooves at the walls in which the gas is expected to be entrapped. This configuration is modeled with alternating no-slip and shear-free boundary conditions at the wall. With respect to the classical turbulent pipe flow, a substantial drag reduction is observed which strongly depends on the grooves’ dimension and on the solid fraction, i.e., the ratio between the solid wall surface and the total surface of the pipe’s circumference. The drag reduction is due to the mean slip velocity at the wall which increases the flow rate at a fixed pressure drop. The enforced boundary conditions also produce peculiar turbulent structures which on the contrary decrease the flow rate. The two concurrent effects provide an overall flow rate increase as demonstrated by means of the mean axial momentum balance. This equation provides the balance between the mean pressure gradient, the Reynolds stress, the mean flow rate, and the mean slip velocity contributions.
Spall response of single-crystal copper
Authors: Turley W. D. , Fensin S. J. , Hixson R. S. , Jones D. R. , La Lone B. M. , Stevens G. D. , Thomas S. A. , Veeser L. R.
Published: February 2018

We performed a series of systematic spall experiments on single-crystal copper in an effort to determine and isolate the effects of crystal orientation, peak stress, and unloading strain rate on the tensile spall strength. Strain rates ranging from 0.62 to 2.2 × 106 s−1 and peak shock stresses in the 5–14 GPa range, with one additional experiment near 50 GPa, were explored as part of this work. Gun-driven impactors, called flyer plates, generated flat top shocks followed by spall. This work highlights the effect of crystal anisotropy on the spall strength by showing that the spall strength decreases in the following order: [100], [110], and [111]. Over the range of stresses and strain rates explored, the spall strength of [100] copper depends strongly on both the strain rate and shock stress. Except at the very highest shock stress, the results for the [100] orientation show linear relationships between the spall strength and both the applied compressive stress and the strain rate. In addition, hydrodynamic computer code simulations of the spall experiments were performed to calculate the relationship between the strain rate near the spall plane in the target and the rate of free surface velocity release during the pullback. As expected, strain rates at the spall plane are much higher than the strain rates estimated from the free surface velocity release rate. We have begun soft recovery experiments and molecular dynamics calculations to understand the unusual recompression observed in the spall signature for [100] crystals.
Approximate deconvolution model for the simulation of turbulent gas-solid flows: An a priori analysis
Authors: Schneiderbauer Simon , Saeedipour Mahdi
Published: February 2018

Highly resolved two-fluid model (TFM) simulations of gas-solid flows in vertical periodic channels have been performed to study closures for the filtered drag force and the Reynolds-stress-like contribution stemming from the convective terms. An approximate deconvolution model (ADM) for the large-eddy simulation of turbulent gas-solid suspensions is detailed and subsequently used to reconstruct those unresolved contributions in an a priori manner. With such an approach, an approximation of the unfiltered solution is obtained by repeated filtering allowing the determination of the unclosed terms of the filtered equations directly. A priori filtering shows that predictions of the ADM model yield fairly good agreement with the fine grid TFM simulations for various filter sizes and different particle sizes. In particular, strong positive correlation (ρ > 0.98) is observed at intermediate filter sizes for all sub-grid terms. Additionally, our study reveals that the ADM results moderately depend on the choice of the filters, such as box and Gaussian filter, as well as the deconvolution order. The a priori test finally reveals that ADM is superior compared to isotropic functional closures proposed recently [S. Schneiderbauer, “A spatially-averaged two-fluid model for dense large-scale gas-solid flows,” AIChE J. 63, 3544–3562 (2017)].
Markov modeling of peptide folding in the presence of protein crowders
Authors: Nilsson Daniel , Mohanty Sandipan , Irbäck Anders
Published: February 2018

We use Markov state models (MSMs) to analyze the dynamics of a β-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin inhibitor (BPTI) and GB1]. In these systems, at the temperature used, the peptide can be folded or unfolded and bound or unbound to crowder molecules. Four or five major free-energy minima can be identified. To estimate the dominant MC relaxation times of the peptide, we build MSMs using a range of different time resolutions or lag times. We show that stable relaxation-time estimates can be obtained from the MSM eigenfunctions through fits to autocorrelation data. The eigenfunctions remain sufficiently accurate to permit stable relaxation-time estimation down to small lag times, at which point simple estimates based on the corresponding eigenvalues have large systematic uncertainties. The presence of the crowders has a stabilizing effect on the peptide, especially with BPTI crowders, which can be attributed to a reduced unfolding rate ku, while the folding rate kf is left largely unchanged.
Using light scattering to resolve Brownian rotation dynamics of optically trapped Au nanorods
Authors: Andres-Arroyo Ana , Reece Peter J.
Published: February 2018

Optically trapped Au nanorods are known to adopt a preferential orientation when trapped in three dimensions at the focus of linearly polarised optical tweezers. Trapped nanorods experience both translational and rotational perturbations due to Brownian motion that are governed by the strength of the trap and associated shape-dependent hydrodynamic properties. In this study, we make use of the strong angular dependent light scattering of the localised surface plasmon resonances to interrogate the rotational dynamics of trapped nanorods principally aligned along the propagation axis of the trapping laser. Our measurements reveal that significant rotational dynamics can be observed whilst maintaining stable translational trapping at low powers.
Barrier to recombination of oppositely charged large polarons
Authors: Emin David
Published: February 2018

Electronic charge carriers in ionic materials can self-trap to form large polarons. Interference between the ionic displacements associated with oppositely charged large polarons increases as they approach one another. Initially, this interference produces an attractive potential that fosters their merger. However, for small enough separations this interference generates a repulsive interaction between oppositely charged large polarons. In suitable circumstances, this repulsion can overwhelm their direct Coulomb attraction. Then, the resulting net repulsion between oppositely charged large polarons constitutes a potential barrier which impedes their recombination.
Comparison of specialist and generalist care
Authors: Horwood C. M. , Hakendorf P. , Thompson C. H.
Published: February 2018

Objective The choice of whether to admit under a specialist or a generalist unit is often made with neither clear rationale nor understanding of its consequences. The present study compared the characteristics and outcomes of patients admitted with community-acquired pneumonia to either a general medicine or respiratory unit. Methods This study was a retrospective cross-sectional study using data from public hospitals in Adelaide, South Australia. Over 5 years there were 9775 overnight, unplanned appropriate adult admissions. Patient length of hospital stay, in-patient mortality rate and 30-day unplanned readmission rate were calculated, with and without adjustment for patient age and comorbidity burden. Results Over 80% of these patients were cared for by a general medicine unit rather than a specialist unit. Patients admitted to a general medicine unit were, on average, 4 years older than those admitted to a respiratory unit. Comorbidity burdens were similar between units at the same hospital. Length of in-patient stay was >1 day shorter for those admitted to a general medicine unit, without significant compromise in mortality or readmission rates. Between each hospital, general medicine units showed a range of mortality rates and length of hospital stay, for which there was no obvious explanation. Conclusions Compared with speciality care, general medicine units can safely and efficiently care for patients presenting to hospital with community-acquired pneumonia. What is known about the topic? Within the narrow range of any specific disease, generalist medical services are often cited as inferior in performance compared with a speciality service. This has implications for hospital resourcing, including both staffing and ward allocation. What does this paper add? This paper demonstrates that most patients admitted with a principal diagnosis of community-acquired pneumonia were admitted to a generalist unit and did not apparently fare worse than patients admitted to a specialist service; patients admitted to a generalist unit spent less time in hospital and there was no difference in mortality or readmission rate compared with patients admitted to a specialist service. What are the implications for practitioners? The provision of generalist services at urban hospitals in Australia provides a safe alternative admission option for patients presenting with pneumonia, and possibly for other common acute medical conditions.
Cochlear implant versus hearing aids
Authors: Gabr Takwa A. , Kotait Mona A.
Published: February 2018

Patients with severe and profound hearing loss (HL) represent a unique challenge in hearing aids (HAs) fitting for whom cochlear implants (CIs) are better choice.

Objectives:

To assess speech perception in children with severe-to-profound HL who are fitted with power HAs or CIs and compare their results with children with better hearing thresholds who are fitted with HAs.

Methods:

Seventy children were participated in this work divided into four groups according to their hearing thresholds: GI: 18 children with moderate HL fitted with HAs, GII: 16 children with severe HL fitted with HAs, GIII: 16 children with profound HL fitted with HAs and GIV: 20 children with profound HL and fitted with CIs.

Results:

Aided speech audiometry showed better results in GI and GIV while GIII showed the worst results among the four groups. P1–N1 of aided speech-evoked cortical auditory-evoked potentials (S-CAEPs) was recorded in all cases in GI and GIV and their latencies showed no significant difference, while GIII showed significantly delayed latencies. There was a significant negative correlation between P1 and N1 latencies and duration of HAs and CIs use in GII and GIV, respectively. Amplitudes of P1 and N2 showed a significant positive correlation with duration of HAs use in GII and GIII, respectively. GI showed a significant positive correlation between SRTs and P1 latency. GII showed significant negative correlations between SD% and N2 latency, while GIV showed a significant positive correlation between SRTs and P2 latency.

Conclusion:

CIs represent a good choice for children with severe-to-profound and profound HL than power HAs. Children with more severe degrees of HL who do well on speech perception measures tend to have better S-CAEPs results with good correspondence between both measures. S-CAEPs and speech perception tests can be used regularly to assess the efficiency of auditory rehabilitation.
Novel overlapping subgraph clustering for the detection of antigen epitopes
Authors: Zhao Liang , Wu Shaogui , Jiang Jiawen , Li Wencui , Luo Jie , Li Jinyan
Published: February 2018

Motivation

Antigens that contain overlapping epitopes have been occasionally reported. As current algorithms mainly take a one-antigen-one-epitope approach to the prediction of epitopes, they are not capable of detecting these multiple and overlapping epitopes accurately, or even those multiple and separated epitopes existing in some other antigens.

Results

We introduce a novel subgraph clustering algorithm for more accurate detection of epitopes. This algorithm takes graph partitions as seeds, and expands the seeds to merge overlapping subgraphs based on the term frequency-inverse document frequency (TF-IDF) featured similarity. Then, the merged subgraphs are each classified as an epitope or non-epitope. Tests of our algorithm were conducted on three newly collected datasets of antigens. In the first dataset, each antigen contains only a single epitope; in the second, each antigen contains only multiple and separated epitopes; and in the third, each antigen contains overlapping epitopes. The prediction performance of our algorithm is significantly better than the state-of-art methods. The lifts of the averaged f-scores on top of the best existing methods are 60, 75 and 22% for the single epitope detection, the multiple and separated epitopes detection, and the overlapping epitopes detection, respectively.

Availability and implementation

The source code is available at github.com/lzhlab/glep/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Homeless in the house of God? An investigation of home and homelessness among undocumented migrants living in a Brussels church
Authors: Damery Shannon
Published: February 2018

The church is often considered a haven and a sanctuary. In the case of a group of undocumented and asylum-seeking Afghans in Brussels, a church was literally a place of refuge. This article explores the home-making practices of Afghan immigrants who were given sanctuary in a Brussels church and who made the church their living space. They slept, ate, socialised, and organised political activities in the church, while also appropriating nearby public spaces to serve various functions in their lives. Home is an increasingly important concept in migration studies, and this article explores home-making through an investigation of what may be lacking in the notion of sanctuary. In this article, home is treated as a series of connections, including connections to people, cultures, places and objects. These connections serve as a way to explore whether the Afghans made the church and surrounding urban space into a home or why they remained homeless despite the proffered sanctuary.
A Prospective Observational Study of the Epidemiology, Management, and Outcomes of Skin and Soft Tissue Infections Due to Carbapenem-Resistant Enterobacteriaceae
Authors: Henig Oryan , Cober Eric , Richter Sandra S , Perez Federico , Salata Robert A , Kalayjian Robert C , Watkins Richard R , Marshall Steve , Rudin Susan D , Domitrovic T Nicholas , Hujer Andrea M , Hujer Kristine M , Doi Yohei , Evans Scott , Fowler Vance G , Bonomo Robert A , van Duin David , Kaye Keith S ,   for the Antibacterial Resistance Leadership Group
Published: February 2018

Background

This study was performed to characterize the epidemiology, management, and outcomes of skin and soft tissue infection (SSTI) and colonization due to carbapenem-resistant Enterobacteriaceae (CRE).

Methods

Patients from the Consortium on Resistance Against Carbapenem in Klebsiella and Other Enterobacteriaceae (CRACKLE-1) from December 24, 2011 to October 1, 2014 with wound cultures positive for CRE were included in the study. Predictors of surgical intervention were analyzed. Molecular typing of isolates was performed using repetitive extragenic palindromic polymerase chain reaction (PCR). Carbapenemase genes were detected using PCR.

Results

One hundred forty-two patients were included: 62 had SSTI (44%) and 56% were colonized. Mean age was 61 years, and 48% were male: median Charlson score was 3 (interquartile range, 1–5). Forty-eight percent of patients were admitted from long-term care facilities (LTCFs), and 31% were from the community. Two strain types (ST258A and ST258B) were identified (73% of 45 tested). Carbapenemase genes were detected in 40 of 45 isolates (blaKPC-3 [47%], blaKPC-2 [42%]). Sixty-eight patients (48%) underwent surgical intervention, 63% of whom had SSTI. Patients admitted from LTCFs were less likely to undergo surgical intervention (odds ratio [OR], 0.36; 95% confidence interval [CI], 0.18–0.71). In multivariable analysis, among patients with SSTI, those admitted from LTCFs were less likely to undergo debridement (OR, 0.18; 95% CI, 0.04–0.93).

Conclusions

Patients admitted from LTCFs with CRE SSTI were less likely to undergo surgical intervention. Sixteen percent of the patients died, and approximately 50% of survivors required more intensive care upon discharge. These findings suggest a unique, impactful syndrome within the CRE infection spectrum. Further studies are needed to assess the role of surgical debridement in management of CRE-SSTI, particularly among LTCF residents.
Associations Between Antiretroviral Treatment and Avascular Bone Necrosis: The Swiss HIV Cohort Study
Authors: Bayard Cornelia , Ledergerber Bruno , Flepp Markus , Lecompte Thanh , Moulin Estelle , Hoffmann Matthias , Weber Rainer , Staehelin Cornelia , Di Benedetto Caroline , Fux Christoph A , Tarr Philip E , Hasse Barbara ,   the Swiss HIV Cohort Study, Aubert V , Battegay M , Bernasconi E , Böni J , Braun DL , Bucher HC , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux CA , Günthard HF , Haerry D , Hasse B , Hirsch HH , Hoffmann M , Hösli I , Kahlert C , Kaiser L , Keiser O , Klimkait T , Kouyos RD , Kovari H , Ledergerber B , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner KJ , Müller N , Nicca D , Pantaleo G , Paioni P , Rauch A , Rudin C , Scherrer AU , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Vernazza P , Wandeler G , Weber R , Yerly S
Published: February 2018

Background

HIV-infected individuals have an increased risk of avascular bone necrosis (AVN). Antiretroviral therapy (ART) and particularly protease inhibitors (PI) have been implicated as a risk factor. We aimed to study the associations of ART with the occurrence of AVN among Swiss HIV Cohort Study participants (SHCS).

Methods

We used incidence density sampling to perform a case control study within the Swiss HIV Cohort Study (SHCS) comparing prospectively collected AVN cases and controls by conditional logistic regression analysis. To evaluate the effect of ART, multivariable models were adjusted for HIV transmission risk group, age, alcohol consumption, use of corticosteroids, CD4 nadir, maximum viral load, and pancreatitis.

Results

We compared 74 AVN cases and 145 controls. Associations with AVN were shown for heterosexual HIV acquisition (odds ratio [OR], 3.4; 95% confidence interval [CI], 1.1–10), alcohol consumption (OR, 2.7; 95% CI, 1.3–5.7), and hyperlipidemia (OR, 3.6; 95% CI, 1.4–9.6). After adding ART substances to the multivariable base model, there was evidence of an association for treatment with tenofovir (TDF) >1 year (OR, 4.4; 95% CI, 1.4–14) with AVN. Neither exposure to specific frequently prescribed ART combinations or ART drug classes nor cumulative ART exposure showed any associations with AVN.

Conclusions

In the HIV-infected population, a combination of risk factors such as heterosexual HIV acquisition, moderate to severe alcohol intake, and hyperlipidemia seem to contribute to AVN. ART does not seem to be a relevant risk factor for AVN. The association of prolonged TDF exposure with AVN needs to be confirmed.
18F-florbetapir Positron Emission Tomography–determined Cerebral β-Amyloid Deposition and Neurocognitive Performance after Cardiac Surgery
Authors: Klinger Rebecca Y. , James Olga G. , Borges-Neto Salvador , Bisanar Tiffany , Li Yi-Ju , Qi Wenjing , Berger Miles , Terrando Niccolò , Newman Mark F. , Doraiswamy P. Murali , Mathew Joseph P.
Published: February 2018

Background

Amyloid deposition is a potential contributor to postoperative cognitive dysfunction. The authors hypothesized that 6-week global cortical amyloid burden, determined by 18F-florbetapir positron emission tomography, would be greater in those patients manifesting cognitive dysfunction at 6 weeks postoperatively.

Methods

Amyloid deposition was evaluated in cardiac surgical patients at 6 weeks (n = 40) and 1 yr (n = 12); neurocognitive function was assessed at baseline (n = 40), 6 weeks (n = 37), 1 yr (n = 13), and 3 yr (n = 9). The association of 6-week amyloid deposition with cognitive dysfunction was assessed by multivariable regression, accounting for age, years of education, and baseline cognition. Differences between the surgical cohort with cognitive deficit and the Alzheimer’s Disease Neuroimaging Initiative cohorts (normal and early/late mild cognitive impairment) was assessed, adjusting for age, education, and apolipoprotein E4 genotype.

Results

The authors found that 6-week abnormal global cortical amyloid deposition was not associated with cognitive dysfunction (13 of 37, 35%) at 6 weeks postoperatively (median standard uptake value ratio [interquartile range]: cognitive dysfunction 0.92 [0.89 to 1.07] vs. 0.98 [0.93 to 1.05]; P = 0.455). In post hoc analyses, global cortical amyloid was also not associated with cognitive dysfunction at 1 or 3 yr postoperatively. Amyloid deposition at 6 weeks in the surgical cohort was not different from that in normal Alzheimer’s Disease Neuroimaging Initiative subjects, but increased over 1 yr in many areas at a rate greater than in controls.

Conclusions

In this study, postoperative cognitive dysfunction was not associated with 6-week cortical amyloid deposition. The relationship between cognitive dysfunction and regional amyloid burden and the rate of postoperative amyloid deposition merit further investigation.
Effect of a Short-term Cycle Ergometer Sprint Training Against Heavy and Light Resistances on Intraocular Pressure Responses
Authors: Vera Jesús , Garcia-Ramos Amador , Redondo Beatriz , Cárdenas David , De Moraes Carlos Gustavo , Jiménez Raimundo
Published: February 2018

Purpose:

The purpose of this study is to determinate the long-term effect of a cycle ergometer sprint training program against heavy and light resistances on baseline intraocular pressure (IOP), and on the acute IOP response to cycling sprints.

Methods:

A total 27 physically active males were randomly assigned to a heavy loads group (HLG, n=9), low loads group (LLG, n=9), and control group (CG, n=9). Participants performed 12 training sessions during 6 weeks (2 sessions per week), and each training session consisted in performing 8 cycling sprints against either heavy (HLG) or light (LLG) resistances. Before and after intervention, they performed an identical protocol, which consisted in performing maximal cycling sprints against 5 different resistances in random order. In these protocols, IOP was measured before and after each sprint by rebound tonometry.

Results:

A Bayesian analysis revealed that baseline IOP was reduced in the LLG after the intervention [Bayes factor (BF01)=0.043 and effect size (ES)=1.255; pretest=15.22±0.94 mm Hg and posttest=15.39±1.02 mm Hg], whereas the HLG did not manifest any baseline IOP change (BF01=2.363 and ES=−0.205; pretest=15.28±1.44 mm Hg and posttest=14.17±1.77 mm Hg). The acute IOP response to maximal sprints was modified for the HLG, showing a more stable IOP response with heavier loads (resistance, 4 and 5) after the intervention (BF01<0.01 in both cases, and ESs=1.847 and 1.920, respectively).

Conclusions:

A short-term cycle ergometer sprint training impacts long-term IOP depending on the level of resistance imposed, showing that training with low loads permits to reduce baseline IOP, whereas training with heavy loads attenuates the acute IOP changes after sprinting against heavy loads.
The medical home for children with autism spectrum disorder: an essential element whose time has come
Authors: Todorow Carlyn , Connell James , Turchi Renee M.
Published: February 2018

Purpose of review

The purpose of this review is to describe the role of the medical home in children with autism spectrum disorder (ASD). A high-quality medical home is essential, given the increase in prevalence of ASD and the array of services, community partners, specialists, therapists, and healthcare team members needed to care for this population.

Recent findings

Providing care through the medical home model results in fewer unmet needs. Care coordination and integration are the aspects of the medical home currently most lacking. Navigating the healthcare landscape for children with ASD may be enhanced with patient navigators, integration of physical and behavioral health, and telehealth services.

Children with ASD have an increased number of medical and mental health needs. Obtaining care via a medical home has been shown to decrease unmet healthcare needs. However, they are less likely to receive care through the medical home model compared with other children with special healthcare needs. Barriers identified by families include a lack of early identification, limited knowledge on educational plans, and unknown community resources. Barriers identified by providers include lack of time, training, and resources. Providing care coordination and family-centered care in a medical home model are essential for children with ASD.
Nucleosome turnover is sufficient to establish varied histone methylation states
Authors: Chory Emma J. , Calarco Joseph P. , Hathaway Nathaniel A. , Bell Oliver , Neel Dana S. , Crabtree Gerald R.
Published: February 2018

Transcription-dependent methylation of histone H3 at lysine 79 (H3K79) is evolutionarily conserved from yeast to mammals, critical for normal development and frequently deregulated by genetic recombination in Mixed Lineage Leukemia. Although this histone modification is associated with gene activity, little is known about the cellular mechanisms of H3K79 methylation regulation. Because no H3K79 demethylase has been discovered, the mechanism of its removal remains unclear. Utilizing chemical-induced-proximity to control histone methylation in vivo we show that the dynamics of methylation state (mono, di, tri-methylation) is genome-context specific. Further, Monte Carlo simulations coupling systems of kinetic reactions with histone turnover rates, suggest that nucleo-some turnover is sufficient to establish varied genome-wide methylation states without active demethylation.
Honest and cheating strategies in a simple model of aggressive communication: the role of spatial correlations
Authors: Számadó Szabolcs , Szántó András
Published: February 2018

The evolution and maintenance of communication in terms of aggressive interactions is a long-debated issue. Several game theoretical models and individual based computer simulations investigated this problem in terms of a simple game of aggressive communication. So far all of these investigations focused on well mixed population of individuals. However, spatial correlations can emerge in nature where individuals or group of individuals defend resources. The extensive literature on cooperative games show that these spatial correlations can be vital in the maintenance and evolution of cooperative strategies, thus it is reasonable to expect that such correlations could play an important role in the evolution of honest communication as well. Here we investigate a traditional game of aggressive communication in a spatially explicit context. We investigate the role of spatial correlations by comparing results of evolvability in well mixed populations with results from spatially explicit populations. Spatial correlations seem to inhibit the evolution of communication in the spatially explicit version of this game. This result is unexpected, and it requires further investigation to understand.
Plasma Membrane Phylloquinone Biosynthesis in Nonphotosynthetic Parasitic Plants
Authors: Gu Xi , Chen Ing-Gin , Harding Scott A. , Nyamdari Batbayar , Ortega Maria A. , Clermont Kristen , Westwood James H. , Tsai Chung-Jui
Published: February 2018

Phylloquinone is a lipophilic naphthoquinone found predominantly in chloroplasts and best known for its function in photosystem I electron transport and disulfide bridge formation of photosystem II subunits. Phylloquinone has also been detected in plasma membrane preparations of heterotrophic tissues with potential transmembrane redox function, but the molecular basis for this noncanonical pathway is unknown. Here we provide evidence of plasma membrane phylloquinone biosynthesis in a nonphotosynthetic holoparasite Phelipanche aegyptiaca. A nonphotosynthetic and nonplastidial role for phylloquinone is supported by transcription of phylloquinone biosynthetic genes during seed germination and haustorium development, by plasma membrane-localization of alternative terminal enzymes, and by detection of phylloquinone in germinated seeds. Comparative gene network analysis with photosynthetically competent parasites revealed a bias of Phelipanche phylloquinone genes toward coexpression with oxidoreductases involved in plasma membrane electron transport. Genes encoding the plasma membrane phylloquinone pathway are also present in several photoautotrophic taxa of Asterids, suggesting an ancient origin of multifunctionality. Our findings suggest that nonphotosynthetic holoparasites exploit alternative targeting of phylloquinone for transmembrane redox signaling associated with parasitism.
Seave: a comprehensive web platform for storing and interrogating human genomic variation
Authors: Gayevskiy Velimir , Roscioli Tony , Dinger Marcel E , Cowley Mark J
Published: February 2018

Capability for genome sequencing and variant calling has increased dramatically, enabling large scale genomic interrogation of human disease. However, discovery is hindered by the current limitations in genomic interpretation, which remains a complicated and disjointed process. We introduce Seave, a web platform that enables variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.
Assessment of Antibody-Dependent Cellular Cytotoxicity by Flow Cytometry
Authors: Duensing Thomas D. , Watson Susan R.
Published: February 2018

A useful feature of therapeutic antibodies is the ability to kill the cells to which they bind. Antibodies are capable of mediating cell killing in a variety of ways. Apoptosis, complement-mediated mechanisms, and antibody-dependent cellular cytotoxicity (ADCC) are all effects that can be assayed to characterize lead antibody candidates. Extensive, multidose characterizations of a series of candidates can be performed in a short amount of time using assays developed for high-throughput flow cytometry systems. Antibodies that contain the Fc portion of the human IgG1 can activate complement-mediated killing. In the ADCC method described here, cytotoxicity is mediated mostly by natural killer (NK) cells. Thus, if an antibody binds to its target on the surface of a tumor cell, Fc receptors on the surface of the NK cells (effector cells) recognize the bound antibody. This leads to the release of cytotoxic granules containing perforin, granzymes, and interferon γ, a cytokine that can stimulate other cells of the immune system such as T cells.
Isolation of Xenopus Oocytes
Authors: Newman Karen , Aguero Tristan , King Mary Lou
Published: February 2018

Xenopus oocytes and oocyte extracts are the starting material for a variety of experimental approaches. Oocytes are obtained by surgical removal of the ovary from anesthetized females. Although oocytes may be used while they remain within their ovarian follicle, it is more practical to work with defolliculated oocytes. Defolliculation can be performed either manually or enzymatically. Here we present a protocol for the isolation and separation of Xenopus oocytes at various developmental stages, and guidelines for maintaining oocytes in culture.
Crystal structure of the triethylammonium salt of 3-[(4-hydroxy-3-methoxyphenyl)(4-hydroxy-2-oxo-2H-chromen-3-yl)methyl]-2-oxo-2H-chromen-4-olate
Authors: Ikram Muhammad , Rehman Sadia , Khan Afzal , Schulzke Carola
Published: February 2018

The reaction between 3,3′-[(3-methoxy-4-hydroxyphenyl)methanediyl]bis(4-hydroxy-2H-chromen-2-one) and triethylamine in methanol yielded the title compound triethylammonium 3-[(4-hydroxy-3-methoxyphenyl)(4-hydroxy-2-oxo-2H-chromen-3-yl)methyl]-2-oxo-2H-chromen-4-olate, C6H16N+·C26H17O8−or (NHEt3)+(C26H17O8)−, which crystallized directly from its methanolic mother liquor. The non-deprotonated coumarol substituent shares its H atom with the deprotonated coumarolate substituent in a short negative charge-assisted hydrogen bond in which the freely refined H atom is moved from its parent O atom towards the acceptor O atom, elongating the covalent O—H bond to 1.18 (3) Å. The respective H atom can therefore be described as being shared by two alcohol O atoms, culminating in the formation of an eight-membered ring.
Crystal structure of octakis(4-methoxypyridinium) bis(4-methoxypyridine-κN)tetrakis(thiocyanato-κN)ferrate(III) bis[(4-methoxypyridine-κN)pentakis(thiocyanato-κN)ferrate(III)] hexakis(thiocyanato-κN)ferrate(III) with iron in three different octahedral coordination environments
Authors: Jochim Aleksej , Jess Inke , Näther Christian
Published: February 2018

The crystal structure of the title salt, (C6H8NO)8[Fe(NCS)4(C6H7NO)2][Fe(NCS)5(C6H7NO)]2[Fe(NCS)6], comprises three negatively charged octahedral FeIIIcomplexes with different coordination environments in which the FeIIIatoms are coordinated by a different number of thiocyanate anions and 4-methoxypyridine ligands. Charge balance is achieved by 4-methoxypyridinium cations. The asymmetric unit consists of three FeIIIcations, one of which is located on a centre of inversion, one on a twofold rotation axis and one in a general position, and ten thiocyanate anions, two 4-methoxypyridine ligands and 4-methoxypyridinium cations (one of which is disordered over two sets of sites). Beside to Coulombic interactions between organic cations and the ferrate(III) anions, weak N—H...S hydrogen-bonding interactions involving the pyridinium N—H groups of the cations and the thiocyanate S atoms of the complex anions are mainly responsible for the cohesion of the crystal structure.
Model validation: local diagnosis, correction and when to quit
Authors: Richardson Jane S. , Williams Christopher J. , Hintze Bradley J. , Chen Vincent B. , Prisant Michael G. , Videau Lizbeth L. , Richardson David C.
Published: February 2018

Traditionally, validation was considered to be a final gatekeeping function, but refinement is smoother and results are better if model validation actively guides corrections throughout structure solution. This shifts emphasis from global to local measures: primarily geometry, conformations and sterics. A fit into the wrong local minimum conformation usually produces outliers in multiple measures. Moving to the right local minimum should be prioritized, rather than small shifts across arbitrary borderlines. Steric criteria work best with all explicit H atoms. `Backrub' motions should be used for side chains and `P-perp' diagnostics to correct ribose puckers. A `water' may actually be an ion, a relic of misfitting or an unmodeled alternate. Beware of wishful thinking in modeling ligands. At high resolution, internally consistent alternate conformations should be modeled and geometry in poor density should not be downweighted. At low resolution,CaBLAMshould be used to diagnose protein secondary structure andERRASERto correct RNA backbone. All atoms should not be forced inside density, beware of sequence misalignment, and very rare conformations such ascis-non-Pro peptides should be avoided. Automation continues to improve, but the crystallographer still must look at each outlier, in the context of density, and correct most of them. For the valid few with unambiguous density and something that is holding them in place, a functional reason should be sought. The expectation is a few outliers, not zero.
Substructure determination using phase-retrieval techniques
Authors: Skubák Pavol
Published: February 2018

Thus far, the application of phase-retrieval methods in crystallography has mainly been aimed at variants of charge flipping or structure-factor flipping. In this work, the relaxed averaged alternating reflections (RAAR) algorithm is applied to determine anomalously scattering substructures from single-wavelength anomalous diffraction (SAD) data of macromolecules. The algorithm has been implemented in a new program,PRASA, and has been shown to significantly outperform charge flipping in determining anomalously scattering substructures on a test sample of 169 SAD data sets with resolutions up to 3.88 Å.
Where is crystallography going?
Authors: Grimes Jonathan M. , Hall David R. , Ashton Alun W. , Evans Gwyndaf , Owen Robin L. , Wagner Armin , McAuley Katherine E. , von Delft Frank , Orville Allen M. , Sorensen Thomas , Walsh Martin A. , Ginn Helen M. , Stuart David I.
Published: February 2018

Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
DIALS: implementation and evaluation of a new integration package
Authors: Winter Graeme , Waterman David G. , Parkhurst James M. , Brewster Aaron S. , Gildea Richard J. , Gerstel Markus , Fuentes-Montero Luis , Vollmar Melanie , Michels-Clark Tara , Young Iris D. , Sauter Nicholas K. , Evans Gwyndaf
Published: February 2018

TheDIALSproject is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.
Technological aspects of silver particle sintering for electronic packaging
Authors: Felba Jan
Published: February 2018

Purpose

This paper aims to find proper technological parameters of low-temperature joining technique by silver sintering to eventually use this technique for reliable electronic packaging.

Design/methodology/approach

Based on the literature and author’s own experience, the factors influencing the nanosized Ag particle sintering results were identified, and their significance was assessed.

Findings

It has been shown that some important technological parameters clearly influence the quality of the joints, and their choice is unambiguous, but the meaning of some parameters is dependent on other factors (interactions), and they should be selected experimentally.

Originality/value

The value of this research is that the importance of all technological factors was analyzed, which makes it easy to choose the technological procedures in the electronic packaging.
When regulatory changes become a driver for business model innovation
Authors: Berti Chiara , Casprini Elena
Published: February 2018

Purpose

The purpose of this paper is to provide an analysis of how an airport’s business model (BM) has been innovated. In particular, it considers a BM innovation owing to an exogenous driver, i.e. a change in the legislative environment.

Design/methodology/approach

The paper presents an in-depth case study. It analyses the case of an Italian regional airport that has been renewed by changes in the National Plan of Transport.

Findings

The paper extends previous research on BM and air transport industry in two ways. First, the authors contribute to Gillen’s (2011) framework, via introducing a new kind of ownership/governance structure, that of long-term concession, characterized by the concession of the comprehensive management to a private company for 30 years. Second, the authors look at how a BM has been implemented and used as a manipulating device over the two phases of the airport development, namely, incubation and generation.

Originality/value

The paper provides an in-depth case study on an airport BM innovation.
Coopetition and institutions: a strategy for Brazilian wineries facing internationalization
Authors: Monticelli Jefferson Marlon , Garrido Ivan Lapuente , de Vasconcellos Silvio Luis
Published: February 2018

Purpose

The purpose of this study is to understand the role institutions play in driving the internationalization of firms in an emerging country through promotion of coopetition. Investigating the relationships between coopetition, institutions and internationalization, especially among firms in emerging countries, is an important approach that has received little attention.

Design/methodology/approach

This study has used a single case study interviewing managers of Brazilian wineries and representatives of formal institutions in an emerging economy. A research framework taking an institutions-based view of strategy and applying it to study coopetition and internationalization is proposed.

Findings

Formal institutions are the most important players in the promotion of coopetition between firms in the Brazilian wine industry. Coopetition enables firms to access new resources and capabilities, promoting and facilitating internationalization, while also increasing firms’ competitiveness in the domestic market. The study also found evidence of certain limiting factors within these relationships, caused by the heterogeneous nature of the firms involved and by the asymmetries in their perceptions of the gains achieved.

Research limitations/implications

As a consequence of the methodology adopted, the results of this study are limited to the Brazilian wine industry. Future research should extend the approach to data collected in different countries and industries. Another promising avenue for research is to explore how decisions of a political nature influence the institutions that coordinate an industry, which would provide a new perspective on the internationalization of the firms involved.

Practical implications

The results offer governments and institutions an opportunity to better understand, and therefore to better manage, their actions in relation to their role in the promotion of the competitiveness of firms and industries, both in international and domestic markets. For firms, the results offer insights into the possible gains and the limitations of coopetition strategies, contributing to their decision-making on involvement. The study also contributes to understanding the competitiveness of the industry investigated.

Originality/value

This study approaches coopetition from the institutional perspective. It also focuses on internationalization of firms from an emerging country, which is characterized by a lack of firm-specific resources. The proposed framework seems promising for future research investigating coopetition and institutions within an integrated analytical framework.
“In sickness and in health, in poverty and in wealth?”
Authors: Roman Pais Seles Bruno Michel , Lopes de Sousa Jabbour Ana Beatriz , Chiappetta Jabbour Charbel Jose , Jugend Daniel
Published: February 2018

Purpose

“Economic crises” and “corporate social responsibility (CSR) initiatives” are two issues that dominate the modern business agenda. Although related, these issues have been analysed separately, and so a significant gap is perpetuated between the two. What are the effects of economic crises on CSR initiatives? Can organisational social initiatives withstand economic crises? The purpose of this paper is to answer these questions.

Design/methodology/approach

An integrative literature review was conducted, considering: the economic and geographical context in which the research was conducted; the focus of each piece of research; the adopted research methods; organisational theories of analytical support; the sectors analysed; and the effects of economic crises on CSR initiatives and environmental management.

Findings

Some of the findings were as follows: most of the studies analysed reported that CSR helps companies to cope with economic crises by increasing the efficiency of investments and establishing better relations with stakeholders and markets; environmental practices are related to negative environmental performance in periods of economic crises; and CSR relates positively to financial performance in periods of economic crises.

Originality/value

This is one of the first integrative literature reviews to investigate what happens to the relationship between businesses and sustainable change management in periods of crises. This paper also offers a future research agenda for the issue, with 12 questions still unanswered by the latest research.