bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear time-varying potential bistable energy harvesting from human motion
Authors: Cao Junyi , Wang Wei , Zhou Shengxi , Inman Daniel J. , Lin Jing
Published: October 2015

A theoretical and experimental investigation into nonlinear bistable energy harvesting with time-varying potential energy is presented. The motivation for examining time-varying potentials comes from the desire to harvest energy from human motion. Time-varying potential energy function of bistable oscillator with respect to the swing angle are established to derive the governing electromechanical model for harvesting vibration energy from the swaying motion during human walking or running. Numerical simulations show good agreement with the experimental potential energy function under different swing angles. Various motion speed treadmill tests are performed to demonstrate the advantage of time-varying bistable harvesters over linear and monostable ones in harvesting energy from human motion.
Mechanism of a high-Tc superconducting flux pump: Using alternating magnetic field to trigger flux flow
Authors: Geng Jianzhao , Coombs T. A.
Published: October 2015

High-Tc Superconducting (HTS) magnets operating in persistent current mode suffer a current decay due to flux creep of superconductor and joint resistance. Flux pumps are able to inject direct current into superconducting circuit to compensate the current decay, without the thermal loss caused by current leads. In this work, we proposed a flux pumping mechanism for HTS coils, with an experimental verification and an analytical model. The basic principle we have used is that flux flow can be triggered when the superconductor carrying a direct current is subjected to a perpendicular AC magnetic field. Low frequency alternating current is induced in a loop of YBCO tape using an AC field. A portion of the tape which we refer to as the “bridge” shorts a superconducting coil. A high frequency AC field is applied perpendicular to the bridge tape when alternating current in the tape reaches one polarity. This triggers a net flux flow and results in a current increase in the coil. The proposed flux pump has clear physics and is easily controllable, which may make it promising in practical use.
Direct observation of electrical properties of grain boundaries in sputter-deposited CdTe using scan-probe microwave reflectivity based capacitance measurements
Authors: Tuteja Mohit , Koirala Prakash , MacLaren Scott , Collins Robert , Rockett Angus
Published: October 2015

Polycrystalline CdTe in 12% efficient solar cells has been studied using scanning microwave impedance microscopy (sMIM). The CdS/CdTe junctions were grown on transparent-conducting-oxide-coated soda lime glass using rf sputter deposition. sMIM based capacitance measurements were performed on the exposed surface of CdCl2 treated CdTe adjacent to thermal-evaporation-deposited Cu/Au back contacts. The sMIM instrument was operated at ∼3 GHz, and capacitance measurements were performed as a function of ac and dc voltage biases applied to the tip, with and without sample illumination. Although dc capacitance measurements are affected by sample topography, the differential capacitance measurement was shown to be topography independent. It was found that the grain boundaries exhibit a depleted carrier concentration as compared to the grain bulk. This depletion effect is enhanced under photo-generated carrier separation or under sufficiently large probe tip biases opposite to the majority carrier charge.
Low resistivity WxV1−xO2-based multilayer structure with high temperature coefficient of resistance for microbolometer applications
Authors: Émond Nicolas , Hendaoui Ali , Chaker Mohamed
Published: October 2015

Materials that exhibit semiconductor-to-metal phase transition (SMT) are commonly used as sensing layers for the fabrication of uncooled microbolometers. The development of highly responsive microbolometers would benefit from using a sensing material that possesses a large thermal coefficient of resistance (TCR) close to room temperature and a resistivity low enough to compromise between noise reduction and high TCR, while it should also satisfies the requirements of current CMOS technology. Moreover, a TCR that remains constant when the IR camera surrounding temperature varies would contribute to achieve reliable temperature measurements without additional corrections steps for TCR temperature dependence. In this paper, the characteristics of the SMT occurring in undoped and tungsten-doped vanadium dioxide thin films deposited on LaAlO3 (100) substrates are investigated. They are further exploited to fabricate a WxV1−xO2 (0 ≤ x ≤ 2.5) multilayer structure exhibiting a bottom-up gradient of tungsten content. This MLS displays a combination of properties that is promising for application to uncooled microbolometer, such as a large TCR of −10.4%/ °C and low resistivity values ranging from 0.012 to 0.10 Ω-cm over the temperature range 22 °C–42 °C.
The graph-theoretic minimum energy path problem for ionic conduction
Authors: Kishida Ippei
Published: October 2015

