bluuebunny/crossref_metadata_2025 huggingface dataset:
Does low-dose methotrexate deserve more respect from clinicians?
Authors: Luu Brent , Rodway George W.
Published: April 2017

Medical errors associated with low-dose methotrexate may be life-threatening. Prescribers should be cognizant of the medication's toxicities and the persistent challenges in preventing adverse events. This article reviews the properties of methotrexate and its common drug-drug interactions. Best practices from the Institute for Safe Medication Practices, aimed at reducing methotrexate errors, are highlighted.
Changes in Personal Relationships During Residency and Their Effects on Resident Wellness: A Qualitative Study
Authors: Law Marcus , Lam Michelle , Wu Diana , Veinot Paula , Mylopoulos Maria
Published: April 2017

Purpose

Residency poses challenges for residents’ personal relationships. Research suggests residents rely on family and friends for support during their training. The authors explored the impact of residency demands on residents’ personal relationships and the effects changes in those relationships could have on their wellness.

Method

The authors used a constructivist grounded theory approach. In 2012–2014, they conducted semistructured interviews with a purposive and theoretical sample of 16 Canadian residents from various specialties and training levels. Data analysis occurred concurrently with data collection, allowing authors to use a constant comparative approach to explore emergent themes. Transcripts were coded; codes were organized into categories and then themes to develop a substantive theory.

Results

Residents perceived their relationships to be influenced by their evolving professional identity: Although personal relationships were important, being a doctor superseded them. Participants suggested they were forced to adapt their personal relationships, which resulted in the evolution of a hierarchy of relationships that was reinforced by the work–life imbalance imposed by their training. This poor work–life balance seemed to result in relationship issues and diminish residents’ wellness. Participants applied coping mechanisms to manage the conflict arising from the adaptation and protect their relationships. To minimize the effects of identity dissonance, some gravitated toward relationships with others who shared their professional identity or sought social comparison as affirmation.

Conclusions

Erosion of personal relationships could affect resident wellness and lead to burnout. Educators must consider how educational programs impact relationships and the subsequent effects on resident wellness.
Plasma Concentration of Itraconazole in Patients With Hematologic Malignancies Treated With Itraconazole Oral Solution
Authors: Marumo Atsushi , Miyawaki Shuichi , Dan Naoaki , Ishiyama Ken
Published: April 2017

Background:

The prophylactic administration of itraconazole (ITCZ) is effective for preventing mycotic infections during chemotherapy in patients with hematologic malignancies. However, fungal infections can occur when the ITCZ does not reach an effective concentration.

Methods:

We conducted a prospective study to monitor the plasma concentration of ITCZ and hydroxyl-ITCZ (OH-ITCZ) weekly and to verify whether the day 3 plasma concentration of ITCZ could predict the subsequent acquisition of an effective plasma concentration.

Results:

A total of 39 patients who underwent 66 courses of chemotherapy were assessed in this study. An effective plasma concentration was achieved on day 7 in 34 of 63 patients (54%) and on day 14 in 35 of 59 patients (59%). A univariate analysis revealed that age, type of chemotherapy, and the body surface area were significantly associated with a high plasma concentration of ITCZ + OH-ITCZ. A linear regression analysis extracted the body surface area and the type of chemotherapy as significant factors. An receiver operating characteristic curve analysis revealed a day 3 plasma ITCZ + OH-ITCZ concentration of >656 ng/mL led to a plasma concentration that exceeded the minimum effective level on day 7; the sensitivity and specificity were 62% and 93%, respectively.

Conclusions:

This study showed that the measurement of the day 3 plasma concentration could lead to a better outcome in patients receiving chemotherapy for hematologic malignancies.
Establishing Content Validity of the CLEFT-Q: A New Patient-reported Outcome Instrument for Cleft Lip/Palate
Authors: Tsangaris Elena , Wong Riff Karen W.Y. , Goodacre Tim , Forrest Christopher R. , Dreise Marieke , Sykes Jonathan , de Chalain Tristan , Harman Karen , O’Mahony Aisling , Pusic Andrea L. , Thabane Lehana , Thoma Achilleas , Klassen Anne F.
Published: April 2017

Background:

The CLEFT-Q is a new patient-reported outcome instrument designed to measure outcomes that matter to patients. The aim of this qualitative study was to establish content validity of the CLEFT-Q in patients who differ by age and culture.

Methods:

Patients aged between 6 and 29 years were recruited from plastic surgery clinics in Canada, India, Ireland, the Philippines, the Netherlands and the United States. Healthcare providers and other experts participated in a focus group or provided individual feedback. Input was sought on all aspects of the CLEFT-Q (item wording, instructions, and response options), and to identify missing content. Patient interviews and expert feedback took place between September 2013 and September 2014.

Results:

Sixty-nine patients and 44 experts participated. The first draft of the CLEFT-Q consisted of 163 items measuring 12 constructs. The first round of feedback identified 92 items that required revision. In total, 3 rounds of interviews, and the involvement of an artist to create pictures for 17 items, were needed to establish content validity. At the conclusion of cognitive interviews, the CLEFT-Q consisted of 13 scales (total 171 items) that measure appearance, health-related quality of life, and facial function. The mean Flesch-Kincaid readability statistic for items was 1.4 (0 to 5.2).

