bluuebunny/crossref_metadata_2025 huggingface dataset:
Utility of Assessing Cytokine Levels for the Differential Diagnosis of Pneumonia in a Pediatric Population*
Authors: Zhou Jian-Ming , Ye Qing
Published: February 2017

Objectives:

Although pneumonia is easily diagnosed, determining the causative agent is difficult due to low pathogen detection rates. We performed a prospective observational study to evaluate the utility of measuring inflammatory cytokine levels to discriminate between pneumonia caused by typical bacteria, respiratory syncytial virus, or Mycoplasma pneumoniae in a pediatric population.

Design:

Serum inflammatory cytokine levels at early stages of the disease were evaluated for pneumonia caused by the three different pathogenic microorganisms.

Setting:

The Children’s Hospital of Zhejiang University School of Medicine, China.

Patients:

One hundred sixty-six patients with bacterial pneumonia, 182 with M. pneumonia, and 167 with respiratory syncytial virus pneumonia.

Measurements and Main Results:

The levels of interleukin-6 for pneumonia were significantly higher with typical bacteria than with either Mycoplasma pneumoniae or respiratory syncytial virus (p < 0.001). The area under the curve for serum concentrations of interleukin-6 was 0.997. A serum interleukin-6 level of greater than or equal to 93.0 pg/mL had 100.0% sensitivity and 99.14% specificity in discriminating bacterial pneumonia from respiratory syncytial virus pneumonia and Mycoplasma pneumoniae pneumonia. The interleukin-6 levels were higher in patients with Mycoplasma pneumoniae pneumonia than in those with respiratory syncytial virus pneumonia (p < 0.001). They also simultaneously had lower interleukin-10 levels than patients with respiratory syncytial virus pneumonia who had interleukin-10 levels comparable to those of patients with bacterial pneumonia, indicating a significant difference in the interleukin-6/interleukin-10 ratio between patients with Mycoplasma pneumoniae pneumonia and respiratory syncytial virus pneumonia (median interleukin-6/interleukin-10 ratio, 2.5 vs 0.5; p < 0.001). At an optimal cut-off value of 0.8, the interleukin-6/interleukin-10 ratio showed 90.3% sensitivity and 88.0% specificity.

Conclusions:

These results suggest that interleukin-6 is a good biomarker for identifying bacterial pneumonia and that the interleukin-6/interleukin-10 ratio is an effective biomarker for discriminating Mycoplasma pneumoniae pneumonia from respiratory syncytial virus pneumonia.
Should Immediate Autologous Breast Reconstruction Be Considered in Women Who Require Postmastectomy Radiation Therapy? A Prospective Analysis of Outcomes
Authors: Billig Jessica , Jagsi Reshma , Qi Ji , Hamill Jennifer B. , Kim Hyungjin M. , Pusic Andrea L. , Buchel Edward , Wilkins Edwin G. , Momoh Adeyiza O.
Published: February 2017

Background:

In women who require postmastectomy radiation therapy, immediate autologous breast reconstruction is often discouraged. The authors prospectively evaluated postoperative morbidity and satisfaction reported by women undergoing delayed or immediate autologous breast reconstruction in the setting of postmastectomy radiation therapy.

Methods:

Patients enrolled in the Mastectomy Reconstruction Outcomes Consortium study, who received postmastectomy radiotherapy and underwent immediate or delayed free abdominally based autologous breast reconstruction, were identified. Postoperative complications at 1 and 2 years after reconstruction were assessed. Patient-reported outcomes were evaluated using the BREAST-Q questionnaire preoperatively and at 1 and 2 years postoperatively. Bivariate analyses and mixed-effects regression models were used to compare outcomes.

Results:

A total of 175 patients met the authors’ inclusion criteria. Immediate reconstructions were performed in 108 patients and delayed reconstructions in 67 patients; 93.5 percent of immediate reconstructions were performed at a single center. Overall complication rates were similar based on reconstructive timing (25.9 percent immediate and 26.9 percent delayed at 1 year; p = 0.54). Patients with delayed reconstruction reported significantly lower prereconstruction scores (p < 0.0001) for Satisfaction with Breasts and Psychosocial and Sexual Well-being than did patients with immediate reconstruction. At 1 and 2 years postoperatively, both groups reported comparable levels of satisfaction in assessed BREAST-Q domains.