A new computational method was developed to analyze the ionic conduction mechanism in crystals through graph theory. The graph was organized into nodes, which represent the crystal structures modeled by ionic site occupation, and edges, which represent structure transitions via ionic jumps. We proposed a minimum energy path problem, which is similar to the shortest path problem. An effective algorithm to solve the problem was established. Since our method does not use randomized algorithm and time parameters, the computational cost to analyze conduction paths and a migration energy is very low. The power of the method was verified by applying it to α-AgI and the ionic conduction mechanism in α-AgI was revealed. The analysis using single point calculations found the minimum energy path for long-distance ionic conduction, which consists of 12 steps of ionic jumps in a unit cell. From the results, the detailed theoretical migration energy was calculated as 0.11 eV by geometry optimization and nudged elastic band method. Our method can refine candidates for possible jumps in crystals and it can be adapted to other computational methods, such as the nudged elastic band method. We expect that our method will be a powerful tool for analyzing ionic conduction mechanisms, even for large complex crystals.
Exploring packaging strategies of nano-embedded thermoelectric generators
Authors: Singha Aniket , Mahanti Subhendra D. , Muralidharan Bhaskaran
Published: October 2015

Embedding nanostructures within a bulk matrix is an important practical approach towards the electronic engineering of high performance thermoelectric systems. For power generation applications, it ideally combines the efficiency benefit offered by low dimensional systems along with the high power output advantage offered by bulk systems. In this work, we uncover a few crucial details about how to embed nanowires and nanoflakes in a bulk matrix so that an overall advantage over pure bulk may be achieved. First and foremost, we point out that a performance degradation with respect to bulk is inevitable as the nanostructure transitions to a multi moded one. It is then shown that a nano embedded system of suitable cross-section offers a power density advantage over a wide range of efficiencies at higher packing fractions, and this range gradually narrows down to the high efficiency regime, as the packing fraction is reduced. Finally, we introduce a metric - the advantage factor, to elucidate quantitatively, the enhancement in the power density offered via nano-embedding at a given efficiency. In the end, we explore the maximum effective width of nano-embedding which serves as a reference in designing generators in the efficiency range of interest.
Lactic Acid Determination in Human Plasma Using Ultrasound-Assisted Emulsification Microextraction Followed by Gas Chromatography
Authors: Shahdousti Parvin , Shojaee Rezvan , Aghamohammadi Mohammad , Harooni Behrang
Published: October 2015

A rapid, sensitive, and accurate analytical method was developed for determination of lactic acid (LA) in human plasma to monitor lactic acidosis. This method was based on an ultrasound-assisted emulsification microextraction (USAEME) method followed by gas chromatography with flame ionization detection (GC–FID). Derivatization of LA was carried out by a low density alcoholic solvent which performs both as an extraction solvent and derivatization agent, simultaneously. In this procedure, 100 μL of binary mixtures of pentan-1-ol with toluene (70 : 30, v/v %) was slowly injected into a 10 mL acidified aqueous sample of LA placed into an ultrasonic water bath. The resulting emulsion was centrifuged and after derivatization, 2 μL of organic phase was analysed by GC–FID. The effective variables were evaluated to optimize the efficiency of USAEME. Under the optimum conditions, good linearity in the range of 0.06–7.77 mmol L–1 was obtained with a correlation coefficient (R2) of 0.991 and a limit of detection (LOD) of 0.04 mmol L–1 for water samples. The inter-day and intra-day repeatability of the proposed method in human plasma were evaluated in terms of the relative standard deviation (RSD %) and were found to be <10 %. The results revealed that the USAEME–GC–FID method can be applied successfully for determination of LA in human plasma samples with satisfactory accuracy and precision.
The concentration-dependent behaviour of nanoparticles
Authors: Baalousha Mohammed , Sikder Mithun , Prasad Ashwini , Lead Jamie , Merrifield Ruth , Chandler G. Thomas
Published: October 2015

Environmental context
Studies of manufactured nanoparticles (NPs) in the environment have been performed almost exclusively at high NP concentrations. These data lead to misunderstandings related to NP fate and effects at relevant environmental concentrations, which are expected to be low. A better understanding of the concentration-dependent behaviour of NPs will improve our understanding of their fate and effects under environmentally realistic conditions.

Abstract
This rapid communication highlights the importance of nanoparticle concentration in determining their environmental fate and behaviour. Notably, two fate processes have been considered: dissolution and aggregation. The decrease in nanoparticle concentration results in increased dissolution and decreased aggregate sizes, inferring higher potential for environmental transport of nanoparticles.
Do Live-Well Temperatures Differ from Ambient Water During Black Bass Tournaments?
Authors: Sullivan Cody , Hasler Caleb , Suski Cory D.
Published: October 2015

Elevated water temperature has been shown to influence mortality during fishing tournaments. However, data on water conditions in live wells are lacking, and the benefits of managing live-well temperature are equivocal. The objective of the current study was to define water temperature in a live well during live-release black bass Micropterus spp. angling tournaments, and to compare live-well temperatures with ambient temperatures in the surrounding lake. For this, thermal loggers were added to live wells during three different tournaments (17 live wells across three tournaments), and anglers fished in the tournament using automatic live-well recirculating pumps (recirculation and aeration occurs and freshwater is pumped in). Live wells were found to be significantly cooler (~1°C) than the epilimnion for two of the three tournaments examined, and 1°C warmer than the epilimnion in the other tournament examined. Based on these findings, fish held in live wells during black bass tournaments do not appear to be experiencing significant thermal differentials relative to ambient water in the lake from which they were caught during live-well confinement. Rather than targeting live wells to mitigate thermal stressors, tournament anglers and organizers should consider other measures to reduce thermal stressors for fish.

