bluuebunny/crossref_metadata_2025 huggingface dataset:
UPML‐ABC and TF/SF boundary for unconditionally stable AH‐FDTD method in conductive medium
Authors: Huang Zheng‐Yu , Shi Li‐Hua , Zhou Yinghui , Chen Bin
Published: September 2015

For analysing the scattering problem in conductive medium with the new unconditionally stable associated Hermite (AH) finite‐difference time‐domain (FDTD) method, the formulation of uniaxial anisotropic perfectly matched layer absorbing boundary condition (UPML‐ABC) and the total‐field/scattered‐field (TF/SF) implementation scheme are deduced. By virtue of AH differential transformation matrix and the eigenvalue transformation, frequency‐dependent parameters of the lossy medium can be well treated in AH‐UPML, without using any additional auxiliary variables. Numerical verification for the scattering of buried conductor in lossy half‐space is performed. Compared with Mur's ABC, UPML increases the absorbing performance by more than 80 dB in AH‐FDTD analysis.
Relative resolution: A hybrid formalism for fluid mixtures
Authors: Chaimovich Aviel , Peter Christine , Kremer Kurt
Published: September 2015

We show here that molecular resolution is inherently hybrid in terms of relative separation. While nearest neighbors are characterized by a fine-grained (geometrically detailed) model, other neighbors are characterized by a coarse-grained (isotropically simplified) model. We notably present an analytical expression for relating the two models via energy conservation. This hybrid framework is correspondingly capable of retrieving the structural and thermal behavior of various multi-component and multi-phase fluids across state space.
The average stress in a suspension of cube-shaped magnetic particles subject to shear and magnetic fields
Authors: Mallavajula Rajesh K. , Archer Lynden A. , Koch Donald L.
Published: September 2015

The effect of a homogeneous magnetic field (H) on the bulk stress in a dilute suspension of weakly Brownian, magnetic cubes suspended in a Newtonian fluid subjected to a linear shear flow is studied. The stresslet on each cube is anisotropic and depends on its orientation. Application of a magnetic field results in anisotropy in the orientation distribution. The steady-state orientation distribution is derived as a function of the angle between the directions of the magnetic field and the fluid vorticity vector and the ratio of the magnetic torque to the viscous torque. Knowledge of the distribution function is used to derive a general expression for the bulk stress in a general linear flow field and a magnetic field. Specific numerical results are obtained for the intrinsic viscosity in a simple shear flow when the magnetic field is either parallel or perpendicular to the vorticity. When the magnetic field is perpendicular to vorticity, we find that the intrinsic viscosity increases at first with increasing shear rate passes through a maximum and then shear thins. The intrinsic viscosity can vary from 3.25 to 5.5 in response to changes in the relative strengths of the shear and magnetic fields. The maximum value of 5.5 is obtained when the magnetic moment of the cube, which is assumed to be parallel to the normal of one of the faces, lies in the flow gradient plane at an angle of π/4 from the flow direction.
Self-focusing of an intense laser pulse interacting with a periodic lattice of metallic nanoparticle
Authors: Sepehri Javan N.
Published: September 2015

The motivation for the present work is the study of self-focusing of an intense laser beam propagating through a periodic array of metallic nanoparticle. Using a perturbative method, a wave equation describing the nonlinear interaction of a laser beam with nanoparticles is derived. Evolution of laser spot size with the Gaussian profile for the circular and linear polarizations is considered. It is found that, in the same intensity, the linear polarization in a special interval of frequency resonantly acts better than the circular one.
Pressure in the Landau-Ginzburg functional: Pascal’s law, nucleation in fluid mixtures, a meanfield theory of amphiphilic action, and interface wetting in glassy liquids
Authors: Chan Ho Yin , Lubchenko Vassiliy
Published: September 2015

We set up the problem of finding the transition state for phase nucleation in multi-component fluid mixtures, within the Landau-Ginzburg density functional. We establish an expression for the coordinate-dependent local pressure that applies to mixtures, arbitrary geometries, and certain non-equilibrium configurations. The expression allows one to explicitly evaluate the pressure in spherical geometry, à la van der Waals. Pascal’s law is recovered within the Landau-Ginzburg density functional theory, formally analogously to how conservation of energy is recovered in the Lagrangian formulation of mechanics. We establish proper boundary conditions for certain singular functional forms of the bulk free energy density that allow one to obtain droplet solutions with thick walls in essentially closed form. The hydrodynamic modes responsible for mixing near the interface are explicitly identified in the treatment; the composition at the interface is found to depend only weakly on the droplet size. Next we develop a Landau-Ginzburg treatment of the effects of amphiphiles on the surface tension; the amphiphilic action is seen as a violation of Pascal’s law. We explicitly obtain the binding potential for the detergent at the interface and the dependence of the down-renormalization of the surface tension on the activity of the detergent. Finally, we argue that the renormalization of the activation barrier for escape from long-lived structures in glassy liquids can be viewed as an action of uniformly seeded, randomly oriented amphiphilic molecules on the interface separating two dissimilar aperiodic structures. This renormalization is also considered as a “wetting” of the interface. The resulting conclusions are consistent with the random first order transition theory.
Rayleigh-type parametric chemical oscillation
Authors: Ghosh Shyamolina , Ray Deb Shankar
Published: September 2015