Conclusion:

Cognitive interviews and expert review allowed us to identify items that required re-wording, re-conceptualizing, or to be removed, as well as any missing items. This process was useful for refining the CLEFT-Q scales for further testing.
Serum Neutrophil Gelatinase–Associated Lipocalin: A Diagnostic Marker in Pediatric Sepsis
Authors: Saleh Nagwan Yossery , Abo El Fotoh Wafaa Moustafa M. , El-Hawy Mahmoud A.
Published: April 2017

Objectives:

Sepsis is a life-threatening condition that arises when the response of the body to infection injures its own tissues and organs. The early prediction of sepsis by current clinical and laboratory methods remains inadequate. Serum neutrophil gelatinase–associated lipocalin level is increased in sepsis irrespective of renal dysfunction. Therefore, we aimed to correlate the serum neutrophil gelatinase–associated lipocalin value determined at admission with clinical progression and severity of disease in critically ill children and to declare its role as a potential diagnostic and prognostic marker for sepsis in critically ill children in the emergency department.

Design:

A prospective cohort study.

Setting:

The study carried out at the PICU of Menoufia University Hospital.

Patients:

We serially enrolled 120 critically ill children admitted to the PICU at 2 fixed days per week in addition to 40 healthy children served as controls.

Interventions:

Clinical examination was performed including calculation of the Pediatric Risk of Mortality and Pediatric Index of Mortality 2. Serum neutrophil gelatinase–associated lipocalin measurement was performed for patients at admission and for the controls. Patients were followed up for 30 days. The discriminatory power of neutrophil gelatinase– associated lipocalin was determined using the receiver-operating characteristic and other predictive likelihood values.

Measurements and Main Results:

Serum neutrophil gelatinase–associated lipocalin level was significantly higher among the total patient cohort and those with sepsis than among the controls (p < 0.001), also in patients with systemic inflammatory response syndrome without sepsis and patients without systemic inflammatory response syndrome (p = 0.04 and <0.001). Furthermore, plasma level of neutrophil gelatinase–associated lipocalin was significantly elevated in nonsurvivors compared with survivors (p < 0. 001). Receiver-operating characteristic curve analysis exhibited an area under the curve of 0.84 for neutrophil gelatinase–associated lipocalin for diagnosis of sepsis, whereas C-reactive protein had an area under the curve of 0.79. Regarding the prognosis, neutrophil gelatinase–associated lipocalin had an area under the curve of 0.74 for prediction of mortality, whereas the area under the curve for Pediatric Risk of Mortality, Pediatric Index of Mortality 2, and C-reactive protein were 0.59, 0.58, and 0.62, respectively.

Conclusion:

Overall, the data support the view that measurement at admission, serum neutrophil gelatinase–associated lipocalin results in substantial added value for early diagnosis and prognostication of sepsis in critically sick children.
Perceived Discrimination and Longitudinal Change in Kidney Function Among Urban Adults
Authors: Beydoun May A. , Poggi-Burke Angedith , Zonderman Alan B. , Rostant Ola S. , Evans Michele K. , Crews Deidra C.
Published: April 2017

Objective

Perceived discrimination has been associated with psychosocial distress and adverse health outcomes. We examined associations of perceived discrimination measures with changes in kidney function in a prospective cohort study, the Healthy Aging in Neighborhoods of Diversity across the Life Span.

Methods

Our study included 1620 participants with preserved baseline kidney function (estimated glomerular filtration rate [eGFR] ≥ 60 mL/min/1.73 m2) (662 whites and 958 African Americans, aged 30–64 years). Self-reported perceived racial discrimination and perceived gender discrimination (PGD) and a general measure of experience of discrimination (EOD) (“medium versus low,” “high versus low”) were examined in relation to baseline, follow-up, and annual rate of change in eGFR using multiple mixed-effects regression (γbase, γrate) and ordinary least square models (γfollow).

Results

Perceived gender discrimination “high versus low PGD” was associated with a lower baseline eGFR in all models (γbase = −3.51 (1.34), p = .009 for total sample). Among white women, high EOD was associated with lower baseline eGFR, an effect that was strengthened in the full model (γbase = −5.86 [2.52], p = .020). Overall, “high versus low” PGD was associated with lower follow-up eGFR (γfollow = −3.03 [1.45], p = .036). Among African American women, both perceived racial discrimination and PGD were linked to lower follow-up kidney function, an effect that was attenuated with covariate adjustment, indicating mediation through health-related, psychosocial, and lifestyle factors. In contrast, EOD was not linked to follow-up eGFR in any of the sex by race groups.