Received April 13, 2015; accepted July 31, 2015
Retention and Stress Effects of Visible Implant Tags When Marking Western Silvery Minnow and Its Application to Other Cyprinids (Family Cyprinidae)
Authors: Neufeld Kenton , Blair Salvatore , Poesch Mark
Published: October 2015

Visible implant tags are commonly used in fisheries research to mark individuals or batches of fish as part of movement and mark–recapture studies. To be effective, these tags generally need to have high retention rates and little impact on the behavior or physiology of the marked individuals. We tested the retention rates of both visible implant elastomer (VIE) and visible implant alphanumeric (VIA) tags in 80–139-mm Western Silvery Minnow Hybognathus argyritis over a 104-d period. We also measured plasma cortisol and lactate to determine the impact of tagging on stress levels. We found that VIE tags had 100% retention and did not cause a significant increase in plasma cortisol levels, though plasma lactate levels were elevated in VIE treatment groups. Overall, VIE tags were found to be suitable for marking Western Silvery Minnow and similar species. Visible implant alphanumeric tags had 36% retention over 104 d and did not cause significant increases in plasma cortisol, though plasma lactate was elevated in the treatment group with both VIE and VIA tags. Given the high retention rates and low stress effects, VIE tags appear to be more beneficial for use with Western Silvery Minnow and similar-sized cyprinids.

Received April 16, 2015; accepted July 29, 2015
General approach to the problem of disruption forces in tokamaks
Authors: Pustovitov V.D.
Published: October 2015

An approach for calculating the force on the vessel wall during plasma disruptions in tokamaks is proposed. It is mainly based on the Maxwell equations and, therefore, is general. Another essential element is the integral force balance on the plasma that strongly constrains the possible solutions. The derived expressions are valid at any disruption scenario and finally give the net forces in terms of the magnetic perturbations behind the wall. The result can be used with magnetic measurements alone. It shows that the geometrical inhomogeneity of the wall and its resistivity are the key factors determining the direction and amplitude of the force.
Efficient APC/C substrate degradation in cells undergoing mitotic exit depends on K11 ubiquitin linkages
Authors: Min Mingwei , Mevissen Tycho E. T. , De Luca Maria , Komander David , Lindon Catherine
Published: October 2015

The ubiquitin proteasome system (UPS) directs programmed destruction of key cellular regulators via posttranslational modification of its targets with polyubiquitin chains. These commonly contain Lys-48 (K48)–directed ubiquitin linkages, but chains containing atypical Lys-11 (K11) linkages also target substrates to the proteasome—for example, to regulate cell cycle progression. The ubiquitin ligase called the anaphase-promoting complex/cyclosome (APC/C) controls mitotic exit. In higher eukaryotes, the APC/C works with the E2 enzyme UBE2S to assemble K11 linkages in cells released from mitotic arrest, and these are proposed to constitute an improved proteolytic signal during exit from mitosis. We tested this idea by correlating quantitative measures of in vivo K11-specific ubiquitination of individual substrates, including Aurora kinases, with their degradation kinetics tracked at the single-cell level. All anaphase substrates tested by this methodology are stabilized by depletion of K11 linkages via UBE2S knockdown, even if the same substrates are significantly modified with K48-linked polyubiquitin. Specific examination of substrates depending on the APC/C coactivator Cdh1 for their degradation revealed Cdh1-dependent enrichment of K11 chains on these substrates, whereas other ubiquitin linkages on the same substrates added during mitotic exit were Cdh1-independent. Therefore we show that K11 linkages provide the APC/C with a means to regulate the rate of substrate degradation in a coactivator-specified manner.
Regulation ofChlamydomonasflagella and ependymal cell motile cilia by ceramide-mediated translocation of GSK3
Authors: Kong Ji Na , Hardin Kara , Dinkins Michael , Wang Guanghu , He Qian , Mujadzic Tarik , Zhu Gu , Bielawski Jacek , Spassieva Stefka , Bieberich Erhard
Published: October 2015

