bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct evidence of strain transfer for InAs island growth on compliant Si substrates
Authors: Marçal L. A. B. , Richard M.-I. , Magalhães-Paniago R. , Cavallo F. , Lagally M. G. , Schmidt O. G. , Schülli T. Ü. , Deneke Ch. , Malachias Angelo
Published: April 2015

Semiconductor heteroepitaxy on top of thin compliant layers has been explored as a path to make inorganic electronics mechanically flexible as well as to integrate materials that cannot be grown directly on rigid substrates. Here, we show direct evidences of strain transfer for InAs islands on freestanding Si thin films (7 nm). Synchrotron X-ray diffraction measurements using a beam size of 300 × 700 nm2 can directly probe the strain status of the compliant substrate underneath deposited islands. Using a recently developed diffraction mapping technique, three-dimensional reciprocal space maps were reconstructed around the Si (004) peak for specific illuminated positions of the sample. The strain retrieved was analyzed using continuous elasticity theory via Finite-element simulations. The comparison of experiment and simulations yields the amount of strain from the InAs islands, which is transferred to the compliant Si thin film.
Acoustic phase-reconstruction near the Dirac point of a triangular phononic crystal
Authors: Yu Si-Yuan , Wang Qing , Zheng Li-Yang , He Cheng , Liu Xiao-Ping , Lu Ming-Hui , Chen Yan-Feng
Published: April 2015

In this work, acoustic phase-reconstruction is studied and experimentally demonstrated in a triangular lattice two-dimensional phononic crystal (PnC) composed of steel rods in air. Owning to the fact that two bands of this triangular lattice PnC touch at the K/K′ point and thus give rise to a conical Dirac cone, acoustic waves transmitting through this PnC can exhibit a pseudo-diffusion transportation feature, producing a reconstructed planar wavefront in the far field away from the interface of the PnC. Such phase reconstruction effect can be utilized in many applications, and here we demonstrate experimentally two important applications: an acoustic collimator and an acoustic cloak operating at a Dirac frequency of 41.3 kHz.
Suppression of endurance degradation by utilizing oxygen plasma treatment in HfO2 resistive switching memory
Authors: Chand Umesh , Huang Chun-Yang , Jieng Jheng-Hong , Jang Wen-Yueh , Lin Chen-Hsi , Tseng Tseung-Yuen
Published: April 2015

Based on the phenomenon of endurance degradation problem caused by no sufficient oxygen ions for resistive switching, we use the oxygen plasma treatment in HfO2 layer to increase the extra available oxygen ions in resistive random access memory devices. To avoid the Ti top electrode directly absorbing the additional oxygen ions from HfO2 layer with oxygen plasma treatment, a thin HfO2 film is inserted to separate them. Therefore, the endurance degradation can be suppressed in the present structure. High speed (30 ns) and large endurance cycles (up to 1010 cycles) are achieved in this device structure for next generation nonvolatile memory application.
Solvent-Dependent Non-Linear Optical Properties of 5,5′-Disubstituted-2,2′-bipyridine Complexes of Ruthenium(II): A Quantum Chemical Perspective
Authors: Janjua Muhammad Ramzan Saeed Ashraf , Jamil Saba , Mahmood Asif , Zafar Atifa , Haroon Muhammad , Bhatti Haq Nawaz
Published: April 2015

In this research article, we reported solvent effects on non-linear optical (NLO) properties of 5,5′-disubstituted-2,2′-bipyridine complexes of ruthenium. The polarizability (α) and hyperpolarizability (β) were calculated in the gas phase. Benzene (ϵ (dielectric constant) = 2.3), THF (ϵ = 7.52), dichloromethane (ϵ = 8.93), acetone (ϵ = 21.01), methanol (ϵ = 33.00), and water (ϵ = 80.10) were used by density functional theory. These solvents cover a wide range of polarities. The results of theoretical investigation showed that the non-linear optical properties were significantly increased with the increase in solvent polarity. The results of this study also showed that similarly to structural modifications, polarity of the medium may play a significant role in modulating the NLO properties.
Reproduction, symbiosis, and the eukaryotic cell
Authors: Godfrey-Smith Peter
Published: April 2015

This paper develops a conceptual framework for addressing questions about reproduction, individuality, and the units of selection in symbiotic associations, with special attention to the origin of the eukaryotic cell. Three kinds of reproduction are distinguished, and a possible evolutionary sequence giving rise to a mitochondrion-containing eukaryotic cell from an endosymbiotic partnership is analyzed as a series of transitions between each of the three forms of reproduction. The sequence of changes seen in this “egalitarian” evolutionary transition is compared with those that apply in “fraternal” transitions, such as the evolution of multicellularity in animals.
Functional Age as an Indicator of Reservoir Senescence
Authors: Miranda L. E. , Krogman Rebecca M.
Published: April 2015

It has been conjectured that reservoirs differ in the rate at which they manifest senescence, but no attempt has been made to find an indicator of senescence that performs better than chronological age. We assembled an indicator of functional age by creating a multimetric scale consisting of 10 metrics descriptive of reservoir environments that were expected to change directionally with reservoir senescence. In a sample of 1,022 U.S. reservoirs, chronological age was not correlated with functional age. Functional age was directly related to percentage of cultivated land in the catchment and inversely related to reservoir depth. Moreover, aspects of reservoir fishing quality and fish population characteristics were related to functional age. A multimetric scale to indicate reservoir functional age presents the possibility for management intervention from multiple angles. If a reservoir is functionally aging at an accelerated rate, action may be taken to remedy the conditions contributing most to functional age. Intervention to reduce scores of selected metrics in the scale can potentially reduce the rate of senescence and increase the life expectancy of the reservoir. This leads to the intriguing implication that steps can be taken to reduce functional age and actually make the reservoir grow younger.

