bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of 1–8 keV K-α x-ray emission from high intensity femtosecond laser produced plasma
Authors: Arora V. , Naik P. A. , Chakera J. A. , Bagchi S. , Tayyab M. , Gupta P. D.
Published: April 2014

We report an experimental study on the optimization of a laser plasma based x-ray source of ultra-short duration K-α line radiation. The interaction of pulses from a CPA based Ti:sapphire laser (10 TW, 45 fs, 10 Hz) system with magnesium, titanium, iron and copper solid target generates bright 1-8 keV K-α x-ray radiation. The x-ray yield was optimized with the laser pulse duration (at fixed fluence) which is varied in the range of 45 fs to 1.4 ps. It showed a maximum at laser pulse duration of ∼740 fs, 420 fs, 350 and 250 fs for Mg (1.3 keV), Ti (4.5 keV), Fe (6.4 keV) and Cu (8.05 keV) respectively. The x-ray yield is observed to be independent of the sign of the chirp. The scaling of the K-α yield (Ix ∝ ILβ) for 45 fs and optimized pulse duration were measured for laser intensities in the region of 3 × 1014 – 8 × 1017. The x-ray yield shows a much faster scaling exponent β = 1.5, 2.1, 2.4 and 2.6 for Mg, Ti, Fe and Cu respectively at optimized pulse duration compared to scaling exponent of 0.65, 1.3, 1.5, and 1.7 obtained for 45 fs duration laser pulses. The laser to x-ray energy conversion efficiencies obtained for different target materials are ηMg = 1.2 × 10−5, ηTi = 3.1 × 10−5, ηFe = 2.7 × 10−5, ηCu = 1.9 × 10−5. The results have been explained from the efficient generation of optimal energy hot electrons at longer laser pulse duration. The faster scaling observed at optimal pulse duration indicates that the x-ray source is generated at the target surface and saturation of x-ray emission would appear at larger laser fluence. An example of utilization of the source for measurement of shock-wave profiles in a silicon crystal by time resolved x-ray diffraction is also presented.
Tunable anisotropic thermal conduction in graphane nanoribbons
Authors: Li Dengfeng , Xu Yong , Chen Xiaobin , Li Bolin , Duan Wenhui
Published: April 2014

Graphane and graphene are both two-dimensional materials but of different bonding configurations, which can result in distinct thermal conduction properties. We simulate thermal conduction in graphane nanoribbons (GANRs) using the nonequilibrium Green's function method. We find anisotropic thermal conduction in GANRs, with zigzag GANRs giving higher thermal conductance than armchair ones. Compared to the graphene counterparts, GANRs show lower ballistic thermal conductance and stronger thermal conductance anisotropy. Furthermore, hydrogen vacancies of GANRs considerably suppress thermal conduction, accompanied by enhanced thermal conductance anisotropy. The tunable thermal conduction, realized by controlling the ribbon width, edge shape, and hydrogen vacancy concentration of GANRs, could be useful for thermal management and thermoelectric applications.
High mobility n-type organic thin-film transistors deposited at room temperature by supersonic molecular beam deposition
Authors: Chiarella F. , Toccoli T. , Barra M. , Aversa L. , Ciccullo F. , Tatti R. , Verucchi R. , Iannotta S. , Cassinese A.
Published: April 2014

In this paper, we report on the fabrication of N,N′-1H,1H-perfluorobutil dicyanoperylenediimide (PDIF-CN2) organic thin-film transistors by Supersonic Molecular Beam Deposition. The devices exhibit mobility up to 0.2 cm2/V s even if the substrate is kept at room temperature during the organic film growth, exceeding by three orders of magnitude the electrical performance of those grown at the same temperature by conventional Organic Molecular Beam Deposition. The possibility to get high-mobility n-type transistors avoiding thermal treatments during or after the deposition could significantly extend the number of substrates suitable to the fabrication of flexible high-performance complementary circuits by using this compound.
Phase contrast and operation regimes in multifrequency atomic force microscopy
Authors: Santos Sergio
Published: April 2014

In amplitude modulation atomic force microscopy the attractive and the repulsive force regimes induce phase shifts above and below 90°, respectively. In the more recent multifrequency approach, however, multiple operation regimes have been reported and the theory should be revisited. Here, a theory of phase contrast in multifrequency atomic force microscopy is developed and discussed in terms of energy transfer between modes, energy dissipation and the kinetic energy and energy transfer associated with externally driven harmonics. The single frequency virial that controls the phase shift might undergo transitions in sign while the average force (modal virial) remains positive (negative).
Role of wrinkles in the corrosion of graphene domain-coated Cu surfaces
Authors: Zhang Y. H. , Zhang H. R. , Wang B. , Chen Z. Y. , Zhang Y. Q. , Wang B. , Sui Y. P. , Zhu B. , Tang C. M. , li X. L. , Xie X. M. , Yu G. H. , Jin Z. , Liu X. Y.
Published: April 2014

