bluuebunny/crossref_metadata_2025 huggingface dataset:
Perspective: Sloppiness and emergent theories in physics, biology, and beyond
Authors: Transtrum Mark K. , Machta Benjamin B. , Brown Kevin S. , Daniels Bryan C. , Myers Christopher R. , Sethna James P.
Published: July 2015

Large scale models of physical phenomena demand the development of new statistical and computational tools in order to be effective. Many such models are “sloppy,” i.e., exhibit behavior controlled by a relatively small number of parameter combinations. We review an information theoretic framework for analyzing sloppy models. This formalism is based on the Fisher information matrix, which is interpreted as a Riemannian metric on a parameterized space of models. Distance in this space is a measure of how distinguishable two models are based on their predictions. Sloppy model manifolds are bounded with a hierarchy of widths and extrinsic curvatures. The manifold boundary approximation can extract the simple, hidden theory from complicated sloppy models. We attribute the success of simple effective models in physics as likewise emerging from complicated processes exhibiting a low effective dimensionality. We discuss the ramifications and consequences of sloppy models for biochemistry and science more generally. We suggest that the reason our complex world is understandable is due to the same fundamental reason: simple theories of macroscopic behavior are hidden inside complicated microscopic processes.
Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5
Authors: Harabuchi Yu , Ono Yuriko , Maeda Satoshi , Taketsugu Tetsuya
Published: July 2015

A global reaction route map is generated for Au5 by the anharmonic downward distortion following method in which 5 minima and 14 transition states (TSs) are located. Through vibrational analyses in the 3N − 7 (N = 5) dimensional space orthogonal to the intrinsic reaction coordinate (IRC), along all the IRCs, four IRCs are found to have valley-ridge transition (VRT) points on the way where a potential curvature changes its sign from positive to negative in a direction orthogonal to the IRC. The detailed mechanisms of bifurcations related to the VRTs are discussed by surveying a landscape of the global reaction route map, and the connectivity of VRT points and minima is clarified. Branching of the products through bifurcations is confirmed by ab initio molecular dynamics simulations starting from the TSs. A new feature of the reaction pathways, unification, is found and discussed.
Millimeter-wave spectroscopy of the FeCO radical in the ν2 and ν3 vibrationally excited states
Authors: Tanaka Keiichi , Nakamura Mitsuhiro , Shirasaka Mitsuaki , Sakamoto Ai , Harada Kensuke , Tanaka Takehiko
Published: July 2015

The pure rotational spectra of the FeCO radical in the ν2 (bending) and ν3 (Fe-C stretching) vibrational states of the ground X̃3Σ− electronic state were observed in the millimeter-wave region. The equilibrium rotational and centrifugal distortion constants were determined to be Be = 4374.631 (58) MHz and De = 1.1666 (20) kHz together with the spin-spin coupling constant λe = 691.89 (37) GHz and spin-rotation coupling constant γe = − 1079.4 (55) MHz with use of the millimeter-wave results and the ν1 IR data. The equilibrium bond length for Fe-C was derived to be 1.725 Å assuming that for C-O to be 1.159 Å. Since the vibronic symmetry of the excited state of bending vibration is 3Π, the analysis of spectrum in the ν2 state required an effective spin-orbit interaction constant of A2 = 6.0219 (61) GHz together with three parity doubling constants of o2 = 36.168 (10) GHz, p2 = 85.18 (34) MHz, and q2 = 4.7024 (17) MHz. The effective spin-orbit interaction constant A2 is attributed to the vibronic mixing of the 3Π excited electronic states. The vibronic mixing also cause the parity doubling constants o2 and p2, but the main contribution to q2 is given by the vibrational l-type doubling.
Bistability in inhomogeneity—Effects of flow coherent structures on the fate of a bistable reaction
Authors: Tang Wenbo , Dhumuntarao Aditya
Published: July 2015

We present a numerical study on the mixing process between two stable states of a chemical reaction model. The two stable states of the reactions are found in practice not to coexist, and a single stable state of homogeneous scalar concentration is achieved over long time. With all other parameters fixed, we find the dependence of the final state on the rate of reaction. Interestingly, with the existence of coherent structures, at a range of intermediate rate of reaction, we find that the final state also depends on the initial locations of the scalar impurity. The exact dependence on initial condition is explored in detail. These results lead to the fundamental understanding on the variability of biogeochemical tracers in the environment induced by nonlinear fluid stirring.
Diffusion phenomena of cells and biomolecules in microfluidic devices
Authors: Yildiz-Ozturk Ece , Yesil-Celiktas Ozlem
Published: July 2015

Biomicrofluidics is an emerging field at the cross roads of microfluidics and life sciences which requires intensive research efforts in terms of introducing appropriate designs, production techniques, and analysis. The ultimate goal is to deliver innovative and cost-effective microfluidic devices to biotech, biomedical, and pharmaceutical industries. Therefore, creating an in-depth understanding of the transport phenomena of cells and biomolecules becomes vital and concurrently poses significant challenges. The present article outlines the recent advancements in diffusion phenomena of cells and biomolecules by highlighting transport principles from an engineering perspective, cell responses in microfluidic devices with emphases on diffusion- and flow-based microfluidic gradient platforms, macroscopic and microscopic approaches for investigating the diffusion phenomena of biomolecules, microfluidic platforms for the delivery of these molecules, as well as the state of the art in biological applications of mammalian cell responses and diffusion of biomolecules.
Note: Vibration energy harvesting based on a round acoustic fence
Authors: Cui Xiao-bin , Huang Cheng-ping , Hu Jun-hui
Published: July 2015

