bluuebunny/crossref_metadata_2025 huggingface dataset:
Trichomes - importance in plant defence and plant breeding.
Authors: Snyder J. C. , Antonious G. F.
Published: August 2014

Trichomes are epidermal hairs that can occur on nearly all plant surfaces. Structures are diverse among higher plants, but generally conserved within taxa. Consequently, trichomes have served as taxonomic characters. Because of their size and location, trichomes often mediate interactions between the plant organ and the external environment. Examples of how trichomes may mediate these interactions between the plant and its abiotic and biotic environment are delineated. A recent progress in breeding for trichome characters is reviewed. Lastly, because the tomato germplasm pool is an extremely rich resource for diversity of trichome characters and crop defence, progress in evaluating and utilizing tomato trichomes for arthropod resistance in tomato and other uses of tomato trichomes is discussed.
Tools for improving environmental sustainability in the hospitality industry.
Authors: Gil-Saura I. , Ruiz M. E.
Published: August 2014

Several organizations have raised the issue of negative effects of transportation and some other activities related to hospitality on the environment. In response to these warnings, a fast-growing tourist segment with a high degree of environmental awareness is pressing the hospitality industry to implement tools to minimize the impact of their activities on climate change. In particular, some applications of information and communication technologies (ICT) offer a direct contribution to the reduction of the demand of supplies and energy by the hospitality industry. Other initiatives, such as eco-friendly labels and environmentally sustainable practices, are being implemented by accommodation establishments. Notwithstanding, the level of use of some of these tools is still reduced. The literature on environmental sustainability and tourism management discusses the level of implementation, and the advantages and challenges of the different environmentally friendly practices. The aim of this review is to present the state of the art on the main tools being used to pursue environmental sustainability in the hospitality industry, and evaluating their potential to reduce the environmental impact of hospitality and tourism activities.
Effects of industrial agriculture on climate change and the mitigation potential of small-scale agro-ecological farms.
Authors: Lin B. B. , Chappell M. J. , Vandermeer J. , Smith G. , Quintero E. , Bezner-Kerr R. , Griffith D. M. , Ketcham S. , Latta S. C. , McMichael P. , McGuire K. L. , Nigh R. , Rocheleau D. , Soluri J. , Perfecto I.
Published: August 2014

According to the Intergovernmental Panel on Climate Change (IPCC), agriculture is responsible for 10-12% of total global anthropogenic emissions and almost a quarter of the continuing increase of greenhouse gas (GHG) emissions. Not all forms of agriculture, however, have equivalent impacts on global warming. Industrial agriculture contributes significantly to global warming, representing a large majority of total agriculture-related GHG emissions. Alternatively, ecologically based methods for agricultural production, predominantly used on small-scale farms, are far less energy-consumptive and release fewer GHGs than industrial agricultural production. Besides generating fewer direct emissions, agro-ecological management techniques have the potential to sequester more GHGs than industrial agriculture. Here, we review the literature on the contributions of agriculture to climate change and show the extent of GHG contributions from the industrial agricultural system and the potential of agro-ecological smallholder agriculture to help reduce GHG emissions. These reductions are achieved in three broad areas when compared with the industrial agricultural system: (1) a decrease in materials used and fluxes involved in the release of GHGs based on agricultural crop management choices; (2) a decrease in fluxes involved in livestock production and pasture management; and (3) a reduction in the transportation of agricultural inputs, outputs and products through an increased emphasis on local food systems. Although there are a number of barriers and challenges towards adopting small-scale agro-ecological methods on the large scale, appropriate incentives can lead to incremental steps towards agro-ecological management that may be able to reduce and mitigate GHG emissions from the agricultural sector.
Applications of acoustics in insect pest management.
Authors: Mankin R. W.
Published: August 2014

Acoustic technology has been applied for many years in studies of insect communication and in the monitoring of calling-insect population levels, geographic distributions and species diversity, as well as in the detection of cryptic insects in soil, wood, container crops and stored products. Acoustic devices of various sizes and power levels have been used successfully to trap insect pests that exhibit phonotaxis or other orientation behaviours, including mosquitoes, midges, mole crickets, field crickets, moths, cockroaches and Tephritid fruit flies. The attractiveness of traps depends on the behaviour, physiological state and age of the target insect, and varies with several environmental factors, including temperature and light level. Widespread adoption of acoustics for trapping has been limited by the costs of instrumentation and the relatively small segments of insect populations (e.g. mate-seeking adults of a limited age-range) that are attracted to a sound source, but trapping effectiveness often can be improved by adding swarm markers, chemical attractants or black lights, and by precisely timing temporal and frequency patterns to match the natural communication signals. There remains potential for using ultrasonic bat-cry signals to disrupt behaviour of night-flying insects, but ultrasonic signals have little effect on insects that are not normally preyed upon by bats. Potential areas for growth in the use of acoustic technology in pest management include the production of signals that disrupt vibrational communication, particularly in the Hemiptera, and the development of control treatments that combine pheromones and precisely patterned sonic or vibrational signals.
Costs of land degradation and benefits of land restoration: a review of valuation methods and suggested frameworks for inclusion into policy-making.
Authors: Quillérou E. , Thomas R. J.
Published: August 2014