Se ha discutido que los reservorios se diferencian entre sí por la tasa a la cual manifiestan senescencia, sin embargo no ha habido esfuerzos para encontrar un indicador de senescencia que funcione mejor que la edad cronológica. Se construyó un indicador de edad funcional mediante una escala multimétrica que consiste en diez métricas descriptivas del ambiente de los reservorios que se previó que cambiaran de dirección a medida que aumenta la senescencia de los reservorios. En una muestra de 1,022 reservorios en los EE.UU., no se encontró correlación entre la edad cronológica y la edad funcional. La edad funcional estuvo directamente relacionada con el porcentaje de tierra cultivada y la capacidad de captación del reservorio, e inversamente relacionada con la profundidad de este. Más aún, algunos aspectos de la calidad para la pesca en el reservorio y características de las poblaciones de peces explotadas, también se relacionaron con la edad funcional. Una escala multimétrica como indicativo de la edad funcional de un reservorio presenta la posibilidad para intervenir en el manejo en varios frentes. Si un reservorio está envejeciendo en términos funcionales a una tasa acelerada, se pueden tomar acciones para remediar aquellas condiciones que más contribuyen con el envejecimiento funcional. La intervención dirigida a reducir las calificaciones sólo de métricas selectas puede potencialmente reducir la tasa de senescencia e incrementar la expectativa de vida del reservorio. Esto da pie a la curiosa implicación que es posible reducir la edad funcional de los reservorios y, de hecho, hacerlos más jóvenes.
Myths that Continue to Impede Progress in Ecosystem-Based Fisheries Management
Authors: Patrick Wesley S. , Link Jason S.
Published: April 2015

Ecosystem-based fisheries management has been perceived as something desirable but pragmatically unachievable due to several impediments identified earlier during its implementation phase. Over the years, many of these impediments have been resolved but not well communicated to stakeholders, managers, scientists, and policymakers. As a result, several past impediments to implementing ecosystem-based fisheries management have taken on a mythical status. Here we identify six common myths, address why they in fact no longer impede ecosystem-based fisheries management, and propose solutions for moving forward. We assert that these myths need not continue to exist and that improved approaches for fisheries are indeed feasible.

El manejo de pesquerías basado en el ecosistema se ha percibido como algo deseable, pero de manera pragmática imposible de lograr debido a ciertos impedimentos que fueron identificados durante la fase de implementación del enfoque. Al pasar de los años, muchos de estos impedimentos se han resuelto pero esto no se le ha comunicado a los interesados en los recursos, manejadores, científicos y funcionarios. Como resultado, muchos obstáculos del pasado que impedían implementar el manejo de pesquerías bajo un enfoque de ecosistema, han adquirido un estatus mítico. Aquí se identifican seis mitos comunes, se ahonda en las razones por cuales actualmente ya no son un obstáculo para este tipo de manejo y se proponen soluciones para avanzar al futuro. Se asevera que no es necesario que estos mitos sigan existiendo y que, de hecho, si son factibles nuevos enfoques para manejo de pesquerías.
What “1989”? A Rhetorical Rhumb on the Topic of Date
Authors: Salazar Philippe-Joseph
Published: April 2015

This article follows a “rhumb” along four nonrhetorical observations on the concepts of date, moment, time, and semelfactive, and nine rhetorical theorems concerning “date” in relation to eidos, eugeneia, credibility, kairos, anagnôrisis, Innerzeitigkeit, evidence, différend, and the sublime, so as to explode our “idiocy” about the topic of date and to offer a rhetorical and phenomenological critique of “date.”
From Fish Soup to Fish Tank: Rhetoric, Politics, and Dialectic in the Polish Revolution of 1989
Authors: Ornatowski Cezar M.
Published: April 2015

The article offers a rhetorical account of the “leap into politics” by the Polish Communist authorities that led to the political transition of 1989. In contrast to accounts of the transition focused on “dialogue” between the authorities and the opposition, this article examines the move toward dialogue from a dramatistic and dialectical perspective—that is, in terms of the shifting principles of motivation, changing rhetorical identities of the key actors, and associated transformations of terms that characterized the transition from a monocentric ideal of the state to a “political” one.
Playing It Again in Post-Communism: The Revolutionary Rhetoric of Viktor Orbán in Hungary
Authors: Szilágyi Anna , Bozóki András
Published: April 2015