Conclusions

Perceived racial and gender discrimination are associated with lower kidney function assessed by glomerular filtration rate and the strength of associations differ by sex and race groups. Perceived discrimination deserves further investigation as a psychosocial risk factors for kidney disease.
Intelligence and Interleukin-6 in Older Adults: The Role of Repetitive Thought
Authors: Segerstrom Suzanne C. , Reed Rebecca G. , Scott April B.
Published: April 2017

Objective

Higher intelligence quotient (IQ) correlates with lower systemic inflammation, consistent with an association between lower IQ and disease risk. The present study examined the role of repetitive thought (RT) in the relationship between IQ and interleukin (IL)-6. RT is thinking attentively, repeatedly, and frequently about oneself and one's world and is characterized by valence (positive-negative), purpose (searching-solving), and total quantity (much-little).

Methods

Estimated IQ and RT dimension scores were assessed at baseline in a sample of older adults (N = 120, mean age = 74 years), who thereafter had blood drawn up to 10 times semiannually (n = 799). Models were adjusted for body mass index, chronological age, and statin medication.

Results

Higher IQ was associated with lower IL-6 (γ = −0.225, SE = 0.111, p = .045). Of the RT dimensions, only more total RT predicted lower IL-6 (γ = −0.037, SE = 0.011, p = .001), an effect that was not moderated by valence or purpose. More total RT accounted for part of the effect of IQ on IL-6 (indirect effect = −0.06 [confidence interval = −0.14 to −0.002]). There was also a significant interaction between IQ and total RT (F(1,119) = 6.97, p = .009), in which more total RT was more strongly associated with lower IL-6 for people with lower IQ.

Conclusions

Although some forms of RT such as worry may have negative health correlates for older adults, engaging in RT per se can be healthy insofar as it also encompasses planning, processing, and coping. Older adults with higher IQ were more likely to engage in RT, but those with average IQ benefitted the most with regard to a marker of systemic inflammation.
Geoffrey Ronald Burbidge. 24 September 1925 — 26 January 2010
Authors: Longair Malcolm , Rees Martin
Published: April 2017

Geoffrey (Geoff) Burbidge's career spanned the tumultuous years when astronomy was transformed from a purely optical science to a multi-wavelength discipline through the development of new types of astronomy—radio, X-ray,γ-ray, cosmic ray physics. These offered new astrophysical and cosmological challenges, which he grasped with relish. To all of these disciplines, Geoff, often in collaboration with his wife Margaret Burbidge (FRS 1964), made pioneering contributions, particularly in the areas of the synthesis of the chemical elements, the physics of extragalactic radio sources, the rotation curves of galaxies, the dark matter problem in clusters of galaxies, the physics of accretion discs and the origin of cosmic rays. He also espoused less popular causes such as the non-cosmological nature of the redshifts of quasars and was sceptical about the standard Big Bang picture of the origin of the large-scale structure and dynamics of the Universe. He was a flamboyant and outspoken astrophysicist who challenged his colleagues about their deeply held views on all aspects of astrophysics and cosmology. His service to the community included five years as director of the US Kitt Peak National Observatory, based in Tucson, Arizona, and as a most effective editor ofAnnual Review of Astronomy and Astrophysicsfor over 30 years and theAstrophysical Journal.
Wsv023 interacted with
Litopenaeus vannamei
γ-tubulin complex associated proteins 2, and decreased the formation of microtubules
Authors: Chen Yihong , Bi Haitao , Li Xiaoyun , Zhang Zezhi , Yue Haitao , Weng Shaoping , He Jianguo
Published: April 2017

A previous study found the key transcription factor of
Litopenaeus vannamei
PERK-eIF2α pathway cyclic AMP-dependent transcription factor 4 (LvATF4) was involved in the transcriptional regulation of white spot syndrome virus (WSSV) gene
wsv023
. Knocked-down expression of LvATF4 reduced the viral copy number and the cumulative mortality of WSSV-infected shrimp. These results suggested that wsv023 may be critical to WSSV infection but the precise function of wsv023 was still unknown. By using co-immunoprecipitation and pull-down assays, we show that wsv023 interacts with
L. vannamei
gamma complex-associated protein 2 (LvGCP2), which is the core protein of the γ-tubulin small complex. Knocked-down, the
wsv023
gene significantly reduced the copy number of WSSV in
L. vannamei
muscle, as well as the cumulative mortality of infected shrimp. And PERK-eIF2α pathway inhibition also showed reduced virus copy number and abrogated shrimp mortality. Furthermore, overexpression of wsv023 inhibited the formation of microtubules in 293T cells. Flow cytometry revealed that WSSV infection similarly decreased the formation of microtubules in
L. vannamei
haemocytes. These findings suggested that wsv023 plays a role in microtubule organization in host cells, which in turn may be beneficial to WSSV.
Modulation of the composite face effect by unintended emotion cues
Authors: Gray Katie L. H. , Murphy Jennifer , Marsh Jade E. , Cook Richard
Published: April 2017