Land degradation has become a growing concern with the current increase in demand for arable land. Sustainable land management and land restoration practices are required in order to meet the demands to provide food and other services. Adoption of improved practices has, however, not been widespread partly because of a lack of clarity on the true economic value and setting of proper financial incentives. This review focuses on the economic costs of land degradation as a prelude to two ongoing initiatives involving the United Nations Convention to Combat Desertification (UNCCD). We review how ecosystem services derived from land have been economically valued to date. Economic valuation has mostly focused on the use value of provisioning services and cultural services, with limited valuation of non-use value of cultural services. Also, no unique valuation method has been applied following methodological developments, varying study objectives and data availability constraints. These factors impair coherent and consistent estimation of the total economic value of land degradation across countries. We identify a need to develop harmonized valuation methods to estimate total economic value under strong data and capacity constraints. We propose two alternative frameworks for harmonized total economic valuation of land degradation at country level to guide further research in making environmental valuation more relevant and practical under strong data and capacity constraints.
Porcine reproductive and respiratory syndrome virus: options for control.
Authors: Chae ChanHee Chae ChanHee
Published: August 2014

Porcine reproductive and respiratory syndrome virus (PRRSV) control has been challenging and frustrating for researchers, veterinarians and producers in the swine industry worldwide since the first discovery of the disease in 1989. The aim of PRRSV control is to reach stability among the breeding females, thereby producing non-infected offspring from a previously infected sow population. The target animals for PRRSV control are the breeding and growing pig population. The procedure for achieving PRRSV control for a breeding herd includes stabilization (mass exposure or mass vaccination), herd closure, introduction of exposed non-shedding replacement gilts (isolation and acclimation) and monitoring stabilization. The procedure for growing pigs includes vaccination and nursery depopulation. The common procedures of PRRSV control include biosecurity and a surveillance programme. This review paper describes several options for each procedure that could be implemented practically in commercial herds.
Emerging trends in the management of disasters and mass casualty incidents.
Authors: Preeti Arora Preeti Arora , Rupa Gunaseelan Rupa Gunaseelan , Rajesh Arora Rajesh Arora
Published: August 2014

Disasters ruthlessly impact the environment, infrastructure, socio-economy and societal development, affecting the lives of individuals and community at large. A proactive disaster management approach focusing on leveraging crucial human resource is imperative to change the outcome of disasters and mass casualty incidents (MCIs). This article presents some emerging trends in disaster management, mainly from a holistic health perspective.
Framework of innovation for a sustainable future in animal agriculture - mini review.
Authors: Kebreab E.
Published: August 2014

Demand for animal products in the future is expected to increase significantly, which has an impact on sustainability of animal agriculture. In this review, the key challenges that must be addressed to improve environmental, social and economic sustainability of animal agriculture is discussed.
Nitrous oxide, climate change and agriculture.
Authors: Skiba U. M. , Rees R. M.
Published: August 2014

Nitrous oxide is an important greenhouse gas with a global warming potential of 298 times that of carbon dioxide. It is also responsible for the destruction of stratospheric ozone. Concentrations of nitrous oxide have shown continuous growth in the atmosphere over the past century, and nitrogen (N) fertilizers and manures applied to agricultural soils are the main anthropogenic source. Precise measurements of emissions from soils are difficult to undertake, as a consequence of high levels of spatial and temporal variability. For this reason, national reports on emissions are based largely on an assumption that a fixed fraction of N is released from N use in agriculture. Attempts to reduce nitrous oxide emissions, resulting from the use of N fertilizer, conflict with the need to maintain or increase food production and to support a growing world population. There is a large regional variation in the growth of emissions, with Asia contributing to the largest growth rates. More efficient management of N fertilizer and improved soil management (particularly in Asia) offer the opportunity to reduce emissions whilst maintaining food production.
Improvement of ligninolytic properties by recombinant expression of glyoxal oxidase gene in hyper lignin-degrading fungus Phanerochaete sordida YK-624
Authors: Yamada Yuto , Wang Jianqiao , Kawagishi Hirokazu , Hirai Hirofumi
Published: August 2014