Conclusions:

From this prospective cohort, immediate autologous breast reconstruction in the setting of postmastectomy radiation therapy appears to be a safe option that may be considered in select patients and centers. Breast aesthetics and quality of life, evaluated from the patient’s perspective, were not compromised by flap exposure to radiation therapy.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Brief Report: Longitudinal Opioid Use Among HIV-Infected Patients, 2000 to 2014
Authors: Brunet Laurence , Napravnik Sonia , Heine Amy D. , Leone Peter A. , Eron Joseph J.
Published: February 2017

Longitudinal opioid prescription use is unknown among HIV-infected patients. Group-based trajectory modeling followed by multinomial logistic regression was used to identify distinct trajectories and their association with baseline characteristics among 1239 HIV-infected UNC CFAR HIV Clinical Cohort participants, 2000–2014. Three trajectories were identified: (1) 72% never/sporadic opioid use (referent group), (2) 11% episodic use (associated with female sex, depression, drug-related diagnoses, antiretroviral therapy use, and undetectable HIV RNA), and (3) 16% chronic use (associated with older age, female sex, and mental health diagnoses). Overall, opioid prescription decreased substantially with longer time in HIV care among both episodic and chronic users.
Detection and Alterations of Acetylcarnitine in Human Skeletal Muscles by 1H MRS at 7 T
Authors: Klepochová Radka , Valkovič Ladislav , Gajdošík Martin , Hochwartner Thomas , Tschan Harald , Krebs Michael , Trattnig Siegfried , Krššák Martin
Published: February 2017

Objectives

The aims of this study were to detect the acetylcarnitine resonance line at 2.13 ppm in the human vastus lateralis and soleus muscles, assess T1 and T2 relaxation times, and investigate the diurnal and exercise-related changes in absolute concentration noninvasively, using proton magnetic resonance spectroscopy at 7 T.

Materials and Methods

All measurements were performed on a 7 T whole-body Magnetom MR system with a 28-channel knee coil. Five healthy, moderately trained volunteers participated in the assessment of the detectability, repeatability, and relaxation times of acetylcarnitine. For the evaluation of the effect of training status, another 5 healthy, normally active volunteers were examined. In addition, normally active volunteers underwent a day-long protocol to estimate diurnal changes and response to the exercise.

Results

Using a long echo time of 350 milliseconds, we were able to detect the acetylcarnitine resonance line at 2.13 ppm in both muscle groups without significant lipid contamination. The T1 of acetylcarnitine in the vastus lateralis muscle was found to be 1807.2 ± 513.1 milliseconds and T2 was found to be 129.9 ± 44.9 milliseconds. Concentrations of acetylcarnitine from the vastus lateralis muscle in moderately trained volunteers were higher than concentrations from normally active volunteers. Acetylcarnitine concentrations changed during the day, tending to be higher in the morning after an overnight fast than after lunch. After 10 minutes of high-intensity exercise, the concentration significantly increased, and 15 minutes after cessation of exercise, a decrease could be observed.

Conclusions

Our results demonstrate an effective detection of acetylcarnitine using a long TE of 350 milliseconds at 7 T in the vastus lateralis and soleus muscles with high repeatability and reliability on a 7 T scanner. Our data emphasize the need for strict standardization, physical activity, and dietary conditions for the measurement of the acetylcarnitine.
Monoenergetic Dual-energy Computed Tomographic Imaging
Authors: Lenga Lukas , Albrecht Moritz H. , Othman Ahmed E. , Martin Simon S. , Leithner Doris , D’Angelo Tommaso , Arendt Christophe , Scholtz Jan-Erik , De Cecco Carlo N. , Schoepf U. Joseph , Vogl Thomas J. , Wichmann Julian L.
Published: February 2017

Monoenergetic imaging is an increasingly used reconstruction technique in postprocessing of dual-energy computed tomography (DECT). The main advantage of this technique is the ability to substantially increase image contrast of structures with uptake of iodinated contrast material. Although monoenergetic imaging was mainly used in oncological DECT applications, recent research has further demonstrated its role in vascular imaging. Using this dedicated postprocessing algorithm, image contrast of vascular structures in the thorax can be increased, a drastic reduction of contrast material is feasible, and even beam-hardening artifacts can be reduced. The aim of this review article is to explain the technical background of this technique, showcase its relevance in cardiothoracic DECT, and provide an outlook on the clinical impact of this technique beyond solely improvements in image quality.
Tumor Size as an Independent Risk Factor for Postoperative Complications in Laparoscopic Low Anterior Resection for Advanced Rectal Cancer: A Multicenter Japanese Study
Authors: Yasui Masayoshi , Takemasa Ichiro , Miyake Yuichiro , Hata Taishi , Ikeda Masataka , Miyake Yasuhiro , Hasegawa Junichi , Ota Hirofumi , Matsuda Chu , Mizushima Tsunekazu , Doki Yuichiro , Mori Masaki
Published: February 2017