An energy harvester based on a round acoustic fence (RAF) has been proposed and studied. The RAF is composed of cylindrical stubs stuck in a circular array on a thin metal plate, which can confine the acoustic energy efficiently. By removing one stub and thus opening a small gap in the RAF, acoustic leakage with larger intensity can be produced at the gap opening. With the vibration source surrounded by the RAF, the energy harvesting at the gap opening has a wide bandwidth and is insensitive to the position of the vibration source. The results may have potential applications in harvesting the energy of various vibration sources in solid structure.
Solvent effects in the helix-coil transition model can explain the unusual biophysics of intrinsically disordered proteins
Authors: Badasyan Artem , Mamasakhlisov Yevgeni Sh. , Podgornik Rudolf , Parsegian V. Adrian
Published: July 2015

We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible states to the number corresponding to a helical conformation. The resulting transition phase diagram is then juxtaposed with the unusual behavior of the secondary structures in Intrinsically Disordered Proteins (IDPs) and a number of similarities are observed, even if the protein folding is a more complex transition than the helix-coil transition. In fact, the deficit in bulky and hydrophobic amino acids observed in IDPs, translated into larger values of phase space volume, allows us to locate the region in parameter space of the helix-coil transition that would correspond to the secondary structure transformations that are intrinsic to conformational transitions in IDPs and that is characterized by a modified phase diagram when compared to globular proteins. Here, we argue how the nature of this modified phase diagram, obtained from a model of the helix-coil transition in a solvent, would illuminate the turned-out response of IDPs to the changes in the environment conditions that follow straightforwardly from the re-entrant (cold denaturation) branch in their folding phase diagram.
Reliable four-point flexion test and model for die-to-wafer direct bonding
Authors: Tabata T. , Sanchez L. , Fournel F. , Moriceau H.
Published: July 2015

For many years, wafer-to-wafer (W2W) direct bonding has been very developed particularly in terms of bonding energy measurement and bonding mechanism comprehension. Nowadays, die-to-wafer (D2W) direct bonding has gained significant attention, for instance, in photonics and microelectro-mechanics, which supposes controlled and reliable fabrication processes. So, whatever the stuck materials may be, it is not obvious whether bonded D2W structures have the same bonding strength as bonded W2W ones, because of possible edge effects of dies. For that reason, it has been strongly required to develop a bonding energy measurement technique which is suitable for D2W structures. In this paper, both D2W- and W2W-type standard SiO2-to-SiO2 direct bonding samples are fabricated from the same full-wafer bonding. Modifications of the four-point flexion test (4PT) technique and applications for measuring D2W direct bonding energies are reported. Thus, the comparison between the modified 4PT and the double-cantilever beam techniques is drawn, also considering possible impacts of the conditions of measures such as the water stress corrosion at the debonding interface and the friction error at the loading contact points. Finally, reliability of a modified technique and a new model established for measuring D2W direct bonding energies is demonstrated.
Magnetohydrodynamic (MHD) flow of Cu-water nanofluid due to a rotating disk with partial slip
Authors: Hayat Tasawar , Rashid Madiha , Imtiaz Maria , Alsaedi Ahmed
Published: July 2015

This paper investigates MHD steady flow of viscous nanofluid due to a rotating disk. Water is treated as a base fluid and copper as nanoparticle. Nanofluid fills the porous medium. Effects of partial slip, viscous dissipation and thermal radiation are also considered. Similarity transformations reduce the nonlinear partial differential equations to ordinary differential equations. Flow and heat transfer characteristics are computed by HAM solutions. Also computations for skin friction coefficient and Nusselt number are presented and examined for pertinent parameters. It is noted that higher velocity slip parameter decreases the radial and azimuthal velocities while temperature decreases for larger values of the thermal slip parameter. Also the rate of heat transfer enhances when the nanoparticle volume fraction increases.
Influence of the anode processes on discharges driven by thermionic emission
Authors: Levko Dmitry
Published: July 2015

The influence of electron reflection and secondary electron emission due to electron impact from the anode on discharges driven by thermionic emission is studied by the self-consistent one-dimensional particle-in-cell Monte Carlo collisions model. Two regimes are considered. In the first regime, the two-stream instability is excited and large anode sheath potential is obtained. It is found that in this regime, the reflected electrons play a significant role. In the second regime, the instability is not excited and the anode sheath potential is small. The dominant anode process in this regime is the secondary electron emission. It is shown that in both regimes, the anode processes significantly influence the plasma parameters.
Establishment and experimental verification of the photoresist model considering interface slip between photoresist and concave spherical substrate
Authors: Yang S. , Bayanheshig  , Zhao X. L. , Xing S. , Jiang Y. X. , Wu N. , Jiao Q. B. , Li W. H. , Tan X.
Published: July 2015