Cilia are important organelles formed by cell membrane protrusions; however, little is known about their regulation by membrane lipids. We characterize a novel activation mechanism for glycogen synthase kinase-3 (GSK3) by the sphingolipids phytoceramide and ceramide that is critical for ciliogenesis in Chlamydomonas and murine ependymal cells, respectively. We show for the first time that Chlamydomonas expresses serine palmitoyl transferase (SPT), the first enzyme in (phyto)ceramide biosynthesis. Inhibition of SPT in Chlamydomonas by myriocin led to loss of flagella and reduced tubulin acetylation, which was prevented by supplementation with the precursor dihydrosphingosine. Immunocytochemistry showed that (phyto)ceramide was colocalized with phospho–Tyr-216-GSK3 (pYGSK3) at the base and tip of Chlamydomonas flagella and motile cilia in ependymal cells. The (phyto)ceramide distribution was consistent with that of a bifunctional ceramide analogue UV cross-linked and visualized by click-chemistry–mediated fluorescent labeling. Ceramide depletion, by myriocin or neutral sphingomyelinase deficiency ( fro/fro mouse), led to GSK3 dephosphorylation and defective flagella and cilia. Motile cilia were rescued and pYGSK3 localization restored by incubation of fro/fro ependymal cells with exogenous C24:1 ceramide, which directly bound to pYGSK3. Our findings suggest that (phyto)ceramide-mediated translocation of pYGSK into flagella and cilia is an evolutionarily conserved mechanism fundamental to the regulation of ciliogenesis.
Focal adhesions are foci for tyrosine-based signal transduction via GIV/Girdin and G proteins
Authors: Lopez-Sanchez Inmaculada , Kalogriopoulos Nicholas , Lo I-Chung , Kabir Firooz , Midde Krishna K. , Wang Honghui , Ghosh Pradipta
Published: October 2015

GIV/Girdin is a multimodular signal transducer and a bona fide metastasis-related protein. As a guanidine exchange factor (GEF), GIV modulates signals initiated by growth factors (chemical signals) by activating the G protein Gαi. Here we report that mechanical signals triggered by the extracellular matrix (ECM) also converge on GIV-GEF via β1 integrins and that focal adhesions (FAs) serve as the major hubs for mechanochemical signaling via GIV. GIV interacts with focal adhesion kinase (FAK) and ligand-activated β1 integrins. Phosphorylation of GIV by FAK enhances PI3K-Akt signaling, the integrity of FAs, increases cell–ECM adhesion, and triggers ECM-induced cell motility. Activation of Gαi by GIV-GEF further potentiates FAK-GIV-PI3K-Akt signaling at the FAs. Spatially restricted signaling via tyrosine phosphorylated GIV at the FAs is enhanced during cancer metastasis. Thus GIV-GEF serves as a unifying platform for integration and amplification of adhesion (mechanical) and growth factor (chemical) signals during cancer progression.
HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS
Authors: Wang Shuang , Zhang Yuchen , Dai Wenrui , Lauter Kristin , Kim Miran , Tang Yuzhe , Xiong Hongkai , Jiang Xiaoqian
Published: October 2015

Motivation: Genome-wide association studies (GWAS) have been widely used in discovering the association between genotypes and phenotypes. Human genome data contain valuable but highly sensitive information. Unprotected disclosure of such information might put individual’s privacy at risk. It is important to protect human genome data. Exact logistic regression is a bias-reduction method based on a penalized likelihood to discover rare variants that are associated with disease susceptibility. We propose the HEALER framework to facilitate secure rare variants analysis with a small sample size.

Results: We target at the algorithm design aiming at reducing the computational and storage costs to learn a homomorphic exact logistic regression model (i.e. evaluate P-values of coefficients), where the circuit depth is proportional to the logarithmic scale of data size. We evaluate the algorithm performance using rare Kawasaki Disease datasets.

Availability and implementation: Download HEALER at http://research.ucsd-dbmi.org/HEALER/

Contact:  shw070@ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Yield per recruit from stocking two different sizes of eel (Anguilla anguilla) in the brackish Roskilde Fjord
Authors: Pedersen Michael I. , Rasmussen Gorm H.
Published: October 2015

Stocking of young eel is widely practised, as a measure, to meet the management target of the EU eel recovery plan. The target of the recovery plan is to increase the escapement to 40% silver eel biomass, relative to pristine conditions. The scientific information to predict the outcome in silver eel biomass from stocking is limited and may depend on whether translocation of wild glass eel or yellow eel is used, or if the stocked eels used are yellow eel from aquaculture. We evaluated the yield from stocking two different sizes, 3 and 9 g eels from aquaculture. A professional fishery recaptured 12.7% of the 3 g and 9.4% of the 9 g eels, originally stocked. Growth rate and mortality rate were different for the two stocked sizes, favouring the small eels. Brutto yield per recruit (YPR) was 13 and 9.2 g and netto YPR was 9.8 and 0.31 g for 3 and 9 g eel, respectively. We conclude that there seems to be no advantage in using larger 9 g eels compared with small 3 g eels for stocking.
Brand Public
Authors: Arvidsson Adam , Caliandro Alessandro
Published: October 2015