This study aimed to identify the risk factors for postoperative complications after laparoscopic low anterior resection for the treatment of advanced rectal cancers. A prospectively maintained database was retrospectively analyzed. Oncological parameters in resected specimens and clinical risk factors for postoperative complications, including anastomotic leakage, were examined in patients with clinical stage II and III upper rectal cancer who underwent laparoscopic low anterior resection, including total mesorectal excision. Pathologic resection margins were negative in all patients. Postoperative complications occurred in 22 patients (25.9%), which is similar to incidence rates in previous studies. In multivariate analysis, tumor size (≥4 cm) and tumor category (T4) were independent risk factors for postoperative complications. Precise pretreatment diagnoses with locoregional evaluations are essential for the selection of appropriate patients for laparoscopic rectal resection. Despite quality results from laparoscopic low anterior resection for the treatment of advanced rectal cancer, we must attempt to reduce postoperative complications.
Benefits of Dexmedetomidine in Management of Post-ECT Agitation
Authors: Narang Puneet , Ianovich Francesca , Sarai Simrat Kaur , Lippmann Steven
Published: February 2017

Electroconvulsive therapy (ECT) is an intervention for patients with a variety of psychiatric conditions. Occasionally, people exhibit dangerous degrees of agitation after this treatment, and some do not respond well to conventional pharmacotherapies. Dexmedetomidine is a central α-2 agonist that can induce significantly calmative effects in persons with post-ECT agitation. The indication for it is in calming individuals with acute and/or recurrent posttreatment agitation. Dexmedetomidine is safe and effective when infused just before, or postictally, at ECT sessions.
Aging parasites produce offspring with poor fitness prospects
Authors: Lippens Cédric , Faivre Bruno , Lechenault Clothilde , Sorci Gabriele
Published: February 2017

Senescing individuals have poor survival prospects and low fecundity. They can also produce offspring with reduced survival and reproductive success. We tested the effect of parental age on the performance of descendants in the nematodeHeligmosomoides polygyrus, an intestinal parasite of rodents. We found that offspring of senescing worms had reduced within-host survival and reduced egg shedding over the first month post-infection compared with offspring produced by young parents. These results suggest that declining offspring quality is a component of senescence in parasitic nematodes and might have evolutionary consequences for the optimal schedule of age-dependent investment into reproductive effort.
Extinction pathways and outbreak vulnerability in a stochastic Ebola model
Authors: Nieddu Garrett T. , Billings Lora , Kaufman James H. , Forgoston Eric , Bianco Simone
Published: February 2017

A zoonotic disease is a disease that can be passed from animals to humans. Zoonotic viruses may adapt to a human host eventually becoming endemic in humans, but before doing so punctuated outbreaks of the zoonotic virus may be observed. The Ebola virus disease (EVD) is an example of such a disease. The animal population in which the disease agent is able to reproduce in sufficient number to be able to transmit to a susceptible human host is called a reservoir. There is little work devoted to understanding stochastic population dynamics in the presence of a reservoir, specifically the phenomena of disease extinction and reintroduction. Here, we build a stochastic EVD model and explicitly consider the impacts of an animal reservoir on the disease persistence. Our modelling approach enables the analysis of invasion and fade-out dynamics, including the efficacy of possible intervention strategies. We investigate outbreak vulnerability and the probability of local extinction and quantify the effective basic reproduction number. We also consider the effects of dynamic population size. Our results provide an improved understanding of outbreak and extinction dynamics in zoonotic diseases, such as EVD.
Control and regulation of pathways via negative feedback
Authors: Sauro Herbert M.
Published: February 2017

The biochemical networks found in living organisms include a huge variety of control mechanisms at multiple levels of organization. While the mechanistic and molecular details of many of these control mechanisms are understood, their exact role in driving cellular behaviour is not. For example, yeast glycolysis has been studied for almost 80 years but it is only recently that we have come to understand the systemic role of the multitude of feedback and feed-forward controls that exist in this pathway. In this article, control theory is discussed as an approach to dissect the control logic of complex pathways. One of the key issues is distinguishing between the terms control and regulation and how these concepts are applied to regulated enzymes such as phosphofructokinase. In doing so, one of the paradoxes in metabolic regulation can be resolved where enzymes such as phosphofructokinase have little control but, nevertheless, possess significant regulatory influence.
Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats
Authors: Han Pu , Deem Michael W.
Published: February 2017

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator–prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria coevolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the re-entrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon.
Surface microtopography modulates sealing zone development in osteoclasts cultured on bone
Authors: Shemesh Michal , Addadi Lia , Geiger Benjamin
Published: February 2017