We analyzed the protective ability of chemical vapor deposition (CVD) graphene domains against corrosion of Cu surfaces. Fresh graphene domains of various shapes were ideal corrosion-inhibiting layers. However, obvious corrosion was found within graphene domains exposed to the air for over a week. Our work demonstrates that the opportunities for corrosion of CVD graphene were provided by wrinkles but not others, such as Cu grain boundaries and graphene domain boundaries, which are always believed the primary factor for inferior quality of the CVD graphene at present.
Accurate measurement of force and displacement with optical tweezers using DNA molecules as metrology standards
Authors: delToro Damian , Smith Douglas E.
Published: April 2014

Optical tweezers facilitate measurement of piconewton-level forces and nanometer-level displacements and have broad applications in biophysics and soft matter physics research. We have shown previously that DNA molecules can be used as metrology standards to define such measurements. Force-extension measurements on two DNA molecules of different lengths can be used to determine four necessary measurement parameters. Here, we show that the accuracy of determining these parameters can be improved by more than 7-fold by incorporating measurements of the DNA overstretching transition and using a multi-step data analysis procedure. This method results in very robust and precise fitting of DNA force-extension measurements to the worm-like chain model. We verify the accuracy through independent measurements of DNA stretching, DNA unzipping, and microsphere contact forces.
A three dimensional thermoplastic microfluidic chip for robust cell capture and high resolution imaging
Authors: Mottet Guillaume , Perez-Toralla Karla , Tulukcuoglu Ezgi , Bidard Francois-Clement , Pierga Jean-Yves , Draskovic Irena , Londono-Vallejo Arturo , Descroix Stephanie , Malaquin Laurent , Louis Viovy Jean
Published: April 2014

We present a low cost microfluidic chip integrating 3D micro-chambers for the capture and the analysis of cells. This device has a simple design and a small footprint. It allows the implementation of standard biological protocols in a chip format with low volume consumption. The manufacturing process relies on hot-embossing of cyclo olefin copolymer, allowing the development of a low cost and robust device. A 3D design of microchannels was used to induce high flow velocity contrasts in the device and provide a selective immobilization. In narrow distribution channels, the liquid velocity induces a shear stress that overcomes adhesion forces and prevents cell immobilization or clogging. In large 3D chambers, the liquid velocity drops down below the threshold for cell attachment. The devices can be operated in a large range of input pressures and can even be handled manually using simple syringe or micropipette. Even at high flow injection rates, the 3D structures protect the captured cell from shear stress. To validate the performances of our device, we implemented immuno-fluorescence labeling and Fluorescence in Situ Hybridization (FISH) analysis on cancer cell lines and on a patient pleural effusion sample. FISH is a Food and Drug Administration approved cancer diagnostic technique that provides quantitative information about gene and chromosome aberration at the single cell level. It is usually considered as a long and fastidious test in medical diagnosis. This process can be easily implanted in our platform, and high resolution fluorescence imaging can be performed with reduced time and computer intensiveness. These results demonstrate the potential of this chip as a low cost, robust, and versatile tool adapted to complex and demanding protocols for medical diagnosis.
Increasing weight gain during pregnancy results in similar increases in lamb birthweights and weaning weights in Merino and non-Merino ewes regardless of sire type
Authors: Paganoni B. L. , Ferguson M. B. , Kearney G. A. , Thompson A. N.
Published: April 2014

Birthweight is the single largest determinant of survival in lambs and can be predicted from ewe liveweight at conception and liveweight changes during pregnancy. These prediction equations are known for Merino ewes, but it is unknown if they are applicable to non-Merino breeds. We tested the hypothesis that increasing conception weights of ewes will increase the birthweights, survival to weaning and weaning weights of their lambs, irrespective of ewe or sire breed, but that non-Merino lamb birthweights would be less responsive than Merino lamb birthweights, to changes in ewe liveweights during pregnancy. Ewe liveweight, lamb birth and weaning weight records from Merino sires mated to Merino ewes (MM), Border Leicester Merino (Maternal) sires mated to Merino ewes, Poll Dorset or Suffolk (Terminal) sires mated to Merino ewes (TM), and Terminal sires mated to Border Leicester Merino ewes (TMAT) were analysed from the 2007 to 2011 lambings of eight information nucleus flocks. Lamb birthweights increased by 0.032 ± 0.0012 kg from MM ewes and 0.024 ± 0.0026 kg from TMAT ewes with every 1-kg increase in conception weight (P < 0.001). Irrespective of breed, for every 1-kg increase in liveweight change during early and late pregnancy, lamb birthweights increased by 0.021 ± 0.0019 kg and 0.034 ± 0.0019 kg and weaning weights by 0.26 ± 0.013 kg and 0.09 ± 0.011 kg, respectively (P < 0.001). Survival to weaning of single, twin and triplet lambs was highest for lambs from TMAT ewes (89.3% ± 1.25, 84.6% ± 1.49 and 73.4% ± 2.35) and lowest for TM ewes (80.2% ± 1.89, 72.8% ± 2.09 and 57.4% ± 2.98; P < 0.001). Coefficients relating ewe liveweight change during pregnancy to lamb birthweights are similar for Merino and Maternal ewes, however conception weights of Maternal ewes are significantly heavier than Merino ewes when run together, and lamb birthweights from Maternal ewes are less responsive to ewe conception weights. The coefficients reported in this paper will enable development of optimum management guidelines for single-, twin- and triple-bearing Maternal ewes.
Role of Anion–π Interactions in the Supramolecular Assembly of Salts Containing Asymmetrical Bis(pyridyl) Cations
Authors: Zhang Zhu-Yan , Deng Zhao-Peng , Huo Li-Hua , Zhang Shu-E , Zhao Hui , Gao Shan
Published: April 2014