The concept of brand community has been used to understand how consumers create value around brands online. Recently consumer researchers have begun to debate the relevance of this concept for understanding brand-related communication on social media. Based on a data set of 8949 tweets about Louis Vuitton gathered on Italian Twitter in 2013, this article addresses these discussions by developing the alternative concept of brand publics that differ from brand communities in three important ways. First, brand publics are social formations that are not based on interaction but on a continuous focus of interest and mediation. Second, participation in brand publics is not structured by discussion or deliberation but by individual or collective affect. Third, in brand publics consumers do not develop a collective identity around the focal brand; rather the brand is valuable as a medium that can offer publicity to a multitude of diverse situations of identity. The conclusion suggests that brand publics might be part of a social media–based consumer culture where publicity rather than identity has become a core value.
Molecular Genetic Alterations in Renal Cell Carcinomas With Tubulocystic Pattern: Tubulocystic Renal Cell Carcinoma, Tubulocystic Renal Cell Carcinoma With Heterogenous Component and Familial Leiomyomatosis-associated Renal Cell Carcinoma. Clinicopathologic and Molecular Genetic Analysis of 15 Cases
Authors: Ulamec Monika , Skenderi Faruk , Zhou Ming , Krušlin Božo , Martínek Petr , Grossmann Petr , Peckova Kvetoslava , Alvarado-Cabrero Isabel , Kalusova Kristyna , Kokoskova Bohuslava , Rotterova Pavla , Hora Milan , Daum Ondrej , Dubova Magdalena , Bauleth Kevin , Slouka David , Sperga Maris , Davidson Whitney , Rychly Boris , Perez Montiel Delia , Michal Michal , Hes Ondrej
Published: October 2015

The characteristic morphologic spectrum of tubulocystic renal cell carcinoma (TC-RCC) may include areas resembling papillary RCC (PRCC). Our study includes 15 RCCs with tubulocystic pattern: 6 TC-RCCs, 1 RCC-high grade with tubulocystic architecture, 5 TC-RCCs with foci of PRCC, 2 with high-grade RCC (HGRCC) not otherwise specified, and 1 with a clear cell papillary RCC/renal angiomyoadenomatous tumor-like component. We analyzed aberrations of chromosomes 7, 17, and Y; mutations of VHL and FH genes; and loss of heterozygosity at chromosome 3p. Genetic analysis was performed separately in areas of classic TC-RCC and in those with other histologic patterns. The TC-RCC component demonstrated disomy of chromosome 7 in 9/15 cases, polysomy of chromosome 17 in 7/15 cases, and loss of Y in 1 case. In the PRCC component, 2/3 analyzable cases showed disomy of chromosome 7 and polysomy of chromosome 17 with normal Y. One case with focal HGRCC exhibited only disomy 7, whereas the case with clear cell papillary RCC/renal angiomyoadenomatous tumor-like pattern showed polysomies of 7 and 17, mutation of VHL, and loss of heterozygosity 3p. FH gene mutation was identified in a single case with an aggressive clinical course and predominant TC-RCC pattern. The following conclusions were drawn: (1) TC-RCC demonstrates variable status of chromosomes 7, 17, and Y even in cases with typical/uniform morphology. (2) The biological nature of PRCC/HGRCC-like areas within TC-RCC remains unclear. Our data suggest that heterogenous TC-RCCs may be associated with an adverse clinical outcome. (3) Hereditary leiomyomatosis-associated RCC can be morphologically indistinguishable from “high-grade” TC-RCC; therefore, in TC-RCC with high-grade features FH gene status should be tested.
MUC1 (VPM654 and EPR1023) Expression in Mucosa of Fallopian Tubes With Ectopic Pregnancy is Altered
Authors: Brito Ledamir R. , Guedes Neto Ernesto de P. , Furich Daniele G. , Savaris Ricardo F.
Published: October 2015

MUC1 is a surface glycoprotein that has an external and an internal domain. A recent report has shown that 1 segment of the external domain is reduced in ectopic pregnancy, suggesting that MUC1 may provide a protective mechanism against ectopic pregnancy. The objective of this study was to analyze the protein expression of 4 antibodies against MUC1 in fallopian tubes with or without ectopic pregnancy. Tissue sections of ectopic pregnancies (n=10) and normal tubes (n=16) derived from surgery were analyzed for the intensity of the staining with 3,3′-diaminobenzidine (DAB). Paraffin sections were submitted to immunohistochemical analysis using 4 different antibodies against different epitopes for MUC1: 214D4, EPR1023, HMFG1, and VPM654. Intensity of the immunostaining (DAB) was measured with ImageJ software. Statistical analysis was performed using Student unpaired t test, Mann-Whitney U test, and ANCOVA. The mean intensity of MUC1 [mean±SD, or median (interquartile)] in the mucosa of fallopian tubes with ectopic pregnancy was higher for EPR1023 (23.73±13.63 vs. 8.5±5.1, P=0.006), and reduced for VPM654 [13.7 (13-16.2) vs. 22.5 (19.5-29.7), P=0.005] compared with normal tubes. No difference was found for 214D4 and HMFG1. The immunoexpression of different epitopes (external and cytoplasmic) of MUC1 expression are altered in tubes with ectopic pregnancy compared with normal tubes, suggesting an association to explain its etiology.
A Novel Technique for the Generation of Multitissue Blocks Using a Carrier
Authors: Frosina Denise , Jungbluth Achim A.
Published: October 2015

