bluuebunny/crossref_metadata_2025 huggingface dataset:
Laparoscopic Hysterectomy With Morcellation Versus Abdominal Hysterectomy for Presumed Fibroids: An Updated Decision Analysis Following the 2014 FDA Safety Communications
Authors: Siedhoff Matthew T. , Doll Kemi M. , Clarke-Pearson Daniel L. , Rutstein Sarah E.
Published: April 2017

(Abstracted from Am J Obstet Gynecol 2017;216:259.e1–259.e6)

Increasing concern that use of electric power morcellation during hysterectomy for benign conditions may result in the spread of an occult leiomyosarcoma (LMS) led the US Food and Drug Administration (FDA) to issue safety communications in April 2014 and November 2014, recommending that this procedure should not be used in perimenopausal and postmenopausal women. These communications significantly changed practice patterns of many gynecologic surgeons, increasing rates of abdominal hysterectomy (AH), and possibly resulting in more complications for patients.
Electronic Fetal Monitoring, Cerebral Palsy, and Caesarean Section: Assumptions Versus Evidence
Authors: Nelson Karin B. , Sartwelle Thomas P. , Rouse Dwight J.
Published: April 2017

(Abstracted from BMJ 2016;355:i6405)

The ever-increasing rate of cesarean delivery may be attributed to a large extent to the extensive use of electronic fetal monitoring (EFM). Initial introduction of EFM was done to enable early identification of fetal asphyxia, thereby preventing mortality or long-term neurological morbidity, particularly cerebral palsy.
Prenatal cfDNA Screening Results Indicative of Maternal Neoplasm: Survey of Current Practice and Management Needs
Authors: Giles Meagan E. , Murphy Lauren , Krstić Nevena , Sullivan Cathy , Hashmi Syed S. , Stevens Blair
Published: April 2017

(Abstracted from Prenat Diagn 2017;37(2):126–132)

The discovery of cell-free fetal DNA (cfDNA) that is free-floating in the serum has led to the development of screening technologies, both in obstetrics and oncology. Circulating cfDNA in the serum of pregnant women is the basis of noninvasive prenatal testing (NIPT).
Nail Matrix Pathology in Cronkhite–Canada Syndrome: The First Case Report
Authors: Chuamanochan Mati , Tovanabutra Napatra , Mahanupab Pongsak , Kongkarnka Sarawut , Chiewchanvit Siri
Published: April 2017

Cronkhite–Canada Syndrome (CCS) presents with gastrointestinal polyposis and the triad of cutaneous abnormalities including nail dystrophy, alopecia, and hyperpigmentation of the skin. The etiology is not well understood. The histology of skin lesion in CCS has not been routinely described. Especially, the nail matrix pathology has not been reported. In this study, the authors report the nail matrix pathology in a patient with CCS. Interestingly, the histologic evaluation revealed matrix hypergranulosis. Because matrix hypergranulosis is commonly found in several inflammatory nail diseases, this discovery points out that an inflammatory process is probably one of the important pathogeneses in CCS.
The Effect of Tranilast 8% Liposomal Gel Versus Placebo on Post-Cesarean Surgical Scars: A Prospective Double-Blind Split-Scar Study
Authors: Kohavi Libi , Sprecher Eli , Zur Eyal , Artzi Ofir
Published: April 2017

BACKGROUND

Tranilast (N-[3, 4-dimethoxycinnamoyl] anthranilic acid), an antiallergic drug, has been shown to attenuate scar formation possibly through inhibition of transforming growth factor beta 1 activity and consequent suppression of collagen synthesis in fibroblasts.

OBJECTIVE

The authors aimed at evaluating the efficacy and safety of tranilast 8% gel in improving the appearance and symptoms of new post-cesarean section surgical wounds.

METHODS

In this prospective double-blind split-scar study, the authors treated each half scar of 26 women with either tranilast 8% liposomal gel or tranilast-free liposomal gel (placebo). Treatment was applied twice daily for 3 months. Twenty women completed the trial. Scar halves were evaluated by 2 investigators and by the patients 9 months after the last application using the Patient and Observer Scar Assessment Scale (POSAS). The participants also rated overall satisfaction and recorded side effects of the treatment.

RESULTS

The mean POSAS scores at 9 months post-treatment were significantly lower for tranilast-treated half scars compared with placebo-treated half scars (p < .001). The women were significantly more satisfied with the tranilast-treated half-scar appearance (p = .002). Three participants reported itching and erythema on the tranilast-treated side.

CONCLUSION

Topical tranilast 8% gel provided significantly better postcaesarian section scar cosmesis and user satisfaction compared with placebo.
CHANGES IN CENTRAL CHOROIDAL THICKNESS AFTER TREATMENT OF DIABETIC MACULAR EDEMA WITH INTRAVITREAL BEVACIZUMAB CORRELATION WITH CENTRAL MACULAR THICKNESS AND BEST-CORRECTED VISUAL ACUITY
Authors: Nourinia Ramin , Ahmadieh Hamid , Nekoei Elnaz , Malekifar Parviz , Tofighi Zahra
Published: April 2017

Purpose:

To assess the effect of intravitreal injection of bevacizumab on central choroidal thickness (CCT) and its relationship with central macular thickness (CMT) and best-corrected visual acuity (BCVA) changes in eyes with center-involving diabetic macular edema.

