bluuebunny/crossref_metadata_2025 huggingface dataset:
Methods of pushing during vaginal delivery and pelvic floor and perineal outcomes: a review
Authors: de Tayrac Renaud , Letouzey Vincent
Published: October 2016

Purpose of review

Over the past 20 years, several randomized studies have compared Valsalva and spontaneous pushing techniques during vaginal delivery. This review summarizes current medical knowledge concerning their maternal and fetal consequences, focusing on pelvic and perineal outcomes.

Recent findings

We selected nine randomized controlled trials comparing Valsalva and spontaneous pushing, and a secondary analysis of a randomized controlled trial comparing different methods of perineal protection. Two trials showed that spontaneous pushing reduces the risk of perineal tears, but no firm conclusions can be drawn given the heterogeneity and inconsistent results of these studies. Conflicting results have been reported regarding the duration of the second stage of labor. Pushing technique does not seem to affect episiotomy, instrumental delivery or cesarean rates. Maternal satisfaction seems to be better after spontaneous pushing. Spontaneous pushing appears to have no adverse effects on neonatal well being, and one study showed a significant improvement in prenatal fetal parameters during the expulsive phase.

Valsalva and spontaneous pushing techniques currently appear comparable in terms of duration, pelvic floor, perineal, and neonatal outcomes. In the absence of strong evidence in favor of either technique, the decision should be guided by patient preference and the clinical situation. Additional, well-designed randomized controlled trials are required.
Open Capsulotomy: An Effective but Overlooked Treatment for Capsular Contracture after Breast Augmentation
Authors: Swanson Eric
Published: October 2016

Background:

The prevailing theory for capsular contracture after breast augmentation is a subclinical capsular infection. A capsulectomy, site change, and implant replacement are recommended. An open capsulotomy leaves the capsule in the patient. Theoretically, such a procedure would be ineffective because it does not remove the infected tissue. Recurrences occurred frequently in women treated in the 1970s when leaky silicone gel implants were in use. Open capsulotomy has not been studied in women implanted with third-generation devices.

Methods:

Seventy-five consecutive women with Baker III/IV capsular contractures after breast augmentation treated with open capsulotomies between 1996 and 2016 were retrospectively evaluated. The original implants were usually saline-filled (72.2%). Replacements were all smooth and round, and 92.6% were also saline-filled.

Results:

Seventeen women (22.7%) developed a recurrent capsular contracture. Two patients (2.7%) experienced a second recurrence. Patients with ruptured silicone gel implants (n = 13) had a significantly greater risk of recurrence (P = 0.01). There was no significant difference in recurrence rates comparing patients whose intact implants were reinserted (12.5%) with women whose intact implants were replaced (18.2%). Povidone–iodine irrigation did not affect the recurrence rate. Capsular contracture was corrected with 1 procedure in 77.3% of patients and 2 procedures in 97.3% of patients.

Conclusions:

Open capsulotomy is a safe and effective treatment that avoids the additional morbidity and cost of a capsulectomy. The findings challenge the infected biofilm theory of capsular contracture. Open capsulotomy deserves reconsideration by plastic surgeons.
Developing an Item Bank to Measure Quality of Life in Individuals With Glaucoma, and the Results of the Interview With Patients: The Effect of Visual Function, Visual Field Progression Rate, Medical, and Surgical Treatments on Quality of Life
Authors: Matsuura Masato , Hirasawa Kazunori , Hirasawa Hiroyo , Yanagisawa Mieko , Murata Hiroshi , Mayama Chihiro , Asaoka Ryo
Published: October 2016

Purpose:

To construct a new item bank to measure quality of life (QOL) in glaucoma patients and to evaluate glaucoma patients’ QOL using the item bank.

Methods:

An item bank of questions was generated through a literature review of QOL instruments useful for glaucoma patients. Using this item bank, a cognitive survey was performed on 203 patients with glaucoma (112 males and 91 females, 61.9±11.9 y old; mean±SD). The results were then analyzed using the Rasch analysis, and the Rasch-derived disability scores were predicted using linear modelling and the following clinical parameters: age, mean total deviation (mTD) in superior and inferior visual field (mTDsup/mTDinf), mTD progression rate, better visual acuity, worse visual acuity, number of eye drops administered per day, number of trabeculectomy procedures experienced in both eyes.

Results:

A total of 23 questionnaires of QOL in glaucoma patients were identified resulting in an item bank of 187 questions related to the following tasks: reading/writing, walking, going out, eating and driving (direct disability) as well as questions concerned with worry/anxiety, social participation, and physical symptoms (indirect disability). In the optimal model for direct disability, age and mTDinf were identified as significant predictors, whereas number of eye drops administered per day and number of trabeculectomy experienced were included in the optimal model for indirect disability.