Bone homeostasis is continuously regulated by the coordinated action of bone-resorbing osteoclasts and bone-forming osteoblasts. Imbalance between these two cell populations leads to pathological bone diseases such as osteoporosis and osteopetrosis. Osteoclast functionality relies on the formation of sealing zone (SZ) rings that define the resorption lacuna. It is commonly assumed that the structure and dynamic properties of the SZ depend on the physical and chemical properties of the substrate. Considering the unique complex structure of native bone, elucidation of the relevant parameters affecting SZ formation and stability is challenging. In this study, we examined in detail the dynamic response of the SZ to the microtopography of devitalized bone surfaces, taken from the same area in cattle femur. We show that there is a significant enrichment in large and stable SZs (diameter larger than 14 µm; lifespan of hours) in cells cultured on rough bone surfaces, compared with small and fast turning over SZ rings (diameter below 7 µm; lifespan approx. 7 min) formed on smooth bone surfaces. Based on these results, we propose that the surface roughness of the physiologically relevant substrate of osteoclasts, namely bone, affects primarily the local stability of growing SZs.
A Maugis–Dugdale cohesive solution for adhesion of a surface with a dimple
Authors: Papangelo A. , Ciavarella M.
Published: February 2017

We study the adhesion of a surface with a ‘dimple’ which shows a mechanism for a bi-stable adhesive system in surfaces with spaced patterns of depressions, leading to adhesion enhancement, high dissipation and hysteresis. Recent studies were limited mainly to the very short range of adhesion (the so-called JKR regime), while we generalize the study to a Maugis cohesive model. A ‘generalized Tabor parameter’, given by the ratio of theoretical strength to elastic modulus, multiplied by the ratio of dimple width to depth has been found. It is shown that bistability disappears for generalized Tabor parameter less than about 2. Introduction of the theoretical strength is needed to have significant results when the system has gone in full contact, unless one postulates alternative limits to full contact, such as air entrapment, contaminants or fine scale roughness. Simple equations are obtained for the pull-off and for the full contact pressure in the entire set of the two governing dimensionless parameters. A qualitative comparison with results of recent experiments with nanopatterned bioinspired dry adhesives is attempted in light of the present model.
Cancer cells exhibit clonal diversity in phenotypic plasticity
Authors: Mathis Robert Austin , Sokol Ethan S. , Gupta Piyush B.
Published: February 2017

Phenotypic heterogeneity in cancers is associated with invasive progression and drug resistance. This heterogeneity arises in part from the ability of cancer cells to switch between phenotypic states, but the dynamics of this cellular plasticity remain poorly understood. Here we apply DNA barcodes to quantify and track phenotypic plasticity across hundreds of clones in a population of cancer cells exhibiting epithelial or mesenchymal differentiation phenotypes. We find that the epithelial-to-mesenchymal cell ratio is highly variable across the different clones in cancer cell populations, but remains stable for many generations within the progeny of any single clone—with a heritability of 0.89. To estimate the effects of combination therapies on phenotypically heterogeneous tumours, we generated quantitative simulations incorporating empirical data from our barcoding experiments. These analyses indicated that combination therapies which alternate between epithelial- and mesenchymal-specific treatments eventually select for clones with increased phenotypic plasticity. However, this selection could be minimized by increasing the frequency of alternation between treatments, identifying designs that may minimize selection for increased phenotypic plasticity. These findings establish new insights into phenotypic plasticity in cancer, and suggest design principles for optimizing the effectiveness of combination therapies for phenotypically heterogeneous tumours.
A morphometric analysis of vegetation patterns in dryland ecosystems
Authors: Mander Luke , Dekker Stefan C. , Li Mao , Mio Washington , Punyasena Surangi W. , Lenton Timothy M.
Published: February 2017

Vegetation in dryland ecosystems often forms remarkable spatial patterns. These range from regular bands of vegetation alternating with bare ground, to vegetated spots and labyrinths, to regular gaps of bare ground within an otherwise continuous expanse of vegetation. It has been suggested that spotted vegetation patterns could indicate that collapse into a bare ground state is imminent, and the morphology of spatial vegetation patterns, therefore, represents a potentially valuable source of information on the proximity of regime shifts in dryland ecosystems. In this paper, we have developed quantitative methods to characterize the morphology of spatial patterns in dryland vegetation. Our approach is based on algorithmic techniques that have been used to classify pollen grains on the basis of textural patterning, and involves constructing feature vectors to quantify the shapes formed by vegetation patterns. We have analysed images of patterned vegetation produced by a computational model and a small set of satellite images from South Kordofan (South Sudan), which illustrates that our methods are applicable to both simulated and real-world data. Our approach provides a means of quantifying patterns that are frequently described using qualitative terminology, and could be used to classify vegetation patterns in large-scale satellite surveys of dryland ecosystems.
Deliberation favours social efficiency by making people disregard their relative shares: evidence from USA and India
Authors: Capraro Valerio , Corgnet Brice , Espín Antonio M. , Hernán-González Roberto
Published: February 2017