Methods:

This prospective interventional case series included 20 eyes of 20 patients with center-involving diabetic macular edema naive to treatment. The BCVA assessment, complete eye examination, enhanced depth optical coherence tomography, and fluorescein angiography were performed at baseline followed by 3 monthly intravitreal injection of bevacizumab. The treated eyes underwent BCVA evaluation and enhanced depth optical coherence tomography at Months 1, 2, 3, and 6 after the first injection. Change of the CCT was the primary outcome measure. Secondary outcome measures included BCVA and CMT changes and their relationship with CCT changes.

Results:

Mean age of patients was 63.1 ± 8.0 (range, 52–75) years. Mean baseline CCT was 265 ± 79 μm, which reduced to 251 ± 81 μm and 232 ± 82 μm at Months 3 and 6, respectively (P < 0.001). Corresponding values for CMT were 470 ± 107 μm, 392 ± 104 μm, and 324 ± 122 μm, respectively (P < 0.001). The BCVA improved from 20/60 at baseline to 20/50 at Month 3 and 20/40 at Month 6 (P = 0.007). Each 1 μm decrease in CCT was associated with 2.74 μm reduction in CMT and 0.1 Early Treatment Diabetic Retinopathy Study letter score improvement in BCVA (P < 0.001 and P = 0.001, respectively).

Conclusion:

After treatment of diabetic macular edema with intravitreal injection of bevacizumab, CCT decreased and this reduction significantly correlated with CMT reduction and vision improvement.
OUTER NUCLEAR LAYER THINNING IN PACHYCHOROID PIGMENT EPITHELIOPATHY
Authors: Ersoz M. Giray , Karacorlu Murat , Arf Serra , Hocaoglu Mumin , Sayman Muslubas Isil
Published: April 2017

Purpose:

To compare the average thicknesses of central inner retinal layers in eyes with pachychoroid pigment epitheliopathy (PPE), with uncomplicated pachychoroid (UCP), and of healthy subjects.

Methods:

Medical records of patients with PPE and UCP were retrospectively reviewed. Twenty-nine eyes with foveal PPE, 30 eyes with UCP, and 29 eyes of healthy subjects were included. Spectral-domain optical coherence tomography with enhanced depth imaging was used for all optical coherence tomography scans. Mean central inner retinal layer thicknesses were measured in 1-mm-diameter circle with Spectralis automated segmentation software and compared between groups.

Results:

The outer nuclear layer (ONL) and the sum of the outer plexiform layer and ONL were significantly thinner in the PPE group than the UCP and control groups (ONL: P < 0.001, P < 0.001; outer plexiform layer + ONL: P = 0.002, P = 0.002, respectively). There was no significant difference between groups regarding thickness of the outer plexiform layer and other inner retinal layers. Eyes with UCP and normal eyes did not differ.

Conclusion:

The ONL is thinner in eyes with PPE. The degenerative process of pachychoroid spectrum diseases may begin with retinal pigment epithelium alterations before subretinal fluid accumulation. The PPE lesions, commonly seen above pachyvessels, may be an indicator of photoreceptor apoptosis.
The Use of GMP-Produced Bone Marrow-Derived Stem Cells in Combination with Extracorporeal Membrane Oxygenation in ARDS: An Animal Model
Authors: Kocyildirim Ergin , Cárdenes Nayra , Ting Antony , Cáceres Eder , BermUdez Christian , Rojas Mauricio
Published: April 2017

Acute respiratory distress syndrome (ARDS) is the result of a wide variety of disorders, which can be associated with different clinical disorders or systemic diseases directly affecting the lungs. Currently, the only existing therapy is limited to supportive care. In a 6 hour pilot study, we analyzed the use of the combination of both stem cell and extracorporeal membrane oxygenation (ECMO) strategies to prevent or treat severe lung injury. A total of 11 sheep were used. Five sheep received Escherichia coli endotoxin as a control group (group 1). Three sheep that received E. coli endotoxin were treated with veno-venous ECMO support in group 2. In group 3, 3 sheep received a dose of clinical grade good manufacturing practice (GMP)-produced MultiPotent Adult Progenitor cells (MAPC) intratracheally after the end of the infusion of E. coli endotoxin, followed by ECMO support. The respiratory parameters by means of blood gas results, measurements of lung injury, inflammatory responses, and integrity of the alveolar capillary barrier after the infusion of these cells were analyzed. Our data suggest that the combination of ECMO and stem cell therapy showed better histopathologic changes with less inflammation. We believe that the combination of stem cells with the ECMO treatment may be useful in future studies investigating the diagnosis, treatment, and prevention of ARDS.
Electrophysiological Studies to Detect Peripheral Neuropathy in Children Treated With Vincristine
Authors: Kavcic Marko , Koritnik Blaz , Krzan Matevz , Velikonja Orjana , Prelog Tomaz , Stefanovic Milica , Debeljak Maruša , Jazbec Janez
Published: April 2017