We consider a nonlinear chemical dynamical system of two phase space variables in a stable steady state. When the system is driven by a time-dependent sinusoidal forcing of a suitable scaling parameter at a frequency twice the output frequency and the strength of perturbation exceeds a threshold, the system undergoes sustained Rayleigh-type periodic oscillation, wellknown for parametric oscillation in pipe organs and distinct from the usual forced quasiperiodic oscillation of a damped nonlinear system where the system is oscillatory even in absence of any external forcing. Our theoretical analysis of the parametric chemical oscillation is corroborated by full numerical simulation of two well known models of chemical dynamics, chlorite-iodine-malonic acid and iodine-clock reactions.
Investigation of long lifetimes in Cu(In,Ga)Se2 by time-resolved photoluminescence
Authors: Maiberg Matthias , Hölscher Torsten , Zahedi-Azad Setareh , Fränzel Wolfgang , Scheer Roland
Published: September 2015

The main objective of time-resolved photoluminescence (TRPL) is to characterize minority carrier recombination in semiconductors. However, trap states in the band gap can lead to artificially long decay times thus distorting the measured minority carrier lifetime. In this work, we propose to measure TRPL under elevated temperature and excitation in order to reduce minority carrier trapping. Taking three Cu(In,Ga)Se2 layers as examples, we show that the decay time decreases with increasing temperature—in accordance with simulations. Under increasing excitation, the decay time can become smaller due to trap saturation but also can become larger due to asymmetric hole and electron lifetimes. By comparison of simulation and experiment, we can find the energy, the density, and the electron capture cross-section of the trap which in the present example of Cu(In,Ga)Se2 films gives values of ∼200 meV, ∼1015 cm−3, and ∼10−13 cm2, respectively.
Investigations of quaternary interdiffusion in a constituent system of high entropy alloys
Authors: Kulkarni Kaustubh , Chauhan Gyanendra Pratap Singh
Published: September 2015

Interdiffusion was investigated at 1000°C in a quaternary Fe-Ni-Co-Cr system, which is an essential constituent of many high-entropy alloys. The relative values of main and cross interdiffusion coefficients determined from concentrations and interdiffusion fluxes developed in a single diffusion couple indicate that significant diffusional interactions exist in this system. Thermodynamic interactions between the binary constituents were analyzed based on the activity coefficient relations and it is shown that the observed diffusional interactions of a component with others are consistent with relative thermodynamic interactions between them.
Surface passivation of c-Si for silicon heterojunction solar cells using high-pressure hydrogen diluted plasmas
Authors: Deligiannis Dimitrios , Vasudevan Ravi , Smets Arno H. M. , van Swaaij René A. C. M. M. , Zeman Miro
Published: September 2015

In this work we demonstrate excellent c-Si surface passivation by depositing a-Si:H in the high-pressure and high hydrogen dilution regime. By using high hydrogen dilution of the precursor gases during deposition the hydrogen content of the layers is sufficiently increased, while the void fraction is reduced, resulting in dense material. Results show a strong dependence of the lifetime on the substrate temperature and a weaker dependence on the hydrogen dilution. After applying a post-deposition annealing step on the samples equilibration of the lifetime occurs independent of the initial nanostructure.
Resonance scattering and radiation force calculations for an elastic cylinder using the translational addition theorem for cylindrical wave functions
Authors: Mitri F. G.
Published: September 2015

The standard Resonance Scattering Theory (RST) of plane waves is extended for the case of any two-dimensional (2D) arbitrarily-shaped monochromatic beam incident upon an elastic cylinder with arbitrary location using an exact methodology based on Graf’s translational addition theorem for the cylindrical wave functions. The analysis is exact as it does not require numerical integration procedures. The formulation is valid for any cylinder of finite size and material that is immersed in a nonviscous fluid. Partial-wave series expansions (PWSEs) for the incident, internal and scattered linear pressure fields are derived, and the analysis is further extended to obtain generalized expressions for the on-axis and off-axis acoustic radiation force components. The wave-fields are expressed using generalized PWSEs involving the beam-shape coefficients (BSCs) and the scattering coefficients of the cylinder. The off-axial BSCs are expressed analytically in terms of an infinite PWSE with emphasis on the translational offset distance d. Numerical computations are considered for a zeroth-order quasi-Gaussian beam chosen as an example to illustrate the analysis. Acoustic resonance scattering directivity diagrams are calculated by subtracting an appropriate background from the expression of the scattered pressure field. In addition, computations for the radiation force exerted on an elastic cylinder centered on the axis of wave propagation of the beam, and shifted off-axially are analyzed and discussed.
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data
Authors: Yang Pengyi , Humphrey Sean J. , James David E. , Yang Yee Hwa , Jothi Raja
Published: September 2015