Paraffin blocks containing several tissues have become a major tool in surgical pathology. As multitissue blocks, they usually consist of few rather large samples and as tissue microarrays (TMAs) they may contain up to several hundred small-sized tissue cores. We developed a novel approach to generate multitissue blocks using a carrier in which tissue samples are inserted. Normal tissues with homogenous consistency such as liver, spleen, and lung seem to be ideal carriers. Carrier tissue size can be freely chosen to accommodate number and size of sample tissues as desired. As the carrier tissue serves as a scaffold for the inserted tissue, even small-sized tissues will stay exactly as placed in the carrier. This makes carrier-based multitissue blocks (CBMTBs) an ideal approach when exact orientation of layers is important, for example in normal GIT tissues. The carrier tissue approach can also be used for few large-sized sample tissues or to generate classical TMAs with sample cores of <1 mm. As the newly generated CBMTB or carrier-based tissue microarray is completely reembedded after assembling, sectioning of CBMTBs is comparable with sectioning a normal solid tissue block producing virtually no sample loss and requiring minimal trimming and consequently vastly increasing yield.
Gene flow despite complex Robertsonian fusions among rock-wallaby (
Petrogale
) species
Authors: Potter Sally , Moritz Craig , Eldridge Mark D. B.
Published: October 2015

Complex Robertsonian rearrangements, with shared arms in different fusions, are expected to prevent gene flow between hybrids through missegregation during meiosis. Here, we estimate gene flow between recently diverged and chromosomally diverse rock-wallabies (
Petrogale
) to test for this form of chromosomal speciation. Contrary to expectations, we observe relatively high admixture among species with complex fusions. Our results reinforce the need to consider alternative roles of chromosome change, together with genic divergence, in driving speciation.
Morpho-elasticity of inflammatory fibrosis: the case of capsular contracture
Authors: Ben Amar Martine , Wu Min , Trejo Miguel , Atlan Michael
Published: October 2015

Inflammatory fibrosis is a wound-healing reaction of the immune system in mammals against aggression. After a signalling cascade, fibroblasts and potentially myofibroblasts make a stiff collagenous tissue inside the body that modifies the original healthy tissue. We focus here on the implant-induced fibrosis that aims to encapsulate the implant with a typical fibrous tissue called the capsule. Focusing on breast capsules, we aim to understand the mechanical properties of these tissues, to test the validity of fibre models that have been established in other contexts such as arteries. For this purpose, we perform force–extension experiments and show that mechanical constitutive laws of these tissues are especially difficult to derive, because models are sensitive to fibre orientation and dispersion, independently of the variation between individuals. In addition, fibre breakdown, and possibly remodelling, occur during the extension experiments. However, the high stiffness of the capsular tissue, compared with the healthy tissue, added to the fact that an inflammatory process has no reason to cease, is at the origin of large compressive stresses
in vivo
, which explains the pain and unaesthetic deformity. We evaluate the stresses responsible for the pain and the buckling instability, which have no reason to stop if the inflammation persists.
A complex carotenoid palette tunes avian colour vision
Authors: Toomey Matthew B. , Collins Aaron M. , Frederiksen Rikard , Cornwall M. Carter , Timlin Jerilyn A. , Corbo Joseph C.
Published: October 2015

The brilliantly coloured cone oil droplets of the avian retina function as long-pass cut-off filters that tune the spectral sensitivity of the photoreceptors and are hypothesized to enhance colour discrimination and improve colour constancy. Although it has long been known that these droplets are pigmented with carotenoids, their precise composition has remained uncertain owing to the technical challenges of measuring these very small, dense and highly refractile optical organelles. In this study, we integrated results from high-performance liquid chromatography, hyperspectral microscopy and microspectrophotometry to obtain a comprehensive understanding of oil droplet carotenoid pigmentation in the chicken (Gallus gallus). We find that each of the four carotenoid-containing droplet types consists of a complex mixture of carotenoids, with a single predominant carotenoid determining the wavelength of the spectral filtering cut-off. Consistent with previous reports, we find that the predominant carotenoid type in the oil droplets of long-wavelength-sensitive, medium-wavelength-sensitive and short-wavelength-sensitive type 2 cones are astaxanthin, zeaxanthin and galloxanthin, respectively. In addition, the oil droplet of the principal member of the double cone contains a mixture of galloxanthin and two hydroxycarotenoids (lutein and zeaxanthin). Short-wavelength-absorbing apocarotenoids are present in all of the droplet types, providing filtering of light in a region of the spectrum where filtering by hydroxy- and ketocarotenoids may be incomplete. Thus, birds rely on a complex palette of carotenoid pigments within their cone oil droplets to achieve finely tuned spectral filtering.
Spectrally tuned structural and pigmentary coloration of birdwing butterfly wing scales
Authors: Wilts Bodo D. , Matsushita Atsuko , Arikawa Kentaro , Stavenga Doekele G.
Published: October 2015