Patients treated with vincristine predictably develop peripheral neuropathy. The aim of our study was to investigate the pattern of vincristine-induced neuropathy in children by nerve conduction studies and somatosensory-evoked potentials (SSEPs). We included data from 39 children who received vincristine for various pediatric malignancies, and we performed initial and follow-up (after a minimum of 4 doses of vincristine 1.5 mg/m2) conduction studies in 27 patients and SSEPs studies in 34 patients. On follow-up the most prevalent symptoms were paresthesias (44%) and constipation (22%), and the most common neurological sign was impaired myotatic reflexes (89%). Performing nerve conduction studies we found that significant reductions were measured for distal amplitudes, distal latencies were prolonged, and conduction velocities were relatively preserved. The most pronounced differences in amplitudes and distal latencies were measured in the peroneal nerves. Changes of SSEPs studies were subtle. Vincristine-induced neuropathy presents with primary axonal involvement and is more pronounced on motor neurons. We found a trend between higher age and higher dose and the degree of neuropathy in our group of patients.
Butyrylcholinesterase as a Blood Biomarker in Neuroblastoma
Authors: Coulter Don W. , Boettner Angela D. , Kortylewicz Zbigniew P. , Enke Stephen P. , Luther Jake A. , Verma Vivek , Baranowska-Kortylewicz Janina
Published: April 2017

Blood-based biomarkers are important in the detection of the disease and in the assessment of responses to therapy. In this study, butyrylcholinesterase was evaluated as a potential biomarker in newly diagnosed neuroblastoma (NB) patients at diagnosis and longitudinally during treatment. Plasma butyrylcholinesterase activities in age-matched and sex-matched children were used as controls. Pretreatment butyrylcholinesterase levels in NB subjects are on an average 2 times lower than butyrylcholinesterase levels in healthy subjects. Significantly, butyrylcholinesterase activities are ∼40% lower in MYCN-amplified as compared with nonamplified disease. As the course of chemotherapy progresses, butyrylcholinesterase activities recover and normalize to control values. The evident response to treatment indicates that plasma butyrylcholinesterase is a good biomarker of tumor response to therapy. Depressed butyrylcholinesterase levels in NB subjects are not caused by hepatic deficits suggesting a specific role for butyrylcholinesterase in NB. Further examination of the mechanism of altered butyrylcholinesterase production require an animal model that best approximates human condition. Studies in mice show that murine NB allografts significantly reduce butyrylcholinesterase activity in plasma. This finding correlates with changes observed in NB patients. In contrast, human NB xenografts produce the opposite effect, that is, butyrylcholinesterase plasma levels rise as the xenograft size increases. In the absence of any liver damage, dissimilarities between butyrylcholinesterase production in murine and human NB models suggest species-specific signaling pathways. This disparity also suggests that human NB xenograft mouse models do not approximate the human disease.
Five Phases of Recovery and Rehabilitation After Allogeneic Stem Cell Transplantation
Authors: van der Lans Mariska C.M. , Witkamp Frederika E. , Oldenmenger Wendy H. , Broers Annoek E.C.
Published: April 2017

Background:

For patients with a hematological malignancy, allogeneic stem cell transplantation (alloSCT) is a treatment modality that may cause a wide range of problems. Little is known about the process of recovery and rehabilitation and the problems that alloSCT patients are confronted with during the first-year posttransplant.

Objective:

This study explored the problems of patients during the first year after alloSCT, to better understand the process of recovery and rehabilitation.

Methods:

In a qualitative study, hemato-oncology patients were interviewed 1-year posttransplant. The semistructured interviews were transcribed verbatim, coded, and analyzed using constant comparative analysis.

Results:

Ten participants were included until saturation of data was reached. The patients had experienced various problems and had gone through an individual process of recovery and rehabilitation. Nevertheless, 5 phases could be distinguished: (1) survive, (2) on the receiving end, (3) bring under control, (4) start recuperation, and (5) retrospection. The duration of each phase varied between patients.

Conclusion:

Although patients experienced individual problems after alloSCT, they all followed a common pathway. Posttransplant care might be improved by adjusting the care to the distinct phases that the patients pass through.

Implications for Practice:

Nurses can play an important role in achieving improvements in posttransplant care by adjusting care to the individual needs of patients within the distinct phases.

Future nursing research should confirm and refine this process of recovery and rehabilitation and assess the effects of improvement measures in alloSCT patients and in other populations.
Exploring the Best Practices of Nursing Research Councils in Magnet® Organizations
Authors: Day Jennifer , Lindauer Cathleen , Parks Joyce , Scala Elizabeth
Published: April 2017

OBJECTIVE

The objective of this descriptive qualitative study was to identify best practices of nursing research councils (NRCs) at Magnet®-designated hospitals.

BACKGROUND

Nursing research (NR) is essential, adding to the body of nursing knowledge. Applying NR to the bedside improves care, enhances patient safety, and is an imperative for nursing leaders.

METHODS

We interviewed NR designees at 26 Magnet-recognized hospitals about the structure and function of their NRCs and used structural coding to identify best practices.