Motivation: Protein phosphorylation is a post-translational modification that underlines various aspects of cellular signaling. A key step to reconstructing signaling networks involves identification of the set of all kinases and their substrates. Experimental characterization of kinase substrates is both expensive and time-consuming. To expedite the discovery of novel substrates, computational approaches based on kinase recognition sequence (motifs) from known substrates, protein structure, interaction and co-localization have been proposed. However, rarely do these methods take into account the dynamic responses of signaling cascades measured from in vivo cellular systems. Given that recent advances in mass spectrometry-based technologies make it possible to quantify phosphorylation on a proteome-wide scale, computational approaches that can integrate static features with dynamic phosphoproteome data would greatly facilitate the prediction of biologically relevant kinase-specific substrates.

Results: Here, we propose a positive-unlabeled ensemble learning approach that integrates dynamic phosphoproteomics data with static kinase recognition motifs to predict novel substrates for kinases of interest. We extended a positive-unlabeled learning technique for an ensemble model, which significantly improves prediction sensitivity on novel substrates of kinases while retaining high specificity. We evaluated the performance of the proposed model using simulation studies and subsequently applied it to predict novel substrates of key kinases relevant to insulin signaling. Our analyses show that static sequence motifs and dynamic phosphoproteomics data are complementary and that the proposed integrated model performs better than methods relying only on static information for accurate prediction of kinase-specific substrates.

Availability and implementation: Executable GUI tool, source code and documentation are freely available at https://github.com/PengyiYang/KSP-PUEL.

Contact:  pengyi.yang@nih.gov or jothi@mail.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Association between malignancy and non-alcoholic Wernicke's encephalopathy: a case report and literature review
Authors: Choi Evan Y. , Gomes William A. , Haigentz Missak , Graber Jerome J.
Published: September 2015

Background

Wernicke's encephalopathy is a serious medical condition associated with high morbidity and mortality caused by deficiency of thiamine. This disease is classically associated with alcoholism, but is underappreciated in the nonalcoholic population. There is growing acknowledgement of the development of Wernicke's encephalopathy in patients with malignancies.

Methods

We conducted a literature review in PubMed for cases of Wernicke's encephalopathy occurring in patients with malignancy. We also present the case of a 47-year-old woman with recurrent laryngeal cancer and multiple hospital admissions for malnutrition. Neurological examination was notable for pendular nystagmus, severe gait ataxia, confusion, and poor memory consolidation. MRI of the brain was significant for T2-weighted fluid-attenuated inversion recovery hyperintensities in periaqueductal regions, medial thalami, and the tectal plate, typical for Wernicke's encephalopathy. She was treated with thiamine repletion, and had marked improvement in her mental status and some improvement in her vision problems and ataxia, although some nystagmus and significant short-term memory impairment persisted.

Results

The literature review yielded dozens of case reports of Wernicke's encephalopathy in patients with malignancy, dominated by cases of patients with malignancies of the gastrointestinal system, followed by those with hematologic malignancies.

Conclusions

Malignancy is an important risk factor for the development of Wernicke's encephalopathy. This diagnosis is underappreciated and difficult for the clinician to discern from multifactorial delirium. Clinicians should be aware to treat at-risk patients with thiamine immediately, especially if multiple risk factors are present.
Intensifying Antiretroviral Therapy With Raltegravir and Maraviroc During Early Human Immunodeficiency Virus (HIV) Infection Does Not Accelerate HIV Reservoir Reduction
Authors: Ostrowski Mario , Benko Erika , Yue Feng Yun , Kim Connie J. , Huibner Sanja , Lee Terry , Singer Joel , Pankovich Jim , Laeyendecker Oliver , Kaul Rupert , Kandel Gabor , Kovacs Colin
Published: September 2015

Background.  Persistent human immunodeficiency virus (HIV) within the CD4+ T-cell reservoir is an obstacle to eradication. We hypothesized that adding raltegravir and maraviroc to standard combination antiretroviral therapy (cART) during early HIV infection could substantially reduce viral reservoirs as a step towards eradication.

Methods.  A prospective, randomized, double-blinded, placebo-controlled pilot trial enrolled 32 participants with documented early (<6 months) HIV infection to either standard cART (emtricitabine/tenofovir/lopinavir/ritonavir) or intensive cART (standard regimen + raltegravir/maraviroc). Human immunodeficiency virus reservoirs were assessed at baseline and at 48 weeks by (1) proviral DNA, (2) cell-associated RNA, and (3) replication-competent virus, all from purified blood CD4+ T cells, and (4) gut proviral DNA. A multiassay algorithm (MAA) on baseline sera estimated timing of infection.

Results.  Thirty individuals completed the study to the 48-week endpoint. The reduction in blood proviral burden was −1.03 log DNA copies/106 CD4+ T cells versus −.84 log in the standard and intensive groups, respectively (P = .056). Overall, there was no significant difference in the rate of decline of HIV-associated RNA, replication-competent virus in blood CD4+ T cells, nor proviral gut HIV DNA to 48 weeks. Individuals who presented with more recent HIV infection had significantly lower virus reservoirs, and cART tended to reduce their reservoirs to a greater extent.