Glyoxal oxidase (GLOX) is a source of the extracellular H2O2 required for the oxidation reactions catalyzed by the ligninolytic peroxidases. In the present study, the GLOX-encoding gene (glx) of Phanerochaete chrysosporium was cloned, and bee2 promoter of P. sordida YK-624 was used to drive the expression of glx. The expression plasmid was transformed into a P. sordida YK-624 uracil auxotrophic mutant (strain UV-64), and 16 clones were obtained as GLOX-introducing transformants. These transformants showed higher GLOX activities than wild-type P. sordida YK-624 and control transformants harboring marker plasmid. RT-PCR analysis indicated that the increased GLOX activity was associated with elevated recombinant glx expression. Moreover, these transformants showed higher ligninolytic activity than control transformants. These results suggest that the ligninolytic properties of white-rot fungi can be improved by recombinant expression of glx.
Non-self-adjoint graphs
Authors: Hussein Amru , Krejčiřík David , Siegl Petr
Published: August 2014

On finite metric graphs we consider Laplace operators, subject to various classes of non-self-adjoint boundary conditions imposed at graph vertices. We investigate spectral properties, existence of a Riesz basis of projectors and similarity transforms to self-adjoint Laplacians. Among other things, we describe a simple way to relate the similarity transforms between Laplacians on certain graphs with elementary similarity transforms between matrices defining the boundary conditions.
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation
Authors: Zhu Fan , Shi Lihong , Li Hongdong , Eksi Ridvan , Engel James Douglas , Guan Yuanfang
Published: August 2014

Motivation: Functional relationship networks, which summarize the probability of co-functionality between any two genes in the genome, could complement the reductionist focus of modern biology for understanding diverse biological processes in an organism. One major limitation of the current networks is that they are static, while one might expect functional relationships to consistently reprogram during the differentiation of a cell lineage. To address this potential limitation, we developed a novel algorithm that leverages both differentiation stage-specific expression data and large-scale heterogeneous functional genomic data to model such dynamic changes. We then applied this algorithm to the time-course RNA-Seq data we collected for ex vivo human erythroid cell differentiation.

Results: Through computational cross-validation and literature validation, we show that the resulting networks correctly predict the (de)-activated functional connections between genes during erythropoiesis. We identified known critical genes, such as HBD and GATA1, and functional connections during erythropoiesis using these dynamic networks, while the traditional static network was not able to provide such information. Furthermore, by comparing the static and the dynamic networks, we identified novel genes (such as OSBP2 and PDZK1IP1) that are potential drivers of erythroid cell differentiation. This novel method of modeling dynamic networks is applicable to other differentiation processes where time-course genome-scale expression data are available, and should assist in generating greater understanding of the functional dynamics at play across the genome during development.

Availability and implementation: The network described in this article is available at http://guanlab.ccmb.med.umich.edu/stageSpecificNetwork.

Contact:  gyuanfan@umich.edu or engel@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Projected ocean warming creates a conservation challenge for river
herring populations
Authors: Lynch Patrick D. , Nye Janet A. , Hare Jonathan A. , Stock Charles A. , Alexander Michael A. , Scott James D. , Curti Kiersten L. , Drew Katherine
Published: August 2014

The term river herring collectively refers to alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis), two anadromous fishes distributed along the east coast of North America. Historically, river herring spawning migrations supported important fisheries, and their spawning runs continue to be of cultural significance to many coastal communities. Recently, substantial declines in spawning run size prompted a petition to consider river herring for listing under the Endangered Species Act (ESA). The ESA status review process requires an evaluation of a species’ response to multiple stressors, including climate change. For anadromous species that utilize a range of habitats throughout their life cycle, the response to a changing global climate is inherently complex and likely varies regionally. River herring occupy marine habitat for most of their lives, and we demonstrate that their relative abundance in the ocean has been increasing in recent years. We project potential effects of ocean warming along the US Atlantic coast on river herring in two seasons (spring and fall), and two future periods (2020–2060 and 2060–2100) by linking species distribution models to projected temperature changes from global climate models. Our analyses indicate that climate change will likely result in reductions in total suitable habitat across the study region, which will alter the marine distribution of river herring. We also project that density will likely decrease for both species in fall, but may increase in spring. Finally, we demonstrate that river herring may have increased sensitivity to climate change under a low abundance scenario. This result could be an important consideration for resource managers when planning for climate change because establishing effective conservation efforts in the near term may improve population resiliency and provide lasting benefits to river herring populations.
Genetic analyses of ling (Molva molva) in the Northeast Atlantic reveal patterns relevant to stock assessments and management advice
Authors: Blanco Gonzalez Enrique , Knutsen Halvor , Jorde Per Erik , Glover Kevin Alan , Bergstad Odd Aksel
Published: August 2014