RESULTS

Most organizations link NR and evidence-based practice. Council membership includes leadership and clinical nurses. Councils conduct scientific reviews for nursing studies, supporting nurse principal investigators. Tracking and reporting of NR vary widely and are challenging. Councils provide education, sponsor research days, and collaborate interprofessionally, including with academic partners.

CONCLUSIONS

Findings from this study demonstrate the need to create formal processes to track and report NR and to develop outcome-focused NR education.
Clarifying the Conundrum: Evidence-Based Practice, Quality Improvement, or Research?
Authors: Carter Eileen J. , Mastro Kari , Vose Courtney , Rivera Reynaldo , Larson Elaine L.
Published: April 2017

Nurses’ active involvement in clinical scholarship is necessary to advance the nursing profession and improve patient outcomes. Yet, definitional confusion and numerous barriers exist to clinical scholarship in and across academic and patient care settings. We discuss factors that pose barriers to the continuum of clinical scholarship and suggest opportunities for clinician-researcher collaborations that promote nurses’ engagement in evidence-based practice, quality improvement, and research.
Actinomyces in Pregnancy: A Review of the Literature
Authors: Estrada Sarah M. , Magann Everett F. , Napolitano Peter G.
Published: April 2017

Importance

Actinomyces is commonly found in many areas of the body where it derives a benefit without harming the host. When it does infect the host during pregnancy, is that infection a threat to the obstetric patient and does that infection cause adverse pregnancy outcomes?

Objective

The aim of this study was to review what is known about Actinomyces infections and the impact of an Actinomyces infection on pregnancy outcomes.

Evidence Acquisition

A PubMed search was undertaken with the search years unlimited to April 1, 2016, and restricted to articles in English. The search terms included “actinomyces,” “pregnancy,” “prenatal,” “maternal,” “actinomyces infection,” “pregnancy,” “chorioamnionitis,” “preterm labor,” “premature birth,” or “postpartum actinomyces.”

Results

Eighteen of the 154 identified articles are the basis of this review. Actinomyces is a rod-like positive bacterium. The diagnosis of an Actinomyces infection can be by culture or Gram stain. Actinomyces is commensal and typically only infects after a mucosal break or lesion. Seventeen cases were identified in pregnancy. Ten cases were complicated by chorioamnionitis and a preterm delivery. A nidus leading to infection was identified in 12 of the cases including women with a cervical cerclage, dental abscesses, appendicitis, renal actinomycosis, and ovarian abscesses. Adverse pregnancy outcomes have been linked with periodontal disease, but treatment did not prevent preterm delivery in a randomized, blinded, controlled trial.

Conclusions

Actinomyces infections in pregnancy are rare but, if they occur, have been linked primarily with preterm deliveries.

Target Audience

Obstetricians and gynecologists, family physicians

Learning Objectives

After completing this activity, the learner should be better able to identify the areas of the body where Actinomyces infections occur and how the infections typically occur, identify the pathophysiologic changes that occur during pregnancy that might lead to an Actinomyces infection and how that infection may affect pregnancy outcomes, and describe the treatment for mild and severe Actinomyces infections.
Noise affects resource assessment in an invertebrate
Authors: Walsh Erin P. , Arnott Gareth , Kunc Hansjoerg P.
Published: April 2017

Anthropogenic noise is a global pollutant, affecting animals across taxa. However, how noise pollution affects resource acquisition is unknown. Hermit crabs (Pagurus bernhardus) engage in detailed assessment and decision-making when selecting a critical resource, their shell; this is crucial as individuals in poor shells suffer lower reproductive success and higher mortality. We experimentally exposed hermit crabs to anthropogenic noise during shell selection. When exposed to noise, crabs approached the shell faster, spent less time investigating it, and entered it faster. Our results demonstrate that changes in the acoustic environment affect the behaviour of hermit crabs by modifying the selection process of a vital resource. This is all the more remarkable given that the known cues used in shell selection involve chemical, visual and tactile sensory channels. Thus, our study provides rare evidence for a cross-modal impact of noise pollution.
Cutting through the smoke: the diversity of microorganisms in deep-sea hydrothermal plumes
Authors: Djurhuus Anni , Mikalsen Svein-Ole , Giebel Helge-Ansgar , Rogers Alex D.
Published: April 2017

There are still notable gaps regarding the detailed distribution of microorganisms between and within insular habitats such as deep-sea hydrothermal vents. This study investigates the community composition of black smoker vent microorganisms in the Southern Hemisphere, and changes thereof along a spatial and chemical gradient ranging from the vent plume to surrounding waters. We sampled two hydrothermal vent fields, one at the South West Indian Ridge (SWIR), the other at the East Scotia Ridge (ESR). Samples were collected across vent fields at varying vertical distances from the origin of the plumes. The microbial data were sequenced on an Illumina MiSeq platform for the 16SrRNA gene. A substantial amount of vent-specific putative chemosynthetic microorganisms were found, particularly in samples from focused hydrothermal venting. Common vent-specific organisms from both vent fields were the generaArcobacter,CaminibacterandSulfurimonasfrom the Epsilonproteobacteria and the SUP05 group from the Gammaproteobacteria. There were no major differences in microbial composition between SWIR and ESR for focused plume samples. However, within the ESR the diffuse flow and focused samples differed significantly in microbial community composition and relative abundance. For Epsilonproteobacteria, we found evidence of niche-specificity to hydrothermal vent environments. This taxon decreased in abundance by three orders of magnitude from the vent orifice to background water. Epsilonproteobacteria distribution followed a distance–decay relationship as vent-effluents mixed with the surrounding seawater. This study demonstrates strong habitat affinity of vent microorganisms on a metre scale with distinct environmental selection.
Ordinary differential equations and Boolean networks in application to modelling of 6-mercaptopurine metabolism
Authors: Lavrova Anastasia I. , Postnikov Eugene B. , Zyubin Andrey Yu. , Babak Svetlana V.
Published: April 2017