Conclusions.  Intensive cART led to no additional reduction in the blood virus reservoir at 48 weeks compared with standard cART. Human immunodeficiency virus reservoir size is smaller earlier in HIV infection. Other novel treatment strategies in combination with early cART will be needed to eliminate the HIV latent reservoir.
Secondary Epiretinal Membrane After Trabeculectomy
Authors: Vieira Luísa , Cabugueira Ana , Borges Bárbara , Carvalho Vanessa , Noronha Manuel , Abegão Pinto Luis , Reina Maria , Dutra Medeiros Marco
Published: September 2015

Purpose:

To determine the frequency of epiretinal membranes (ERM) in eyes with primary open-angle glaucoma subjected to trabeculectomy.

Methods:

We conducted a retrospective study on patients subjected to trabeculectomy with at least a 6-month follow-up. Ophthalmologic examination and spectral-domain optical coherence tomography (SD-OCT) were analyzed. Eyes with previous surgical or laser treatments or other pathologies (other than glaucoma and ERM) were excluded.

Results:

A total of 50 eyes (40 patients) were included in this study. The mean follow-up time after surgery was 27.8 months. After surgery, 9 eyes (18%) had preretinal macular fibrosis and 19 eyes (38%) had cellophane macular reflex. Of the 16 eyes with a preoperative macular SD-OCT, 3 (18.8%) developed ERM and 4 (25%) progressed from cellophane macular reflex to preretinal macular fibrosis, after surgery. The ERM frequency did not differ significantly between eyes subjected to trabeculectomy with or without the use of antimetabolites (P=0.08), or between eyes subjected to simple or combined surgery (phacotrabeculectomy) (P=0.09).

Conclusion:

Trabeculectomy may predispose one to the appearance and progression of ERM. Further studies are needed to clarify this intriguing relation.
Lateral Canthal Tendon Disinsertion: Clinical Characteristics and Anatomical Correlates
Authors: Shriver Erin M. , Erickson Benjamin P. , Kossler Andrea L. , Tse David T.
Published: September 2015

Purpose:

To highlight features of lateral canthal tendon disinsertion (LCTD), provide an algorithm for systematic assessment, and describe the anatomic genesis of signs and symptoms.

Methods:

Retrospective case series of consecutive patients with lateral canthal tendon disinsertion, who underwent lateral canthal tendon fixation by a single surgeon (DTT) between 2004 and 2011.

Results:

One hundred and seventeen eyes in 90 patients underwent lateral canthal tendon fixation. Average age was 69.3 ± 17.9 years. Twenty-three percentage of eyes had undergone lower eyelid blepharoplasty and 52% had undergone lateral canthal tightening; 35% had no previous periocular surgery. Patients with purely involutional lateral canthal tendon disinsertion were significantly older (76.1 ± 7.8 years of age; p < 0.03). Six key features associated with lateral canthal tendon disinsertion were identified. On static evaluation: 1) a blunted or vertically displaced lateral canthal angle; 2) a narrow horizontal fissure with reduced temporal scleral triangle; and 3) pseudo eyelid retraction. On dynamic evaluation with attempted closure: 4) medial and inferior movement of the lateral commissure; 5) incomplete apposition of the eyelid margins in the absence of anterior lamellar shortage; and 6) temporal eyelid imbrication. Improved blink dynamics with manual lateral canthal tendon complex repositioning (“the thumb test”) predicted a favorable outcome with surgical tightening in 95.7% of cases.

Conclusions:

Lateral canthal tendon disinsertion results in altered eyelid fissure symmetry, blink dynamics, and lacrimal pump function. The authors recommend the mnemonic—A.B.C.: for Aperture configuration, Blink dynamics, and eyelid Closure—to structure the examination of all symptomatic patients. Manual restoration of the disinserted lateral canthal tendon with the “thumb test” predicts favorable outcomes with surgical fixation.
Pseudomonas Aeruginosa: A Masquerader in Sino-Orbital Infections
Authors: Chen Xi , Bleier Benjamin S. , Lefebvre Daniel R. , Lee Nahyoung Grace
Published: September 2015

Purpose:

To report 2 immunocompromised patients with sino-orbital necrotizing pseudomonas infections and review the literature.

Methods:

This is a noncomparative, retrospective case series, and review. The clinical data of 2 patients with histopathologic and microbiologic diagnoses of pseudomonas sinus infections causing orbital cellulitis were obtained from medical records. A retrospective literature review was performed on all reported cases of periorbital pseudomonas infections.

Results:

One patient with acquired immune deficiency syndrome was noted to have orbital cellulitis with clear visualization of eschar in the middle turbinate on nasal endoscopy. A second patient also had orbital cellulitis with ophthalmoplegia and presence of eschar in the sinus. Both patients had some degree of erosion through the lamina papyracea found on orbital imaging and both had intact vision without optic neuropathy. Pseudomonas infection was confirmed in both cases with permanent histopathology and cultures from conservative sinus debridement.