The ling, Molva molva, is a commercially exploited demersal gadid fish distributed throughout the Northeast Atlantic. Here, we provide the first study of population genetic structure by genotyping 6 geographically distinct samples with 11 microsatellite DNA markers. The results rejected the hypothesis of a single ling stock in the Northeast Atlantic, and rather suggested the existence of two or more groups, with the main grouping represented by a western (comprising Rockall and Iceland) and an eastern group (Faroe Bank, Norway). Significant genetic differences coincide with an expanse of deep water that probably limits connectivity facilitated by migration. Retention in gyres and directional oceanic circulation may also prevent drift and admixture during planktonic life stages. On the other hand, the apparent absence of genetic differentiation within the eastern part of the distribution range indicates gene flow, perhaps by larval drift and migration, over considerable distances. Our findings should contribute to improving stock assessments and monitoring and thus fisheries management advice for the ling.
Coexisting Aortic Stenosis and Left Ventricular Outflow Tract Obstruction
Authors: Haddy Steven M.
Published: August 2014

Supplemental Digital Content is available in the text.
High‐ and Low‐Dose Oral Delayed‐Release Mesalamine in Children With Mild‐to‐Moderately Active Ulcerative Colitis
Authors: Winter Harland S. , Krzeski Piotr , Heyman Melvin B. , Ibarguen‐Secchia Eduardo , Iwanczak Barbara , Kaczmarski Maciej , Kierkus Jaroslaw , Kolaček Sanja , Osuntokun Bankole , Quiros J. Antonio , Shah Manoj , Yacyshyn Bruce , Dunnmon Preston M.
Published: August 2014

Objective:

The aim of the study was to assess the safety and efficacy of high‐ and low‐dose oral, delayed‐release mesalamine in a randomized, double‐blind, active control study of children with mild‐to‐moderately active ulcerative colitis.

Methods:

Patients ages 5 to 17 years, with a Pediatric Ulcerative Colitis Activity Index (PUCAI) score of ≥10 to ≤55 and a truncated Mayo Score of ≥1 for both rectal bleeding and stool frequency, were enrolled. They received body weight–dependent doses of oral, delayed‐release mesalamine for 6 weeks in a low‐ (27–71 mg · g−1 · day−1) or high‐dose group (53–118 mg · g−1 · day−1). The primary endpoint was treatment success, defined as the proportion of patients who achieved remission (PUCAI score <10) or partial response (PUCAI score ≥10 with a decrease from baseline by ≥20 points). Secondary endpoints included truncated Mayo Score and global assessment of change of disease activity.

Results:

The modified intent‐to‐treat population included 81 of 83 patients enrolled. Treatment success by PUCAI was achieved by 23 of 41 (56%) and 22 of 40 (55%) patients in the mesalamine low‐ and high‐dose groups, respectively (P = 0.924). Truncated Mayo Score (low‐dose 30 [73%] and high‐dose 28 [70%] patients) and other efficacy results did not differ between the groups. The type and severity of adverse events were consistent with those reported in previous studies of adults with ulcerative colitis and did not differ between groups.

Conclusions:

Both low‐ and high‐dose oral, delayed‐release mesalamine doses were equally effective as short‐term treatment of mild‐to‐moderately active ulcerative colitis in children, without a specific benefit or risk to using either dose.
Application of Failure Mode Effect Analysis to Improve the Care of Septic Patients Admitted Through the Emergency Department
Authors: Alamry Ahmed , Al Owais Souzan M. , Marini Abdellatif M. , Al-Dorzi Hasan , Alsolamy Sami , Arabi Yaseen
Published: August 2014

Background

Failure mode effect analysis (FMEA) is a proactive multistep tool used to analyze risks, identify failures before they occur, and prioritize preventive measures.

Methods

A multidisciplinary team trained on FMEA methodology analyzed the process of treatment of septic patients and recorded processes under 3 major phases (recognition of severe sepsis, referral, and resuscitation). The team identified potential failure modes in each process; assigned severity, occurrence, and detection scores for each; and calculated the risk priority numbers (RPNs). Finally, higher-priority failure modes (RPN of ≥300) were analyzed to redesign the care process.

Results

We identified 27 processes and 48 failure modes with a mean RPN of 270. Twenty-two high-risk failures were identified by RPN of 300 or higher. All identified critical processes were related to phase 1 (recognition of sepsis) and phase 3 (resuscitation). The most critical process seemed to be related to the initial workup and treatment of septic patients, with 4 potential failure modes and a total RPN of 1485.