A thickness distribution model of photoresist spin-coating on concave spherical substrate (CSS) has been developed via both theoretical studies and experimental verification. The stress of photoresist on rotating CSS is analyzed and the boundary conditions of hydrodynamic equation are presented under the non-lubricating condition. Moreover, a multivariable polynomial equation of photoresist-layer thickness distribution is derived by analyzing and deducing the flow equation where the evaporation rate, substrate topography, interface slip between liquid and CSS, and the variation of rotational speed and photoresist parameters are considered in detail. Importantly, the photoresist-layer thickness at various CSS rotational speeds and liquid concentrations can be obtained according to the theoretical equation. The required photoresist viscosity and concentration parameters of different photoresist coating thickness under a certain coating speeds can be also solved through this equation. It is noted that the calculated theoretical values are well consistent with the experimental results which were measured with various CSS rotational speeds and liquid concentrations at steady state. Therefore, both our experimental results and theoretical analysis provide the guidance for photoresist dilution and pave the way for potential improvements and microfabrication applications in the future.
Mechanical rupture explains a bacterium’s puzzling “pop”
Authors: Smart Ashley G.
Published: July 2015

Experiments suggest that dividing Staphylococcus cells are designed to crack under pressure.
Nonproliferation treaty talks end in acrimony
Authors: Kramer David
Published: July 2015

Issues of nuclear nonproliferation and disarmament take a back seat to a Middle East regional nuclear-free zone.
Brighter and faster: The promise and challenge of the x-ray free-electron laser
Authors: Bucksbaum Philip H. , Berrah Nora
Published: July 2015

Starting with the Linac Coherent Light Source in 2009, free-electron lasers are using x rays in new ways. Early results are wowing scientists the world over.
A host-specific habitat former controls biodiversity across ecological transitions in a rocky intertidal facilitation cascade
Authors: Thomsen Mads S. , Metcalfe Isis , South Paul , Schiel David R.
Published: July 2015

Few studies have quantified facilitation cascades from rocky intertidal systems, across ecological transition zones, or where the secondary facilitator is an obligate epiphyte. Here, we address these research gaps. We first quantified distributions of the seaweed host Hormosira banksii and its obligate epiphyte Notheia anomala at different tidal elevations in summer and winter at Kaikoura, New Zealand. This analysis showed that the host and the epiphyte were, in both seasons, most abundant at ‘high’ and ‘low’ tidal elevations respectively, probably driven by contrasting responses to competitors and desiccation. We subsequently quantified richness and abundances of mobile invertebrates associated with Hormosira and various levels of epiphytic Notheia. Hormosira fronds were collected from different elevations, seasons, diurnal cycles, with different neighbouring algae and following an epiphyte-removal experiment. All tests showed positive density-dependent effects of Notheia-epiphytism on richness and abundances of invertebrates, with strongest facilitation occurring at the transition from intertidal to subtidal habitats. Our results support a growing number of facilitation cascade studies from different ecosystems and habitats, and suggest that habitat formation–driven facilitation cascades may be particularly common in marine benthic systems where epibiosis can be a dominant life form.
Zinc and nickel binary mixtures act additively on the tropical mysid Mysidopsis juniae
Authors: Pitombeira de Figuerêdo Lívia , Nilin Jeamylle , Queiroz da Silva Allyson , Pinheiro Damasceno Évila , Loureiro Susana , Veras Costa-Lotufo Letícia
Published: July 2015

Heavy metals may appear in the environment as a result of different anthropogenic activities, such as agriculture practices, industry and mining. They can reach aquatic environments as complex mixtures, and single chemical toxicity as a baseline for risk assessment can underestimate the impairment of ecosystems. The aim of the present study was to evaluate combined toxicity of binary mixtures of zinc and nickel to the tropical mysid Mysidopsis juniae. Acute toxicity was assessed and mixture toxicity was modelled using the conceptual models for concentration addition and independent action to predict whether both metals act additively or whether they interact with each other inside the organism. For that, the observed mortality data were compared with the modelled data. For the single toxicity assessment, results showed that nickel induced higher toxicity than did zinc, with lethal concentrations to 50% of the organisms of 180±30μgL–1 and 260±40μg zinc L–1 respectively. In binary mixtures, both metals acted additively and no interactions were predicted by using the conceptual models. The present study has highlighted the need to fill the gaps in toxicity studies using marine species and approaches that can help improve the assessment of accurate risk in the environment.
Freezability of Andalusian donkey (Equus asinus) spermatozoa: effect of extenders and permeating cryoprotectants
Authors: Acha D. , Hidalgo M. , Ortiz I. , Gálvez M. J. , Carrasco J. J. , Gómez-Arrones V. , Dorado J.
Published: July 2015

The aim of this study was to compare the effect of two semen extenders and four permeating cryoprotectants on post-thaw sperm quality of Andalusian donkeys. First, 32 ejaculates were pooled, split and frozen in either Gent B or INRA 96 with egg yolk and glycerol. Second, 12 pooled semen samples were simultaneously frozen in Gent B (glycerol) or Gent A containing ethylene glycol (EG; 1 or 1.5%) or dimethyl sulfoxide (DMSO; 1.5 or 2%). Finally, nine pooled samples were simultaneously cryopreserved in Gent A containing 1% EG (as control), dimethylformamide (DMFA; 1 or 2.5%) or a combination of 1% EG and 1.5% DMFA. Gent B yielded a higher (P < 0.01) post-thaw sperm motility than modified INRA96. EG 1% increased the sperm membrane integrity (P < 0.001), whereas DMSO affected sperm motility and membrane integrity (P < 0.001). DMFA 2.5% yielded higher (P < 0.001) values for sperm motility and membrane integrity. We concluded that Gent B improves in vitro post-thaw sperm quality of donkey spermatozoa, but the replacement of glycerol with 1% EG or 2.5% DMFA increased sperm protection against cryodamage. The use of DMSO for freezing donkey semen was unsuccessful and a toxic effect is suspected. These extenders should be included in the pre-freeze test for each donkey.
Land management within capability: a new scheme to guide sustainable land management in New South Wales, Australia
Authors: Gray Jonathan M. , Chapman Greg A. , Murphy Brian W.
Published: July 2015