Self-assembly of three flexible bis(pyridyl) molecules with different inorganic acids (HPF6, HClO4, and HNO3) leads to the formation of eight salts, which exhibit diverse architectures involving hydrogen bonding and anion–π interactions. The three types of inorganic anions in these salts formed anion–π interactions with HM+ and H2M2+ except for 2, in which the six F atoms were involved in hydrogen bonds. Anion–π interactions produced diverse motifs of one (anion)-to-one (cation) in 1, 3, 4, and 6, two (anion)-to-one (cation) in 5 and 7, and (4,4) layer in 8. Hydrogen bonds resulted in interesting supramolecular architectures, such as right- and left-handed helical chains in 3, 2-fold interpenetrating networks in 5, and 3-fold interpenetrating networks in 8. Structural analyses indicated that the conformations of the three flexible asymmetrical bis(pyridyl) molecules and the non-covalent bonding interactions, such as hydrogen bonds and anion···π interactions, play crucial roles in the final architectures of these salts. Thermogravimetric analyses indicated that the thermal stability of the eight salts decreased in the order of perchlorates, hexafluorophosphates, and nitrates. The emission intensity of the perchlorates is much stronger than that of the hexafluorophosphates, nitrates, and their corresponding organic molecules in the solid state at room temperature.
In utero exposure to the oestrogen mimic diethylstilbestrol disrupts gonadal development in a viviparous reptile
Authors: Parsley Laura M. , Wapstra Erik , Jones Susan M.
Published: April 2014

The ubiquitous presence of endocrine-disrupting chemicals (EDCs) in the environment is of major concern. Studies on oviparous reptiles have significantly advanced knowledge in this field; however, 30% of reptilian species are viviparous (live-bearing), a parity mode in which both yolk and a placenta support embryonic development, thus exposure to EDCs may occur via multiple routes. In this first study of endocrine disruption in a viviparous lizard (Niveoscincus metallicus), we aimed to identify effects of the oestrogen mimic diethylstilbestrol (DES) on gonadal development. At the initiation of sexual differentiation, pregnant N. metallicus were treated with a single dose of DES at 100 or 10 µg kg­–1, a vehicle solvent or received no treatment. There was no dose-response effect, but the testes of male neonates born to DES-exposed mothers showed reduced organisation of seminiferous tubules and a lack of germ cells compared with those from control groups. The ovaries of female neonates born to DES-exposed mothers exhibited phenotypic abnormalities of ovarian structure, oocytes and follicles compared with controls. The results indicate that, in viviparous lizards, maternal exposure to oestrogenic EDCs during gestation may have profound consequences for offspring reproductive fitness.
Predicting the number of daily human-caused bushfires to assist suppression planning in south-west Western Australia
Authors: Plucinski M. P. , McCaw W. L. , Gould J. S. , Wotton B. M.
Published: April 2014

Data from bushfire incidents in south-west Western Australia from the Departments of Parks and Wildlife and Fire and Emergency Services were used to develop models that predict the number of human-caused bushfires within 10 management areas. Fire incident data were compiled with weather variables, binary classifications of day types (e.g. school days) and counts of the number of fires that occurred over recent days. Models were developed using negative binomial regression with a dataset covering 3 years and evaluated using data from an independent year. A common model form that included variables relating to fuel moisture content, the number of recent human-caused bushfires, work day (binary classification separating weekends and public holidays from other days) and rainfall was applied to all areas. The model had reasonable fit statistics across all management areas, but showed enough day-to-day prediction variability to be of practical use only in the more densely populated management areas, which were dominated by deliberate ignitions. The findings of this study should be of interest to fire managers in Mediterranean climatic regions where a variety of practices are used to manage wildfires.
Exploring the use of economic evaluation in Australian wildland fire management decision-making
Authors: Clayton Helena , Mylek Melinda R. , Schirmer Jacki , Cary Geoffrey J. , Dovers Stephen R.
Published: April 2014