When upper and lower regions from different
emotionless
faces are aligned to form a facial composite, observers ‘fuse’ the two halves together, perceptually. The illusory distortion induced by task-irrelevant (‘distractor’) halves hinders participants' judgements about task-relevant (‘target’) halves. This composite-face effect reveals a tendency to integrate feature information from disparate regions of intact upright faces, consistent with theories of holistic face processing. However, observers frequently perceive emotion in ostensibly neutral faces, contrary to the intentions of experimenters. This study sought to determine whether this ‘perceived emotion’ influences the composite-face effect. In our first experiment, we confirmed that the composite effect grows stronger as the strength of distractor emotion increased. Critically, effects of distractor emotion were induced by weak emotion intensities, and were incidental insofar as emotion cues hindered image matching, not emotion labelling
per se
. In Experiment 2, we found a correlation between the presence of perceived emotion in a set of ostensibly neutral distractor regions sourced from commonly used face databases, and the strength of illusory distortion they induced. In Experiment 3, participants completed a sequential matching composite task in which half of the distractor regions were rated high and low for perceived emotion, respectively. Significantly stronger composite effects were induced by the high-emotion distractor halves. These convergent results suggest that perceived emotion increases the strength of the composite-face effect induced by supposedly emotionless faces. These findings have important implications for the study of holistic face processing in typical and atypical populations.
Body size affects the strength of social interactions and spatial organization of a schooling fish (Pseudomugil signifer)
Authors: Romenskyy Maksym , Herbert-Read James E. , Ward Ashley J. W. , Sumpter David J. T.
Published: April 2017

While a rich variety of self-propelled particle models propose to explain the collective motion of fish and other animals, rigorous statistical comparison between models and data remains a challenge. Plausible models should be flexible enough to capture changes in the collective behaviour of animal groups at their different developmental stages and group sizes. Here, we analyse the statistical properties of schooling fish (Pseudomugil signifer) through a combination of experiments and simulations. We make novel use of a Boltzmann inversion method, usually applied in molecular dynamics, to identify the effective potential of the mean force of fish interactions. Specifically, we show that larger fish have a larger repulsion zone, but stronger attraction, resulting in greater alignment in their collective motion. We model the collective dynamics of schools using a self-propelled particle model, modified to include varying particle speed and a local repulsion rule. We demonstrate that the statistical properties of the fish schools are reproduced by our model, thereby capturing a number of features of the behaviour and development of schooling fish.
Classification of self-assembling protein nanoparticle architectures for applications in vaccine design
Authors: Indelicato G. , Burkhard P. , Twarock R.
Published: April 2017

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.
Group cohesion in foraging meerkats: follow the moving ‘vocal hot spot’
Authors: Gall Gabriella E. C. , Manser Marta B.
Published: April 2017

Group coordination, when ‘on the move’ or when visibility is low, is a challenge faced by many social living animals. While some animals manage to maintain cohesion solely through visual contact, the mechanism of group cohesion through other modes of communication, a necessity when visual contact is reduced, is not yet understood. Meerkats (Suricata suricatta), a small, social carnivore, forage as a cohesive group while moving continuously. While foraging, they frequently emit ‘close calls’, soft close-range contact calls. Variations in their call rates based on their local environment, coupled with individual movement, produce a dynamic acoustic landscape with a moving ‘vocal hotspot’ of the highest calling activity. We investigated whether meerkats follow such a vocal hotspot by playing back close calls of multiple individuals to foraging meerkats from the front and back edge of the group simultaneously. These two artificially induced vocal hotspots caused the group to spatially elongate and split into two subgroups. We conclude that meerkats use the emergent dynamic call pattern of the group to adjust their movement direction and maintain cohesion. Our study describes a highly flexible mechanism for the maintenance of group cohesion through vocal communication, for mobile species in habitats with low visibility and where movement decisions need to be adjusted continuously to changing environmental conditions.
Geometric decompositions of collective motion
Authors: Mischiati Matteo , Krishnaprasad P. S.
Published: April 2017

Collective motion in nature is a captivating phenomenon. Revealing the underlying mechanisms, which are of biological and theoretical interest, will require empirical data, modelling and analysis techniques. Here, we contribute a geometric viewpoint, yielding a novel method of analysing movement. Snapshots of collective motion are portrayed as tangent vectors on configuration space, with length determined by the total kinetic energy. Using the geometry of fibre bundles and connections, this portrait is split into orthogonal components each tangential to a lower dimensional manifold derived from configuration space. The resulting decomposition, when interleaved with classical shape space construction, is categorized into a family of kinematic modes—including rigid translations, rigid rotations, inertia tensor transformations, expansions and compressions. Snapshots of empirical data from natural collectives can be allocated to these modes and weighted by fractions of total kinetic energy. Such quantitative measures can provide insight into the variation of the driving goals of a collective, as illustrated by applying these methods to a publicly available dataset of pigeon flocking. The geometric framework may also be profitably employed in the control of artificial systems of interacting agents such as robots.
Flow through a very porous obstacle in a shallow channel
Authors: Creed M. J. , Draper S. , Nishino T. , Borthwick A. G. L.
Published: April 2017