A new evaluation scheme, land management within capability (LMwC), used to guide sustainable land management in New South Wales (NSW), is presented. The scheme semi-quantitatively categorises the potential impacts of specific land-management actions and compares these with the inherent physical capability of the land in relation to a range of land-degradation hazards. This leads to the derivation of LMwC indices, which signify the sustainability of land-management practices at the scale of individual sites up to broader regions. The LMwC scheme can be used to identify lands at greatest risk from various land-degradation hazards. It can help to guide natural resource agencies at local, regional and state levels to target priorities and promote sustainable land management across their lands. Few other schemes that assess the sustainability of a given land-management regime in a semi-quantitative yet pragmatic manner are found in the literature. The scheme has particular application for regional soil-monitoring programs and it was applied in such a program over NSW in 2008–09. The results suggested that the hazards most poorly managed across the state are wind erosion, soil acidification and soil organic carbon decline. The LMwC scheme, or at least its underlying concepts, could be readily applied to other jurisdictions.
GABA-mediated repulsive coupling between circadian clock neurons in the SCN encodes seasonal time
Authors: Myung Jihwan , Hong Sungho , DeWoskin Daniel , De Schutter Erik , Forger Daniel B. , Takumi Toru
Published: July 2015

Significance

How animals track the seasons has long been a mystery. We found a mechanism that explains how day length is encoded within the neuronal network of suprachiasmatic nucleus (SCN). Using an integrated approach combining experiments and modeling, we find evidence for changes in the coupling in the SCN that divides the clock oscillations into two clusters as a function of day length. We show that asymmetric distribution of intracellular chloride across the SCN causes this coupling change. Blocking GABA or chloride import erases the oscillator organization formed by day-length entrainment. These demonstrate that coupling through GABA is a key ingredient of day-length encoding in the SCN.
Supercooled spin liquid state in the frustrated pyrochlore Dy
2
Ti
2
O
7
Authors: Kassner Ethan R. , Eyvazov Azar B. , Pichler Benjamin , Munsie Timothy J. S. , Dabkowska Hanna A. , Luke Graeme M. , Davis J. C. Séamus
Published: July 2015

Significance

Frustrated magnetic pyrochlore systems, in which there are many possible favored spin configurations, may host a variety of exotic magnetic phases. For example, some models predict that Dy
2
Ti
2
O
7
hosts a fluid of mobile magnetic “monopoles” that interact via a magnetic Coulomb interaction. Here, we introduce a novel measurement technique that realizes periodic boundary conditions, and use it to examine the magnetization transport dynamics of tori of Dy
2
Ti
2
O
7
. We identify multiple phenomena in the dynamics of Dy
2
Ti
2
O
7
that are characteristic of a supercooled magnetic liquid approaching a glass transition. This highly unusual classical spin liquid forms in a structurally ordered crystal and therefore it may constitute the approach to a novel magnetic glass state.
Brook Trout Distribution, Genetics, and Population Characteristics in the Driftless Area of Minnesota
Authors: Hoxmeier R. John H. , Dieterman Douglas J. , Miller Loren M.
Published: July 2015

The Driftless Area in southeastern Minnesota is on the southwestern edge of the native range of Brook Trout Salvelinus fontinalis. It was assumed that native Brook Trout were extirpated from this region in the early 1900s due to degraded stream conditions and stockings of eastern-origin Brook Trout and European Brown Trout Salmo trutta. Our objectives were to examine Brook Trout populations in the region to determine their spatial and genetic distribution and quantify population characteristics. Information on presence or absence of Brook Trout was gathered by electrofishing 174 streams in southeastern Minnesota. Brook Trout were present in 68% of coldwater streams compared with only in 3% in the early 1970s. The increase is likely due to increasing stream discharge throughout the Driftless Area, enabling recolonization or successful establishment of stocked populations. Streams with higher base flow discharge also had higher abundance, larger size at maturity, and larger Brook Trout present. Genetic data on 74 populations were analyzed to characterize genetic variation within populations, assess genetic structure among populations, and determine possible origins. Numerous populations were not associated with known hatchery sources but were primarily composed of geographic groupings that could represent remnant lineages. Although population characteristics were similar among genetic origins, potentially remnant populations should be given conservation priority because they have proven their ability to sustain themselves in this region. Management actions that emphasize maintaining or increasing stream base flows throughout the region will likely enhance remnant Brook Trout populations in the Driftless Area.