Wildland fire managers make daily decisions about ways to allocate scarce resources to meet policy objectives. Making these decisions has become more challenging as the frequency and size of fires increase, as does associated risk to assets and costs of management. There is growing interest in using economic evaluation to inform resource allocation decisions, but little work has examined the economic evaluation needs of wildland fire managers, their current use of economic information and the factors that aid or hinder use. This study examined these issues through a survey of Australian wildland fire managers in fire management and policy roles. We found that despite strong interest in economic evaluation, managers have limited familiarity with most evaluation methods or use of the information derived. Several actions can improve the use and usefulness of economic evaluation for wildland fire managers: first, building capacity of managers to both commission and use economic information; second, integrating analysis of market and non-market benefits and costs as part of economic evaluation and third, better integrating economic evaluation with the broader context of decision-making processes.
Long-term persistence and vicariance within the Australian Monsoonal Tropics: the case of the giant cave and tree geckos (Pseudothecadactylus)
Authors: Oliver Paul M. , Laver Rebecca J. , Smith Katie L. , Bauer Aaron M.
Published: April 2014

The Australian Monsoonal Tropics (AMT) are one of the largest unbroken areas of savannah woodland in the world. The history of the biota of this region is poorly understood; however, data from fossil deposits indicate that the climate was more mesic in the past, and that biodiversity has been shaped by attenuation and turnover as arid conditions expanded and intensified through the Miocene and Plio-Pleistocene. The giant cave and tree geckos (Pseudothecadactylus) are distributed across three disjunct regions of relatively high rainfall in the AMT (the north-west Kimberley, the ‘Top End’, and Cape York). We present an analysis of the diversity and biogeography of this genus based on mitochondrial (ND2) and nuclear (RAG-1) loci. These data indicate that the three widely allopatric lineages of Pseudothecadactylus diverged around the mid-Miocene, a novel pattern of relatively long-term persistence that has not previously been documented within the AMT. Two Pseudothecadactylus species endemic to sandstone scarps in the west Kimberley Region and ‘Top End’ also include divergent mitochondrial lineages, indicative of deep intraspecific coalescence times within these regions. Pseudothecadactylus is a highly relictual lineage with an extant distribution that has been shaped by a history of attenuation, isolation and persistence in the face of increasingly arid conditions. The low ecological and morphological diversity of Pseudothecadactylus also contrasts with its diverse sister lineage of geckos in New Caledonia, further underlining the relictual nature of standing diversity in the former.
Hst3 is turned over by a replication stress-responsive SCF
Cdc4
phospho-degron
Authors: Edenberg Ellen R. , Vashisht Ajay A. , Topacio Benjamin R. , Wohlschlegel James A. , Toczyski David P.
Published: April 2014

Significance

Acetylation and deacetylation of histone H3K56 is important for genomic stability, replication, and the response to DNA damage and replication stress. One of the key regulators of H3K56 acetylation in budding yeast is Hst3, a cell-cycle– and damage-regulated histone deacetylase for the mark. Previously, Hst3 was known to be transcriptionally regulated. In this paper, we show that Hst3 is controlled posttranscriptionally by protein degradation. Specifically, Hst3 protein is degraded by SCF
Cdc4
recognizing a small phospho-degron. We also find that the degradation of Hst3 increases in response to replication stress through the same phospho-degron.
The nature and extent of contributions by defective ribosome products to the HLA peptidome
Authors: Bourdetsky Dmitry , Schmelzer Christian E. H. , Admon Arie
Published: April 2014

Significance

Rapid degradation of newly synthesized proteins, followed by presentation of the resulting peptides by the MHC molecules, serves as an early alert for the immune system during pathogen infection. This study defines the relative contribution to the MHC peptidome of defective ribosome products (DRiPs), which are newly synthesized and rapidly degraded proteins, vs. mature proteins, degraded at the end of their functional lifetimes (retirees). The rates of synthesis of the individual MHC peptides and their source proteins were followed using stable isotope labeling and quantitative proteomics and peptidomics analyses. We conclude that DRiPs are a significant source of MHC peptides. Many of these DRiPs are misassembled surplus subunits of protein complexes and therefore are degraded soon after synthesis.
Colloidal aggregation and dynamics in anisotropic fluids
Authors: Mondiot Frédéric , Botet Robert , Snabre Patrick , Mondain-Monval Olivier , Loudet Jean-Christophe
Published: April 2014

Significance

The formulation of colloidal particle/liquid crystal (LC) composites is a well-identified route toward the design of smart responsive materials with tunable optical or mechanical properties. However, the particles aggregate because they distort the intrinsic order of LC phases, which costs elastic energy. For micrometer-sized inclusions, the resulting elastic forces dominate the coarsening of the system. In this paper, we find a previously unidentified regime where elastic interactions no longer prevail when the particles are downsized to the nanometer scale. Instead, the system evolution is governed by an anisotropic Brownian diffusion coupled to attractive depletion interactions. This finding opens up new possibilities to better control the clustering of colloids in such media. We provide both experimental evidence and numerical simulations.
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
Authors: Leung Alvin , Bader Gary D. , Reimand Jüri
Published: April 2014

Summary: Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery. HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks.

Availability and implementation: HyperModules is available in Cytoscape App Store and as a command line tool at www.baderlab.org/Sofware/HyperModules .