Conclusions:

A new item bank to measure QOL in glaucoma patients was developed and evaluated. Age and mTDinf were found to be related to direct disability while medical and surgical treatments were related to indirect disability.
Using Hemospray Improves the Cost-effectiveness Ratio in the Management of Upper Gastrointestinal Nonvariceal Bleeding
Authors: Barkun Alan N. , Adam Viviane , Lu Yidan , Chen Yen-I , Martel Myriam
Published: October 2016

Goals:

We compared the cost-effectiveness of traditional recommended endoscopic hemostatic therapies and Hemospray alone or in combination when treating nonvariceal upper gastrointestinal bleeding (NVUGIB).

Background:

Hemospray (TC-325) is a novel endoscopic hemostatic powder, achieving hemostasis through adherence to actively bleeding biological surfaces.

Study:

A decision tree of patients with NVUGIB assessed 4 possible treatment strategies: traditional therapy alone (T), Hemospray alone (H), traditional therapy completed by Hemospray if needed (T+H), or Hemospray completed by traditional therapy if needed (H+T). Using published probabilities, effectiveness was the likelihood of avoiding rebleeding over 30 days. Costs in 2014 US$ were based on the US National Inpatient Sample. A third-party payer perspective was adopted. Sensitivity and subgroup analyses were performed.

Results:

For all patients, T+H was more efficacious (97% avoiding rebleeding) and less expensive (average cost per patient of US$9150) than all other approaches. The second most cost-effective approach was H+T (5.57% less effective and US$635 more per patient). Sensitivity analyses showed T+H followed by a strategy of H+T remained more cost-effective than H or T alone when varying all probability assumptions across plausible ranges. Subgroup analysis showed that the inclusion of H (especially alone) was least adapted for ulcers and was more cost-effective when treating lesions at low risk of delayed rebleeding.

Conclusions:

Hemospray improves the effectiveness of traditional hemostasis, being less costly in most NVUGIB patient populations. A Hemospray first approach is most cost-effective for nonulcer bleeding lesions at low risk of delayed hemorrhage.
Cardiac arrests within the emergency department: an Utstein style report, causation and survival factors
Authors: Tan Sing C. , Leong Benjamin Sieu-Hon
Published: October 2016

Background

Emergency Department Cardiac Arrests are typically classified with in-hospital cardiac arrests, but are yet to be well described as a distinct clinical entity. This study provides an Utstein style report on Emergency Department Cardiac Arrests, and identifies factors associated with survival.

Patients and methods

Patients who experienced a cardiac arrest in the Emergency Department of the National University Hospital, Singapore, between January 2010 and August 2012 were studied. Data were collected retrospectively and potential survival factors were assessed with a multivariate logistic regression.

Results

One hundred and six cases were identified for analysis. Most patients were male and 43.4% had a presumed cardiac diagnosis. All arrests were witnessed and received Advanced Cardiac Life Support interventions immediately. Out of the total, 31.1% of arrests occurred during or immediately after intubation. Overall, 48.1% of patients survived to hospital discharge. Patients with a shockable rhythm had the highest survival rate (70.8%), followed by asytole (20.8%) and pulseless electrical activity (15.1%). In all, 91.3% of survivors with a premorbid Cerebral Performance Category score of 1 were discharged with a similar Cerebral Performance Category score.

Variables associated with survival to hospital discharge were a shockable initial rhythm (odds ratio 12.1; 95% confidence interval, 3.1–47.6) and a time to return of spontaneous circulation of less than 10 min (odds ratio 4.1; 95% confidence interval, 1.0–16.9).

Conclusion

This is the first Utstein style report on Emergency Department Cardiac Arrests. A high survival rate with good neurological outcomes was found in this population. The initial rhythm and time to return of spontaneous circulation have been identified as survival factors and may be used to guide decision-making during resuscitation.
The Malta Childhood National Body Mass Index Study
Authors: Grech Victor , Aquilina Samuel , Camilleri Erin , Spiteri Karl , Busuttil Maria‐Louisa , Sant'Angelo Victoria F. , Calleja Neville
Published: October 2016

Objectives:

Obesity is a chronic disease that often commences in childhood. More than a quarter of Maltese children are overweight or obese. The present study was carried out to measure height and weight (and body mass index) for all school children in Malta to precisely quantify the extent of the problem.

Methods:

Schooling in Malta is provided by: free state schools, subsidized Roman Catholic church–run schools, and independent private schools. All were included. Physical education teachers were trained in measurements on identical stadiometers. Bespoke spreadsheets were created using World Health Organization cut‐offs for underweight, overweight, and obesity.

Results:

The present study included more than 46,027 children in more than 145 schools (ages 4.7–17 years). Less than 10% were unmeasured. Approximately 40% of school‐aged children in Malta are overweight or obese. The proportion of obese was greater than that of overweight. Levels of overweight and obesity were significantly different: State>Church>Independent schools. Overall, and for both sexes and for school types, there was a trend for overweight and obesity to peak in years 5 to 8, then decline slightly. Overweight and obesity was secondary>primary schools, and boys>girls. The underweight group was small with no significant difference between the school types.