Received July 25, 2014; accepted March 17, 2015
Evaluating the Ability of Tiger Muskellunge to Eradicate Brook Trout in Idaho Alpine Lakes
Authors: Koenig Martin K. , Meyer Kevin A. , Kozfkay Joseph R. , DuPont Joseph M. , Schriever Edward B.
Published: July 2015

In western North America, nonnative Brook Trout Salvelinus fontinalis in alpine lakes threaten the persistence of native trout and often offer limited sport fishing opportunity as they are prone to stunting. Stocking tiger muskellunge (Northern Pike Esox lucius × Muskellunge E. masquinongy), which are reproductively sterile, may be an option to eradicate Brook Trout in some alpine lakes. We used floating gill nets to survey 17 alpine lake Brook Trout populations, then stocked 13 lakes with tiger muskellunge, with four additional lakes serving as controls. Tiger muskellunge were stocked at a mean TL of 317 mm and a density of 40 fish/ha. Brook Trout were resampled for 4 or 5 years after stocking to evaluate changes in Brook Trout TL and CPUE (fish/net-night). Declines in CPUE were substantial for both treatment and control lakes but were significantly greater in treatment lakes. Mean Brook Trout CPUE in treatment lakes declined from 23.1 fish/net-night to 2.3 fish/net-night 5 years after stocking tiger muskellunge, whereas in control lakes, CPUE declined from 25.5 fish/net-night to 7.8 fish/net-night 5 years later. Complete eradication appeared to occur in two lakes within 2 years, and in two more lakes by year 5. In lakes where tiger muskellunge were stocked, the proportion of Brook Trout ≥250 mm TL in the catch increased significantly in years 1, 2, and 4 after stocking (compared with prestocking data), whereas no increase occurred in control lakes. Tiger muskellunge were most successful in reducing Brook Trout CPUE in lakes with no inlets or outlets, while elevation and lake area may also have played a role. Our results suggest tiger muskellunge can improve the size structure and potentially eradicate Brook Trout populations from some alpine lakes. However, we recommend combining any tiger muskellunge stocking with other conventional removal methods to increase the likelihood of successful eradication.

Received October 27, 2014; accepted March 22, 2015
Climate Change Adaptation and Restoration of Western Trout Streams: Opportunities and Strategies
Authors: Williams Jack E. , Neville Helen M. , Haak Amy L. , Colyer Warren T. , Wenger Seth J. , Bradshaw Stan
Published: July 2015

Climate change is contributing to the severity and rate of stream degradation by changing the timing of peak flows, altering flow regimes, creating more frequent and intense disturbances, and increasing stream temperatures. Herein we describe three case studies of trout stream adaptation that address existing and climate-driven causes of degradation through habitat restoration. The case studies vary in geography and complexity, but all include restoration efforts intended to address multiple causes of stream degradation and improve the resilience of these streams to floods, droughts, and wildfires. Four elements of successful climate adaptation projects emerge: (1) habitat assessments that help drive project location and design, (2) projects that directly address climate change impacts and increase habitat resilience, (3) projects that combine to achieve watershed-scale impacts, and (4) projects that include sufficient monitoring to determine their effectiveness. We describe solutions to common challenges in conducting climate change adaptation, including how to balance scientific assessments with opportunities when choosing projects, how smaller projects can be aggregated to achieve watershed-scale benefits, and how citizen science efforts can augment monitoring programs.

El cambio climático está contribuyendo a incrementar la severidad y la tasa de degradación de los ríos a través de la alteración en la estacionalidad del flujo máximo, modificación del régimen de flujos, generación de perturbaciones más frecuentes e intensas e incremento de la temperatura de los ríos. Aquí se describen tres casos de estudio de la adaptación de ríos en donde habita la trucha, en los que se abordan las causas de la degradación que son provocadas por el cambio climático, mediante la restauración del hábitat. Los casos de estudio varían en cuanto a ubicación geográfica y complejidad, pero en todos se contemplan esfuerzos de restauración enfocados a abordar múltiples causas de degradación de ríos y mejoramiento de la resiliencia de éstos ante inundaciones, sequías e incendios naturales. Se consideraron cuatro elementos para lograr una adaptación exitosa al cambio climático: 1) evaluaciones del hábitat que ayuden a diseñar y establecer dónde llevar a cabo los proyectos; 2) proyectos que aborden directamente los impactos del cambio climático y el incremento en la resiliencia del hábitat; 3) proyectos que, al combinarse, logren resultados a nivel de cuenca hidrológica; y 4) proyectos que incluyan un monitoreo suficiente como para que se pueda determinar su efectividad. También se describen soluciones a los clásicos retos que implica la adaptación al cambio climático, incluyendo cómo encontrar un balance entre evaluaciones científicas y elección de proyectos, cómo se pueden integrar varios proyectos pequeños para conseguir beneficios a escala de cuenca y cómo se puede incrementar el monitoreo mediante esfuerzos ciudadanos.
Two generalizations of homogeneity in groups with applications to regular semigroups
Authors: Araújo João , Cameron Peter
Published: July 2015

LetXXbe a finite set such that|X|=n|X|=nand leti⩽j⩽ni\leqslant j \leqslant n. A groupG⩽SnG\leqslant \mathcal {S}_{n}is said to be(i,j)(i,j)-homogeneous if for everyI,J⊆XI,J\subseteq X, such that|I|=i|I|=iand|J|=j|J|=j, there existsg∈Gg\in Gsuch thatIg⊆JIg\subseteq J. (Clearly(i,i)(i,i)-homogeneity isii-homogeneity in the usual sense.)