This longitudinal case study about the political rhetoric of Viktor Orbán—prime minister of Hungary between 1998 and 2002, and since 2010, respectively—demonstrates that the first, remarkable personal experiences in public communication may have a major impact (“imprinting”) on the future behavior of political actors. Orbán gave a memorably radical talk on June 16, 1989, urging Hungary’s democratic transition from Communism. The study uses critical discourse analysis and links it to media scholarship on live media events to show that Orbán became hostage of his own rhetoric and speech situation for the two decades that followed his 1989 entry.
The Rhetorical Contours of Pre- and Post-1989 China: A Genealogical, Ethical Study
Authors: Chou Senkou
Published: April 2015

This article situates the extraordinary events of 1989 within the symbolic and politicoeconomic context of Reform-era China. It sees 1989 as a threshold moment for the political culture and a turning point for the collective ethos. The article argues that the vitalistic 1980s made for an ethical existence for the demos, culminating in the “poetics” of 1989, while the post-1989 era witnessed a homogenization of the Chinese ethical imaginary. The latter is the very exigency that drives this study. Drawing on the ethical understandings of Deleuze and Burke, the article calls for the return and fusion of the ethical and the political, and points to a reason for pietas toward the world and the demos. The article is informed by a genealogical understanding of history and a ritualistic-dramatistic understanding of political life. Its central concern is the retransformation of the soul of the Chinese people in the here and now.
A Nonmuscle Myosin Light Chain Kinase–Dependent Gene Signature in Peripheral Blood Mononuclear Cells is Linked to Human Asthma Severity and Exacerbation Status
Authors: Zhou Tong , Wang Ting , Garcia Joe G. N.
Published: April 2015

Asthma is increasingly recognized as a heterogeneous disease influenced by complex genetic and environmental contributions. Myosin light chain kinase (MLCK; gene symbol, MYLK), especially the nonmuscle isoform nmMLCK, is a cytoskeleton protein known to be related to human asthma susceptibility and severity, findings confirmed in preclinical models of asthmatic inflammation. In this study, we define the central capacity for a nmMLCK‐influenced gene signature in human peripheral blood mononuclear cells to predict human asthma severity and exacerbation status. We refined this signature from a list of nmMLCK‐influenced genes identified in lung tissues of nmMLCK knockout mice exposed to inflammatory stimuli (ventilator‐induced lung injury), with subsequent identification of nmMLCK‐influenced genes in a list of human asthma severity–related genes expressed in blood. The enriched nmMLCK‐influenced gene signature successfully predicted human asthma severity and exacerbation status in both discovery and validation human asthma cohorts. These findings validate the central role played by nmMLCK in asthma susceptibility, severity, and exacerbation and further provide novel gene signatures as effective asthma biomarkers for severity, exacerbation, and prognosis.
Symbol length in the Brauer group of a field
Authors: Matzri Eliyahu
Published: April 2015

We bound the symbol length of elements in the Brauer group of a field

K
K

containing a

C
m

C_m

field (for example any field containing an algebraically closed field or a finite field), and solve the local exponent-index problem for a

C
m

C_m

field

F
F

. In particular, for a

C
m

C_m

field

F
F

, we show that every

F
F

central simple algebra of exponent

p
t

p^t

is similar to the tensor product of at most

len
⁡
(

p
t

,
F
)
≤
t
(

p

m
−
1

−
1
)

\operatorname {len}(p^t,F)\leq t(p^{m-1}-1)

symbol algebras of degree

p
t

p^t

. We then use this bound on the symbol length to show that the index of such algebras is bounded by

(

p
t

)

(

p

m
−
1

−
1
)

(p^t)^{(p^{m-1}-1)}

, which in turn gives a bound for any algebra of exponent

n
n

via the primary decomposition. Finally for a field

K
K

containing a

C
m

C_m

field

F
F

, we show that every

F
F

central simple algebra of exponent

p
t

p^t

and degree

p
s

p^s

is similar to the tensor product of at most

len
⁡
(

p
t

,

p
s

,
K
)
≤
len
⁡
(

p
t

,
L
)

\operatorname {len}(p^t,p^s,K)\leq \operatorname {len}(p^t,L)

symbol algebras of degree

p
t

p^t

, where

L
L

is a

C

m
+

ed
L

⁡
(
A
)
+

p

s
−
t

−
1

C_{m+\operatorname {ed}_L(A)+p^{s-t}-1}

field.
Matroids of gain graphs in applied discrete geometry
Authors: Tanigawa Shin-ichi
Published: April 2015

A

Γ
\Gamma

-gain graph is a graph whose oriented edges are labeled invertibly from a group

Γ
\Gamma

. Zaslavsky proposed two matroids associated with

Γ
\Gamma

-gain graphs, called frame matroids and lift matroids, and investigated linear representations of them. Each matroid has a canonical representation over a field

F

\mathbb {F}

if

Γ
\Gamma

is isomorphic to a subgroup of

F

×

\mathbb {F}^{\times }

in the case of frame matroids or

Γ
\Gamma

is isomorphic to an additive subgroup of

F

\mathbb {F}

in the case of lift matroids. The canonical representation of the frame matroid of a complete graph is also known as a Dowling geometry, as it was first introduced by Dowling for finite groups

Γ
\Gamma

.