Conclusions:

The present study has confirmed high levels of overweight and obesity in Maltese children. It also provides proof of concept of scalability by demonstrating the feasibility of undertaking a relatively inexpensive study of an entire childhood population. The modus operandi (utilizing physical education teachers) could relatively easily be up scaled for any country.
Causative agents, diseases, epidemiology and diagnosis of sexually transmitted infections
Authors: Casillas-Vega Néstor , Morfín-Otero Rayo , García Santos , Camacho-Ortiz Adrian , Garza-González Elvira
Published: October 2016

Sexually transmitted infections (STIs) are caused by more than 30 species; the organisms with the highest frequency and clinical importance are Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, Mycoplasma genitalium, the hepatitis B and C viruses, the human immunodeficiency virus, the human papillomavirus, the herpes simplex virus type 1 and type 2 and Trichomonas vaginalis. Most of these infections are present without symptoms, and when they are present, the most common clinical manifestations of sexually transmitted diseases include vaginal discharge, genital ulcers and abdominal pain in women. Worldwide more than 1 million people acquire an STI per day, and an estimated 500 million people are infected each year with one of the next four STIs: chlamydia, gonorrhoea, syphilis or trichomoniasis. More than 290 million women are infected with human papillomavirus, and more than 530 million people have the virus that causes herpes simplex virus type 2 at this time. Such infections can have serious consequences beyond the immediate effects of the infection itself, that is transmission from mother to child during pregnancy and childbirth, and chronic diseases. Given the importance of these illnesses, in this review, we present the most important aspects of the causative agents, diseases, epidemiology and diagnosis of STIs.
Moving In and Out of the What-Ifs
Authors: Schroeder Dawn , Duggleby Wendy , Cameron Brenda L.
Published: October 2016

Background:

In families where genetic testing for the breast cancer 1 and 2 genes (BRCA1/2) has not identified a deleterious mutation, the risk for hereditary breast cancer (HBC) can still be high when there is a strong family history. Little is known about how an awareness of risk for HBC impacts the everyday lives of unaffected women (no personal history for breast and/or ovarian cancer) in these families.

Objective:

The aim of this study is to explore how unaffected women, living in BRCA1/2-negative families, experience living with risk for HBC.

Methods:

van Manen’s hermeneutic phenomenological approach guided this study. Unaffected at-risk women were recruited from a hereditary breast and ovarian cancer clinic in Western Canada.

Results:

Nine women participated in 20 open-ended conversations. Phenomenological reflection on the 4 life existentials (lived space, body, time, and relations) revealed “Moving In and Out of the What-Ifs” as an overarching description that was communicated through the following themes: “Just Moving Along: Living a Normal Life,” “Moving Into Those Dark Spaces,” “Is there Something Wrong With Me”? “Markings in Time,” “Living in the Moment,” “Being Cared For,” and “Keeping Me Grounded.”

Conclusions:

The findings reveal how knowledge from predictive medicine impacts the lives of women and the importance of supportive relations and provides a foundation for future research into how health is perceived.

Implications for Practice:

The findings inform the practices of healthcare professionals as they engage in discussions with women living with risk for HBC and highlight the importance of a supportive relationship.
Clinical subtypes and genetic heterogeneity: of lumping and splitting in Parkinson disease
Authors: von Coelln Rainer , Shulman Lisa M.
Published: October 2016

Purpose of review

Recent studies on clinical, genetic and pathological heterogeneity of Parkinson disease have renewed the old debate whether we should think of Parkinson disease as one disease with variations, or as a group of independent diseases that happen to present with similar phenotypes. Here, we provide an overview of where the debate is coming from, and how recent findings in clinical subtyping, genetics and clinico-pathological correlation have shaped this controversy over the last few years.

Recent findings

New and innovative clinical diagnostic criteria for Parkinson disease have been proposed and await validation. Studies using functional imaging or wearable biosensors, as well as biomarker studies, provide new support for the validity of the traditional clinical subtypes of Parkinson disease (tremor-dominant versus akinetic-rigid or postural instability/gait difficulty). A recent cluster analysis (as unbiased data-driven approach to subtyping) included a wide spectrum of nonmotor variables, and showed correlation of the proposed subtypes with disease progression in a longitudinal analysis. New genetic factors contributing to Parkinson disease susceptibility continue to be identified, including rare mutations causing monogenetic disease, common variants with small effect size and risk factors (like mutations in the gene for glucocerebrosidase) that fall in between the two other categories. Recent studies show some limited correlation between genetic factors and clinical heterogeneity. Despite some variations in patterns of pathology, Lewy bodies are still the hallmark of Parkinson disease, including the vast majority of genetic subgroups.