Conclusions:

Pseudomonas sino-orbital infections must be considered in the differential diagnosis in cases of eschar and orbital wall erosion especially when vision is preserved in immunocompromised individuals. This finding obviates the need for radical debridement including orbital exenteration, which can be indicated in cases of invasive fungal disease.
Local Resection and Brachytherapy for Primary Orbital Rhabdomyosarcoma: Outcome and Failure Pattern Analysis
Authors: Schoot Reineke A. , Saeed Peerooz , Freling Nicole J. , Blank Leo E. C. M. , Pieters Bradley R. , van der Grient Johan N. B. , Strackee Simon D. , Bras Johannes , Caron Huib N. , Merks Johannes H. M.
Published: September 2015

Purpose:

Survival in patients with orbital rhabdomyosarcoma (RMS) is excellent. Therefore, new local treatment modalities, such as brachytherapy, have been developed to minimize adverse events. Since 1990, patients with orbital RMS and a residual tumor after induction chemotherapy were eligible for resection and brachytherapy. Otherwise patients received external beam radiotherapy. In this study, the authors describe the outcome for 20 patients with primary orbital RMS. The aim was to assess risk factors for treatment failure in this single center cohort.

Methods:

In this retrospective cohort study, the authors reviewed imaging studies, surgery reports, histology reports, and radiotherapy plans in a multidisciplinary setting. The authors included 20 consecutive patients with orbital RMS, treated between 1990 and 2007, (median age: 7.4 years, range: 0.7–16.1; median follow up: 11.5 years).

Results:

After induction chemotherapy, 12 patients were treated with surgery and brachytherapy, 2 with external beam radiotherapy, and in 5 patients who achieved complete remission, local treatment was withheld. In 1 patient, brachytherapy was incorrectly withheld after delayed surgery. Seven patients relapsed (no local treatment, N = 2; surgery and brachytherapy, N = 2; external beam radiotherapy, N = 2; surgery only, N = 1). The authors found no patient, tumor, or treatment characteristics that predisposed for treatment failure. Ten-year-overall survival and event-free survival were 89% and 65%, respectively.

Conclusions:

Overall survival in this cohort of orbital RMS patients was good, including surgery and brachytherapy as treatment modality for orbital RMS resulted in an effective local treatment approach with fewer adverse events than external beam radiotherapy. The authors could not identify factors predisposing for treatment failure.
Systemic Intravenous Lidocaine for the Treatment of Complex Regional Pain Syndrome: A Case Report and Literature Review
Authors: Rickard Joshua P. , Kish Troy
Published: September 2015

Complex regional pain syndrome (CRPS) was described in 1864 by Mitchell et al as a condition characterized by many unique symptoms. Although symptoms may differ from patient to patient, the most common complaints are painful swelling in upper or lower extremities or changes in the skin. CRPS has been given many different names since it was first mentioned in the literature in 1851. The most common alternative names include causalgia, aglodystrophy, and sympathetic dystrophy syndrome. This condition is generally diagnosed in older adults because of trauma, nerve damage, and coronary artery disease; however, there are cases of CRPS affecting the pediatric and young adult population. The fourth edition of the diagnostic and treatment guidelines of CRPS published by Harden et al in 2013 suggest many different pharmacologic treatment options for these patients. Intravenous lidocaine is used to block the sodium channels in neuronal membranes, thus stopping initiation and conduction of impulses associated with neuropathic and inflammatory pain. The use of regional intravenous lidocaine (by applying a tourniquet on the affected extremity) has been well-documented in the literature with a successful decrease in pain symptoms. A unique case of the use of systemic intravenous lidocaine will be presented.
Beyond contact-based transmission networks: the role of spatial coincidence
Authors: Richardson Thomas O. , Gorochowski Thomas E.
Published: September 2015

Animal societies rely on interactions between group members to effectively communicate and coordinate their actions. To date, the transmission properties of interaction networks formed by direct physical contacts have been extensively studied for many animal societies and in all cases found to inhibit spreading. Such direct interactions do not, however, represent the only viable pathways. When spreading agents can persist in the environment, indirect transmission via ‘same-place, different-time’ spatial coincidences becomes possible. Previous studies have neglected these indirect pathways and their role in transmission. Here, we use rock ant colonies, a model social species whose flat nest geometry, coupled with individually tagged workers, allowed us to build temporally and spatially explicit interaction networks in which edges represent either direct physical contacts or indirect spatial coincidences. We show how the addition of indirect pathways allows the network to enhance or inhibit the spreading of different types of agent. This dual-functionality arises from an interplay between the interaction-strength distribution generated by the ants' movement and environmental decay characteristics of the spreading agent. These findings offer a general mechanism for understanding how interaction patterns might be tuned in animal societies to control the simultaneous transmission of harmful and beneficial agents.
Recoverability in quantum information theory
Authors: Wilde Mark M.
Published: September 2015