We consider two approaches to modelling the cell metabolism of 6-mercaptopurine, one of the important chemotherapy drugs used for treating acute lymphocytic leukaemia: kinetic ordinary differential equations, and Boolean networks supplied with one controlling node, which takes continual values. We analyse their interplay with respect to taking into account ATP concentration as a key parameter of switching between different pathways. It is shown that the Boolean networks, which allow avoiding the complexity of general kinetic modelling, preserve the possibility of reproducing the principal switching mechanism.
The mountains of giants: an anthropometric survey of male youths in Bosnia and Herzegovina
Authors: Grasgruber Pavel , Popović Stevo , Bokuvka Dominik , Davidović Ivan , Hřebíčková Sylva , Ingrová Pavlína , Potpara Predrag , Prce Stipan , Stračárová Nikola
Published: April 2017

The aim of this anthropometric survey, conducted between 2015 and 2016 in Bosnia and Herzegovina (BiH), was to map local geographical differences in male stature and some other anthropometric characteristics (sitting height, arm span). In addition, to investigate the main environmental factors influencing physical growth, the documented values of height would be compared with available nutritional and socioeconomic statistics. Anthropometric data were collected in 3192 boys aged approximately 18.3 years (17–20 years), from 97 schools in 37 towns. When corrected for population size in the examined regions, the average height of young males in BiH is 181.2 cm (181.4 cm in the Bosniak-Croat Federation, 180.9 cm in Republika Srpska). The regional variation is considerable—from 179.7 cm in the region of Doboj to 184.5 cm in the region of Trebinje. These results fill a long-term gap in the anthropological research of the Western Balkans and confirm older reports that the population of the Dinaric Alps is distinguished by extraordinary physical stature. Together with the Dutch, Montenegrins and Dalmatians, men from Herzegovina (183.4 cm) can be regarded as the tallest in the world. Because both nutritional standards and socioeconomic conditions are still deeply suboptimal, the most likely explanation of this exceptional height lies in specific genetic factors associated with the spread of Y haplogroup I-M170. The genetic potential for height in this region could then be the greatest in the world. Future studies should further elucidate the roots of this intriguing phenomenon, which touches an important aspect of human biodiversity.
Multiple phase transitions in an agent-based evolutionary model with neutral fitness
Authors: King Dawn M. , Scott Adam D. , Bahar Sonya
Published: April 2017

Null models are crucial for understanding evolutionary processes such as speciation and adaptive radiation. We analyse an agent-based null model, considering a case without selection—neutral evolution—in which organisms are defined only by phenotype. Universal dynamics has previously been demonstrated in a related model on a neutral fitness landscape, showing that this system belongs to the directed percolation (DP) universality class. The traditional null condition of neutral fitness (where fitness is defined as the number of offspring each organism produces) is extended here to include equal probability of death among organisms. We identify two types of phase transition: (i) a non-equilibrium DP transition through generational time (i.e. survival), and (ii) an equilibrium ordinary percolation transition through the phenotype space (based on links between mating organisms). Owing to the dynamical rules of the DP reaction–diffusion process, organisms can only sparsely fill the phenotype space, resulting in significant phenotypic diversity within a cluster of mating organisms. This highlights the necessity of understanding hierarchical evolutionary relationships, rather than merely developing taxonomies based on phenotypic similarity, in order to develop models that can explain phylogenetic patterns found in the fossil record or to make hypotheses for the incomplete fossil record of deep time.
Multifunctional scanning ion conductance microscopy
Authors: Page Ashley , Perry David , Unwin Patrick R.
Published: April 2017

Scanning ion conductance microscopy (SICM) is a nanopipette-based technique that has traditionally been used to image topography or to deliver species to an interface, particularly in a biological setting. This article highlights the recent blossoming of SICM into a technique with a much greater diversity of applications and capability that can be used either standalone, with advanced control (potential–time) functions, or in tandem with other methods. SICM can be used to elucidate functional information about interfaces, such as surface charge density or electrochemical activity (ion fluxes). Using a multi-barrel probe format, SICM-related techniques can be employed to deposit nanoscale three-dimensional structures and further functionality is realized when SICM is combined with scanning electrochemical microscopy (SECM), with simultaneous measurements from a single probe opening up considerable prospects for multifunctional imaging. SICM studies are greatly enhanced by finite-element method modelling for quantitative treatment of issues such as resolution, surface charge and (tip) geometry effects. SICM is particularly applicable to the study of living systems, notably single cells, although applications extend to materials characterization and to new methods of printing and nanofabrication. A more thorough understanding of the electrochemical principles and properties of SICM provides a foundation for significant applications of SICM in electrochemistry and interfacial science.
Robust identification of harmonic oscillator parameters using the adjoint Fokker–Planck equation
Authors: Boujo E. , Noiray N.
Published: April 2017