A theoretical model, informed by numerical simulations based on the shallow water equations, is developed to predict the flow passing through and around a uniform porous obstacle in a shallow channel, where background friction is important. This problem is relevant to a number of practical situations, including flow through aquatic vegetation, the performance of arrays of turbines in tidal channels and hydrodynamic forces on offshore structures. To demonstrate this relevance, the theoretical model is used to (i) reinterpret core flow velocities in existing laboratory-based data for an array of emergent cylinders in shallow water emulating aquatic vegetation and (ii) reassess the optimum arrangement of tidal turbines to generate power in a tidal channel. Comparison with laboratory-based data indicates a maximum obstacle resistance (or minimum porosity) for which the present theoretical model is valid. When the obstacle resistance is above this threshold the shallow water equations do not provide an adequate representation of the flow, and the theoretical model over-predicts the core flow passing through the obstacle. The second application of the model confirms that natural bed resistance increases the power extraction potential for a partial tidal fence in a shallow channel and alters the optimum arrangement of turbines within the fence.
Evanescent wave boundary layers in metamaterials and sidestepping them through a variational approach
Authors: Srivastava Ankit , Willis John R.
Published: April 2017

All metamaterial applications are based upon the idea that extreme material properties can be achieved through appropriate dynamic homogenization of composites. This homogenization is almost always done for infinite domains and the results are then applied to finite samples. This process ignores the evanescent waves which appear at the boundaries of such finite samples. In this paper, we first clarify the emergence and purpose of these evanescent waves in a model problem consisting of an interface between a layered composite and a homogeneous medium. We show that these evanescent waves form boundary layers on either side of the interface beyond which the composite can be represented by appropriate infinite domain homogenized relations. We show that if one ignores the boundary layers, then the displacement and stress fields are discontinuous across the interface. Therefore, the scattering coefficients at such an interface cannot be determined through the conventional continuity conditions involving only propagating modes. Here, we propose an approximate variational approach for sidestepping these boundary layers. The aim is to determine the scattering coefficients without the knowledge of evanescent modes. Through various numerical examples we show that our technique gives very good estimates of the actual scattering coefficients beyond the long wavelength limit.
Element analysis: a wavelet-based method for analysing time-localized events in noisy time series
Authors: Lilly Jonathan M.
Published: April 2017

A method is derived for the quantitative analysis of signals that are composed of superpositions of isolated, time-localized ‘events’. Here, these events are taken to be well represented as rescaled and phase-rotated versions of generalized Morse wavelets, a broad family of continuous analytic functions. Analysing a signal composed of replicates of such a function using another Morse wavelet allows one to directly estimate the properties of events from the values of the wavelet transform at its own maxima. The distribution of events in general power-law noise is determined in order to establish significance based on an expected false detection rate. Finally, an expression for an event’s ‘region of influence’ within the wavelet transform permits the formation of a criterion for rejecting spurious maxima due to numerical artefacts or other unsuitable events. Signals can then be reconstructed based on a small number of isolated points on the time/scale plane. This method, termed
element analysis
, is applied to the identification of long-lived eddy structures in ocean currents as observed by along-track measurements of sea surface elevation from satellite altimetry.
Wave directional spreading from point field measurements
Authors: McAllister M. L. , Venugopal V. , Borthwick A. G. L.
Published: April 2017

Ocean waves have multidirectional components. Most wave measurements are taken at a single point, and so fail to capture information about the relative directions of the wave components directly. Conventional means of directional estimation require a minimum of three concurrent time series of measurements at different spatial locations in order to derive information on local directional wave spreading. Here, the relationship between wave nonlinearity and directionality is utilized to estimate local spreading without the need for multiple concurrent measurements, following Adcock & Taylor (Adcock & Taylor 2009
Proc. R. Soc. A
465
, 3361–3381. (
doi:10.1098/rspa.2009.0031
)), with the assumption that directional spreading is frequency independent. The method is applied to measurements recorded at the North Alwyn platform in the northern North Sea, and the results compared against estimates of wave spreading by conventional measurement methods and hindcast data. Records containing freak waves were excluded. It is found that the method provides accurate estimates of wave spreading over a range of conditions experienced at North Alwyn, despite the noisy chaotic signals that characterize such ocean wave data. The results provide further confirmation that Adcock and Taylor's method is applicable to metocean data and has considerable future promise as a technique to recover estimates of wave spreading from single point wave measurement devices.
The deferred limit method for long waves in a curved waveguide
Authors: Chapman C. J. , Sorokin S. V.
Published: April 2017

This paper presents a technique, based on a deferred approach to a limit, for analysing the dispersion relation for propagation of long waves in a curved waveguide. The technique involves the concept of an analytically satisfactory pair of Bessel functions, which is different from the concept of a numerically satisfactory pair, and simplifies the dispersion relations for curved waveguide problems. Details are presented for long elastic waves in a curved layer, for which symmetric and antisymmetric waves are strongly coupled. The technique gives high-order corrections to a widely used approximate dispersion relation based a kinematic hypothesis, and determines rigorously which of its coefficients are exact.
Deformed quons and bi-coherent states
Authors: Bagarello F.
Published: April 2017

We discuss how a q-mutation relation can be deformed replacing a pair of conjugate operators with two other and unrelated operators, as it is done in the construction of pseudo-fermions, pseudo-bosons and truncated pseudo-bosons. This deformation involves interesting mathematical problems and suggests possible applications to pseudo-hermitian quantum mechanics. We construct bi-coherent states associated to