The fact that the quantum relative entropy is non-increasing with respect to quantum physical evolutions lies at the core of many optimality theorems in quantum information theory and has applications in other areas of physics. In this work, we establish improvements of this entropy inequality in the form of physically meaningful remainder terms. One of the main results can be summarized informally as follows: if the decrease in quantum relative entropy between two quantum states after a quantum physical evolution is relatively small, then it is possible to perform a recovery operation, such that one can perfectly recover one state while approximately recovering the other. This can be interpreted as quantifying how well one can reverse a quantum physical evolution. Our proof method is elementary, relying on the method of complex interpolation, basic linear algebra and the recently introduced Rényi generalization of a relative entropy difference. The theorem has a number of applications in quantum information theory, which have to do with providing physically meaningful improvements to many known entropy inequalities.
Temporal variability and cooperative breeding: testing the bet-hedging hypothesis in the acorn woodpecker
Authors: Koenig Walter D. , Walters Eric L.
Published: September 2015

Cooperative breeding is generally considered an adaptation to ecological constraints on dispersal and independent breeding, usually due to limited breeding opportunities. Although benefits of cooperative breeding are typically thought of in terms of increased mean reproductive success, it has recently been proposed that this phenomenon may be a bet-hedging strategy that reduces variance in reproductive success (fecundity variance) in populations living in highly variable environments. We tested this hypothesis using long-term data on the polygynandrous acorn woodpecker (
Melanerpes formicivorus
). In general, fecundity variance decreased with increasing sociality, at least when controlling for annual variation in ecological conditions. Nonetheless, decreased fecundity variance was insufficient to compensate for reduced
per capita
reproductive success of larger, more social groups, which typically suffered lower estimated mean fitness. We did, however, find evidence that sociality in the form of larger group size resulted in increased fitness in years following a small acorn crop due to reduced fecundity variance. Bet-hedging, although not the factor driving sociality in general, may play a role in driving acorn woodpecker group living when acorns are scarce and ecological conditions are poor.
Decreasing sleep requirement with increasing numbers of neurons as a driver for bigger brains and bodies in mammalian evolution
Authors: Herculano-Houzel Suzana
Published: September 2015

Mammals sleep between 3 and 20 h d
−1
, but what regulates daily sleep requirement is unknown. While mammalian evolution has been characterized by a tendency towards larger bodies and brains, sustaining larger bodies and brains requires increasing hours of feeding per day, which is incompatible with a large sleep requirement. Mammalian evolution, therefore, must involve mechanisms that tie increasing body and brain size to decreasing sleep requirements. Here I show that daily sleep requirement decreases across mammalian species and in rat postnatal development with a decreasing ratio between cortical neuronal density and surface area, which presumably causes sleep-inducing metabolites to accumulate more slowly in the parenchyma. Because addition of neurons to the non-primate cortex in mammalian evolution decreases this ratio, I propose that increasing numbers of cortical neurons led to decreased sleep requirement in evolution that allowed for more hours of feeding and increased body mass, which would then facilitate further increases in numbers of brain neurons through a larger caloric intake per hour. Coupling of increasing numbers of neurons to decreasing sleep requirement and increasing hours of feeding thus may have not only allowed but also driven the trend of increasing brain and body mass in mammalian evolution.
Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment withEscherichia coli
Authors: Lenski Richard E. , Wiser Michael J. , Ribeck Noah , Blount Zachary D. , Nahum Joshua R. , Morris J. Jeffrey , Zaman Luis , Turner Caroline B. , Wade Brian D. , Maddamsetti Rohan , Burmeister Alita R. , Baird Elizabeth J. , Bundy Jay , Grant Nkrumah A. , Card Kyle J. , Rowles Maia , Weatherspoon Kiyana , Papoulis Spiridon E. , Sullivan Rachel , Clark Colleen , Mulka Joseph S. , Hajela Neerja
Published: September 2015

Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population’s mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories ofEscherichia colipopulations over 50,000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10,000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely— or at least for a long time—even in a constant environment.
A sucrose-binding site provides a lead towards an isoform-specific inhibitor of the cancer-associated enzyme carbonic anhydrase IX
Authors: Pinard Melissa A. , Aggarwal Mayank , Mahon Brian P. , Tu Chingkuang , McKenna Robert
Published: September 2015