Evidence of clinical, genetic and pathological heterogeneity of Parkinson disease continues to emerge, but clearly defined subtypes that hold up in more than one of these domains remain elusive. For research to identify such subtypes, splitting is likely the way forward; until then, for clinical practice, lumping remains the more pragmatic approach.
Trade-off between disease resistance and crop yield: a landscape-scale mathematical modelling perspective
Authors: Vyska Martin , Cunniffe Nik , Gilligan Christopher
Published: October 2016

The deployment of crop varieties that are partially resistant to plant pathogens is an important method of disease control. However, a trade-off may occur between the benefits of planting the resistant variety and a yield penalty, whereby the standard susceptible variety outyields the resistant one in the absence of disease. This presents a dilemma: deploying the resistant variety is advisable only if the disease occurs and is sufficient for the resistant variety to outyield the infected standard variety. Additionally, planting the resistant variety carries with it a further advantage in that the resistant variety reduces the probability of disease invading. Therefore, viewed from the perspective of a grower community, there is likely to be an optimal trade-off and thus an optimal cropping density for the resistant variety. We introduce a simple stochastic, epidemiological model to investigate the trade-off and the consequences for crop yield. Focusing on susceptible–infected–removed epidemic dynamics, we use the final size equation to calculate the surviving host population in order to analyse the yield, an approach suitable for rapid epidemics in agricultural crops. We identify a single compound parameter, which we call the efficacy of resistance and which incorporates the changes in susceptibility, infectivity and durability of the resistant variety. We use the compound parameter to inform policy plots that can be used to identify the optimal strategy for given parameter values when an outbreak is certain. When the outbreak is uncertain, we show that for some parameter values planting the resistant variety is optimal even when it would not be during the outbreak. This is because the resistant variety reduces the probability of an outbreak occurring.
Body reserves mediate trade-offs between life-history traits: new insights from small pelagic fish reproduction
Authors: Brosset Pablo , Lloret Josep , Muñoz Marta , Fauvel Christian , Van Beveren Elisabeth , Marques Virginie , Fromentin Jean-Marc , Ménard Frédéric , Saraux Claire
Published: October 2016

Limited resources in the environment prevent individuals from simultaneously maximizing all life-history traits, resulting in trade-offs. In particular, the cost of reproduction is well known to negatively affect energy investment in growth and maintenance. Here, we investigated these trade-offs during contrasting periods of high versus low fish size and body condition (before/after 2008) in the Gulf of Lions. Female reproductive allocation and performance in anchovy (
Engraulis encrasicolus
) and sardine (
Sardina pilchardus
) were examined based on morphometric historical data from the 1970s and from 2003 to 2015. Additionally, potential maternal effects on egg quantity and quality were examined in 2014/2015. After 2008, the gonadosomatic index increased for sardine and remained steady for anchovy, while a strong decline in mean length at first maturity indicated earlier maturation for both species. Regarding maternal effects, for both species egg quantity was positively linked to fish size but not to fish lipid reserves, while the egg quality was positively related to lipid reserves. Atresia prevalence and intensity were rather low regardless of fish condition and size. Finally, estimations of total annual numbers of eggs spawned indicated a sharp decrease for sardine since 2008 but a slight increase for anchovy during the last 5 years. This study revealed a biased allocation towards reproduction in small pelagic fish when confronted with a really low body condition. This highlights that fish can maintain high reproductive investment potentially at the cost of other traits which might explain the present disappearance of old and large individuals in the Gulf of Lions.
Perceptual impairment in face identification with poor sleep
Authors: Beattie Louise , Walsh Darragh , McLaren Jessica , Biello Stephany M. , White David
Published: October 2016

Previous studies have shown impaired memory for faces following restricted sleep. However, it is not known whether lack of sleep impairs performance on face identification tasks that do not rely on recognition memory, despite these tasks being more prevalent in security and forensic professions—for example, in photo-ID checks at national borders. Here we tested whether poor sleep affects accuracy on a standard test of face-matching ability that does not place demands on memory: the Glasgow Face-Matching Task (GFMT). In Experiment 1, participants who reported sleep disturbance consistent with insomnia disorder show impaired accuracy on the GFMT when compared with participants reporting normal sleep behaviour. In Experiment 2, we then used a sleep diary method to compare GFMT accuracy in a control group to participants reporting poor sleep on three consecutive nights—and again found lower accuracy scores in the short sleep group. In both experiments, reduced face-matching accuracy in those with poorer sleep was not associated with lower confidence in their decisions, carrying implications for occupational settings where identification errors made with high confidence can have serious outcomes. These results suggest that sleep-related impairments in face memory reflect difficulties in perceptual encoding of identity, and point towards metacognitive impairment in face matching following poor sleep.
Coping with a changing environment: the effects of early life stress
Authors: Vindas Marco A. , Madaro Angelico , Fraser Thomas W. K. , Höglund Erik , Olsen Rolf E. , Øverli Øyvind , Kristiansen Tore S.
Published: October 2016