A groupG⩽SnG\leqslant \mathcal {S}_{n}is said to have thekk-universal transversal property if given any setI⊆XI\subseteq X(with|I|=k|I|=k) and any partitionPPofXXintokkblocks, there existsg∈Gg\in Gsuch thatIgIgis a section forPP. (That is, the orbit of eachkk-subset ofXXcontains a section for eachkk-partition ofXX.)

In this paper we classify the groups with thekk-universal transversal property (with the exception of two classes of22-homogeneous groups) and the(k−1,k)(k-1,k)-homogeneous groups (for2>k⩽⌊n+12⌋2>k\leqslant \lfloor \frac {n+1}{2}\rfloor). As a corollary of the classification we prove that a(k−1,k)(k-1,k)-homogeneous group is also(k−2,k−1)(k-2,k-1)-homogeneous, with two exceptions; and similarly, but with no exceptions, groups having thekk-universal transversal property have the(k−1)(k-1)-universal transversal property.

A corollary of all the previous results is a classification of the groups that together with any rankkktransformation onXXgenerate a regular semigroup (for1⩽k⩽⌊n+12⌋1\leqslant k\leqslant \lfloor \frac {n+1}{2}\rfloor).

The paper ends with a number of challenges for experts in number theory, group and/or semigroup theory, linear algebra and matrix theory.
Application of a ℤ₃-orbifold construction to the lattice vertex operator algebras associated to Niemeier lattices
Authors: Sagaki Daisuke , Shimakura Hiroki
Published: July 2015

By applying Miyamoto’s

Z

3

\mathbb {Z}_{3}

-orbifold construction to the lattice vertex operator algebras associated to Niemeier lattices and their automorphisms of order

3
3

, we construct holomorphic vertex operator algebras of central charge

24
24

whose Lie algebras of the weight one spaces are of types

A

2
,
3

6

A_{2,3}^6

,

E

6
,
3

G

2
,
1

3

E_{6,3}G_{2,1}^{3}

, and

A

5
,
3

D

4
,
3

A

1
,
1

3

A_{5,3}D_{4,3}A_{1,1}^{3}

, which correspond to No. 6, No. 17, and No. 32 on Schellekens’ list, respectively.
ProFET: Feature engineering captures high-level protein functions
Authors: Ofer Dan , Linial Michal
Published: July 2015

Motivation: The amount of sequenced genomes and proteins is growing at an unprecedented pace. Unfortunately, manual curation and functional knowledge lag behind. Homologous inference often fails at labeling proteins with diverse functions and broad classes. Thus, identifying high-level protein functionality remains challenging. We hypothesize that a universal feature engineering approach can yield classification of high-level functions and unified properties when combined with machine learning approaches, without requiring external databases or alignment.

Results: In this study, we present a novel bioinformatics toolkit called ProFET (Protein Feature Engineering Toolkit). ProFET extracts hundreds of features covering the elementary biophysical and sequence derived attributes. Most features capture statistically informative patterns. In addition, different representations of sequences and the amino acids alphabet provide a compact, compressed set of features. The results from ProFET were incorporated in data analysis pipelines, implemented in python and adapted for multi-genome scale analysis. ProFET was applied on 17 established and novel protein benchmark datasets involving classification for a variety of binary and multi-class tasks. The results show state of the art performance. The extracted features’ show excellent biological interpretability. The success of ProFET applies to a wide range of high-level functions such as subcellular localization, structural classes and proteins with unique functional properties (e.g. neuropeptide precursors, thermophilic and nucleic acid binding). ProFET allows easy, universal discovery of new target proteins, as well as understanding the features underlying different high-level protein functions.

Availability and implementation: ProFET source code and the datasets used are freely available at https://github.com/ddofer/ProFET.

Contact:  michall@cc.huji.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Depletion of enteroantigen-activated CD4+ T cells: effects on proliferation and pathogenicity
Authors: Belmaáti Mohammed-Samir , Claesson Mogens H.
Published: July 2015

Naive CD4+ T cells depleted of natural Treg (CD25+) cells proliferate extensively when exposed to a fecal extract [enteroantigen (eAg)] pulsed on antigen-presenting cells (APC). When transplanted into SCID recipient mice, the CD25-depleted T cells induce a chronic colitis with a lethal course. We observed here that if T cells, pre-activated for 48h by eAg from BALB/c or SCID mice, are removed and then reexposed to either of the two sources of antigen, these T cells have completely lost their anti-eAg proliferative capacity in vitro. This observation indicates that eAgs derived from Balb/c and SCID mice are recognized by similar subsets of T cells. However, when transferred into SCID mice, eAg-activation-depleted T cells are still capable of inducing a severe colitis fully comparable with the disease induced by naive CD4+ T cells
Radial distributions of arm–gas offsets as an observational test of spiral theories
Authors: Baba Junichi , Morokuma-Matsui Kana , Egusa Fumi
Published: July 2015