Contact:  Juri.Reimand@utoronto.ca or Gary.Bader@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online
A risk-based approach to evaluating northeast US fish community vulnerability to climate change
Authors: Gaichas S. K. , Link J. S. , Hare J. A.
Published: April 2014

Risk assessment methods are used worldwide to evaluate threats posed by fisheries and other impacts on living marine resources, and to prioritize management of these threats. We derive a simplified risk analysis for aggregate fish communities as a preliminary tool to identify priorities for further detailed assessment. Because some of the largest observed rates of sea surface temperature increase are on the northeast US continental shelf, we focused on climate change-driven risks to marine communities in this region. We evaluated climate vulnerability for six communities across two ecosystems: both commercial and non-commercial demersal fish, pelagic fish, and benthic invertebrates in the Gulf of Maine (GOM) and Mid-Atlantic bight (MAB). We first evaluated the probability that anticipated climate changes (e.g. warming water, decreased salinity, increased acidity, altered boundary currents) would occur in these regions, and rated the potential severity of change over the next 10 years. Then, we evaluated the sensitivity of each biological community in each region using 12 attributes (e.g. habitat and prey specificity, temperature and acidity sensitivity, larval dispersal, adult mobility, population productivity, etc.). Exposure to the key climate risks was related to community sensitivity in each region for an overall assessment of climate vulnerability. Climate risks from increased surface water temperature, sea level rise, and earlier spring were rated moderate to high in both regions, with additional moderate to high risks in the GOM from increased bottom temperature, stratification, and river inputs. Benthic invertebrates were rated most sensitive, with demersals intermediate and pelagics lowest. Two MAB communities were rated more sensitive than corresponding GOM communities, but greater short-term climate risks in the GOM indicated increased exposure for GOM communities. Overall, this simple analysis may help prioritize short-term regional climate risk management action, thus addressing key conditions related to fishery fluctuations beyond fishing itself.
Addressing Patient Safety in Rapid Response Activations for Nonhospitalized Persons
Authors: Lakshminarayana Pradeep H. , Darby Joseph M. , Simmons Richard L.
Published: April 2014

Background

Rapid response teams (RRTs) have been widely accepted as useful adjuncts to the care of inpatients with unanticipated emergencies. One study suggested that leadership of such teams could be assigned to midlevel providers, especially when nonhospitalized person (NHP)–related emergencies occur. However, in our tertiary medical center, a critical care medicine (CCM) physician always leads all RRT events including those related to NHPs.

Objective

In this study, we postulate reasons in favor of a single structured RRT led by an intensivist for both inpatients and NHPs.

Methods

An observational study conducted at an academic medical center. Demographic and clinical characteristics of NHP-related RRT events were evaluated over a 9-month period.

Measurements and Main Results

Rapid response teams were activated 1,952 times, of which, 154 events were NHP related. Only 42 RRT activations occurred for employees and visitors. Most of the NHP activations (112 events) occurred in response to events involving persons who were on the premises because of preexisting illnesses, either visiting physician offices (46 events), undergoing ambulatory diagnostic procedures (30 events), in transit to the emergency department (13 events), or undergoing emergency psychiatry evaluation (11 events). Most patients (83 NHPs) required admission to the hospital including 22 NHPs to intensive care units (ICUs) either directly from the event location or subsequently from the emergency department. The physician team leader admitted 20 NHPs directly from the scene, of which, 13 were admitted directly to ICUs.

Conclusion

Nonhospitalized patients requiring RRT activation often have complex pre-existent illnesses. A standardized team composition for both inpatients and NHPs in crisis is an appropriate administrative structure enhancing patient safety in hospitals where ambulatory and inpatient facilities are combined.
Disclosing Adverse Events to Patients: International Norms and Trends
Authors: Wu Albert W. , McCay Layla , Levinson Wendy , Iedema Rick , Wallace Gordon , Boyle Dennis J. , McDonald Timothy B. , Bismark Marie M. , Kraman Steve S. , Forbes Emma , Conway James B. , Gallagher Thomas H.
Published: April 2014

Objectives

There is a growing expectation in health systems around the world that patients will be fully informed when adverse events occur. However, current disclosure practices often fall short of this expectation.

Methods

We reviewed trends in policy and practice in 5 countries with extensive experience with adverse event disclosure: the United States, the United Kingdom, Canada, New Zealand, and Australia.

Results

We identified 5 themes that reflect key challenges to disclosure: (1) the challenge of putting policy into large-scale practice, (2) the conflict between patient safety theory and patient expectations, (3) the conflict between legal privilege for quality improvement and open disclosure, (4) the challenge of aligning open disclosure with liability compensation, and (5) the challenge of measurement related to disclosure.

Conclusions

Potential solutions include health worker education coupled with incentives to embed policy into practice, better communication about approaches beyond the punitive, legislation that allows both disclosure to patients and quality improvement protection for institutions, apology protection for providers, comprehensive disclosure programs that include patient compensation, delinking of patient compensation from regulatory scrutiny of disclosing physicians, legal and contractual requirements for disclosure, and better measurement of its occurrence and quality. A longer-term solution involves educating the public and health care workers about patient safety.
Beta-diversity on deep-sea wood falls reflects gradients in energy availability
Authors: McClain Craig , Barry James
Published: April 2014

Wood falls on the deep-sea floor represent a significant source of energy into the food-limited deep sea. Unique communities of primarily wood- and sulfide-obligate species form on these wood falls. However, little is known regarding patterns and drivers of variation in the composition of wood fall communities through space and time, and thus, how wood falls contribute to deep-sea biodiversity. Eighteen
Acacia
logs varying in size were placed and retrieved after five years at a 3200 m site in the Pacific Ocean. We found that the taxonomic composition and structure of deep-sea wood fall communities varied considerably and equated with considerable differences in energy usage and availability. Our findings suggest that natural variability in wood falls may contribute significantly to deep-sea diversity.
Systems level approach reveals the correlation of endoderm differentiation of mouse embryonic stem cells with specific microstructural cues of fibrin gels
Authors: Task Keith , D'Amore Antonio , Singh Satish , Candiello Joe , Jaramillo Maria , Wagner William R. , Kumta Prashant , Banerjee Ipsita
Published: April 2014

Stem cells receive numerous cues from their associated substrate that help to govern their behaviour. However, identification of influential substrate characteristics poses difficulties because of their complex nature. In this study, we developed an integrated experimental and systems level modelling approach to investigate and identify specific substrate features influencing differentiation of mouse embryonic stem cells (mESCs) on a model fibrous substrate, fibrin. We synthesized a range of fibrin gels by varying fibrinogen and thrombin concentrations, which led to a range of substrate stiffness and microstructure. mESCs were cultured on each of these gels, and characterization of the differentiated cells revealed a strong influence of substrate modulation on gene expression patterning. To identify specific substrate features influencing differentiation, the substrate microstructure was quantified by image analysis and correlated with stem cell gene expression patterns using a statistical model. Significant correlations were observed between differentiation and microstructure features, specifically fibre alignment. Furthermore, this relationship occurred in a lineage-specific manner towards endoderm. This systems level approach allows for identification of specific substrate features from a complex material which are influential to cellular behaviour. Such analysis may be effective in guiding the design of scaffolds with specific properties for tissue engineering applications.
Stochastic holin expression can account for lysis time variation in the bacteriophageλ
Authors: Singh Abhyudai , Dennehy John J.
Published: April 2014

The inherent stochastic nature of biochemical processes can drive differences in gene expression between otherwise identical cells. While cell-to-cell variability in gene expression has received much attention, randomness in timing of events has been less studied. We investigate event timing at the single-cell level in a simple system, the lytic pathway of the bacterial virus phageλ. In individual cells, lysis occurs on average at 65 min, with an s.d. of 3.5 min. Interestingly, mutations in the lysis protein, holin, alter both the lysis time (LT) mean and variance. In our analysis, LT is formulated as the first-passage time (FPT) for cellular holin levels to cross a critical threshold. Exact analytical formulae for the FPT moments are derived for stochastic gene expression models. These formulae reveal how holin transcription and translation efficiencies independently modulate the LT mean and variation. Analytical expressions for the LT moments are used to evaluate previously published single-cell LT data forλphages with mutations in the holin sequence or its promoter. Our results show that stochastic holin expression is sufficient to account for the intercellular LT differences in both wild-type phages, and phage variants where holin transcription and the threshold for lysis have been experimentally altered. Finally, our analysis reveals regulatory motifs that enhance the robustness of lysis timing to cellular noise.
The aerodynamic cost of flight in the short-tailed fruit bat (Carollia perspicillata): comparing theory with measurement
Authors: von Busse Rhea , Waldman Rye M. , Swartz Sharon M. , Voigt Christian C. , Breuer Kenneth S.
Published: April 2014

Aerodynamic theory has long been used to predict the power required for animal flight, but widely used models contain many simplifications. It has been difficult to ascertain how closely biological reality matches model predictions, largely because of the technical challenges of accurately measuring the power expended when an animal flies. We designed a study to measure flight speed-dependent aerodynamic power directly from the kinetic energy contained in the wake of bats flying in a wind tunnel. We compared these measurements with two theoretical predictions that have been used for several decades in diverse fields of vertebrate biology and to metabolic measurements from a previous study using the same individuals. A high-accuracy displaced laser sheet stereo particle image velocimetry experimental design measured the wake velocities in the Trefftz plane behind four bats flying over a range of speeds (3–7 m s−1). We computed the aerodynamic power contained in the wake using a novel interpolation method and compared these results with the power predicted by Pennycuick's and Rayner's models. The measured aerodynamic power falls between the two theoretical predictions, demonstrating that the models effectively predict the appropriate range of flight power, but the models do not accurately predict minimum power or maximum range speeds. Mechanical efficiency—the ratio of aerodynamic power output to metabolic power input—varied from 5.9% to 9.8% for the same individuals, changing with flight speed.
Comparative finite-element analysis: a single computational modelling method can estimate the mechanical properties of porcine and human vertebrae
Authors: Robson Brown K. , Tarsuslugil S. , Wijayathunga V. N. , Wilcox R. K.
Published: April 2014