Ongoing rapid domestication of Atlantic salmon implies that individuals are subjected to evolutionarily novel stressors encountered under conditions of artificial rearing, requiring new levels and directions of flexibility in physiological and behavioural coping mechanisms. Phenotypic plasticity to environmental changes is particularly evident at early life stages. We investigated the performance of salmon, previously subjected to an unpredictable chronic stress (UCS) treatment at an early age (10 month old parr), over several months and life stages. The UCS fish showed overall higher specific growth rates compared with unstressed controls after smoltification, a particularly challenging life stage, and after seawater transfer. Furthermore, subjecting fish to acute stress at the end of the experiment, we found that UCS groups had an overall lower hypothalamic catecholaminergic and brain stem serotonergic response to stress compared with control groups. In addition, serotonergic activity was negatively correlated with final growth rates, which implies that serotonin responsive individuals have growth disadvantages. Altogether, our results may imply that a subdued monoaminergic response in stressful farming environments may be beneficial, because in such situations individuals may be able to reallocate energy from stress responses into other life processes, such as growth.
Seven and up: individual differences in male voice fundamental frequency emerge before puberty and remain stable throughout adulthood
Authors: Fouquet Meddy , Pisanski Katarzyna , Mathevon Nicolas , Reby David
Published: October 2016

Voice pitch (the perceptual correlate of fundamental frequency,
F
0) varies considerably even among individuals of the same sex and age, communicating a host of socially and evolutionarily relevant information. However, due to the almost exclusive utilization of cross-sectional designs in previous studies, it remains unknown whether these individual differences in voice pitch emerge before, during or after sexual maturation, and whether voice pitch remains stable into adulthood. Here, we measured the
F
0 parameters of men who were recorded once every 7 years from age 7 to 56 as they participated in the British television documentary
Up Series
. Linear mixed models revealed significant effects of age on all
F
0 parameters, wherein
F
0 mean, minimum, maximum and the standard deviation of
F
0 showed sharp pubertal decreases between age 7 and 21, yet remained remarkably stable after age 28. Critically, men's pre-pubertal
F
0 at age 7 strongly predicted their
F
0 at every subsequent adult age, explaining up to 64% of the variance in post-pubertal
F
0. This finding suggests that between-individual differences in voice pitch that are known to play an important role in men's reproductive success are in fact largely determined by age 7, and may therefore be linked to prenatal and/or pre-pubertal androgen exposure.
Tumbling of a Brownian particle in an extensional flow
Authors: Plan Emmanuel Lance Christopher VI Medil , Vincenzi Dario
Published: October 2016

The phenomenon of tumbling of microscopic objects is commonly associated with shear flows. We address the question of whether tumbling can also occur in stretching-dominated flows. To answer this, we study the dynamics of a semi-flexible trumbbell in a planar extensional velocity field. We show that the trumbbell undergoes a random tumbling-through-folding motion. The probability distribution of long tumbling times is exponential with a time scale exponentially increasing with the Weissenberg number.
Network rewiring dynamics with convergence towards a star network
Authors: Whigham P. A. , Dick G. , Parry M.
Published: October 2016

Network rewiring as a method for producing a range of structures was first introduced in 1998 by Watts & Strogatz (
Nature
393
, 440–442. (
doi:10.1038/30918
)). This approach allowed a transition from regular through small-world to a random network. The subsequent interest in scale-free networks motivated a number of methods for developing rewiring approaches that converged to scale-free networks. This paper presents a rewiring algorithm (RtoS) for undirected, non-degenerate, fixed size networks that transitions from regular, through small-world and scale-free to star-like networks. Applications of the approach to models for the spread of infectious disease and fixation time for a simple genetics model are used to demonstrate the efficacy and application of the approach.
Deleterious localized stress fields: the effects of boundaries and stiffness tailoring in anisotropic laminated plates
Authors: Groh R. M. J. , Weaver P. M.
Published: October 2016

The safe design of primary load-bearing structures requires accurate prediction of stresses, especially in the vicinity of geometric discontinuities where deleterious three-dimensional stress fields can be induced. Even for thin-walled structures significant through-thickness stresses arise at edges and boundaries, and this is especially precarious for laminates of advanced fibre-reinforced composites because through-thickness stresses are the predominant drivers in delamination failure. Here, we use a higher-order equivalent single-layer model derived from the Hellinger–Reissner mixed variational principle to examine boundary layer effects in laminated plates comprising constant-stiffness and variable-stiffness laminae and deforming statically in cylindrical bending. The results show that zigzag deformations, which arise due to layerwise differences in the transverse shear moduli, drive boundary layers towards clamped edges and are therefore critically important in quantifying localized stress gradients. The relative significance of the boundary layer scales with the degree of layerwise anisotropy and the thickness to characteristic length ratio. Finally, we demonstrate that the phenomenon of alternating positive and negative transverse shearing deformation through the thickness of composite laminates, previously only observed at clamped boundaries, can also occur at other locations as a result of smoothly varying the material properties over the in-plane dimensions of the laminate.
Characterization of the surface roughness of sand particles using an advanced fractal approach
Authors: Yang Hongwei , Baudet Béatrice A. , Yao Ting
Published: October 2016

The surface roughness of soil grains affects the mechanical behaviour of soils, but the characterization of real soil grain roughness is still limited in both quantity and quality. A new method is proposed, which applies the power spectral density (PSD), typically used in tribology, to optical interferometry measurements of soil grain surfaces. The method was adapted to characterize the roughness of soil grains separately from their shape, allowing the scale of the roughness to be determined in the form of a wavevector range. The surface roughness can be characterized by a roughness value and a fractal dimension, determined based on the stochastic formation process of the surface. When combined with other parameters, the fractal dimension provides additional information about the surface structure and roughness to the value of roughness alone. Three grain sizes of a quarzitic sand were tested. The parameters determined from the PSD analysis were input directly into a Weierstrass–Mandelbrot function to reconstruct successfully a fractal surface.
Strong influence of palaeoclimate on the structure of modern African mammal communities
Authors: Rowan John , Kamilar Jason M. , Beaudrot Lydia , Reed Kaye E.
Published: October 2016

Ecological research often assumes that species are adapted to their current climatic environments. However, climate fluctuations over geologic timescales have influenced species dispersal and extinction, which in turn may affect community structure. Modern community structure is likely to be the product of both palaeoclimate and modern climate, with the relative degrees of influence of past and present climates unknown. Here, we assessed the influence of climate at different time periods on the phylogenetic and functional trait structure of 203 African mammal communities. We found that the climate of the mid-Holocene (approx. 6000 years ago) and Last Glacial Maximum (approx. 22 000 years ago) were frequently better predictors of community structure than modern climate for mammals overall, carnivorans and ungulates. Primate communities were more strongly influenced by modern climate than palaeoclimate. Overall, community structure of African mammals appears to be related to the ecological flexibility of the groups considered here and the regions of continental Africa that they occupy. Our results indicate that the future redistribution, expansion and contraction of particular biomes due to human activity, such as climate and land-use change, will differentially affect mammal groups that vary in their sensitivity to environmental change.
Capuchins, space, time and memory: an experimental test of what-where-when memory in wild monkeys
Authors: Janson Charles H.
Published: October 2016

There is considerable controversy about the existence, extent and adaptive value of integrated multimodal memory in non-human animals. Building on prior results showing that wild capuchin monkeys in Argentina appear to recall both the location and amount of food at patches they had previously visited, I tested whether they also track and use elapsed time as a basis for decisions about which feeding patches to visit. I presented them with an experimental array of eight feeding sites, at each of which food rewards increased with increasing elapsed time since the previous visit, similar to the pattern of ripe fruit accumulation in natural feeding trees. Over the course of 68 days, comprising two distinct renewal rate treatments, one group repeatedly visited sites in the feeding array, generating 212 valid choices between sites. Comparison of observations against simulated movements and multinomial statistical models shows that the monkeys' choices were most consistent with dynamic memory for elapsed time specific to each of the eight sites. Thus, it appears that capuchin monkeys possess and use integrated memories of prior food patch use, including where the patch is relative to their current location, how productive the patch is and how long it has been since they last visited the patch. Natural selection to use such integrated memories in foraging tasks may provide an ecologically relevant basis for the evolution of complex intelligence in primates.
Evolution of bacterial recombinase A (
recA
) in eukaryotes explained by addition of genomic data of key microbial lineages
Authors: Hofstatter Paulo G. , Tice Alexander K. , Kang Seungho , Brown Matthew W. , Lahr Daniel J. G.
Published: October 2016

Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic
recA
genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria–eukaryote) and/or secondary (eukaryote–eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the
recA
genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by
Dictyostelium
. We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial
recA
homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.
Genetic basis of priority effects: insights from nectar yeast
Authors: Dhami Manpreet K. , Hartwig Thomas , Fukami Tadashi
Published: October 2016

Priority effects, in which the order of species arrival dictates community assembly, can have a major influence on species diversity, but the genetic basis of priority effects remains unknown. Here, we suggest that nitrogen scavenging genes previously considered responsible for starvation avoidance may drive priority effects by causing rapid resource depletion. Using single-molecule sequencing, we
de novo
assembled the genome of the nectar-colonizing yeast,
Metschnikowia reukaufii
, across eight scaffolds and complete mitochondrion, with gap-free coverage over gene spaces. We found a high rate of tandem gene duplication in this genome, enriched for nitrogen metabolism and transport. Both high-capacity amino acid importers,
GAP1
and
PUT4
, present as tandem gene arrays, were highly expressed in synthetic nectar and regulated by the availability and quality of amino acids. In experiments with competitive nectar yeast,
Candida rancensis
, amino acid addition alleviated suppression of
C. rancensis
by early arrival of
M. reukaufii
, corroborating that amino acid scavenging may contribute to priority effects. Because niche pre-emption via rapid resource depletion may underlie priority effects in a broad range of microbial, plant and animal communities, nutrient scavenging genes like the ones we considered here may be broadly relevant to understanding priority effects.
Temporal patterns of local adaptation in soil pseudomonads
Authors: Kraemer Susanne A. , Kassen Rees
Published: October 2016