Groups make decisions on both the production and the distribution of resources. These decisions typically involve a tension between increasing the total level of group resources (i.e. social efficiency) and distributing these resources among group members (i.e. individuals' relative shares). This is the case because the redistribution process may destroy part of the resources, thus resulting in socially inefficient allocations. Here we apply a dual-process approach to understand the cognitive underpinnings of this fundamental tension. We conducted a set of experiments to examine the extent to which different allocation decisions respond to intuition or deliberation. In a newly developed approach, we assess intuition and deliberation at both the trait level (using the Cognitive Reflection Test, henceforth CRT) and the state level (through the experimental manipulation of response times). To test for robustness, experiments were conducted in two countries: the USA and India. Despite absolute-level differences across countries, in both locations we show that: (i) time pressure and low CRT scores are associated with individuals' concerns for their relative shares and (ii) time delay and high CRT scores are associated with individuals' concerns for social efficiency. These findings demonstrate that deliberation favours social efficiency by overriding individuals' intuitive tendency to focus on relative shares.
Horizontal and vertical movements of Caribbean reef sharks (
Carcharhinus perezi
): conservation implications of limited migration in a marine sanctuary
Authors: Shipley Oliver N. , Howey Lucy A. , Tolentino Emily R. , Jordan Lance K. B. , Ruppert Jonathan L. W. , Brooks Edward J.
Published: February 2017

Despite the ecological and economic importance of the Caribbean reef shark (
Carcharhinus perezi
), little data exist regarding the movements and habitat use of this predator across its range. We deployed 11 pop-up satellite archival tags on Caribbean reef sharks captured in the northeast Exuma Sound, The Bahamas, to assess their horizontal and vertical movements throughout the water column. Sharks showed high site fidelity to The Bahamas suggesting Bahamian subpopulations remain protected within the Bahamian Shark Sanctuary. Depth data indicate that Caribbean reef sharks spent a significant proportion (72–91%) of their time above 50 m in narrow vertical depth bands, which varied considerably on an individual basis. This may be indicative of high site fidelity to specific bathymetric features. Animals exhibited three broadly categorized sporadic off-bank excursions (more than 50 m excursions) down to a depth of 436.1 m, which were more frequent during the night. These deeper excursions during night may be indicative of foraging in relation to prey on mesophotic reefs, as well as diel-vertically migrating prey from the deeper meso- and bathypelagic zones. These vertical movements suggest that Caribbean reef sharks can be significant vectors of ecosystem connectivity further warranting holistic multi-system management and conservation approaches.
Cultural influence of social information use in pedestrian road-crossing behaviours
Authors: Pelé Marie , Bellut Caroline , Debergue Elise , Gauvin Charlotte , Jeanneret Anne , Leclere Thibault , Nicolas Lucie , Pontier Florence , Zausa Diorne , Sueur Cédric
Published: February 2017

Social information use is common in a wide range of group-living animals, notably in humans. The role it plays in decision-making could be a key to understanding how social groups make collective decisions. The observation of road-crossing behaviours in the presence of other individuals is an ideal means to study the influence of social information on decision-making. This study investigated the influence of culture on social information used by pedestrians in a potentially dangerous scenario, namely road crossing. We scored the collective crossing of pedestrians at four locations in Nagoya (Japan) and three locations in Strasbourg (France). French pedestrians cross against the lights much more often (41.9%) than Japanese ones (2.1%). Individuals deciding to cross the road were strongly influenced by the behaviour and the presence of other pedestrians, especially in Japan, where a stronger conformism was noted. However, Japanese pedestrians were half as likely to be influenced by social information as their French counterparts when crossing at the red light, as they were more respectful of rules. Men show riskier behaviour than women (40.6% versus 25.7% of rule-breaking, respectively), deciding quickly and setting off earlier than women. Further related studies could help target specific preventive, culture-specific solutions for pedestrian safety.
February precipitation in the wintering grounds of the lesser whitethroat,Sylvia curruca: is it a cue for migration onset?
Authors: Aloni Irith , Markman Shai , Ziv Yaron
Published: February 2017

Numerous studies report shifts in bird migration phenology, presumably owing to global warming. However, most studies focus on migration patterns in the Northern Hemisphere. In this study, we investigated associations between weather conditions in African wintering grounds of the lesser whitethroat,Sylvia curruca,and spring arrival time in Eilat, Israel. Using multivariate regression models, we analysed a 30-year dataset in order to examine correlations between median springtime arrival and 46 climate variables of the wintering quarters. The model obtained exhibited a highly statistical fit, involving mean precipitation in February and March with negative effects and number of wet days during November–February. February precipitation levels were also the major factor associated with the interquartile range of arrival time. Interestingly and contrary to published results, annual or seasonal precipitation showed no correlation with spring arrival time, nor did temperature. Moreover, winter in this region falls into dry season with negligible rainfall quantities. Hence, it is unlikely that precipitation effect on habitat productivity is a driving force of migration, as suggested by other studies. Instead, we propose that precipitation in February acts as a cue for the birds, indicating the approach of spring and migration time.
Repeatability of circadian behavioural variation revealed in free-ranging marine fish
Authors: Alós Josep , Martorell-Barceló Martina , Campos-Candela Andrea
Published: February 2017