In this paper, we extend these matroids in two ways. The first one is extending the rank function of each matroid, based on submodular functions over

Γ
\Gamma

. The resulting rank function generalizes that of the union of frame matroids or lift matroids. Another one is extending the canonical linear representation of the union of

d
d

copies of a frame matroid or a lift matroid, based on linear representations of

Γ
\Gamma

on a

d
d

-dimensional vector space. We show that linear matroids of the latter extension are indeed special cases of the first extension, as in the relation between Dowling geometries and frame matroids. We also discuss an attempt to unify the extension of frame matroids and that of lift matroids.

This work is motivated by recent results in the combinatorial rigidity of symmetric graphs. As special cases, we give several new results on this topic, including combinatorial characterizations of the symmetry-forced rigidity of generic body-bar frameworks with point group symmetries or crystallographic symmetries and the symmetric parallel redrawability of generic bar-joint frameworks with point group symmetries or crystallographic symmetries.
Combining otolith microstructure and trace elemental analyses to infer the arrival of juvenile Pacific bluefin tuna in the California current ecosystem
Authors: Baumann Hannes , Wells R. J. D. , Rooker Jay R. , Zhang Saijin , Baumann Zofia , Madigan Daniel J. , Dewar Heidi , Snodgrass Owyn E. , Fisher Nicholas S.
Published: April 2015

Juvenile Pacific bluefin tuna (PBT, Thunnus orientalis) are known to migrate from western Pacific spawning grounds to their eastern Pacific nursery and feeding grounds in the California Current Large Marine Ecosystem (CCLME), but the timing, durations, and fraction of the population that makes these migrations need to be better understood for improved management. To complement recent work focused on stable isotope and radiotracer approaches (“tracer toolbox”; Madigan et al., 2014) we explored the suitability of combining longitudinal analyses of otolith microstructure and trace elemental composition in age ∼1–2 PBT (n = 24, 66–76 cm curved fork length) for inferring the arrival of individuals in the CCLME. Element:Ca ratios in transverse otolith sections (9–12 rows, triplicate ablations from primordium to edge, ø50 μm) were quantified for eight elements: Li, Mg, Mn, Co, Cu, Zn, Sr, and Ba, which was followed by microstructure analysis to provide age estimates corresponding to each ablation spot. Age estimates from otoliths ranged from 328 to 498 d post-hatch. The combined elemental signatures of four elements (Ba, Mg, Co, Cu) showed a significant increase at the otolith edge in approximately half of the individuals (30–60 d before catch). Given the different oceanographic properties of oligotrophic open Pacific vs. high nutrient, upwelling CCLME waters, this signal is consistent with the entry of the fish into the CCLME, which was estimated to occur primarily in July after a transoceanic migration of ∼1.5–2.0 months. Our approach comprises a useful addition to the available tracer toolbox and can provide additional and complementary understanding of trans-Pacific migration patterns in PBT.
Critically endangered western gray whales migrate to the eastern North Pacific
Authors: Mate Bruce R. , Ilyashenko Valentin Yu. , Bradford Amanda L. , Vertyankin Vladimir V. , Tsidulko Grigory A. , Rozhnov Vyacheslav V. , Irvine Ladd M.
Published: April 2015

Western North Pacific gray whales (WGWs), once considered extinct, are critically endangered with unknown migratory routes and reproductive areas. We attached satellite-monitored tags to seven WGWs on their primary feeding ground off Sakhalin Island, Russia, three of which subsequently migrated to regions occupied by non-endangered eastern gray whales (EGWs). A female with the longest-lasting tag visited all three major EGW reproductive areas off Baja California, Mexico, before returning to Sakhalin Island the following spring. Her 22 511 km round-trip is the longest documented mammal migration and strongly suggests that some presumed WGWs are actually EGWs foraging in areas historically attributed to WGWs. The observed migration routes provide evidence of navigational skills across open water that break the near-shore north–south migratory paradigm of EGWs. Despite evidence of genetic differentiation, these tagging data indicate that the population identity of whales off Sakhalin Island needs further evaluation.
Poor health is associated with use of anthropogenic resources in an urban carnivore
Authors: Murray Maureen , Edwards Mark A. , Abercrombie Bill , St. Clair Colleen Cassady
Published: April 2015

Rates of encounters between humans and wildlife are increasing in cities around the world, especially when wildlife overlap with people in time, space and resources. Coyotes (Canis latrans) can make use of anthropogenic resources and reported rates of conflict have increased in cities across North America. This increase may be linked to individual differences in the use of human food and developed areas. We compared the relationships between coyote age, sex or health and the use of anthropogenic resources, which we defined as using developed areas over large home ranges, being active during the day, and consuming anthropogenic food. To do so, we applied GPS collars to 19 coyotes and sampled hair for stable isotope analysis. Eleven coyotes appeared to be healthy and eight were visibly infested with sarcoptic mange (Sarcoptes scabiei), a mite that causes hair loss. Diseased coyotes used more developed areas, had larger monthly home ranges, were more active during the day, and assimilated less protein than coyotes that appeared to be healthy. We speculate that anthropogenic food provides a low-quality but easily accessible food source for diseased coyotes, which in turn may increase reliance on it and other anthropogenic resources to promote encounters with people.
Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources
Authors: De Smet Birgit , Mayo Mark , Peeters Charlotte , Zlosnik James E. A. , Spilker Theodore , Hird Trevor J. , LiPuma John J. , Kidd Timothy J. , Kaestli Mirjam , Ginther Jennifer L. , Wagner David M. , Keim Paul , Bell Scott C. , Jacobs Jan A. , Currie Bart J. , Vandamme Peter
Published: April 2015