Significant advances in the functional analysis of musculoskeletal systems require the development of modelling techniques with improved focus, accuracy and validity. This need is particularly visible in the fields, such as palaeontology, where unobservable parameters may lie at the heart of the most interesting research questions, and where models and simulations may provide some of the most innovative solutions. Here, we report on the development of a computational modelling method to generate estimates of the mechanical properties of vertebral bone across two living species, using elderly human and juvenile porcine specimens as cases with very different levels of bone volume fraction and mineralization. This study is presented in two parts; part I presents the computational model development and validation, and part II the virtual loading regime and results. This work paves the way for the future estimation of mechanical properties in fossil mammalian bone.
Common mechanics of mode switching in locomotion of limbless and legged animals
Authors: Kuroda Shigeru , Kunita Itsuki , Tanaka Yoshimi , Ishiguro Akio , Kobayashi Ryo , Nakagaki Toshiyuki
Published: April 2014

Crawling using muscular waves is observed in many species, including planaria, leeches, nemertea, aplysia, snails, chitons, earthworms and maggots. Contraction or extension waves propagate along the antero-posterior axis of the body as the crawler pushes the ground substratum backward. However, the observation that locomotory waves can be directed forward or backward has attracted much attention over the past hundred years. Legged organisms such as centipedes and millipedes exhibit parallel phenomena; leg tips form density waves that propagate backward or forward. Mechanical considerations reveal that leg-density waves play a similar role to locomotory waves in limbless species, and that locomotory waves are used by a mechanism common to both legged and limbless species to achieve crawling. Here, we report that both mode switching of the wave direction and friction control were achieved when backward motion was induced in the laboratory. We show that the many variations of switching in different animals can essentially be classified in two types according to mechanical considerations. We propose that during their evolution, limbless crawlers first moved in a manner similar to walking before legs were obtained. Therefore, legged crawlers might have learned the mechanical mode of movement involved in walking long before obtaining legs.
Linear patterning of mesenchymal condensations is modulated by geometric constraints
Authors: Klumpers Darinka D. , Mao Angelo S. , Smit Theo H. , Mooney David J.
Published: April 2014

The development of the vertebral column starts with the formation of a linear array of mesenchymal condensations, forming the blueprint for the eventual alternating pattern of bone and cartilage. Despite growing insight into the molecular mechanisms of morphogenesis, the impact of the physical aspects of the environment is not well understood. We hypothesized that geometric boundary conditions may play a pivotal role in the linear patterning of condensations, as neighbouring tissues provide physical constraints to the cell population. To study the process of condensation and the patterning thereof under tightly controlled geometric constraints, we developed a novelin vitromodel that combines micropatterning with the established micromass assay. The spacing and alignment of condensations changed with the width of the cell adhesive patterns, a phenomenon that could not be explained by cell availability alone. Moreover, the extent of chondrogenic commitment was increased on substrates with tighter geometric constraints. When thein vivopattern of condensations was investigated in the developing vertebral column of chicken embryos, the measurements closely fit into the quantitative relation between geometric constraints and inter-condensation distance foundin vitro. Together, these findings suggest a potential role of geometric constraints in skeletal patterning in a cellular process of self-organization.
Modelled three-dimensional suction accuracy predicts prey capture success in three species of centrarchid fishes
Authors: Kane Emily A. , Higham Timothy E.
Published: April 2014

Prey capture is critical for survival, and differences in correctly positioning and timing a strike (accuracy) are likely related to variation in capture success. However, an ability to quantify accuracy under natural conditions, particularly for fishes, is lacking. We developed a predictive model of suction hydrodynamics and applied it to natural behaviours using three-dimensional kinematics of three centrarchid fishes capturing evasive and non-evasive prey. A spheroid ingested volume of water (IVW) with dimensions predicted by peak gape and ram speed was verified with known hydrodynamics for two species. Differences in capture success occurred primarily with evasive prey (64–96% success).Micropterus salmoideshad the greatest ram and gape when capturing evasive prey, resulting in the largest and most elongate IVW. Accuracy predicted capture success, although other factors may also be important. The lower accuracy previously observed inM. salmoideswas not replicated, but this is likely due to more natural conditions in our study. Additionally, we discuss the role of modulation and integrated behaviours in shaping the IVW and determining accuracy. With our model, accuracy is a more accessible performance measure for suction-feeding fishes, which can be used to explore macroevolutionary patterns of prey capture evolution.
A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure
Authors: Greenbury Sam F. , Johnston Iain G. , Louis Ard A. , Ahnert Sebastian E.
Published: April 2014