Conclusions

Patient safety and care reliability issues are a major concern in health care. This study suggests that tools such as FMEA can enable a detailed analysis of the care process of septic patients by outlining potential failure modes and guiding improvement efforts.
Sociocultural Factors Influencing Incident Reporting Among Physicians and Nurses: Understanding Frames Underlying Self- and Peer-Reporting Practices
Authors: Hewitt Tanya , Chreim Samia , Forster Alan
Published: August 2014

Objectives

Voluntary reporting of incidents is a common approach for improving patient safety. Reporting behaviors may vary because of different frames within and across professions, where frames are templates that individuals hold and that guide interpretation of events. Our objectives were to investigate frames of physicians and nurses who report into a voluntary incident reporting system as well as to understand enablers and inhibitors of self-reporting and peer reporting.

Methods

This is a qualitative case study—confidential in-depth interviews with physicians and nurses in General Internal Medicine in a Canadian tertiary care hospital.

Results

Frames that health care practitioners use in their reporting practices serve as enablers and inhibitors for self-reporting and peer reporting. Frames that inhibit reporting are shared by physicians and nurses, such as the fear of blame frame regarding self-reporting and the tattletale frame regarding peer reporting. These frames are underpinned by a focus on the individual, despite the organizational message of reporting for learning. A learning frame is an enabler to incident reporting. Viewing the objective of voluntary incident reporting as learning allows practitioners to depersonalize incident reporting. The focus becomes preventing recurrence and not the individual reporting or reported on.

Conclusions

Physicians and nurses use various frames that bound their views of self and peer incident reporting—further progress should incorporate an understanding of these deep-seated views and beliefs.
Organizational, Cultural, and Psychological Determinants of Smart Infusion Pump Work Arounds: A Study of 3 U.S. Health Systems
Authors: Dunford Benjamin B. , Perrigino Matthew , Tucker Sharon J. , Gaston Cynthia L. , Young Jim , Vermace Beverly J. , Walroth Todd A. , Buening Natalie R. , Skillman Katherine L. , Berndt Dawn
Published: August 2014

Objectives

We investigated nurse perceptions of smart infusion medication pumps to provide evidence-based insights on how to help reduce work around and improve compliance with patient safety policies. Specifically, we investigated the following 3 research questions: (1) What are nurses' current attitudes about smart infusion pumps? (2) What do nurses think are the causes of smart infusion pump work arounds? and (3) To whom do nurses turn for smart infusion pump training and troubleshooting?

Methods

We surveyed a large number of nurses (N = 818) in 3 U.S.-based health care systems to address the research questions above. We assessed nurses' opinions about smart infusion pumps, organizational perceptions, and the reasons for work arounds using a voluntary and anonymous Web-based survey. Using qualitative research methods, we coded open-ended responses to questions about the reasons for work arounds to organize responses into useful categories.

Results

The nurses reported widespread satisfaction with smart infusion pumps. However, they reported numerous organizational, cultural, and psychological causes of smart pump work arounds. Of 1029 open-ended responses to the question “why do smart pump work arounds occur?” approximately 44% of the causes were technology related, 47% were organization related, and 9% were related to individual factors. Finally, an overwhelming majority of nurses reported seeking solutions to smart pump problems from coworkers and being trained primarily on the job.

Discussion and Conclusions

Hospitals may significantly improve adherence to smart pump safety features by addressing the nontechnical causes of work arounds and by providing more leadership and formalized training for resolving smart pump–related problems.
Preterm birth is associated with an increased fundamental frequency of spontaneous crying in human infants at term-equivalent age
Authors: Shinya Yuta , Kawai Masahiko , Niwa Fusako , Myowa-Yamakoshi Masako
Published: August 2014

Human infant crying has been researched as a non-invasive tool for assessing neurophysiological states at an early developmental stage. Little is known about the acoustic features of spontaneous cries in preterm infants, although their pain-induced cries are at a higher fundamental frequency (
F
0
) before term-equivalent age. In this study, we investigated the effects of gestational age, body size at recording and intrauterine growth retardation (IUGR) on the
F
0
of spontaneous cries in healthy preterm and full-term infants at term-equivalent age. We found that shorter gestational age was significantly associated with higher
F
0
, although neither smaller body size at recording nor IUGR was related to increased
F
0
in preterm infants. These findings suggest that the increased
F
0
of spontaneous cries is not caused by their smaller body size, but instead might be caused by more complicated neurophysiological states owing to their different intrauterine and extrauterine experiences.
Size matters: plasticity in metabolic scaling shows body-size may modulate responses to climate change
Authors: Carey Nicholas , Sigwart Julia D.
Published: August 2014

Variability in metabolic scaling in animals, the relationship between metabolic rate (

R

) and body mass (

M

), has been a source of debate and controversy for decades.