Theories of stellar spiral arms in disk galaxies can be grouped into two classes based on the longevity of a spiral arm. Although the quasi-stationary density wave theory supposes that spirals are rigidly rotating, long-lived patterns, the dynamic spiral theory predicts that spirals are differentially rotating, transient, recurrent patterns. In order to distinguish between the two spiral models from observations, we performed hydrodynamic simulations with steady and dynamic spiral models. Hydrodynamic simulations in steady spiral models demonstrated that the dust lane locations relative to the stellar spiral arms (hereafter, arm–gas offsets) depend on radius, regardless of the strength and pitch angle of the spiral and the model of the interstellar medium. In contrast, we found that the dynamic spiral models show no systematic radial dependence of the arm–gas offsets. The arm–gas offset radial profile method, together with the other test methods, will help us to distinguish between the two spiral models in observed spiral galaxies.
Antioxidants Protect Calsequestrin-1 Knockout Mice from Halothane- and Heat-induced Sudden Death
Authors: Michelucci Antonio , Paolini Cecilia , Canato Marta , Wei-Lapierre Lan , Pietrangelo Laura , De Marco Alessandro , Reggiani Carlo , Dirksen Robert T. , Protasi Feliciano
Published: July 2015

AbstractAbstract

Antioxidant pretreatment with N-acetylcysteine and Trolox protected calsequestrin-1-null mice from otherwise lethal episodes triggered by exposure to either halothane or heat stress. The results support evidence for a potential role of oxidative stress in life-threatening events of malignant hyperthermia and heat stress.

Background:

Mice lacking calsequestrin-1 (CASQ1-null), a Ca2+-binding protein that modulates the activity of Ca2+ release in the skeletal muscle, exhibit lethal hypermetabolic episodes that resemble malignant hyperthermia in humans when exposed to halothane or heat stress.

Methods:

Because oxidative species may play a critical role in malignant hyperthermia crises, we treated CASQ1-null mice with two antioxidants, N-acetylcysteine (NAC, Sigma-Aldrich, Italy; provided ad libitum in drinking water) and (±)-6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid (Trolox, Sigma-Aldrich; administered by intraperitoneal injection), before exposure to halothane (2%, 1 h) or heat (41°C, 1 h).

Results:

NAC and Trolox significantly protected CASQ1-null mice from lethal episodes, with mortality being 79% (n = 14), 25% (n = 16), and 20% (n = 5) during halothane exposure and 86% (n = 21), 29% (n = 21), and 33% (n = 6) during heat stress in untreated, NAC-treated, and Trolox-treated mice, respectively. During heat challenge, an increase in core temperature in CASQ1-null mice (42.3° ± 0.1°C, n=10) was significantly reduced by both NAC and Trolox (40.6° ± 0.3°C, n = 6 and 40.5° ± 0.2°C, n = 6). NAC treatment of CASQ1-null muscles/mice normalized caffeine sensitivity during in vitro contracture tests, Ca2+ transients in single fibers, and significantly reduced the percentage of fibers undergoing rhabdomyolysis (37.6 ± 2.5%, 38/101 fibers in 3 mice; 11.6 ± 1.1%, 21/186 fibers in 5 mice). The protective effect of antioxidant treatment likely resulted from mitigation of oxidative stress, because NAC reduced mitochondrial superoxide production, superoxide dismutase type-1 expression, and 3-nitrotyrosine expression, and increased both reduced glutathione and reduced glutathione/oxidized glutathione ratio.

Conclusion:

These studies provide a deeper understanding of the mechanisms that underlie hyperthermic crises in CASQ1-deficient muscle and demonstrate that antioxidant pretreatment may prevent them.
Achieving Kaiser Permanente quality
Authors: McHugh Matthew D. , Aiken Linda H. , Eckenhoff Myra E. , Burns Lawton R.
Published: July 2015

Background:

The Kaiser Permanente model of integrated health delivery is highly regarded for high-quality and efficient health care. Efforts to reproduce Kaiser’s success have mostly failed. One factor that has received little attention and that could explain Kaiser’s advantage is its commitment to and investment in nursing as a key component of organizational culture and patient-centered care.

Purpose:

The aim of this study was to investigate the role of Kaiser’s nursing organization in promoting quality of care.

Methodology:

This was a cross-sectional analysis of linked secondary data from multiple sources, including a detailed survey of nurses, for 564 adult, general acute care hospitals from California, Florida, Pennsylvania, and New Jersey in 2006–2007. We used logistic regression models to examine whether patient (mortality and failure-to-rescue) and nurse (burnout, job satisfaction, and intent-to-leave) outcomes in Kaiser hospitals were better than in non-Kaiser hospitals. We then assessed whether differences in nursing explained outcomes differences between Kaiser and other hospitals. Finally, we examined whether Kaiser hospitals compared favorably with hospitals known for having excellent nurse work environments—Magnet hospitals.

Findings:

Patient and nurse outcomes in Kaiser hospitals were significantly better compared with non-Magnet hospitals. Kaiser hospitals had significantly better nurse work environments, staffing levels, and more nurses with bachelor’s degrees. Differences in nursing explained a significant proportion of the Kaiser outcomes advantage. Kaiser hospital outcomes were comparable with Magnet hospitals, where better outcomes have been largely explained by differences in nursing.

Implications:

An important element in Kaiser’s success is its investment in professional nursing, which may not be evident to systems seeking to achieve Kaiser’s advantage. Our results suggest that a possible strategy for achieving outcomes like Kaiser may be for hospitals to consider Magnet designation, a proven and cost-effective strategy to improve process of care through investments in nursing.
Distributed leadership in health care teams
Authors: Chreim Samia , MacNaughton Kate
Published: July 2015

Background and Purpose:

Recent literature has been critical of research that adopts a narrow focus on single leaders and on leadership attributes and has called for attention to leadership that is distributed among individuals and to practices in which leaders engage. We conducted a study of health care teams where we attended to role distribution among leadership constellation members and to loose or tight coupling practices between leaders and the remainder of the team. This focus provides insights into how leadership can be practiced and structured to enhance team functioning.