We present a model-based output-only method for identifying from time series the parameters governing the dynamics of stochastically forced oscillators. In this context, suitable models of the oscillator’s damping and stiffness properties are postulated, guided by physical understanding of the oscillatory phenomena. The temporal dynamics and the probability density function of the oscillation amplitude are described by a Langevin equation and its associated Fokker–Planck equation, respectively. One method consists in fitting the postulated analytical drift and diffusion coefficients with their estimated values, obtained from data processing by taking the short-time limit of the first two transition moments. However, this limit estimation loses robustness in some situations—for instance when the data are band-pass filtered to isolate the spectral contents of the oscillatory phenomena of interest. In this paper, we use a robust alternative where the adjoint Fokker–Planck equation is solved to compute Kramers–Moyal coefficients exactly, and an iterative optimization yields the parameters that best fit the observed statistics simultaneously in a wide range of amplitudes and time scales. The method is illustrated with a stochastic Van der Pol oscillator serving as a prototypical model of thermoacoustic instabilities in practical combustors, where system identification is highly relevant to control.
Statistical emulation of landslide-induced tsunamis at the Rockall Bank, NE Atlantic
Authors: Salmanidou D. M. , Guillas S. , Georgiopoulou A. , Dias F.
Published: April 2017

Statistical methods constitute a useful approach to understand and quantify the uncertainty that governs complex tsunami mechanisms. Numerical experiments may often have a high computational cost. This forms a limiting factor for performing uncertainty and sensitivity analyses, where numerous simulations are required. Statistical emulators, as surrogates of these simulators, can provide predictions of the physical process in a much faster and computationally inexpensive way. They can form a prominent solution to explore thousands of scenarios that would be otherwise numerically expensive and difficult to achieve. In this work, we build a statistical emulator of the deterministic codes used to simulate submarine sliding and tsunami generation at the Rockall Bank, NE Atlantic Ocean, in two stages. First we calibrate, against observations of the landslide deposits, the parameters used in the landslide simulations. This calibration is performed under a Bayesian framework using Gaussian Process (GP) emulators to approximate the landslide model, and the discrepancy function between model and observations. Distributions of the calibrated input parameters are obtained as a result of the calibration. In a second step, a GP emulator is built to mimic the coupled landslide-tsunami numerical process. The emulator propagates the uncertainties in the distributions of the calibrated input parameters inferred from the first step to the outputs. As a result, a quantification of the uncertainty of the maximum free surface elevation at specified locations is obtained.
Large gyres as a shallow-water asymptotic solution of Euler’s equation in spherical coordinates
Authors: Constantin A. , Johnson R. S.
Published: April 2017

Starting from the Euler equation expressed in a rotating frame in spherical coordinates, coupled with the equation of mass conservation and the appropriate boundary conditions, a thin-layer (i.e. shallow water) asymptotic approximation is developed. The analysis is driven by a single, overarching assumption based on the smallness of one parameter: the ratio of the average depth of the oceans to the radius of the Earth. Consistent with this, the magnitude of the vertical velocity component through the layer is necessarily much smaller than the horizontal components along the layer. A choice of the size of this speed ratio is made, which corresponds, roughly, to the observational data for gyres; thus the problem is characterized by, and reduced to an analysis based on, a single small parameter. The nonlinear leading-order problem retains all the rotational contributions of the moving frame, describing motion in a thin spherical shell. There are many solutions of this system, corresponding to different vorticities, all described by a novel vorticity equation: this couples the vorticity generated by the spin of the Earth with the underlying vorticity due to the movement of the oceans. Some explicit solutions are obtained, which exhibit gyre-like flows of any size; indeed, the technique developed here allows for many different choices of the flow field and of any suitable free-surface profile. We comment briefly on the next order problem, which provides the structure through the layer. Some observations about the new vorticity equation are given, and a brief indication of how these results can be extended is offered.
Known mutator alleles do not markedly increase mutation rate in clinicalSaccharomyces cerevisiaestrains
Authors: Skelly Daniel A. , Magwene Paul M. , Meeks Brianna , Murphy Helen A.
Published: April 2017

Natural selection has the potential to act on all phenotypes, including genomic mutation rate. Classic evolutionary theory predicts that in asexual populations, mutator alleles, which cause high mutation rates, can fix due to linkage with beneficial mutations. This phenomenon has been demonstrated experimentally and may explain the frequency of mutators found in bacterial pathogens. By contrast, in sexual populations, recombination decouples mutator alleles from beneficial mutations, preventing mutator fixation. In the facultatively sexual yeastSaccharomyces cerevisiae, segregating alleles ofMLH1andPMS1have been shown to be incompatible, causing a high mutation rate when combined. These alleles had never been found together naturally, but were recently discovered in a cluster of clinical isolates. Here we report that the incompatible mutator allele combination only marginally elevates mutation rate in these clinical strains. Genomic and phylogenetic analyses provide no evidence of a historically elevated mutation rate. We conclude that the effect of the mutator alleles is dampened by background genetic modifiers. Thus, the relationship between mutation rate and microbial pathogenicity may be more complex than once thought. Our findings provide rare observational evidence that supports evolutionary theory suggesting that sexual organisms are unlikely to harbour alleles that increase their genomic mutation rate.
Stable producer–scrounger dynamics in wild birds: sociability and learning speed covary with scrounging behaviour
Authors: Aplin L. M. , Morand-Ferron J.
Published: April 2017