Strong divergent selection leading to local adaptation is often invoked to explain the staggering diversity of bacteria in microbial ecosystems. However, examples of specialization by bacterial clones to alternative niches in nature are rare. Here, we investigate the extent of local adaptation in natural isolates of pseudomonads and their relatives to their soil environments across both space and time. Though most isolates grew well in most environments, patchily distributed low-quality environments were found to drive specialization. In contrast to experimental evolution work on microbial adaptation, temporal adaptation was stronger than spatial adaptation among the isolates and environments we sampled. Time-shift analysis of fitness across two seasons of growth revealed an unexpectedly strong effect of preadaptation. This pattern of apparent future adaptation may be caused by unknown abiotic properties of these environments, phages, bacterial competitors or general mechanisms of ecological niche release, and warrants future study.
Density-dependent changes in effective area occupied for sea-bottom-associated marine fishes
Authors: Thorson James T. , Rindorf Anna , Gao Jin , Hanselman Dana H. , Winker Henning
Published: October 2016

The spatial distribution of marine fishes can change for many reasons, including density-dependent distributional shifts. Previous studies show mixed support for either the proportional-density model (PDM; no relationship between abundance and area occupied, supported by ideal-free distribution theory) or the basin model (BM; positive abundance–area relationship, supported by density-dependent habitat selection theory). The BM implies that fishes move towards preferred habitat as the population declines. We estimate the average relationship using bottom trawl data for 92 fish species from six marine regions, to determine whether the BM or PDM provides a better description for sea-bottom-associated fishes. We fit a spatio-temporal model and estimate changes in effective area occupied and abundance, and combine results to estimate the average abundance–area relationship as well as variability among taxa and regions. The average relationship is weak but significant (0.6% increase in area for a 10% increase in abundance), whereas only a small proportion of species–region combinations show a negative relationship (i.e. shrinking area when abundance increases). Approximately one-third of combinations (34.6%) are predicted to increase in area more than 1% for every 10% increase in abundance. We therefore infer that population density generally changes faster than effective area occupied during abundance changes. Gadiformes have the strongest estimated relationship (average 1.0% area increase for every 10% abundance increase) followed by Pleuronectiformes and Scorpaeniformes, and the Eastern Bering Sea shows a strong relationship between abundance and area occupied relative to other regions. We conclude that the BM explains a small but important portion of spatial dynamics for sea-bottom-associated fishes, and that many individual populations merit cautious management during population declines, because a compressed range may increase the efficiency of harvest.
Improving trust, improving schools
Authors: Brown Chris , Daly Alan , Liou Yi-Hwa
Published: October 2016

Purpose

– Many governments worldwide are now promoting the importance of research-informed efforts at improvement. At the same time research is yet to make sustained impact on the practices of teachers. Given the importance of the issue and the lack of progress in this area, the purpose of this paper is to examine what drives teachers’ perceptions that their school: first, encourages the use of research evidence to support improvements to teaching; and second, whether school improvement strategies are grounded in research on effective practice.

Design/methodology/approach

– Reviewing extant literature, the authors hypothesize that teachers’ perceptions of research use are related to their perceptions of: the presence of in-school organizational learning (OL) factors; whether they work in high-trust environments; and also to the frequency and quality of their “expertise-seeking” interactions. Using a survey instrument to measure OL, trust, and school research use climate, the authors gather data from 828 teachers in 43 schools. The authors then use social network analysis to quantify teachers’ professional relationships; with hierarchical linear regression employed to explore multilevel relationships between variables. Social network diagrams are also used to visualize the patterns of relationships between teachers/study variables.

Findings

– The analysis indicates that teachers who report the climate of their schools to be focussed on learning, experimentation, and valuing new ideas, tend to also report more use of research/evidence. Likewise, teachers who had more frequent and useful interactions around teaching and learning also report more research/evidence use (RE Use) in their schools. Finally, and perhaps most powerfully, is that higher levels of perceived trust in the school are also associated with reporting higher levels of RE Use.

Originality/value

– The results illustrate the importance of learning and trust in facilitating the types of relations needed to provide teachers with access to the research/evidence centered social capital that resides within a school. The work expands the notions of what is necessary to support the use of research/evidence in schools by placing more relational elements of the improvement equation front and center.
Beam monitor calibration in scanned light‐ion beams
Authors: Palmans Hugo , Vatnitsky Stanislav M.
Published: October 2016

Purpose

To propose a formalism for the reference dosimetry of scanned light‐ion beams consistent with IAEA TRS‐398 and Alfonso et al. [Med. Phys. 35, 5179–5186 (2008)]. To identify machine‐specific reference (msr) fields and plan‐class specific reference (pcsr) fields consistent with the definitions given by Alfonso et al. To review the literature of beam monitor calibration in scanned beams using three different methods in terms of this common formalism.