Methodology:

A qualitative, multicase study of four teams was conducted. Data collection involved 44 interviews with almost all the members of the teams and 18 team meeting observations. Thematic analysis was conducted by the two authors.

Findings:

Leadership constellations can give rise to leadership role overlaps and gaps that may create ambiguity within teams, ambiguity is diminished if the leaders can agree on which leader assumes ultimate authority in an area, the presence of more leaders does not necessarily entail more comprehensive fulfillment of team needs, and teams’ needs for tight or loose leadership practices are influenced by contextual factors that we elaborate.

Practice Implications:

(a) It is important to recognize areas of overlap and gaps in leadership roles and to provide clarity about role boundaries to avoid ambiguity. Role mapping exercises and open discussions should be considered. (b) Attempting to spread formal leadership responsibilities informally among individuals is not always a workable strategy for addressing team needs. (c) Organizations need to examine critically the allocation of resources to leadership activities.
The influence of organization tenure on nurses’ perceptions of multiple work process improvement initiatives
Authors: Edwardson Nicholas , Gregory Sean , Gamm Larry
Published: July 2015

Background:

A nurse’s optimism or skepticism toward an organization-mandated change initiative largely depends on their experience with similar change initiatives and their unit’s and organization’s track record with previous change efforts. Thus, depending on the context, organization tenure can work in favor or against any particular change initiative. However, few studies have examined the impact of organization tenure on perceptions toward change initiatives. The few studies that have been conducted have yielded mixed results and have only targeted single or similar work initiatives.

Purpose:

The aim of this study was to examine how organization tenure impacts nurses’ perceptions toward a diverse array of work process improvement initiatives.

Methodology:

The data are derived from a survey of 421 medical-surgical nurses representing 41 units across four hospitals. The survey was designed to capture nurses’ perceptions toward three change initiatives—AIDET (Acknowledge, Introduce, Duration, Explanation, and Thank You), hourly rounding, and discharge phone calls—and their impact across two subscales—patient care and individual work change.

Findings:

Organization tenure is significantly and negatively associated with change receptivity for the non-patient safety-oriented initiative (AIDET). This negative relationship dissipates as we evaluate more patient safety-oriented work process initiatives (hourly rounding and discharge phone calls).

Practice Implications:

Significant differences in nurses’ perceptions toward change do exist depending on how long they have worked for their employer. For non-patient safety-oriented change initiatives, veteran-to-the-organization nurses may exhibit more recalcitrance than their new-to-the-organization counterparts. However, our findings also suggest the presence of a patient safety exception rule where veteran-to-the-organization nurses do not exhibit differences in opinion than their new-to-the-organization counterparts for patient safety-oriented change initiatives.
Experiences of Young Adults With Pacemakers and/or Implantable Cardioverter Defibrillators
Authors: Larimer Karen , Durmus Julie , Florez Elizabeth
Published: July 2015

Background:

The number of implanted devices (pacemakers [PMs] and implantable cardioverter defibrillators [ICDs]) is increasing. Because of technological advances, these devices are used in greater numbers in children and adolescents. Challenges of having these devices have been well studied in adults, but little is known about the lived experiences from the perspective of young adults.

Objective:

This study explored the lived experiences, coping behaviors, and challenges of young adults who had cardiac devices implanted during childhood.

Methods:

A descriptive qualitative study design was used. Purposive sampling was used to identify young adults aged 18 to 29 years, living with a PM and/or ICD. Participants were interviewed about their experiences and challenges related to living with a PM or ICD, with common themes identified and analyzed.

Results:

A total of 6 participants were interviewed for this study. The challenges of living with a PM and/or ICD included insecurity about physical appearance, device compliance, physical sensations of the device, future uncertainty, and limited support. The identified coping behaviors utilized by the participants were confrontation, acceptance, educating others, spreading awareness, avoidance, and humor. The overall lived experiences described were appreciation for device benefits, fear of device malfunction, and attracting attention.

Conclusions:

The lived experiences of young recipients often mirror that of older adults; however, it is clear that there are challenges and coping behaviors unique to young adults living with a PM and/or ICD. It is important to educate healthcare providers about the unique challenges that young adults may face so they can provide the appropriate support to this population.
Fatal Neuroleptic Malignant Syndrome Associated With Quetiapine
Authors: Schattner Ami , Kitroser Ella , Cohen Joel D.
Published: July 2015

Acute psychosis developed in an elderly patient with Parkinson disease and she was admitted and treated with quetiapine (Seroquel). One day later, high fever unexplained by infection appeared associated with restlessness, confusion, convulsion, leukocytosis, and extreme serum creatine kinase levels. She died of neuroleptic malignant syndrome (NMS) despite intensive treatment. Quetiapine is an atypical neuroleptic agent, rarely associated with NMS in the absence of other contributing drugs. Our case strongly establishes quetiapine-induced NMS (Naranjo scale 6) and is also unique in the abrupt onset and severe refractory course. The steep increase in the prescription of quetiapine worldwide mandates better recognition of this severe adverse reaction, which is fortunately rare, to allow immediate drug withdrawal and appropriate treatment.