The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here, we introduce a rich, intuitive and biologically realistic genotype–phenotype (GP) map that serves as a model of self-assembling biological structures, such as protein complexes, and remains computationally and analytically tractable. Our GP map arises naturally from the self-assembly of polyomino structures on a two-dimensional lattice and exhibits a number of properties:redundancy(genotypes vastly outnumber phenotypes),phenotype bias(genotypic redundancy varies greatly between phenotypes),genotype component disconnectivity(phenotypes consist of disconnected mutational networks) andshape space covering(most phenotypes can be reached in a small number of mutations). We also show that the mutational robustness of phenotypes scales very roughly logarithmically with phenotype redundancy and is positively correlated with phenotypic evolvability. Although our GP map describes the assembly of disconnected objects, it shares many properties with other popular GP maps for connected units, such as models for RNA secondary structure or the hydrophobic-polar (HP) lattice model for protein tertiary structure. The remarkable fact that these important properties similarly emerge from such different models suggests the possibility that universal features underlie a much wider class of biologically realistic GP maps.
Energy storage inherent in large tidal turbine farms
Authors: Vennell Ross , Adcock Thomas A. A.
Published: April 2014

While wind farms have no inherent storage to supply power in calm conditions, this paper demonstrates that large tidal turbine farms in channels have short-term energy storage. This storage lies in the inertia of the oscillating flow and can be used to exceed the previously published upper limit for power production by currents in a tidal channel, while simultaneously maintaining stronger currents. Inertial storage exploits the ability of large farms to manipulate the phase of the oscillating currents by varying the farm's drag coefficient. This work shows that by optimizing how a large farm's drag coefficient varies during the tidal cycle it is possible to have some flexibility about when power is produced. This flexibility can be used in many ways, e.g. producing more power, or to better meet short predictable peaks in demand. This flexibility also allows trading total power production off against meeting peak demand, or mitigating the flow speed reduction owing to power extraction. The effectiveness of inertial storage is governed by the frictional time scale relative to either the duration of a half tidal cycle or the duration of a peak in power demand, thus has greater benefits in larger channels.
Nonlinear magneto-viscoelasticity of transversally isotropic magneto-active polymers
Authors: Saxena Prashant , Hossain Mokarram , Steinmann Paul
Published: April 2014

Iron-filled magnetorheological polymers, when cured in the presence of a magnetic field, result in having a transversely isotropic structure with iron particles forming chains along the direction of applied magnetic induction. In this work, we model the magneto-viscoelastic deformation (and magnetization) process of such polymers. Components of the deformation gradient and the applied magnetic induction in the direction of anisotropy are considered to be additional arguments of the energy density function. The existence of internal damping mechanisms is considered by performing a multiplicative decomposition of the deformation gradient and an additive decomposition of the magnetic induction into equilibrium and non-equilibrium parts. Energy density functions and evolution laws of the internal variables are proposed that agree with the laws of thermodynamics. In the end, we present solutions of some standard deformation cases to illustrate the theory. In particular, it is shown that the orientation of resultant magnetic field and principal stress directions change with time owing to viscoelastic evolution.
Strong links between genomic and anatomical diversity in both mammalian olfactory chemosensory systems
Authors: Garrett Eva C. , Steiper Michael E.
Published: April 2014

Mammalian olfaction comprises two chemosensory systems: the odorant-detecting main olfactory system (MOS) and the pheromone-detecting vomeronasal system (VNS). Mammals are diverse in their anatomical and genomic emphases on olfactory chemosensation, including the loss or reduction of these systems in some orders. Despite qualitative evidence linking the genomic evolution of the olfactory systems to specific functions and phenotypes, little work has quantitatively tested whether the genomic aspects of the mammalian olfactory chemosensory systems are correlated to anatomical diversity. We show that the genomic and anatomical variation in these systems is tightly linked in both the VNS and the MOS, though the signature of selection is different in each system. Specifically, the MOS appears to vary based on absolute organ and gene family size while the VNS appears to vary according to the relative proportion of functional genes and relative anatomical size and complexity. Furthermore, there is little evidence that these two systems are evolving in a linked fashion. The relationships between genomic and anatomical diversity strongly support a role for natural selection in shaping both the anatomical and genomic evolution of the olfactory chemosensory systems in mammals.
Locomotor function shapes the passive mechanical properties and operating lengths of muscle
Authors: Azizi E.
Published: April 2014

Locomotor muscles often perform diverse roles, functioning as motors that produce mechanical energy, struts that produce force and brakes that dissipate mechanical energy. In many vertebrate muscles, these functions are not mutually exclusive and a single muscle often performs a range of mechanically diverse tasks. This functional diversity has obscured the relationship between a muscle's locomotor function and its mechanical properties. I use hopping in toads as a model system for comparing muscles that primarily produce mechanical energy with muscles that primarily dissipate mechanical energy. During hopping, hindlimb muscles undergo active shortening to produce mechanical energy and propel the animal into the air, whereas the forelimb muscles undergo active lengthening to dissipate mechanical energy during landing. Muscles performing distinct mechanical functions operate on different regions of the force–length curve. These findings suggest that a muscle's operating length may be shaped by potential trade-offs between force production and sarcomere stability. In addition, the passive force–length properties of hindlimb and forelimb muscles vary, suggesting that passive stiffness functions to restrict the muscle's operating lengthin vivo. These results inform our understanding of vertebrate muscle variation by providing a clear link between a muscle's locomotor function and its mechanical properties.