R

is proportional to

M
b

, the precise value of

b

much debated, but historically considered equal in all organisms. Recent metabolic theory, however, predicts

b

to vary among species with ecology and metabolic level, and may also vary within species under different abiotic conditions. Under climate change, most species will experience increased temperatures, and marine organisms will experience the additional stressor of decreased seawater pH (‘ocean acidification’). Responses to these environmental changes are modulated by myriad species-specific factors. Body-size is a fundamental biological parameter, but its modulating role is relatively unexplored. Here, we show that changes to metabolic scaling reveal asymmetric responses to stressors across body-size ranges;

b

is systematically decreased under increasing temperature in three grazing molluscs, indicating smaller individuals were more responsive to warming. Larger individuals were, however, more responsive to reduced seawater pH in low temperatures. These alterations to the allometry of metabolism highlight abiotic control of metabolic scaling, and indicate that responses to climate warming and ocean acidification may be modulated by body-size.
Shiing-Shen Chern. 26 October 1911 — 3 December 2004
Authors: Hitchin Nigel J.
Published: August 2014

Shiing-Shen Chern was a towering figure in mathematics, both for his contributions to differential geometry and as a source of inspiration and encouragement for all mathematicians, and particularly those in China. Born in the final year of the Qing dynasty, and educated at a time when China was only beginning to set up Western-style universities, he lived to preside over the 2002 International Congress of Mathematicians in Beijing. He was a co-founder of the Mathematical Sciences Research Institute in Berkeley and its first Director in 1981; he also set up the Nankai Institute for Mathematics in 1985. His contributions to differential geometry were of foundational importance for the global viewpoint that developed in the postwar years, and the mathematical tools he introduced are now the common currency in geometry, topology and even aspects of theoretical physics.
Programming chemistry in DNA-addressable bioreactors
Authors: Fellermann Harold , Cardelli Luca
Published: August 2014

We present a formal calculus, termed the
chemtainer calculus
, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis.
Masticatory biomechanics in the rabbit: a multi-body dynamics analysis
Authors: Watson Peter J. , Gröning Flora , Curtis Neil , Fitton Laura C. , Herrel Anthony , McCormack Steven W. , Fagan Michael J.
Published: August 2014

Multi-body dynamics is a powerful engineering tool which is becoming increasingly popular for the simulation and analysis of skull biomechanics. This paper presents the first application of multi-body dynamics to analyse the biomechanics of the rabbit skull. A model has been constructed through the combination of manual dissection and three-dimensional imaging techniques (magnetic resonance imaging and micro-computed tomography). Individual muscles are represented with multiple layers, thus more accurately modelling muscle fibres with complex lines of action. Model validity was sought through comparing experimentally measured maximum incisor bite forces with those predicted by the model. Simulations of molar biting highlighted the ability of the masticatory system to alter recruitment of two muscle groups, in order to generate shearing or crushing movements. Molar shearing is capable of processing a food bolus in all three orthogonal directions, whereas molar crushing and incisor biting are predominately directed vertically. Simulations also show that the masticatory system is adapted to process foods through several cycles with low muscle activations, presumably in order to prevent rapidly fatiguing fast fibres during repeated chewing cycles. Our study demonstrates the usefulness of a validated multi-body dynamics model for investigating feeding biomechanics in the rabbit, and shows the potential for complementing and eventually reducingin vivoexperiments.
Temporally dynamic habitat suitability predicts genetic relatedness among caribou
Authors: Yannic Glenn , Pellissier Loïc , Le Corre Maël , Dussault Christian , Bernatchez Louis , Côté Steeve D.
Published: August 2014

Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its ability to explain the genetic relatedness among individuals. We assessed habitat selection using locations of collared individuals in migratory herds and static occurrences from sedentary groups. Connectivity models based on habitat use outperformed a baseline isolation-by-distance model in explaining genetic relatedness, suggesting that variations in landscape features such as snow, vegetation productivity and land use modulate connectivity among populations. Connectivity surfaces derived from habitat use were the best predictors of genetic relatedness. The relationship between connectivity surface and genetic relatedness varied in time and peaked during the rutting period. Landscape permeability in the period of mate searching is especially important to allow gene flow among populations. Our study highlights the importance of considering temporal variations in habitat selection for optimizing connectivity across heterogeneous landscape and counter habitat fragmentation.
Three-way interactions between mosquito population, viral strain and temperature underlying chikungunya virus transmission potential
Authors: Zouache Karima , Fontaine Albin , Vega-Rua Anubis , Mousson Laurence , Thiberge Jean-Michel , Lourenco-De-Oliveira Ricardo , Caro Valérie , Lambrechts Louis , Failloux Anna-Bella
Published: August 2014