The colourful wing patterns of butterflies play an important role for enhancing fitness; for instance, by providing camouflage, for interspecific mate recognition, or for aposematic display. Closely related butterfly species can have dramatically different wing patterns. The phenomenon is assumed to be caused by ecological processes with changing conditions, e.g. in the environment, and also by sexual selection. Here, we investigate the birdwing butterflies,
Ornithoptera
, the largest butterflies of the world, together forming a small genus in the butterfly family Papilionidae. The wings of these butterflies are marked by strongly coloured patches. The colours are caused by specially structured wing scales, which act as a chirped multilayer reflector, but the scales also contain papiliochrome pigments, which act as a spectral filter. The combined structural and pigmentary effects tune the coloration of the wing scales. The tuned colours are presumably important for mate recognition and signalling. By applying electron microscopy, (micro-)spectrophotometry and scatterometry we found that the various mechanisms of scale coloration of the different birdwing species strongly correlate with the taxonomical distribution of
Ornithoptera
species.
Multimodal signalling in the North American barn swallow: a phenotype network approach
Authors: Wilkins Matthew R. , Shizuka Daizaburo , Joseph Maxwell B. , Hubbard Joanna K. , Safran Rebecca J.
Published: October 2015

Complex signals, involving multiple components within and across modalities, are common in animal communication. However, decomposing complex signals into traits and their interactions remains a fundamental challenge for studies of phenotype evolution. We apply a novel phenotype network approach for studying complex signal evolution in the North American barn swallow (Hirundo rustica erythrogaster). We integrate model testing with correlation-based phenotype networks to infer the contributions of female mate choice and male–male competition to the evolution of barn swallow communication. Overall, the best predictors of mate choice were distinct from those for competition, while moderate functional overlap suggests males and females use some of the same traits to assess potential mates and rivals. We interpret model results in the context of a network of traits, and suggest this approach allows researchers a more nuanced view of trait clustering patterns that informs new hypotheses about the evolution of communication systems.
The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection
Authors: Lind Martin I. , Yarlett Kylie , Reger Julia , Carter Mauricio J. , Beckerman Andrew P.
Published: October 2015

Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustaceanDaphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments.
Convergent evolution of vascular optimization in kelp (Laminariales)
Authors: Drobnitch Sarah Tepler , Jensen Kaare H. , Prentice Paige , Pittermann Jarmila
Published: October 2015

Terrestrial plants and mammals, although separated by a great evolutionary distance, have each arrived at a highly conserved body plan in which universal allometric scaling relationships govern the anatomy of vascular networks and key functional metabolic traits. The universality of allometric scaling suggests that these phyla have each evolved an ‘optimal’ transport strategy that has been overwhelmingly adopted by extant species. To truly evaluate the dominance and universality of vascular optimization, however, it is critical to examine other, lesser-known, vascularized phyla. The brown algae (Phaeophyceae) are one such group—as distantly related to plants as mammals, they have convergently evolved a plant-like body plan and a specialized phloem-like transport network. To evaluate possible scaling and optimization in the kelp vascular system, we developed a model of optimized transport anatomy and tested it with measurements of the giant kelp,
Macrocystis pyrifera
, which is among the largest and most successful of macroalgae. We also evaluated three classical allometric relationships pertaining to plant vascular tissues with a diverse sampling of kelp species.
Macrocystis pyrifera
displays strong scaling relationships between all tested vascular parameters and agrees with our model; other species within the Laminariales display weak or inconsistent vascular allometries. The lack of universal scaling in the kelps and the presence of optimized transport anatomy in
M. pyrifera
raises important questions about the evolution of optimization and the possible competitive advantage conferred by optimized vascular systems to multicellular phyla.
Artificial light at night desynchronizes strictly seasonal reproduction in a wild mammal
Authors: Robert Kylie A. , Lesku John A. , Partecke Jesko , Chambers Brian
Published: October 2015

Change in day length is an important cue for reproductive activation in seasonally breeding animals to ensure that the timing of greatest maternal investment (e.g. lactation in mammals) coincides with favourable environmental conditions (e.g. peak productivity). However, artificial light at night has the potential to interfere with the perception of such natural cues. Following a 5-year study on two populations of wild marsupial mammals exposed to different night-time levels of anthropogenic light, we show that light pollution in urban environments masks seasonal changes in ambient light cues, suppressing melatonin levels and delaying births in the tammar wallaby. These results highlight a previously unappreciated relationship linking artificial light at night with induced changes in mammalian reproductive physiology, and the potential for larger-scale impacts at the population level.
Food provisioning alters infection dynamics in populations of a wild rodent
Authors: Forbes Kristian M. , Henttonen Heikki , Hirvelä-Koski Varpu , Kipar Anja , Mappes Tapio , Stuart Peter , Huitu Otso
Published: October 2015