There has been extensive game-theoretic modelling of conditions leading to equilibria of producer–scrounger dichotomies in groups. However there is a surprising paucity of experimental evidence in wild populations. Here, we examine producer–scrounger games in five subpopulations of birds feeding at a socially learnt foraging task. Over four weeks, a bimodal distribution of producers and scroungers emerged in all areas, with pronounced and consistent individual tactic specialization persisting over 3 years. Tactics were unrelated to exploratory personality, but correlated with latency to contact and learn the foraging task, with the late arrivers and slower learners more likely to adopt the scrounging role. Additionally, the social environment was also important: at the broad scale, larger subpopulations with a higher social density contained proportionally more scroungers, while within subpopulations scroungers tended to be central in the social network and be observed in larger foraging flocks. This study thus provides a rare example of a stable, dimorphic distribution of producer–scrounger tactics in a wild population. It further gives support across multiple scales for a major prediction of social foraging theory; that the frequency of scroungers increases with group size.
Dry habitats were crucibles of domestication in the evolution of agriculture in ants
Authors: Branstetter Michael G. , Ješovnik Ana , Sosa-Calvo Jeffrey , Lloyd Michael W. , Faircloth Brant C. , Brady Seán G. , Schultz Ted R.
Published: April 2017

The evolution of ant agriculture, as practised by the fungus-farming ‘attine’ ants, is thought to have arisen in the wet rainforests of South America about 55–65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The ‘out-of-the-rainforest’ hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture is very likely to have occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favoured the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.
Open data and digital morphology
Authors: Davies Thomas G. , Rahman Imran A. , Lautenschlager Stephan , Cunningham John A. , Asher Robert J. , Barrett Paul M. , Bates Karl T. , Bengtson Stefan , Benson Roger B. J. , Boyer Doug M. , Braga José , Bright Jen A. , Claessens Leon P. A. M. , Cox Philip G. , Dong Xi-Ping , Evans Alistair R. , Falkingham Peter L. , Friedman Matt , Garwood Russell J. , Goswami Anjali , Hutchinson John R. , Jeffery Nathan S. , Johanson Zerina , Lebrun Renaud , Martínez-Pérez Carlos , Marugán-Lobón Jesús , O'Higgins Paul M. , Metscher Brian , Orliac Maëva , Rowe Timothy B. , Rücklin Martin , Sánchez-Villagra Marcelo R. , Shubin Neil H. , Smith Selena Y. , Starck J. Matthias , Stringer Chris , Summers Adam P. , Sutton Mark D. , Walsh Stig A. , Weisbecker Vera , Witmer Lawrence M. , Wroe Stephen , Yin Zongjun , Rayfield Emily J. , Donoghue Philip C. J.
Published: April 2017

Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.
Climatic niche evolution is faster in sympatric than allopatric lineages of the butterfly genusPyrgus
Authors: Pitteloud Camille , Arrigo Nils , Suchan Tomasz , Mastretta-Yanes Alicia , Vila Roger , Dincă Vlad , Hernández-Roldán Juan , Brockmann Ernst , Chittaro Yannick , Kleckova Irena , Fumagalli Luca , Buerki Sven , Pellissier Loïc , Alvarez Nadir
Published: April 2017

Understanding how speciation relates to ecological divergence has long fascinated biologists. It is assumed that ecological divergence is essential to sympatric speciation, as a mechanism to avoid competition and eventually lead to reproductive isolation, while divergence in allopatry is not necessarily associated with niche differentiation. The impact of the spatial context of divergence on the evolutionary rates of abiotic dimensions of the ecological niche has rarely been explored for an entire clade. Here, we compare the magnitude of climatic niche shifts between sympatric versus allopatric divergence of lineages in butterflies. By combining next-generation sequencing, parametric biogeography and ecological niche analyses applied to a genus-wide phylogeny of PalaearcticPyrgusbutterflies, we compare evolutionary rates along eight climatic dimensions across sister lineages that diverged in large-scale sympatry versus allopatry. In order to examine the possible effects of the spatial scale at which sympatry is defined, we considered three sets of biogeographic assignments, ranging from narrow to broad definition. Our findings suggest higher rates of niche evolution along all climatic dimensions for sister lineages that diverge in sympatry, when using a narrow delineation of biogeographic areas. This result contrasts with significantly lower rates of climatic niche evolution found in cases of allopatric speciation, despite the biogeographic regions defined here being characterized by significantly different climates. Higher rates in allopatry are retrieved when biogeographic areas are too widely defined—in such a case allopatric events may be recorded as sympatric. Our results reveal the macro-evolutionary significance of abiotic niche differentiation involved in speciation processes within biogeographic regions, and illustrate the importance of the spatial scale chosen to define areas when applying parametric biogeographic analyses.
Evolution and multiple roles of the Pancrustacea specific transcription factorzeldain insects
Authors: Ribeiro Lupis , Tobias-Santos Vitória , Santos Danielle , Antunes Felipe , Feltran Geórgia , de Souza Menezes Jackson , Aravind L. , Venancio Thiago Motta , Fonseca Rodrigo Nunes da
Published: April 2017