Repeatable between-individual differences in the behavioural manifestation of underlying circadian rhythms determine chronotypes in humans and terrestrial animals. Here, we have repeatedly measured three circadian behaviours, awakening time, rest onset and rest duration, in the free-ranging pearly razorfish,Xyrithchys novacula, facilitated by acoustic tracking technology and hidden Markov models. In addition, daily travelled distance, a standard measure of daily activity as fish personality trait, was repeatedly assessed using a State-Space Model. We have decomposed the variance of these four behavioural traits using linear mixed models and estimated repeatability scores (R) while controlling for environmental co-variates: year of experimentation, spatial location of the activity, fish size and gender and their interactions. Between- and within-individual variance decomposition revealed significantRs in all traits suggesting high predictability of individual circadian behavioural variation and the existence of chronotypes. The decomposition of the correlations among chronotypes and the personality trait studied here into between- and within-individual correlations did not reveal any significant correlation at between-individual level. We therefore propose circadian behavioural variation as an independent axis of the fish personality, and the study of chronotypes and their consequences as a novel dimension in understanding within-species fish behavioural diversity.
Polarimetry of
Pinctada fucata
nacre indicates myostracal layer interrupts nacre structure
Authors: Metzler Rebecca A. , Jones Joshua A. , D'Addario Anthony J. , Galvez Enrique J.
Published: February 2017

The inner layer of many bivalve and gastropod molluscs consists of iridescent nacre, a material that is structured like a brick wall with bricks consisting of crystalline aragonite and mortar of organic molecules. Myostracal layers formed during shell growth at the point of muscle attachment to the shell can be found interspersed within the nacre structure. Little has been done to examine the effect the myostracal layer has on subsequent nacre structure. Here we present data on the structure of the myostracal and nacre layers from a bivalve mollusc,
Pinctada fucata
. Scanning electron microscope imaging shows the myostracal layer consists of regular crystalline blocks. The nacre before the layer consists of tablets approximately 400 nm thick, while after the myostracal layer the tablets are approximately 500 nm thick. A new technique, imaging polarimetry, indicates that the aragonite crystals within the nacre following the myostracal layer have greater orientation uniformity than before the myostracal layer. The results presented here suggest a possible interaction between the myostracal layer and subsequent shell growth.
Early animal farming and zoonotic disease dynamics: modelling brucellosis transmission in Neolithic goat populations
Authors: Fournié Guillaume , Pfeiffer Dirk U. , Bendrey Robin
Published: February 2017

Zoonotic pathogens are frequently hypothesized as emerging with the origins of farming, but evidence of this is elusive in the archaeological records. To explore the potential impact of animal domestication on zoonotic disease dynamics and human infection risk, we developed a model simulating the transmission of
Brucella melitensis
within early domestic goat populations. The model was informed by archaeological data describing goat populations in Neolithic settlements in the Fertile Crescent, and used to assess the potential of these populations to sustain the circulation of
Brucella
. Results show that the pathogen could have been sustained even at low levels of transmission within these domestic goat populations. This resulted from the creation of dense populations and major changes in demographic characteristics. The selective harvesting of young male goats, likely aimed at improving the efficiency of food production, modified the age and sex structure of these populations, increasing the transmission potential of the pathogen within these populations. Probable interactions between Neolithic settlements would have further promoted pathogen maintenance. By fostering conditions suitable for allowing domestic goats to become reservoirs of
Brucella melitensis
, the early stages of agricultural development were likely to promote the exposure of humans to this pathogen.
Ambidextrous ungulates have more flexible behaviour, bolder personalities and migrate less
Authors: Found R. , St. Clair C. C.
Published: February 2017