Nine Burkholderia cepacia complex (Bcc) bacteria were isolated during environmental surveys for the ecological niche of Burkholderia pseudomallei, the aetiological agent of melioidosis, in the Northern Territory of Australia. They represented two multi-locus sequence analysis-based clusters, referred to as Bcc B and Bcc L. Three additional environmental and clinical Bcc B isolates were identified upon deposition of the sequences in the PubMLST database. Analysis of the concatenated nucleotide sequence divergence levels within both groups (1.4 and 1.9 %, respectively) and towards established Bcc species (4.0 and 3.9 %, respectively) demonstrated that the two taxa represented novel Bcc species. All 12 isolates were further characterized using 16S rRNA and recA gene sequence analysis, RAPD analysis, DNA base content determination, fatty acid methyl ester analysis and biochemical profiling. Analysis of recA gene sequences revealed a remarkable diversity within each of these taxa, but, together, the results supported the affiliation of the two taxa to the Bcc. Bcc B strains can be differentiated from most other Bcc members by the assimilation of maltose. Bcc L strains can be differentiated from other Bcc members by the absence of assimilation of N-acetylglucosamine. The names Burkholderia stagnalis sp. nov. with type strain LMG 28156T ( = CCUG 65686T) and Burkholderia territorii sp. nov. with type strain LMG 28158T ( = CCUG 65687T) are proposed for Bcc B and Bcc L bacteria, respectively.
Draconibacterium sediminis sp. nov., isolated from river sediment
Authors: Du Juan , Lai Qiliang , Liu Yang , Dong Chunming , Xie Yanrong , Shao Zongze
Published: April 2015

A Gram-reaction-negative, facultatively anaerobic and rod-shaped bacterium, designated strain JN14CK-3T, was isolated from surface sediment of the Jiulong River of China and was characterized phenotypically and phylogenetically. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain JN14CK-3T belonged to the genus Draconibacterium, with the highest sequence similarity (98.3 %) to Draconibacterium orientale FH5T. By contrast, strain JN14CK-3T shared low 16S rRNA gene sequence similarities ( < 91.0 %) with other type strains. The sole respiratory quinone was MK-7.The polar lipids were phosphatidylethanolamine and several unidentified phospholipids and lipids. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, C17:0 2-OH, iso-C16:0 3-OH and iso-C17:0 3-OH. The G+C content of the genomic DNA was 40.9 mol%. The digital DNA–DNA hybridization value and average nucleotide identity (ANI) between strain JN14CK-3T and D. orientale FH5T were 34.2 ± 2.5 % and 87.1 %, respectively. The combined genotypic and phenotypic data showed that strain JN14CK-3T represents a novel species of the genus Draconibacterium, for which the name Draconibacterium
sediminis sp. nov. is proposed, with the type strain JN14CK-3T ( = MCCC 1A00734T = KCTC 42152T).
Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor
Authors: Koeck Daniela E. , Ludwig Wolfgang , Wanner Gerhard , Zverlov Vladimir V. , Liebl Wolfgang , Schwarz Wolfgang H.
Published: April 2015

Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the familyLachnospiraceae. As a representative of the whole group of isolates, strain T3/55Twas further characterized. The closest relative of T3/55Tamong the taxa with validly published names isMobilitalea sibirica, sharing 93.9 % 16S rRNA gene sequence similarity. Strain T3/55Twas catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1 %) were 16 : 0 dimethyl acetal, 16 : 0 fatty acid methyl ester and 16 : 0 aldehyde. The DNA G+C content was 36.6 mol%. A novel genus and species,Herbinix hemicellulosilyticagen. nov., sp. nov., is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T( = DSM 29228T = CECT 8801T), represents the type strain ofHerbinix hemicellulosilyticagen. nov., sp. nov.
Simulation of population development in the predator-prey system under changing conditions of interaction
Authors: Tetearing Alexandr N.
Published: April 2015

The numerical models of populations behaviour, simulated under changing condition of populations interaction (the hungry or full-fed populations, the existence of persons in the personal areas or in the common territory), demonstrate the increase, reduction or damping of oscillations amplitude, that corresponds qualitatively to known experimental data, obtained for real population of bacteria.
An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types
Authors: Park Sunho , Kim Seung-Jun , Yu Donghyeon , Pena-Llopis Samuel , Gao Jianjiong , Park Jin Suk , Tang Hao , Chen Beibei , Kim Jiwoong , Norris Jessie , Wang Xinlei , Chen Min , Kim Minsoo , Yong Jeongsik , WarDak Zabi , Choe Kevin S , Story Michael , Starr Timothy K. , Cheong Jaeho , Hwang Tae Hyun
Published: April 2015