Interactions between pathogens and their insect vectors in nature are under the control of both genetic and non-genetic factors, yet most studies on mosquito vector competence for human pathogens are conducted in laboratory systems that do not consider genetic and/or environmental variability. Evaluating the risk of emergence of arthropod-borne viruses (arboviruses) of public health importance such as chikungunya virus (CHIKV) requires a more realistic appraisal of genetic and environmental contributions to vector competence. In particular, sources of variation do not necessarily act independently and may combine in the form of interactions. Here, we measured CHIKV transmission potential by the mosquito
Aedes albopictus
in all combinations of six worldwide vector populations, two virus strains and two ambient temperatures (20°C and 28°C). Overall, CHIKV transmission potential by
Ae. albopictus
strongly depended on the three-way combination of mosquito population, virus strain and temperature. Such genotype-by-genotype-by-environment (G × G × E) interactions question the relevance of vector competence studies conducted with a simpler set of conditions. Our results highlight the need to account for the complex interplay between vectors, pathogens and environmental factors to accurately assess the potential of vector-borne diseases to emerge.
Prediction of phylogeographic endemism in an environmentally complex biome
Authors: Carnaval Ana Carolina , Waltari Eric , Rodrigues Miguel T. , Rosauer Dan , VanDerWal Jeremy , Damasceno Roberta , Prates Ivan , Strangas Maria , Spanos Zoe , Rivera Danielle , Pie Marcio R. , Firkowski Carina R. , Bornschein Marcos R. , Ribeiro Luiz F. , Moritz Craig
Published: August 2014

Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current and past climatic variation on the genetic diversity of 25 vertebrates in the Brazilian Atlantic rainforest. We identify two divergent bioclimatic domains within the forest and high turnover around the Rio Doce. Independent modelling of these domains demonstrates that endemism patterns are subject to different climatic drivers. Past climate dynamics, specifically areas of relative stability, predict phylogeographic endemism in the north. Conversely, contemporary climatic heterogeneity better explains endemism in the south. These results accord with recent speleothem and fossil pollen studies, suggesting that climatic variability through the last 250 kyr impacted the northern and the southern forests differently. Incorporating sub-regional differences in climate dynamics will enhance our ability to understand those processes shaping high phylogeographic and species endemism, in the Neotropics and beyond.
A quantitative analysis of objective feather colour assessment: measurements in the lab are more reliable than in the field
Authors: Vaquero-Alba Iker , McGowan Andrew , Pincheira-Donoso Daniel , Evans Matthew R. , Dall Sasha R.X.
Published: August 2014

The evolution of animal colouration is importantly driven by sexual selection operating on traits used to transmit information to rivals and potential mates, which therefore, have major impacts on fitness. Reflectance spectrometry has become a standard colour-measuring tool, especially after the discovery of tetrachromacy in birds and their ability to detect UV. Birds? plumage patterns may be invisible to humans, necessitating a reliable and objective way of assessing colouration not dependent on human vision. Plumage colouration measurements can be taken directly on live birds in the field or in the lab (e.g. on collected feathers). Therefore, it is essential to determine which sampling method yields more repeatable and reliable measures, and which of the available quantitative approaches best assess the repeatability of these measures. Using a spectrophotometer, we measured melanin-based colouration in barn swallows? (Hirundo rustica) plumage. We assessed the repeatability of measures obtained with both traditional sampling methods separately to quantitatively determine their reliability. We used the ANOVA-based method for calculating the repeatability of measurements from two years separately, and the GLMM-based method to calculate overall adjusted repeatabilities for both years. We repeated the assessment for the whole reflectance spectrum range and only the human-visible part, to assess the influence of the UV component on the reliabilities of sampling methodologies. Our results reveal very high repeatability for lab measurements and a lower, still moderate to high repeatability, for field measurements. Both increased when limited to only the human-visible part, for all plumage patches except the throat, where we observed the opposite trend. Repeatability between sampling methods was quite low including the whole spectrum, but moderate including only the human-visible part. Our results suggest higher reliability for measurements in the lab and higher power and accuracy of the GLMM-based method. They also suggest UV reflectance differences amongst different plumage patches.
Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems
Authors: Simon Marianne , Jardillier Ludwig , Deschamps Philippe , Moreira David , Restoux Gwendal , Bertolino Paola , López‐García Purificación
Published: August 2014

Although inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well known. Some molecular surveys of lakes exist, but little information is available from smaller, shallower and often ephemeral freshwater systems, despite their global distribution and ecological importance. We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2–5 μm size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France. Our study revealed a wide diversity of small protists, with 812 stringently defined operational taxonomic units (OTUs) belonging to the recognized eukaryotic supergroups (SAR − Stramenopiles, Alveolata, Rhizaria − Archaeplastida, Excavata, Amoebozoa, Opisthokonta) and to groups of unresolved phylogenetic position (Cryptophyta, Haptophyta, Centrohelida, Katablepharida, Telonemida, Apusozoa). Some OTUs represented deep‐branching lineages (Cryptomycota, Aphelida, Colpodellida, Tremulida, clade‐10 Cercozoa, HAP‐1 Haptophyta). We identified several lineages previously thought to be marine including, in addition to MAST‐2 and MAST‐12, already detected in freshwater, MAST‐3 and possibly MAST‐6. Protist community structures were different in the five ecosystems. These differences did not correlate with geographical distances, but seemed to be influenced by environmental parameters.
Mental health trajectories and their embeddedness in work and family circumstances: a latent state‐trait approach to life‐course trajectories
Authors: Cullati Stéphane , Courvoisier Delphine S. , Burton‐Jeangros Claudine
Published: August 2014