Studies of wildlife have shown consistent individual variation in behavioural plasticity, which affects the rate of adaptation to changing environments. More flexible individuals may thus be more prone to habituation and conflict behaviour, but these applications of personality to wildlife management are little explored. Behavioural lateralization reflects cerebral specialization that may predict diverse expressions of behavioural plasticity. We recorded front-limb biases (i.e. handedness) in wild elk (Cervus canadensis), a species with facultative migration and high rates of habituation inside protected areas. Less lateralized elk responded more strongly to the application of aversive conditioning (predator-resembling chases by humans) by increasing their average flight response distances, but these same animals were also quicker to reduce their flight responses (i.e. habituate) when human approaches were benign. Greater laterality was correlated with, but not completely predicted by, bolder personalities, which we quantified via five correlated behavioural metrics. Lastly, lateralized elk were three times more likely to migrate, whereas less lateralized animals were similarly likely to remain near humans year-round. Lateralized behaviours can provide insight into behavioural flexibility enabling certain individuals to more quickly adapt to human-disturbed landscapes, and offer an especially productive arena for collaborative work by behaviourists, conservation biologists and wildlife managers.
A wave theory of heat transport with applications to Kapitsa resistance and thermal rectification
Authors: Budaev Bair V. , Bogy David B.
Published: February 2017

We develop a theory of thermal transport in nanoscale-layered structures based on wave processes. The theory incorporates two fundamental principles, first, that the spectra of thermally excited waves are determined by the temperature differential and the heat flux, and second, that the wave fields in the heat exchanging domains are coupled. The developed method includes classical theories as special cases that are valid in larger scales, and it naturally explains such phenomena as interface thermal resistance (Kapitsa resistance) and thermal rectification (asymmetry of thermal transport). Numerical examples demonstrate the feasibility of the approach, and they show good agreement with measurements of Kapitsa resistance reported in the literature.
An experimental study of ultrasonic vibration and the penetration of granular material
Authors: Firstbrook David , Worrall Kevin , Timoney Ryan , Suñol Francesc , Gao Yang , Harkness Patrick
Published: February 2017

This work investigates the potential use of direct ultrasonic vibration as an aid to penetration of granular material. Compared with non-ultrasonic penetration, required forces have been observed to reduce by an order of magnitude. Similarly, total consumed power can be reduced by up to 27%, depending on the substrate and ultrasonic amplitude used. Tests were also carried out in high-gravity conditions, displaying a trend that suggests these benefits could be leveraged in lower gravity regimes.
Bioinspired turbine blades offer new perspectives for wind energy
Authors: Cognet V. , Courrech du Pont S. , Dobrev I. , Massouh F. , Thiria B.
Published: February 2017

Wind energy is becoming a significant alternative solution for future energy production. Modern turbines now benefit from engineering expertise, and a large variety of different models exists, depending on the context and needs. However, classical wind turbines are designed to operate within a narrow zone centred around their optimal working point. This limitation prevents the use of sites with variable wind to harvest energy, involving significant energetic and economic losses. Here, we present a new type of bioinspired wind turbine using elastic blades, which passively deform through the air loading and centrifugal effects. This work is inspired from recent studies on insect flight and plant reconfiguration, which show the ability of elastic wings or leaves to adapt to the wind conditions and thereby to optimize performance. We show that in the context of energy production, the reconfiguration of the elastic blades significantly extends the range of operating regimes using only passive, non-consuming mechanisms. The versatility of the new turbine model leads to a large increase of the converted energy rate, up to 35%. The fluid/elasticity mechanisms involved for the reconfiguration capability of the new blades are analysed in detail, using experimental observations and modelling.
Signals, cues and the nature of mimicry
Authors: Jamie Gabriel A.
Published: February 2017

‘Mimicry’ is used in the evolutionary and ecological literature to describe diverse phenomena. Many are textbook examples of natural selection's power to produce stunning adaptations. However, there remains a lack of clarity over how mimetic resemblances are conceptually related to each other. The result is that categories denoting the traditional subdivisions of mimicry are applied inconsistently across studies, hindering attempts at conceptual unification. This review critically examines the logic by which mimicry can be conceptually organized and analysed. It highlights the following three evolutionarily relevant distinctions. (i) Are the model's traits being mimicked signals or cues? (ii) Does the mimic signal a fitness benefit or fitness cost in order to manipulate the receiver's behaviour? (iii) Is the mimic's signal deceptive? The first distinction divides mimicry into two broad categories: ‘signal mimicry’ and ‘cue mimicry’. ‘Signal mimicry’ occurs when mimic and model share the same receiver, and ‘cue mimicry’ when mimic and model have different receivers or when there is no receiver for the model's trait. ‘Masquerade’ fits conceptually within cue mimicry. The second and third distinctions divide both signal and cue mimicry into four types each. These are the three traditional mimicry categories (aggressive, Batesian and Müllerian) and a fourth, often overlooked category for which the term ‘rewarding mimicry’ is suggested. Rewarding mimicry occurs when the mimic's signal is non-deceptive (as in Müllerian mimicry) but where the mimic signals a fitness benefit to the receiver (as in aggressive mimicry). The existence of rewarding mimicry is a logical extension of the criteria used to differentiate the three well-recognized forms of mimicry. These four forms of mimicry are not discrete, immutable types, but rather help to define important axes along which mimicry can vary.
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Authors: Dutoit Ludovic , Vijay Nagarjun , Mugal Carina F. , Bossu Christen M. , Burri Reto , Wolf Jochen , Ellegren Hans
Published: February 2017

Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird species—collared flycatcher and hooded crow—and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman'sρ= 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.
Human visual search behaviour is far from ideal
Authors: Nowakowska Anna , Clarke Alasdair D. F. , Hunt Amelia R.
Published: February 2017

Evolutionary pressures have made foraging behaviours highly efficient in many species. Eye movements during search present a useful instance of foraging behaviour in humans. We tested the efficiency of eye movements during search using homogeneous and heterogeneous arrays of line segments. The search target is visible in the periphery on the homogeneous array, but requires central vision to be detected on the heterogeneous array. For a compound search array that is heterogeneous on one side and homogeneous on the other, eye movements should be directed only to the heterogeneous side. Instead, participants made many fixations on the homogeneous side. By comparing search of compound arrays to an estimate of search performance based on uniform arrays, we isolate two contributions to search inefficiency. First, participants make superfluous fixations, sacrificing speed for a perceived (but not actual) gain in response certainty. Second, participants fixate the homogeneous side even more frequently than predicted by inefficient search of uniform arrays, suggesting they also fail to direct fixations to locations that yield the most new information.
A Sign of Disparity: Racial/Ethnic Composition of Treatment Centers is an Independent Risk Factor in SPRINT Trial
Authors: Matlock Matthew , Dang Na Le , Brown David , Joshua Swamidass S.
Published: February 2017

The racial composition of treatment centers in the SPRINT trial is an independent risk factor for myocardial infarction (MI) and stroke. Independent of individual race or ethnicity, patients face a 39% increase in relative risk of MI or stroke when associated to treatment centers with a high proportion of African Americans. The magnitude of this effect is comparable to smoking. This suggests the strong influence of social determinants on health outcomes among hypertensive patients.
Global Cropland Connectivity: A Risk Factor for Invasion and Saturation by Emerging Pathogens and Pests
Authors: Xing Y. , Hernandez Nopsa J. F. , Andersen K. F. , Andrade-Piedra J. , Beed F. D. , Blomme G. , Carvajal-Yepes M. , Coyne D. L. , Cuellar W. J. , Forbes G. A. , Kreuze J. F. , Kroschel J. , Kumar P. L. , Legg J. P. , Parker M. , Schulte-Geldermann E. , Sharma K. , Garrett K. A.
Published: February 2017

The geographic pattern of cropland is an important risk factor for invasion and saturation by crop-specific pathogens and arthropods. Understanding cropland networks supports smart pest sampling and mitigation strategies. We evaluate global networks of cropland connectivity for key vegetatively-propagated crops (banana and plantain, cassava, potato, sweetpotato, and yam) important for food security in the tropics. For each crop, potential movement between geographic location pairs was evaluated using a gravity model, with associated uncertainty quantification. The highly-linked hub and bridge locations in cropland connectivity risk maps are likely priorities for surveillance and management, and for tracing intra-region movement of pathogens and pests. Important locations are identified beyond those locations that simply have high crop density. Cropland connectivity risk maps provide a new risk component for integration with other factors – such as climatic suitability, genetic resistance, and trade routes – to inform Pest Risk Assessment and mitigation.
SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks
Authors: Dalle Pezze Piero , Le Novère Nicolas
Published: February 2017

Background:The rapid growth of the number of mathematical models in Systems Biology fostered the development of many tools to simulate and analyse them. The reliability and precision of these tasks often depend on multiple repetitions and they can be optimised if executed as pipelines. In addition, new formal analyses can be performed on these repeat sequences, revealing important insights about the accuracy of model predictions.

Results:Here we introduce SBpipe, an open source software tool for automating repetitive tasks in model building and simulation. Using basic configuration files, SBpipe builds a sequence of repeated model simulations or parameter estimations, performs analyses from this generated sequence, and finally generates a LaTeX/PDF report. The parameter estimation pipeline offers analyses of parameter profile likelihood and parameter correlation using samples from the computed estimates. Specific pipelines for scanning of one or two model parameters at the same time are also provided. Pipelines can run on multicore computers, Sun Grid Engine (SGE), or Load Sharing Facility (LSF) clusters, speeding up the processes of model building and simulation. SBpipe can execute models implemented in Copasi, Python or coded in any other programming language using Python as a wrapper module. Future support for other software simulators can be dynamically added without affecting the current implementation.

Conclusions:SBpipe allows users to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis. The source code and documentation of this project are freely available at the web site:https://pdp10.github.io/sbpipe/.