Identification of altered pathways that are clinically relevant across human cancers is a key challenge in cancer genomics. We developed a network-based algorithm to integrate somatic mutation data with gene networks and pathways, in order to identify pathways altered by somatic mutations across cancers. We applied our approach to The Cancer Genome Atlas (TCGA) dataset of somatic mutations in 4,790 cancer patients with 19 different types of malignancies. Our analysis identified cancer-type-specific altered pathways enriched with known cancer-relevant genes and drug targets. Consensus clustering using gene expression datasets that included 4,870 patients from TCGA and multiple independent cohorts confirmed that the altered pathways could be used to stratify patients into subgroups with significantly different clinical outcomes. Of particular significance, certain patient subpopulations with poor prognosis were identified because they had specific altered pathways for which there are available targeted therapies. These findings could be used to tailor and intensify therapy in these patients, for whom current therapy is suboptimal.
Genome of octoploid plant maca (Lepidium meyenii) illuminates genomic basis for high altitude adaptation in the central Andes
Authors: Zhang Jing , Tian Yang , Yan Liang , Zhang Guanghui , Wang Xiao , Zeng Yan , Zhang Jiajin , Ma Xiao , Tan Yuntao , Long Ni , Wang Yangzi , Ma Yujin , Xue Yu , Hao Shumei , Yang Shengchao , Wang Wen , Zhang Liangsheng , Dong Yang , Chen Wei , Sheng Jun
Published: April 2015

Maca (Lepidium meyeniiWalp, 2n = 8× = 64) of Brassicaceae family is an Andean economic plant cultivated on the 4000-4500 meters central sierra in Peru. Considering the rapid uplift of central Andes occurred 5 to 10 million years ago (Mya), an evolutionary question arises on how plants like maca acquire high altitude adaptation within short geological period. Here, we report the high-quality genome assembly of maca, in which two close-spaced maca-specific whole genome duplications (WGDs, ∼ 6.7 Mya) were identified. Comparative genomics between maca and close-related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway and secondary metabolite biosynthesis via WGDs. Retention and subsequent evolution of many duplicated genes may account for the morphological and physiological changes (i.e. small leaf shape and loss of vernalization) in maca for high altitude environment. Additionally, some duplicated maca genes under positive selection were identified with functions in morphological adaptation (i.e.MYB59) and development (i.e.GDPD5andHDA9). Collectively, the octoploid maca genome sheds light on the important roles of WGDs in plant high altitude adaptation in the Andes.
Genomic prediction of celiac disease targeting HLA-positive individuals
Authors: Abraham Gad , Rohmer Alexia , Tye-Din Jason A , Inouye Michael
Published: April 2015

Background: Genomic prediction aims to leverage genome-wide genetic data towards better disease diagnostics and risk scores. We have previously published a genomic risk score (GRS) for celiac disease (CD), a common and highly heritable autoimmune disease, which differentiates between CD cases and population-based controls at a clinically-relevant predictive level, improving upon other gene-based approaches. HLA risk haplotypes, particularly HLA-DQ2.5, are necessary but not sufficient for CD, with at least one HLA risk haplotype present in up to half of most Caucasian populations. Here, we assess a genomic prediction strategy that specifically targets this common genetic susceptibility subtype, utilizing a supervised learning procedure for CD that leverages known HLA-DQ2.5 risk. Methods: Using L1/L2-regularized support-vector machines trained on large European case-control datasets, we constructed novel CD GRSs specific to individuals with HLA-DQ2.5 risk haplotypes (GRS-DQ2.5) and compared them with the predictive power of the existing CD GRS (GRS14) as well as two haplotype-based approaches, externally validating the results in a North American case-control study. Results: Consistent with previous observations, both the existing GRS14 and the GRS-DQ2.5 had better predictive performance than the HLA haplotype approaches. GRS-DQ2.5 models, based on directly genotyped or imputed markers, achieved similar levels of predictive performance (AUC = 0.718-0.73), which were substantially higher than those obtained from the DQ2.5 zygosity alone (AUC = 0.558), the HLA risk haplotype method (AUC = 0.634), or the generic GRS14 (AUC = 0.679). In a screening model of at-risk individuals, the GRS-DQ2.5 lowered the number of unnecessary follow-up tests for CD across most sensitivity levels. Relative to a baseline implicating all DQ2.5-positive individuals for follow-up, the GRS-DQ2.5 resulted in a net saving of 2.2 unnecessary follow-up tests for each justified test while still capturing 90% of DQ2.5-positive CD cases. Conclusions: Genomic risk scores for CD that target genetically at-risk sub-groups improve predictive performance beyond traditional approaches and may represent a useful strategy for prioritizing individuals at increase risk of disease, thus potentially reducing unnecessary follow-up diagnostic tests.
A surface model using the eccentric shell and multi-point constraint for warpage prediction of plastics
Authors: Zhang Shi , Zhang Yun , Shi Songxin , Huang Zhigao , Zhou Huamin
Published: April 2015

Purpose

– The purpose of this paper is to propose a new surface model combining the eccentric shell with multi-point constraint (MPC) for warpage prediction of injection molded plastics.