Mental health trajectories are known to be influenced by work and family circumstances. However, few studies have examined both of these influences simultaneously in a longitudinal manner. The life‐course perspective stresses the importance of examining trajectories in terms of both stable and dynamic components. In this article we use structural equation models (latent state‐trait, LST) to distinguish the stable and situational components of mental health trajectories and hypothesise that situational mental health is influenced by satisfaction with work and family, and this effect differs by gender. An analysis of data from a nationally representative sample of 1616 working Swiss residents (2000–2006) shows that mental health trajectories are mostly stable and only slightly sensitive to situational influences. However, situational influences in a given wave do predict situational influences in the next wave. Satisfaction with work and family influences situational mental health in both genders, but the impact is greater for men. In conclusion, the LST approach allows for the examination of mental health trajectories from a life‐course perspective by distinguishing stable and situational components. Mental health trajectories are more stable and constant than they are dependent on work and family circumstances, and men are more sensitive to family circumstances than women.
Changes in Serum Asymmetric Dimethylarginine and Endothelial Markers Levels With Varying Periods of Hemodialysis
Authors: Yaman Alper , Karabag Funda , Demir Serap , Koken Tulay
Published: August 2014

Asymmetric dimethylarginine (ADMA) as a uremia toxin is accumulated in end‐stage renal disease (ESRD) patients. Elevated ADMA level has been shown to be predictive of cardiovascular diseases (CVDs) and all‐cause mortality in ESRD. Therefore, we investigated the effect of prolonged hemodialysis (HD) treatment on the levels of serum ADMA, arginine, nitric oxide (NO), soluble intercellular adhesion molecule‐1 (sICAM‐1) and soluble vascular cell adhesion molecule‐1 (sVCAM‐1). Seventy‐five patients (M/F = 40/35) with chronic renal failure (CRF) and who were on HD were divided into five groups with differing treatment periods of HD; from 6 to 24 months to 97–120 months. Fifteen apparently healthy subjects acted as controls. The serum levels of ADMA, sICAM‐1 and sVCAM‐1 were increased in all patient groups compared to the control group. No significant difference was observed when the patient groups were compared in terms of HD treatment periods. Nitric oxide levels were lower in the three groups who were treated for periods of 49–72, 73–96, 97–120 months compared to the control group. The L‐arginine to ADMA ratio was decreased in all patient groups compared to controls. Consequently, our investigations have shown that in HD continued for more than 4 years NO levels began to decrease significantly and the levels of serum ADMA, sICAM‐1 and sVCAM‐1 levels increased although this increase was not affected by the period in which hemodialysis treatment was applied.
Alcohol expectancies in childhood: change with the onset of drinking and ability to predict adolescent drunkenness and binge drinking
Authors: Jester Jennifer M. , Wong Maria M. , Cranford James A. , Buu Anne , Fitzgerald Hiram E. , Zucker Robert A.
Published: August 2014

Aims

We examined the relationship between alcohol expectancies in childhood and onset of drinking, binge drinking and drunkenness in adolescence and the influence of drinking onset on expectancy development.

Design

A prospective, longitudinal study of children assessed for alcohol expectancies and drinking at four time‐points between ages 6 and 17 years.

Setting

Community study of families at high risk for alcoholism conducted in a four‐county area in the Midwestern United States.

Participants

The study involved 614 children; 460 were children of alcoholics and 70% were male.

Measurements

Expectancies about alcohol effects were measured using the Beverage Opinion Questionnaire and child's drinking by the Drinking and Drug History—Youth Form.

Findings

Partial factor invariance was found for expectancy factors from ages 6 to 17 years. Survival analysis showed that social/relaxation expectancies in childhood predicted time to onset of binge drinking and first time drunk (Wald χ2, 1 d.f. = 3.8, P = 0.05 and 5.0, P < 0.05, respectively). The reciprocal effect was also present; when adolescents began drinking, there was an increase in social/relaxation expectancy and a concomitant increase in slope of the expectancy changes lasting throughout adolescence.

Conclusions

A reciprocal relationship exists between childhood alcohol expectancies and the development of alcohol involvement. Higher expectancies for positive effects predict earlier onset of problem drinking. Onset of use, in turn, predicts an increase in rate of development of positive expectancies.