Methods

Four types of msr fields are identified as those that are meant to calibrate the beam monitor for scanned beams with particular energies. Two types of pcsr fields are identified as those that are meant to apply one or more tuning factors to the entire delivery chain.

Results

The formalism establishes the energy‐dependent relation between the number of particles incident on the phantom surface and the beam monitor reading and distinguishes three routes to determine the beam monitor calibration function: (i) the use of a calibrated reference ionization chamber in a single‐layer scanned beam, (ii) the use of a cross‐calibrated large‐area parallel plate ionization chamber in a single‐energy beamlet, and (iii) the use of a calibrated reference ionization chamber in a box field to adjust a calibration curve obtained by a Faraday cup or an ionization chamber. Examples of all three methods and comparisons between them from the literature are analysed.

Conclusions

The formalism can form the basis of future dosimetry recommendations for scanned particle beams and the analysis of the literature data in terms of this formalism can form the basis of data compilations for the application of the dosimetry procedures.
Whole‐body bone segmentation from MRI for PET/MRI attenuation correction using shape‐based averaging
Authors: Arabi Hossein , Zaidi Habib
Published: October 2016

Purpose

The authors evaluate the performance of shape‐based averaging (SBA) technique for whole‐body bone segmentation from MRI in the context of MRI‐guided attenuation correction (MRAC) in hybrid PET/MRI. To enhance the performance of the SBA scheme, the authors propose to combine it with statistical atlas fusion techniques. Moreover, a fast and efficient shape comparison‐based atlas selection scheme was developed and incorporated into the SBA method.

Methods

Clinical studies consisting of PET/CT and MR images of 21 patients were used to assess the performance of the SBA method. In addition, the authors assessed the performance of simultaneous truth and performance level estimation (STAPLE) and the selective and iterative method for performance level estimation (SIMPLE) combined with SBA. In addition, a local shape comparison scheme (L‐Shp) was proposed to improve the performance of SBA. The SIMPLE method was applied globally (G‐SIMPLE) while STAPLE method was employed at both global (G‐STAPLE) and local (L‐STAPLE) levels. The evaluation was performed based on the accuracy of extracted whole‐body bones, fragmentation, and computation time achieved by the different methods. The majority voting (MV) atlas fusion scheme was also evaluated as a conventional and commonly used method. MRI‐guided attenuation maps were generated using the different segmentation methods. Thereafter, quantitative analysis of PET attenuation correction was performed using CT‐based attenuation correction as reference.

Results

The SBA and MV methods resulted in considerable underestimation of bone identification (Dice ≈ 0.62) and high factious fragmentation error of contiguous structures. Applying global atlas selection or regularization (G‐STAPLE and G‐SIMPLE) to the SBA method enhanced bone segmentation accuracy up to a Dice = 0.66. The best results were achieved when applying the L‐STAPLE method with a Dice of 0.76 and the L‐Shp method with a Dice of 0.75. However, L‐STAPLE required up to five‐fold increased computation time compared to the L‐Shp method. Moreover, both L‐STAPLE and L‐Shp methods resulted in less than 3% SUV mean relative error and 6% SUV mean absolute error in bony structures owing to superior bone identification accuracy. The quantitative analysis using joint histograms revealed good correlation between PET‐MRAC images using the proposed L‐Shp algorithm and the corresponding reference PET‐CT images.

Conclusions

The performance of SBA was enhanced through application of local atlas weighting or regularization schemes (L‐STAPLE and L‐Shp). Bone recognition, fragmentation of the contiguous structures, and quantitative PET uptake recovery improved dramatically using these methods while the proposed L‐Shp method significantly reduced the computation time.
Aeroacoustical coupling and synchronization of organ pipes
Authors: Fischer Jost Leonhardt , Bader Rolf , Abel Markus
Published: October 2016

A synchronization experiment on two mutual interacting organ pipes is compared with a theoretical model which takes into account the coupling mechanisms by the underlying first principles of fluid mechanics and aeroacoustics. The focus is on the Arnold-tongue, a mathematical object in the parameter space of detuning and coupling strength which quantitatively captures the interaction of the synchronized sound sources. From the experiment, a nonlinearly shaped Arnold-tongue is obtained, describing the coupling of the synchronized pipe–pipe system. This is in contrast to the linear shaped Arnold-tongue found in a preliminary experiment of the coupled system pipe-loudspeaker. To understand the experimental result, a coarse-grained model of two nonlinear coupled self-sustained oscillators is developed. The model, integrated numerically, is in very good agreement with the synchronization experiment for separation distances of the pipes in the far field and in the intermediate field. The methods introduced open the door for a deeper understanding of the fundamental processes of sound generation and the coupling mechanisms on mutual interacting acoustic oscillators.