While pathogens are often assumed to limit the growth of wildlife populations, experimental evidence for their effects is rare. A lack of food resources has been suggested to enhance the negative effects of pathogen infection on host populations, but this theory has received little investigation. We conducted a replicated two-factor enclosure experiment, with introduction of the bacteriumBordetella bronchisepticaand food supplementation, to evaluate the individual and interactive effects of pathogen infection and food availability on vole populations during a boreal winter. We show that prior to bacteria introduction, vole populations were limited by food availability.Bordetella bronchisepticaintroduction then reduced population growth and abundance, but contrary to predictions, primarily in food supplemented populations. Infection prevalence and pathological changes in vole lungs were most common in food supplemented populations, and are likely to have resulted from increased congregation and bacteria transmission around feeding stations.Bordetella bronchiseptica-infected lungs often showed protozoan co-infection (consistent withHepatozoon erhardovae), together with more severe inflammatory changes. Using a multidisciplinary approach, this study demonstrates a complex picture of interactions and underlying mechanisms, leading to population-level effects. Our results highlight the potential for food provisioning to markedly influence disease processes in wildlife mammal populations.
The interdependent nature of multi-loci associations can be revealed by 4C-Seq
Authors: Jiang Tingting , Raviram Ramya , Rocha Pedro P. , Snetkova Valentina , Proudhon Charlotte , Badri Sana , Bonneau Richard , Skok Jane A. , Kluger Yuval
Published: October 2015

Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that these associations act in isolation of other interacting partners within the genome. Indeed, the influence of multi-loci interactions in gene control remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise interactions involving theTcrbandIgkantigen receptor enhancers, in addition to novel tri-loci associations. We further show that enhancer deletions not only interfere with tri-loci interactions in which they participate, but they also disrupt pairwise interactions between other partner enhancers and this disruption is linked to a reduction in their transcriptional output. These findings underscore the functional importance of hubs and provide new insight into chromatin organization as a whole. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings.
Critical success factors of Lean Six Sigma deployment: a current review
Authors: Abu Bakar Fairul Anwar , Subari Khairanum , Mohd Daril Mohd Amran
Published: October 2015

Purpose

– The purpose of this paper is to review and gather the latest critical success factors (CSF) of Lean Six Sigma (LSS) deployment and implementation into a comprehensive list of factors.

Design/methodology/approach

– The approach taken by authors in this study was to analyze the latest literature review starting 2010 onwards and focus on CSFs of LSS (not dedicated as Lean or Six Sigma) by excluding other improvement methodologies or initiatives, e.g. Lean, Six Sigma, TQM, TRIZ etc.

Findings

– Five significant CSFs were identified (initially 97 CSFs listed from 13 papers) out of nine groups/headers listed in clustering analysis using Affinity Diagram tool and new headers mapping.

Practical implications

– Most of the organisations were aware of the success story on LSS, but did not scrutinize or consider its CSFs. By knowing the outcome of this paper, it can help open eyes regarding readiness before implementing LSS.

Originality/value

– At the end of this paper, the authors tried to cluster the CSFs similarities that could intentionally provide the guidelines and references to industries/companies for successful deployment and implementation of LSS in future endeavours.
Combining Lean and Six Sigma in the context of Systems Engineering design
Authors: Sreeram TR , Thondiyath Asokan
Published: October 2015

Purpose

– The purpose of this paper is to present a combined framework for system design using Six Sigma and Lean concepts. Systems Engineering has evolved independently and there are numerous tools and techniques available to address issues that may arise in the design of systems. In the context of systems design, the application of Six Sigma and Lean concepts results in a flexible and adaptable framework. A combined framework is presented here that allows better visualization of the system-level components and their interactions at parametric level, and it also illuminates gaps that make way for continuous improvement. The Deming’s Plan-Do-Check-Act is the basis of this framework. Three case studies are presented to evaluate the application of this framework in the context of Systems Engineering design. The paper concludes with a summary of advantages of using a combined framework, its limitations and scope for future work.

Design/methodology/approach

– Six Sigma, Lean and Systems Engineering approaches combined into a framework for collaborative product development.

Findings

– The present framework is not rigid and does not attempt to force fit any tools or concepts. The framework is generic and allows flexibility through a plug and play type of implementation. This is important, as engineering change needs vary constantly to meet consumer demands. Therefore, it is important to engrain flexibility in the development of a foundational framework for design-encapsulating improvements and innovation. From a sustainability perspective, it is important to develop techniques that drive rationality in the decisions, especially during tradeoffs and conflicts.

Research limitations/implications

– Scalability of the approach for large systems where complex interactions exist. Besides, the application of negotiation techniques for more than three persons poses a challenge from a mathematical context. Future research should address these in the context of systems design using Six Sigma and Lean techniques.

Practical implications

– This paper provides a flexible framework for combining the three techniques based on Six Sigma, Lean and Systems Engineering.

Social implications

– This paper will influence the construction of agent-based systems, particularly the ones using the Habermas’s theory of social action as the basis for product development.

Originality/value

– This paper has not been published in any other journal or conference.