D

-pseudo-quons, and we show that they share many of their properties with ordinary coherent states. In particular, we find conditions for these states to exist, to be eigenstates of suitable annihilation operators and to give rise to a resolution of the identity. Two examples are discussed in details, one connected to an unbounded similarity map, and the other to a bounded map.
Key functional role of the optical properties of coral skeletons in coral ecology and evolution
Authors: Enríquez Susana , Méndez Eugenio R. , Hoegh-Guldberg Ove , Iglesias-Prieto Roberto
Published: April 2017

Multiple scattering of light on coral skeleton enhances light absorption efficiency of coral symbionts and plays a key role in the regulation of their internal diffuse light field. To understand the dependence of this enhancement on skeleton meso- and macrostructure, we analysed the scattering abilities of naked coral skeletons for 74 Indo-Pacific species. Sensitive morphotypes to thermal and light stress, flat-extraplanate and branching corals, showed the most efficient structures, while massive-robust species were less efficient. The lowest light-enhancing scattering abilities were found for the most primitive colonial growth form: phaceloid. Accordingly, the development of highly efficient light-collecting structures versus the selection of less efficient but more robust holobionts to cope with light stress may constitute a trade-off in the evolution of modern symbiotic scleractinian corals, characterizing two successful adaptive solutions. The coincidence of the most important structural modifications with epitheca decline supports the importance of the enhancement of light transmission across coral skeleton in modern scleractinian diversification, and the central role of these symbioses in the design and optimization of coral skeleton. Furthermore, the same ability that lies at the heart of the success of symbiotic corals as coral-reef-builders can also explain the ‘Achilles's heel’ of these symbioses in a warming ocean.
Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system
Authors: Solbakken Monica Hongrø , Voje Kjetil Lysne , Jakobsen Kjetill Sigurd , Jentoft Sissel
Published: April 2017

Host-intrinsic factors as well as environmental changes are known to be strong evolutionary drivers defining the genetic foundation of immunity. Using a novel set of teleost genomes and a time-calibrated phylogeny, we here investigate the family of Toll-like receptor (
TLR
) genes and address the underlying evolutionary processes shaping the diversity of the first-line defence. Our findings reveal remarkable flexibility within the evolutionary design of teleost innate immunity characterized by prominent
TLR
gene losses and expansions. In the order of Gadiformes, expansions correlate with the loss of major histocompatibility complex class II (
MHCII
) and diversifying selection analyses support that this has fostered new immunological innovations in
TLR
s within this lineage. In teleosts overall,
TLRs
expansions correlate with species latitudinal distributions and maximum depth. By contrast, lineage-specific gene losses overlap with well-described changes in palaeoclimate (global ocean anoxia) and past Atlantic Ocean geography. In conclusion, we suggest that the evolvability of the teleost immune system has most likely played a prominent role in the survival and successful radiation of this lineage.
Hydrodynamic regime determines the feeding success of larval fish through the modulation of strike kinematics
Authors: China Victor , Levy Liraz , Liberzon Alex , Elmaliach Tal , Holzman Roi
Published: April 2017

Larval fishes experience extreme mortality rates, with 99% of a cohort perishing within days after starting to actively feed. While recent evidence suggests that hydrodynamic factors contribute to constraining larval feeding during early ontogeny, feeding is a complex process that involves numerous interacting behavioural and biomechanical components. How these components change throughout ontogeny and how they contribute to feeding remain unclear. Using 339 observations of larval feeding attempts, we quantified the effects of morphological and behavioural traits on feeding success ofSparus auratalarvae during early ontogeny. Feeding success was determined using high-speed videography, under both natural and increased water viscosity treatments. Successful strikes were characterized by Reynolds numbers that were an order of magnitude higher than those of failed strikes. The pattern of increasing strike success with increasing age was driven by the ontogeny of traits that facilitate the transition to higher Reynolds numbers. Hence, the physical growth of a larva plays an important role in its transition to a hydrodynamic regime of higher Reynolds numbers, in which suction feeding is more effective.
Adaptation to a latitudinal thermal gradient within a widespread copepod species: the contributions of genetic divergence and phenotypic plasticity
Authors: Pereira Ricardo J. , Sasaki Matthew C. , Burton Ronald S.
Published: April 2017

Understanding how populations adapt to heterogeneous thermal regimes is essential for comprehending how latitudinal gradients in species diversification are formed, and how taxa will respond to ongoing climate change. Adaptation can occur by innate genetic factors, by phenotypic plasticity, or by a combination of both mechanisms. Yet, the relative contribution of such mechanisms to large-scale latitudinal gradients of thermal tolerance across conspecific populations remains unclear. We examine thermal performance in 11 populations of the intertidal copepodTigriopus californicus, ranging from Baja California Sur (Mexico) to British Columbia (Canada). Common garden experiments show that survivorship to acute heat-stress differs between populations (by up to 3.8°C in LD50values), reflecting a strong genetic thermal adaptation. Using a split-brood experiment with two rearing temperatures, we also show that developmental phenotypic plasticity is beneficial to thermal tolerance (by up to 1.3°C), and that this effect differs across populations. Although genetic divergence in heat tolerance strongly correlates with latitude and temperature, differences in the plastic response do not. In the context of climate warming, our results confirm the general prediction that low-latitude populations are most susceptible to local extinction because genetic adaptation has placed physiological limits closer to current environmental maxima, but our results also contradict the prediction that phenotypic plasticity is constrained at lower latitudes.
Rapid polygenic response to secondary contact in a hybrid species
Authors: Sætre Glenn-Peter , Cuevas Angélica , Hermansen Jo S. , Elgvin Tore O. , Fernández Laura Piñeiro , Sæther Stein A. , Cascio Sætre Camilla Lo , Eroukhmanoff Fabrice
Published: April 2017

Secondary contact between closely related species can have genetic consequences. Competition for essential resources may lead to divergence in heritable traits that reduces interspecific competition leading to increased rate of genetic divergence. Conversely, hybridization and backcrossing can lead to genetic convergence. Here, we study a population of a hybrid species, the Italian sparrow (Passer italiae), before and after it came into secondary contact with one of its parent species, the Spanish sparrow (P. hispaniolensis), in 2013. We demonstrate strong consequences of interspecific competition: Italian sparrows were kept away from a popular feeding site by its parent species, resulting in poorer body condition and a significant drop in population size. Although no significant morphological change could be detected, after only 3 years of sympatry, the Italian sparrows had diverged significantly from the Spanish sparrows across a set of 81 protein-coding genes. These temporal genetic changes are mirrored by genetic divergence observed in older sympatric Italian sparrow populations within the same area of contact. Compared with microallopatric birds, sympatric ones are genetically more diverged from Spanish sparrows. Six significant outlier genes in the temporal and spatial comparison (i.e. showing the greatest displacement) have all been found to be associated with learning and neural development in other bird species.
A case of polymicrobial anaerobic spondylodiscitis due to Parvimonas micra and Fusobacterium nucleatum
Authors: Cleaver Leanne M , Palanivel Shara , Mack Damien , Warren Simon
Published: April 2017

Introduction. Here, we present a case of polymicrobial anaerobic spondylodiscitis.

Case Presentation. A forty-five year-old female patient was referred to a specialist orthopaedic hospital with an eight week history of back pain without fevers. X-ray imaging and magnetic resonance imaging showed acute osteomyelitis of the twelfth thoracic and first lumbar vertebrae. Prolonged enrichment cultures grew Parvimonas micra and Fusobacterium nucleatum, identified by matrix-assisted laser desorption ionisation-time of flight (MALDI-ToF) mass spectrometry (MS). The patient was successfully treated with six weeks of intravenous ertapenem and oral clindamycin.

Conclusion. Anaerobic discitis is rare, and polymicrobial discitis is rarer still. A PubMed literature review revealed only seven cases of F. nucleatum discitis and only twelve cases of P. micra discitis; this includes only one other reported case of a polymicrobial discitis due to infection with both anaerobes. We emphasise the importance of prolonging enrichment culture and the use of fast yet accurate identification of anaerobes using MALDI-ToF MS in these infections.
Acceleration of Nucleotide Semi-Global Alignment with Adaptive Banded Dynamic Programming
Authors: Suzuki Hajime , Kasahara Masahiro
Published: April 2017

Motivation

Pairwise alignment of nucleotide sequences has previously been carried out using the seed- and-extend strategy, where we enumerate seeds (shared patterns) between sequences and then extend the seeds by Smith-Waterman-like semi-global dynamic programming to obtain full pairwise alignments. With the advent of massively parallel short read sequencers, algorithms and data structures for efficiently finding seeds have been extensively explored. However, recent advances in single-molecule sequencing technologies have enabled us to obtain millions of reads, each of which is orders of magnitude longer than those output by the short-read sequencers, demanding a faster algorithm for the extension step that accounts for most of the computation time required for pairwise local alignment. Our goal is to design a faster extension algorithm suitable for single-molecule sequencers with high sequencing error rates (e.g., 10-15%) and with more frequent insertions and deletions than substitutions.

Results

We propose an adaptive banded dynamic programming algorithm for calculating pairwise semi-global alignment of nucleotide sequences that allows a relatively high insertion or deletion rate while keeping band width relatively low (e.g., 32 or 64 cells) regardless of sequence lengths. Our new algorithm eliminated mutual dependences between elements in a vector, allowing an efficient Single-Instruction-Multiple-Data parallelization. We experimentally demonstrate that our algorithm runs approximately 5× faster than the extension alignment algorithm in NCBI BLAST+ while retaining similar sensitivity (recall).

We also show that our extension algorithm is more sensitive than the extension alignment routine in DALIGNER, while the computation time is comparable.

Availability

The implementation of the algorithm and the benchmarking scripts are available athttps://github.com/ocxtal/adaptivebandbench.

Contact

mkasa@edu.k.u-tokyo.ac.jp
The yeast Mig1 transcriptional repressor is dephosphorylated by glucose-dependent and independent mechanisms
Authors: Shashkova Sviatlana , Wollman Adam J.M. , Leake Mark C. , Hohmann Stefan
Published: April 2017

Saccharomyces cerevisiaeAMPK/Snf1 regulates glucose derepression of genes required for utilization of alternative carbon sources through the transcriptional repressor Mig1. It has been suggested that the Glc7-Reg1 phosphatase dephosphorylates Mig1. Here we report that Mig1 is dephosphorylated by Glc7-Reg1 in an apparently glucose-dependent mechanism but also by a mechanism independent of glucose and Glc7-Reg1. In addition to serine/threonine phosphatases another process including tyrosine phosphorylation seems crucial for Mig1 regulation. Taken together, Mig1 dephosphorylation appears to be controlled in a complex manner, in line with the importance for rapid and sensitive regulation upon altered glucose concentrations in the growth medium.
Leveraging population-based clinical quantitative phenotyping for drug repositioning
Authors: Brown Adam S , Rasooly Danielle , Patel Chirag J
Published: April 2017

Computational drug repositioning methods can scalably nominate approved drugs for new diseases, with reduced risk of unforeseen side effects. The majority of methods eschew individual-level phenotypes despite the promise of biomarker-driven repositioning. In this study, we propose a framework for discovering serendipitous interactions between drugs and routine clinical phenotypes in cross-sectional observational studies. Key to our strategy is the use of a healthy and non-diabetic population derived from the National Health and Nutrition Examination Survey, mitigating risk for confounding by indication. We combine complementary diagnostic phenotypes (fasting glucose and glucose response) and associate them with prescription drug usage. We then sought confirmation of phenotype-drug associations in un-identifiable member claims data from Aetna using a retrospective self-controlled case analysis approach. We identify bupropion hydrochloride as a plausible antidiabetic agent, suggesting that surveying otherwise healthy individuals cross-sectional studies can discover new drug repositioning hypotheses that have applicability to longitudinal clinical practice.
The Calcineurin-FoxO-MuRF1 Signaling Pathway Regulates Myofibril Integrity in Cardiomyocytes
Authors: Shimizu Hirohito , Langenbacher Adam , Huang Jie , Wang Kevin , Otto Georg W. , Geisler Robert , Wang Yibin , Chen Jau-Nian
Published: April 2017

Altered Ca2+handling is often present in diseased hearts undergoing structural remodeling and functional deterioration. The influences of Ca2+signaling on cardiac function have been examined extensively, but whether Ca2+directly regulates sarcomere structure has remained elusive. Using a mutant zebrafish model lackingNCX1activity in the heart, we explored the impacts of impaired Ca2+homeostasis on myofibril integrity. Gene expression profiling analysis revealed that the E3 ubiquitin ligase MuRF1 is upregulated inncx1-deficient hearts. Intriguingly, knocking down MuRF1 activity or inhibiting proteasome activity preserved myofibril integrity inncx1deficient hearts, revealing a MuRF1-mediated proteasome degradation mechanism that is activated in response to abnormal Ca2+homeostasis. Furthermore, we detected an accumulation of the MuRF1 regulator FoxO in the nuclei ofncx1-deficient cardiomyocytes. Overexpression of FoxO in wild type cardiomyocytes induced MuRF1 expression and caused myofibril disarray, whereas inhibiting Calcineurin activity attenuated FoxO-mediated MuRF1 expression and protected sarcomeres from degradation inncx1-deficient hearts. Together, our findings reveal a novel mechanism by which Ca2+overload disrupts the myofibril integrity in heart muscle cells by activating a Calcineurin-FoxO-MuRF1-proteosome signaling pathway.
The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae
Authors: Neves Lauren T. , Douglass Stephen , Spreafico Roberto , Venkataramanan Srivats , Kress Tracy L. , Johnson Tracy L.
Published: April 2017

In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio–temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5′ ends of protein-coding genes, and has been implicated in transcription regulation. Here we show that splicing of intron-containing genes in cells lacking H2A.Z is impaired, particularly under suboptimal splicing conditions. Cells lacking H2A.Z are especially dependent on a functional U2 snRNP (small nuclear RNA [snRNA] plus associated proteins), as H2A.Z shows extensive genetic interactions with U2 snRNP-associated proteins, and RNA sequencing (RNA-seq) reveals that introns with nonconsensus branch points are particularly sensitive to H2A.Z loss. Consistently, H2A.Z promotes efficient spliceosomal rearrangements involving the U2 snRNP, as H2A.Z loss results in persistent U2 snRNP association and decreased recruitment of downstream snRNPs to nascent RNA. H2A.Z impairs transcription elongation, suggesting that spliceosome rearrangements are tied to H2A.Z's role in elongation. Depletion of disassembly factor Prp43 suppresses H2A.Z-mediated splice defects, indicating that, in the absence of H2A.Z, stalled spliceosomes are disassembled, and unspliced RNAs are released. Together, these data demonstrate that H2A.Z is required for efficient pre-mRNA splicing and indicate a role for H2A.Z in coordinating the kinetics of transcription elongation and splicing.