Design/methodology/approach

– In this paper, three benchmark tests and a practical example are implemented to evaluate the performance of the new surface model and existing models.

Findings

– The results demonstrate that the proposed model could give satisfactory solutions and has advantages over the existing models.

Practical implications

– More precisely predicted warpage field for injection molded plastics can be achieved with the purposed model, such as that in the practical case.

Originality/value

– The surface models are efficient and still popular for practical injection molding analysis. However, the existing models for warpage prediction cannot properly represent the true strain energy and obey material continuity assumption, and also they have not been assessed rigorously by benchmark tests. To overcome above-mentioned difficulty, a new surface model is proposed, which employs the eccentric shell without shear factor and MPC equation that ensuring material continuity. The results from experiment illustrate that the new model is superior to existing models.
A fictitious crack XFEM with two new solution algorithms for cohesive crack growth modeling in concrete structures
Authors: Zhang Xiaodong , Bui Tinh Quoc
Published: April 2015

Purpose

– The purpose of this paper is to achieve numerical simulation of cohesive crack growth in concrete structures.

Design/methodology/approach

– The extended finite element method (XFEM) using four-node quadrilateral element associated with the fictitious cohesive crack model is used. A mixed-mode traction-separation law is assumed for the cohesive crack in the fracture process zone (FPZ). Enrichments are considered for both partly and fully cracked elements, and it thus makes the evolution of crack to any location inside the element possible. In all. two new solution procedures based on Newton-Raphson method, which differ from the approach suggested by Zi and Belytschko (2003), are presented to solve the nonlinear system of equations. The present formulation results in a symmetric tangent matrix, conveniently in finite element implementation and programming.

Findings

– The inconvenience in solving the inversion of an unsymmetrical Jacobian matrix encountered in the existing approach is avoided. Numerical results evidently confirm the accuracy of the proposed approach. It is concluded that the developed XFEM approach is especially suitable in simulating cohesive crack growth in concrete structures.

Research limitations/implications

– Multiple cracks and crack growth in reinforced concretes should be considered in further studies.

Practical implications

– The research paper presents a very useful and accurate numerical method for engineering application problems that has ability to numerically simulate the cohesive crack growth of concrete structures.

Originality/value

– The research paper provides a new numerical approach using two new solution procedures in solving nonlinear system of equations for cohesive crack growth in concrete structures that is very convenient in programming and implementation.
Discrete element modeling of vibrating tillage tools
Authors: Keppler Istvan , Hudoba Zoltan , Oldal Istvan , Csatar Attila , Fenyvesi Laszlo
Published: April 2015

Purpose

– The analysis of the effect of tool vibrations on the measured and simulated draught forces of cultivator tools. This paper aims to discuss this issue.

Design/methodology/approach

– Soil bin measurements and discrete element method (DEM)-based simulations.

Findings

– The soil-tool interaction induced free vibrations of cultivator tools have significant impact on the measured draught force, and the simulations made by using vibrating tools give similar results.

Research limitations/implications

– Accurate calibration of discrete element model parameters can be done based on the reproduction of the whole Mohr-Coulomb failure line. Draught force ratio – velocity ratio values seem to be independent of tool geometry and soil conditions in case of velocity ratio higher than 2.

Practical implications

– DEM-based numerical simulations can be used for modeling the effect of tool vibration on the draught force values. During discrete element simulations of soil-tool interaction, the effect of tool vibration may not be neglected.

Originality/value

– The paper demonstrates that during the discrete element modelling of the soil-tool interaction, the tool vibration phenomenon should not be neglected.
Guest editorial: games for learning and dialogue on humanitarian work
Authors: Harteveld Casper , Suarez Pablo
Published: April 2015

Purpose

– The purpose of this guest editorial is to provide the introduction and context of the Special Issue on Games for Learning and Dialogue on Humanitarian Work. The Special Issue aims to promote the development, deployment, and analysis of games for the humanitarian sector: it investigates how games can meaningfully engage people and organizations in experiencing, understanding and improving complex systems.

Design/methodology/approach

– The editorial describes the need and motivation for building a body of knowledge on the use of games in the humanitarian sector. It further gives an overview of the three papers included in this Special Issue and how they contribute to building such a body of knowledge.

Findings

– Games enable participants to experience the complexity of humanitarian systems, linking decisions with consequences. Even though game-like approaches have been used for decades in disaster management, there is little written about it. The papers included in this Special Issue provide insights and frameworks to learn from, ranging from online tools that reveal inefficiencies in supply chains, to simulated emergency response exercises, to applied improvisation. In addition, the current papers highlight the need for more empirical study of the impact of games.

Research implications/limitations

– The Special Issue describes three unique cases, which by no means cover the entire practice of games in the humanitarian sector. However, they do provide insight into the diversity of game-like approaches and signal the current state of practice and research of games for learning and dialogue on humanitarian work.

Practical implications

– This editorial gives an overview of how games could be used in practice and why they are relevant for humanitarian work. It further highlights how the contributions in the Special Issue may help in improving humanitarian work.