Human carbonic anhydrase (CA; EC 4.2.1.1) isoform IX (CA IX) is an extracellular zinc metalloenzyme that catalyzes the reversible hydration of CO2 to HCO3
−, thereby playing a role in pH regulation. The majority of normal functioning cells exhibit low-level expression of CA IX. However, in cancer cells CA IX is upregulated as a consequence of a metabolic transition known as the Warburg effect. The upregulation of CA IX for cancer progression has drawn interest in it being a potential therapeutic target. CA IX is a transmembrane protein, and its purification, yield and crystallization have proven challenging to structure-based drug design, whereas the closely related cytosolic soluble isoform CA II can be expressed and crystallized with ease. Therefore, we have utilized structural alignments and site-directed mutagenesis to engineer a CA II that mimics the active site of CA IX. In this paper, the X-ray crystal structure of this CA IX mimic in complex with sucrose is presented and has been refined to a resolution of 1.5 Å, an R
cryst of 18.0% and an R
free of 21.2%. The binding of sucrose at the entrance to the active site of the CA IX mimic, and not CA II, in a non-inhibitory mechanism provides a novel carbohydrate moiety binding site that could be further exploited to design isoform-specific inhibitors of CA IX.
Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide
Authors: Srikannathasan Velupillai , Wohlkonig Alexandre , Shillings Anthony , Singh Onkar , Chan Pan F. , Huang Jianzhong , Gwynn Michael N. , Fosberry Andrew P. , Homes Paul , Hibbs Martin , Theobald Andrew J. , Spitzfaden Claus , Bax Benjamin D.
Published: September 2015

Fluoroquinolone drugs such as moxifloxacin kill bacteria by stabilizing the normally transient double-stranded DNA breaks created by bacterial type IIA topoisomerases. Previous crystal structures of Staphylococcus aureus DNA gyrase with asymmetric DNAs have had static disorder (with the DNA duplex observed in two orientations related by the pseudo-twofold axis of the complex). Here, 20-base-pair DNA homoduplexes were used to obtain crystals of covalent DNA-cleavage complexes of S. aureus DNA gyrase. Crystals with QPT-1, moxifloxacin or etoposide diffracted to between 2.45 and 3.15 Å resolution. A G/T mismatch introduced at the ends of the DNA duplexes facilitated the crystallization of slightly asymmetric complexes of the inherently flexible DNA-cleavage complexes.
Structure and binding properties of a cameloid nanobody raised against KDM5B
Authors: Wiuf Anders , Kristensen Line Hyltoft , Kristensen Ole , Dorosz Jerzy , Jensen Jonas , Gajhede Michael
Published: September 2015

The histone demethylase KDM5B is considered to be a promising target for anticancer therapy. Single-chain antibodies from llama (nanobodies) have been raised to aid in crystallization and structure determination of this enzyme. The antigen-binding properties of 15 of these nanobodies have been characterized. The crystal structure of one of these (NB17) has been determined to a resolution of 1.85 Å. NB17 crystallizes in space groupP4322 with six molecules in the asymmetric unit. The six molecules in the asymmetric unit pack as an entity with approximateD3 symmetry with interactions mediated by the CDR loops, which could act as a crystallization nucleus. NB17 does not bind to monomeric KDM5B residues 1–820, but is found to bind to aggregates formed after incubation at 310 K.
Purification, crystallization and X-ray crystallographic analysis of human RAB11(S20V), a constitutively active GTP-binding form
Authors: Kim Chang Min , Choi Jae Young , Yoon Jong Hwan , Park Hyun Ho
Published: September 2015

RAB11, a member of the Ras superfamily of small G proteins, is involved in the regulation of vesicle trafficking during endosome recycling. Substitution of Ser20 by Val20 in Rab11 [RAB11(S20V)] inhibits its GTP hydrolysis activity and produces a constitutively active GTP-binding form. In this study, the RAB11(S20V) mutant was overexpressed inEscherichia coliwith an engineered C-terminal His tag. RAB11(S20V) was then purified to homogeneity and was crystallized at 293 K. X-ray diffraction data were collected to a resolution of 2.4 Å from a crystal belonging to space groupI4, with unit-cell parametersa = 74.11,b= 74.11,c= 149.44 Å. The asymmetric unit was estimated to contain two molecules of RAB11(S20V).
Extension of resolution and oligomerization-state studies of 2,4′-dihydroxyacetophenone dioxygenase fromAlcaligenessp. 4HAP
Authors: Guo J. , Erskine P. , Coker A. R. , Gor J. , Perkins S. J. , Wood S. P. , Cooper J. B.
Published: September 2015

The enzyme 2,4′-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid. This enzyme is a very unusual dioxygenase in that it cleaves a C—C bond in a substituent of the aromatic ring rather than within the ring itself. Whilst it has been shown that DAD is a tetramer in solution, the recently solved crystal structure of theAlcaligenessp. 4HAP enzyme was in fact dimeric rather than tetrameric. Since the use of limited chymotrypsinolysis, which apparently results in removal of the first 20 or so N-terminal residues of DAD, was necessary for crystallization of the protein, it was investigated whether this was responsible for the change in its oligomerization state. Gel-filtration and analytical ultracentrifugation studies were conducted, which confirmed that chymotrypsinolysed DAD has an apparent molecular weight of around 40 kDa, corresponding to a dimer. In contrast, the native enzyme has a molecular weight in the 70–80 kDa region, as expected for the tetramer. The structural basis for tetramerization has been investigated by the use of several docking servers, and the results are remarkably consistent with the tetrameric structure of a homologous cupin protein fromRalstonia eutropha(PDB entry 3ebr).
An active site–tail interaction in the structure of hexahistidine-taggedThermoplasma acidophilumcitrate synthase
Authors: Murphy Jesse R. , Donini Stefano , Kappock T. Joseph
Published: September 2015

Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophileThermoplasma acidophilum(TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open' structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site–tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.
Structural analysis of SepL, an enteropathogenicEscherichia colitype III secretion-system gatekeeper protein
Authors: Burkinshaw Brianne J. , Souza Sergio A. , Strynadka Natalie C. J.
Published: September 2015

During infection, enteropathogenicEscherichia coliassembles a complex multi-protein type III secretion system that traverses the bacterial membranes and targets the host cell membrane to directly deliver virulence or effector proteins to the host cytoplasm. As this secretion system is composed of more than 20 proteins, many of which form oligomeric associations, its assembly must be tightly regulated. A protein called the gatekeeper, or SepL, ensures that the secretion of the translocon component, which inserts into the host membrane, occurs before the secretion of effectors. The crystal structure of the gatekeeper SepL was determined and compared with the structures of SepL homologues from other bacterial pathogens in order to identify SepL residues that may be critical for its role in type III secretion-system assembly.
Structure of a catalytic dimer of the α- and β-subunits of the F-ATPase fromParacoccus denitrificansat 2.3 Å resolution
Authors: Morales-Ríos Edgar , Montgomery Martin G. , Leslie Andrew G. W. , García-Trejo José J. , Walker John E.
Published: September 2015

The structures of F-ATPases have predominantly been determined from mitochondrial enzymes, and those of the enzymes in eubacteria have been less studied.Paracoccus denitrificansis a member of the α-proteobacteria and is related to the extinct protomitochondrion that became engulfed by the ancestor of eukaryotic cells. TheP. denitrificansF-ATPase is an example of a eubacterial F-ATPase that can carry out ATP synthesis only, whereas many others can catalyse both the synthesis and the hydrolysis of ATP. Inhibition of the ATP hydrolytic activity of theP. denitrificansF-ATPase involves the ζ inhibitor protein, an α-helical protein that binds to the catalytic F1domain of the enzyme. This domain is a complex of three α-subunits and three β-subunits, and one copy of each of the γ-, δ- and ∊-subunits. Attempts to crystallize the F1–ζ inhibitor complex yielded crystals of a subcomplex of the catalytic domain containing the α- and β-subunits only. Its structure was determined to 2.3 Å resolution and consists of a heterodimer of one α-subunit and one β-subunit. It has no bound nucleotides, and it corresponds to the `open' or `empty' catalytic interface found in other F-ATPases. The main significance of this structure is that it aids in the determination of the structure of the intact membrane-bound F-ATPase, which has been crystallized.
The structure of the death receptor 4–TNF-related apoptosis-inducing ligand (DR4–TRAIL) complex
Authors: Ramamurthy Vidhyashankar , Yamniuk Aaron P. , Lawrence Eric J. , Yong Wei , Schneeweis Lumelle A. , Cheng Lin , Murdock Melissa , Corbett Martin J. , Doyle Michael L. , Sheriff Steven
Published: September 2015

The structure of death receptor 4 (DR4) in complex with TNF-related apoptosis-inducing ligand (TRAIL) has been determined at 3 Å resolution and compared with those of previously determined DR5–TRAIL complexes. Consistent with the high sequence similarity between DR4 and DR5, the overall arrangement of the DR4–TRAIL complex does not differ substantially from that of the DR5–TRAIL complex. However, subtle differences are apparent. In addition, solution interaction studies were carried out that show differences in the thermodynamics of binding DR4 or DR5 with TRAIL.
Home is where the shell is: predicting turtle home range sizes
Authors: Slavenko Alex , Itescu Yuval , Ihlow Flora , Meiri Shai
Published: September 2015

Home range is the area traversed by an animal in its normal activities. The size of home ranges is thought to be tightly linked to body size, through size effect on metabolic requirements. Due to the structure of Eltonian food pyramids, home range sizes of carnivores are expected to exceed those of herbivorous species. The habitat may also affect home range size, with reduced costs of locomotion or lower food abundance in, for example, aquatic habitats selecting for larger home ranges. Furthermore, home range of males in polygamous species may be large due to sexual selection for increased reproductive output.

Comparative studies on home range sizes have rarely been conducted on ectotherms. Because ectotherm metabolic rates are much lower than those of endotherms, energetic considerations of metabolic requirements may be less important in determining the home range sizes of the former, and other factors such as differing habitats and sexual selection may have an increased effect.

We collected literature data on turtle home range sizes. We used phylogenetic generalized least squares analyses to determine whether body mass, sex, diet, habitat and social structure affect home range size.

Turtle home range size increases with body mass. However, body mass explains relatively little of the variation in home range size. Aquatic turtles have larger home ranges than semiaquatic species. Omnivorous turtles have larger home ranges than herbivores and carnivores, but diet is not a strong predictor. Sex and social structure are unrelated to home range size.

We conclude that energetic constraints are not the primary factor that determines home range size in turtles, and energetic costs of locomotion in different habitats probably play a major role.