Gene regulatory networks (GRN) evolve as a result of the coevolutionary process acting on transcription factors and the cis-regulatory modules (CRMs) they bind. The zinc-finger transcription factor (TF)zelda(zld) is essential for maternal zygotic transition (MZT) inDrosophila melanogaster, where it directly binds over thousand CRMs to regulate chromatin accessibility.D. melanogasterdisplays a long germ type of embryonic development, where all segments are simultaneously generated along the whole egg. However, it remains unclear ifzldis also involved in MZT of short-germ insects (including those from basal lineages) or in other biological processes. Here we show thatzldis an innovation of the Pancrustacea lineage, being absent in more distant arthropods (e.g. chelicerates) and other organisms. To better understandzld’sancestral function, we thoroughly investigated its roles in a short-germ beetle,Tribolium castaneum, using molecular biology and computational approaches. Our results demonstrate roles forzldnot only during the MZT, but also in posterior segmentation and patterning of imaginal disc derived structures. Further, we also demonstrate thatzldis critical for posterior segmentation in the hemipteranRhodnius prolixus, indicating this function predates the origin of holometabolous insects and was subsequently lost in long-germ insects. Our results unveil new roles ofzldin maintaining pluripotent state of progenitor cells at the posterior region and suggest that changes in expression ofzld(and probably other pioneer TFs) are critical in the evolution of insect GRNs.
When Group Means Fail: Can One Size Fit All?
Authors: Grandy Thomas H. , Lindenberger Ulman , Werkle-Bergner Markus
Published: April 2017

The present study examined whether a cognitive process model that is inferred based on group data holds, and is meaningful, at the level of the individual person. Investigation of this issue is tantamount to questioning that the same set and configuration of cognitive processes is present within all individuals, a usually untested assumption in standard group-based experiments. Search from memory as assessed with the Sternberg memory scanning paradigm is among the most widely studied phenomena in cognitive psychology. According to the original memory scanning model, search is serial and exhaustive. Here we critically examined the validity of this model across individuals and practice. 32 younger adults completed 1488 trials of the Sternberg task distributed over eight sessions. In the first session, group data followed the pattern predicted by the original model, replicating earlier findings. However, data from the first session were not sufficiently reliable for identifying whether each individual complied with the serial exhaustive search model. In sessions six to eight, when participants performed near asymptotic levels of performance, between-person differences were reliable, group data deviated substantially from the original memory search model, and the model fit only 13 of the 32 participants’ data. Our findings challenge the proposition that one general memory search process exists within a group of healthy younger adults, and questions the testability of this proposition at the individual level in single-session experiments. Implications for cognitive psychology and cognitive neuroscience are discussed with reference to earlier work emphasizing the explicit consideration of potentially existent individual differences.
The Influence of Parkinson’s Disease and Neurotypical Aging on Cognitive Performance Among Volunteers for an Exercise-based Rehabilitative Intervention
Authors: McKay J. Lucas , Bozzorg Ariyana , Nocera Joe , Hackney Madeleine E.
Published: April 2017

PURPOSE

To determine the impact of aging versus combined aging and disease on cognition in older adults with and without Parkinson’s disease (PD) who were volunteers for exercise based rehabilitation research.

METHODS

We used a multiple linear regression approach to analyze cognitive outcome measures of rehabilitation volunteers with and without PD.

RESULTS

Significant associations were identified between increased age and decreased performance on 8 of the 14 outcomes analyzed after controlling for false discovery rate. Of those 8 outcomes, multivariate regression analyses demonstrated an effect of disease on performance in only 4/8. In all cases, PD was associated with superior, rather than decreased performance after controlling for age. Results were unaffected by sex and education. Post-hoc comparison with available age norms demonstrated that differences between PD and Non-PD volunteers could be primarily attributed to the Non-PD group substantially underperforming versus age norms.

CONCLUSIONS

In rehabilitative exercise studies using volunteers, many cognitive domains decline with increasing age, consistent with previous neuropsychological studies without a rehabilitation component. However, older “neurotypical” volunteers may potentially underperform PD volunteers after controlling for age. This may be an important design consideration for rehabilitation studies with cognitive outcomes.

IMPLICATIONS FOR REHABILITATION

An increasing number of rehabilitation studies incorporate cognitive outcomes.

Whether the overall cognitive profile of rehabilitation volunteers differs from that of neurotypical aging remains to be established.

Rehabilitation volunteers with Parkinson’s disease may outperform putatively neurotypical volunteers after controlling for covariates.

Cognitive impairments associated with PD in neuropsychological studies may not generalize to exercise rehabilitation volunteers.