Originality/value

– Although review papers and Special Issues have appeared on particular topics such as climate change, to our knowledge no significant academic attention has been given to humanitarian work with regards to games.
The value of fourth-party logistics services in the humanitarian supply chain
Authors: Abidi Hella , de Leeuw Sander , Klumpp Matthias
Published: April 2015

Purpose

– The purpose of this paper is to identify the value of fourth-party logistics (4PL) services in a humanitarian supply chain. Furthermore, it shows a framework for a fourth-party humanitarian logistics concept.

Design/methodology/approach

– The research paper presents a framework of fourth-party humanitarian logistics based on the four core components described by Christopher (2005) which was evaluated with a nonlinear approach called analytical hierarchy process (AHP). The AHP method explores qualitative and quantitative decision-making criteria in case of solving multi-attribute and complex problems. In total, seven experts from academia and practice have contributed to this research, resulting in a better understanding of the decisive needs of humanitarian supply chain actors for implementing and integrating a 4PL concept.

Findings

– The research shows an increased value for humanitarian supply chain actors of establishing a 4PL concept. The results present a positive influence of 4PL in complex disasters environments and provide key drivers for increasing and simplifying collaboration between the humanitarian supply chain actors.

Research limitations/implications

– Future research has to consider different disaster types and needs to further emphasize the added value for beneficiaries of implementing a 4PL concept in a humanitarian supply chain environment. Further research should preferably also consider case studies in order to analyse challenges, drawbacks and benefits of this concept (qualitative and quantitative factors) in a real-life humanitarian supply chain setting.

Practical implications

– The research offers managerial insights into the use of a 4PL concept in the humanitarian supply chain environment to improve efficiency due to an improved collaboration between the humanitarian supply chain actors.

Originality/value

– The research paper investigates an under-researched topic in the humanitarian supply chain environment. For humanitarian supply chain actors outsourcing their activities to a 4PL service provider could secure collaboration, increase service levels as well as efficiency and therefore create additional value.
Effects of inviting customers to share responsibility in the context of impersonal service
Authors: Ku Hsuan-Hsuan , Hsu Ko-Hsin
Published: April 2015

Purpose

– The purpose of this paper is to investigate how customers respond to a service provider’s invitation to share responsibility for the experience of an “impersonal” service that is not customized but available to all customers on an equal footing; specifically to assess the extent to which the tendency to psychological reactance moderates their responses.

Design/methodology/approach

– Four studies investigate the effects of such invitations on perceptions of shared responsibility, the mechanism underlying that process, the effect of trait reactance on susceptibility to an invitation, and the extent to which a predisposition to reactance moderates the effect of an invitation on willingness to share blame for service failure.

Findings

– Service customers are more likely to feel a sense of shared responsibility and less likely to experience reactance in response to a “reciprocal” invitation to participate in “co-creation” of the experience than to a more “unilateral” invitation. That heightened perception of shared responsibility was restricted to low-reactance individuals, who were also more willing to share the blame for service failure in response to a unilateral invitation and even more so when it was reciprocal. The willingness of high-reactance individuals was unaffected by the type of invitation.

Originality/value

– Whereas the relevant literature has focussed mainly on person-to-person service transactions, the studies reported here show how customers may be converted into active partners in an “impersonal” service encounter.
Effects of short RNA structural analogues against hepatitis C virus genotypes 2, 3 and 4 in replicon cells
Authors: Elshaffei Ismail M , Gupta Nidhi , Wu Catherine H , Wu David C , Hammad Lamiaa N , Abo‐Elmatty Dina M , Mesbah Noha M , Wu George Y
Published: April 2015

Objective

To determine whether computer‐predicted short RNA structural analogues could inhibit hepatitis C virus (HCV) genotype 2a, 3a and 4a replication in cultured cells.

Methods

Short RNA sequences, X12, X12a and X12b, designed to be identical in secondary structure to the X region in the 3′‐untranslated region (3′‐UTR) of the HCV 1b genome, as well as shorter stem‐loop components of X region, were inserted into a plasmid and transfected into separate Huh7.5 human hepatoma cells stably transfected with subgenomic replicons for genotypes 2a, 3a and 4a. All replicons included a firefly luciferase reporter gene. After 48 h of plasmid transfection, the inhibition of HCV replication was determined by HCV RNA isolation and quantification by real‐time polymerase chain reaction and luciferase assays.

Results

All the secondary structural analogues to genotype 1b X region cross‐inhibited genotype 2a, 3a and 4a replicons. The maximum inhibition by genotype 1b X region structural analogues was obtained against genotype 2a cells in which X12, X12a and X12b inhibited replication by 30%, 63% and 72%, respectively (P < 0.05 for all), compared to an unrelated hepatitis B viral analogue.

Conclusions

Despite substantial sequence dissimilarity, HCV RNA genotype 1b X region analogues cross‐inhibited the replication of HCV genotypes 2a, 3a and 4a. Particular conformations and not the sequence of the stem‐loops of the X region are involved in HCV replication.
Metaproteomics of complex microbial communities in biogas plants
Authors: Heyer Robert , Kohrs Fabian , Reichl Udo , Benndorf Dirk
Published: April 2015

Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full‐scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed.