bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal system‐level organization of the switch from glycolytic to gluconeogenic operation in yeast
Authors: Zampar Guillermo G , Kümmel Anne , Ewald Jennifer , Jol Stefan , Niebel Bastian , Picotti Paola , Aebersold Ruedi , Sauer Uwe , Zamboni Nicola , Heinemann Matthias
Published: April 2013

The diauxic shift in Saccharomyces cerevisiae is an ideal model to study how eukaryotic cells readjust their metabolism from glycolytic to gluconeogenic operation. In this work, we generated time‐resolved physiological data, quantitative metabolome (69 intracellular metabolites) and proteome (72 enzymes) profiles. We found that the diauxic shift is accomplished by three key events that are temporally organized: (i) a reduction in the glycolytic flux and the production of storage compounds before glucose depletion, mediated by downregulation of phosphofructokinase and pyruvate kinase reactions; (ii) upon glucose exhaustion, the reversion of carbon flow through glycolysis and onset of the glyoxylate cycle operation triggered by an increased expression of the enzymes that catalyze the malate synthase and cytosolic citrate synthase reactions; and (iii) in the later stages of the adaptation, the shutting down of the pentose phosphate pathway with a change in NADPH regeneration. Moreover, we identified the transcription factors associated with the observed changes in protein abundances. Taken together, our results represent an important contribution toward a systems‐level understanding of how this adaptation is realized.
Soil organic carbon concentrations and storage in irrigated cotton cropping systems sown on permanent beds in a Vertosol with restricted subsoil drainage
Authors: Hulugalle N. R. , Weaver T. B. , Finlay L. A. , Heimoana V.
Published: April 2013

Long-term studies of soil organic carbon dynamics in two- and three-crop rotations in irrigated cotton (Gossypium hirsutum L.) based cropping systems under varying stubble management practices in Australian Vertosols are relatively few. Our objective was to quantify soil organic carbon dynamics during a 9-year period in four irrigated, cotton-based cropping systems sown on permanent beds in a Vertosol with restricted subsoil drainage near Narrabri in north-western New South Wales, Australia. The experimental treatments were: cotton–cotton (CC); cotton–vetch (Vicia villosa Roth. in 2002–06, Vicia benghalensis L. in 2007–11) (CV); cotton–wheat (Triticum aestivum L.), where wheat stubble was incorporated (CW); and cotton–wheat–vetch, where wheat stubble was retained as in-situ mulch (CWV). Vetch was terminated during or just before flowering by a combination of mowing and contact herbicides, and the residues were retained as in situ mulch. Estimates of carbon sequestered by above- and below-ground biomass inputs were in the order CWV >> CW = CV > CC. Carbon concentrations in the 0–1.2 m depth and carbon storage in the 0–0.3 and 0–1.2 m depths were similar among all cropping systems. Net carbon sequestration rates did not differ among cropping systems and did not change significantly with time in the 0–0.3 m depth, but net losses occurred in the 0–1.2 m depth. The discrepancy between measured and estimated values of sequestered carbon suggests that either the value of 5% used to estimate carbon sequestration from biomass inputs was an overestimate for this site, or post-sequestration losses may have been high. The latter has not been investigated in Australian Vertosols. Future research efforts should identify the cause and quantify the magnitude of these losses of organic carbon from soil.
Stability and viability of novel perennial ryegrass host–Neotyphodium endophyte associations
Authors: Tian P. , Le T.-N. , Smith K. F. , Forster J. W. , Guthridge K. M. , Spangenberg G. C.
Published: April 2013

The temperate pasture grass Lolium perenne L. is commonly found in association with the fungal endophyte Neotyphodium lolii. Viability of both seed and endophyte was evaluated by inoculation of individual genotypes from the host cultivar Bronsyn with six distinct endophyte strains. The resulting populations were subjected to either long-term storage under various temperature conditions, or accelerated ageing (AA) treatments. High temperature storage was detrimental to endophyte viability. The AA variables (relative humidity [RH] and time) and subsequent temperature and duration of storage significantly (P < 0.05) affected both seed germination and endophyte viability. Significant interaction effects between the AA treatment and storage conditions were also observed. Endophyte viability following AA treatment was inversely correlated with both increasing RH and duration of treatment. Differential responses between different endophytes within the Bronsyn host were also apparent. The standard endophyte (SE) strain and the novel endophytes AR1 and AR37 exhibited higher viability than NEA2, NEA3, and NEA6 during seed storage, suggesting the importance of identification and selection for compatible symbiotic associations in agronomic varieties. The observed similarity between assessments of endophyte viability after AA treatments and following long-term storage confirmed the capacity of moderate conditions (e.g. 80% RH for 7 days or 100% RH for 4 days) to predict variation in viability between different endophyte strains.
Zona pellucida birefringence and meiotic spindle visualisation of human oocytes are not influenced by IVM technology
Authors: Omidi Marjan , Khalili Mohammad Ali , Ashourzadeh Sareh , Rahimipour Marzieh
Published: April 2013

The aim of the present study was to investigate the relationship between the presence of the meiotic spindle and zona pellucida (ZP) birefringence with morphology of in vivo- and in vitro-matured human oocytes. Germinal vesicles (n = 47) and MI (n = 38) oocytes obtained from stimulated ovaries of patients undergoing intracytoplasmic sperm injection (ICSI) underwent IVM. Using a PolScope (OCTAX PolarAID; Octax, Herbon, Germany), the presence of spindles and ZP birefringence was assessed in both in vivo-matured (n = 56) and IVM (n = 56) oocytes. In addition, the morphology of each matured oocyte was evaluated microscopically. There were insignificant differences for ZP birefringence and meiotic spindle between the in vivo-matured and IVM MII oocytes. Subanalysis revealed that the rates of morphologically abnormal oocytes did not differ significantly between the two groups, except in the case of irregular shape (P = 0.001), refractile body (P = 0.001) and fragmented polar body (P = 0.03), which were higher in IVM oocytes. In the case of in vivo-matured oocytes, a significantly higher percentage of oocytes with intracytoplasmic and both intra- and extracytoplasmic abnormalities have a low birefringent ZP (P = 0.007 and P = 0.02, respectively). There was no relationship between morphological abnormalities and spindle detection. The findings suggest that clinical IVM is a safe technology that maintains the high maturation rate and integrity of oocytes. In addition, the use of the non-invasive PolScope is recommended for the detection of oocytes most suitable for ICSI.
Emergent relation between surface vapor conductance and relative humidity profiles yields evaporation rates from weather data
Authors: Salvucci Guido D. , Gentine Pierre
Published: April 2013

The ability to predict terrestrial evapotranspiration (
E
) is limited by the complexity of rate-limiting pathways as water moves through the soil, vegetation (roots, xylem, stomata), canopy air space, and the atmospheric boundary layer. The impossibility of specifying the numerous parameters required to model this process in full spatial detail has necessitated spatially upscaled models that depend on effective parameters such as the surface vapor conductance (
C

surf

).
C

surf

accounts for the biophysical and hydrological effects on diffusion through the soil and vegetation substrate. This approach, however, requires either site-specific calibration of
C

surf

to measured
E
, or further parameterization based on metrics such as leaf area, senescence state, stomatal conductance, soil texture, soil moisture, and water table depth. Here, we show that this key, rate-limiting, parameter can be estimated from an emergent relationship between the diurnal cycle of the relative humidity profile and
E
. The relation is that the vertical variance of the relative humidity profile is less than would occur for increased or decreased evaporation rates, suggesting that land–atmosphere feedback processes minimize this variance. It is found to hold over a wide range of climate conditions (arid–humid) and limiting factors (soil moisture, leaf area, energy). With this relation, estimates of
E
and
C

surf

can be obtained globally from widely available meteorological measurements, many of which have been archived since the early 1900s. In conjunction with precipitation and stream flow, long-term
E
estimates provide insights and empirical constraints on projected accelerations of the hydrologic cycle.
Ontogeny and phylogeny of language
Authors: Yang Charles
Published: April 2013

How did language evolve? A popular approach points to the similarities between the ontogeny and phylogeny of language. Young children’s language and nonhuman primates’ signing both appear formulaic with limited syntactic combinations, thereby suggesting a degree of continuity in their cognitive abilities. To evaluate the validity of this approach, as well as to develop a quantitative benchmark to assess children’s language development, I propose a formal analysis that characterizes the statistical profile of grammatical rules. I show that very young children’s language is consistent with a productive grammar rather than memorization of specific word combinations from caregivers’ speech. Furthermore, I provide a statistically rigorous demonstration that the sign use of Nim Chimpsky, the chimpanzee who was taught American Sign Language, does not show the expected productivity of a rule-based grammar. Implications for theories of language acquisition and evolution are discussed.
Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil
Authors: Gonçalves Vanessa Faria , Stenderup Jesper , Rodrigues-Carvalho Cláudia , Silva Hilton P. , Gonçalves-Dornelas Higgor , Líryo Andersen , Kivisild Toomas , Malaspinas Anna-Sapfo , Campos Paula F. , Rasmussen Morten , Willerslev Eske , Pena Sergio Danilo J.
Published: April 2013

There is a consensus that modern humans arrived in the Americas 15,000–20,000 y ago during the Late Pleistocene, most probably from northeast Asia through Beringia. However, there is still debate about the time of entry and number of migratory waves, including apparent inconsistencies between genetic and morphological data on Paleoamericans. Here we report the identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil. The identification of these two Polynesian haplogroups was confirmed in independent replications in Brazil and Denmark, ensuring reliability of the data. Parallel analysis of 12 other Botocudo individuals yielded only the well-known Amerindian mtDNA haplogroup C1. Potential scenarios to try to help understand these results are presented and discussed. The findings of this study may be relevant for the understanding of the pre-Columbian and/or post-Columbian peopling of the Americas.
Common mechanism unites membrane poration by amyloid and antimicrobial peptides
Authors: Last Nicholas B. , Miranker Andrew D.
Published: April 2013

Poration of bacterial membranes by antimicrobial peptides such as magainin 2 is a significant activity performed by innate immune systems. Pore formation by soluble forms of amyloid proteins such as islet amyloid polypeptide (IAPP) is implicated in cell death in amyloidoses. Similarities in structure and poration activity of these two systems suggest a commonality of mechanism. Here, we investigate and compare the mechanisms by which these peptides induce membrane leakage and bacterial cell death through the measurement of liposome leakage kinetics and bacterial growth inhibition. For both systems, leakage occurs through the nucleation-dependent formation of stable membrane pores. Remarkably, we observe IAPP and magainin 2 to be fully cross-cooperative in the induction of leakage and inhibition of bacterial growth. The effects are dramatic, with mixtures of these peptides showing activities >100-fold greater than simple sums of the activities of individual peptides. Direct protein–protein interactions cannot be the origin of cooperativity, as IAPP and its enantiomer
D
-IAPP are equally cross-cooperative. We conclude that IAPP and magainin 2 induce membrane leakage and cytotoxicity through a shared, cross-cooperative, tension-induced poration mechanism.
Pathway-based personalized analysis of cancer
Authors: Drier Yotam , Sheffer Michal , Domany Eytan
Published: April 2013

We introduce Pathifier, an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample. We demonstrate the algorithm’s performance on three colorectal cancer datasets and two glioblastoma multiforme datasets and show that our multipathway-based representation is reproducible, preserves much of the original information, and allows inference of complex biologically significant information. We discovered several pathways that were significantly associated with survival of glioblastoma patients and two whose scores are predictive of survival in colorectal cancer: CXCR3-mediated signaling and oxidative phosphorylation. We also identified a subclass of proneural and neural glioblastoma with significantly better survival, and an EGF receptor-deregulated subclass of colon cancers.
Flagella stator homologs function as motors for myxobacterial gliding motility by moving in helical trajectories
Authors: Nan Beiyan , Bandaria Jigar N. , Moghtaderi Amirpasha , Sun Im-Hong , Yildiz Ahmet , Zusman David R.
Published: April 2013

Significance

Gliding is a form of enigmatic bacterial surface motility that does not use visible external structures such as flagella or pili. This study characterizes the single-molecule dynamics of the
Myxococcus xanthus
gliding motor protein AglR, a homolog of the
Escherichia coli
flagella stator protein MotA. However, the
Myxococcus
motors, unlike flagella stators, lack peptidoglycan-binding domains. With photoactivatable localization microscopy (PALM), we found that these motor proteins move actively within the cell membrane and generate torque by accumulating in clusters that exert force on the gliding surface. Our model unifies gliding and swimming with conserved power-generating modules.
Modeling Ewing sarcoma tumors in vitro with 3D scaffolds
Authors: Fong Eliza Li Shan , Lamhamedi-Cherradi Salah-Eddine , Burdett Emily , Ramamoorthy Vandhana , Lazar Alexander J. , Kasper F. Kurtis , Farach-Carson Mary C. , Vishwamitra Deeksha , Demicco Elizabeth G. , Menegaz Brian A. , Amin Hesham M. , Mikos Antonios G. , Ludwig Joseph A.
Published: April 2013

The pronounced biological influence of the tumor microenvironment on cancer progression and metastasis has gained increased recognition over the past decade, yet most preclinical antineoplastic drug testing is still reliant on conventional 2D cell culture systems. Although monolayer cultures recapitulate some of the phenotypic traits observed clinically, they are limited in their ability to model the full range of microenvironmental cues, such as ones elicited by 3D cell–cell and cell–extracellular matrix interactions. To address these shortcomings, we established an ex vivo 3D Ewing sarcoma model that closely mimics the morphology, growth kinetics, and protein expression profile of human tumors. We observed that Ewing sarcoma cells cultured in porous 3D electrospun poly(ε-caprolactone) scaffolds not only were more resistant to traditional cytotoxic drugs than were cells in 2D monolayer culture but also exhibited remarkable differences in the expression pattern of the insulin-like growth factor-1 receptor/mammalian target of rapamycin pathway. This 3D model of the bone microenvironment may have broad applicability for mechanistic studies of bone sarcomas and exhibits the potential to augment preclinical evaluation of antineoplastic drug candidates for these malignancies.
Recent thymic emigrants are the preferential precursors of regulatory T cells differentiated in the periphery
Authors: Paiva Ricardo S. , Lino Andreia C. , Bergman Marie-Louise , Caramalho Íris , Sousa Ana E. , Zelenay Santiago , Demengeot Jocelyne
Published: April 2013

Most Forkhead box P3
+
(Foxp3
+
) CD4 regulatory T cell (Treg) precursors are newly formed thymocytes that acquire Foxp3 expression on antigen encounter in the thymus. Differentiation of Treg, however, can also occur in the periphery. What limits this second layer of self- and nonself-reactive Treg production in physiological conditions remains to be understood. In this work, we tested the hypothesis that, similarly to thymic Treg, the precursors of peripheral Treg are immature T cells. We show that CD4
+
CD8
−
Foxp3
−
thymocytes and recent thymic emigrants (RTEs), contrarily to peripheral naïve mature cells, efficiently differentiate into Treg on transfer into lymphopenic mice. By varying donor and recipient mice and conducting ex vivo assays, we document that the preferential conversion of newly formed T cells does not require intrathymic preactivation, is cell-intrinsic, and correlates with low and high sensitivity to natural inhibitors and inducers of Foxp3 expression, such as IL-6, T-cell receptor triggering, and TGF-β. Finally, ex vivo analysis of human thymocytes and peripheral blood T cells revealed that human RTE and newly developed T cells share an increased potential to acquire a FOXP3
bright
CD25
high
Treg phenotype. Our findings indicating that RTEs are the precursors of Tregs differentiated in the periphery should guide the design of Treg-based therapies.
Dictyostelium
Ric8 is a nonreceptor guanine exchange factor for heterotrimeric G proteins and is important for development and chemotaxis
Authors: Kataria Rama , Xu Xuehua , Fusetti Fabrizia , Keizer-Gunnink Ineke , Jin Tian , van Haastert Peter J. M. , Kortholt Arjan
Published: April 2013

Heterotrimeric G proteins couple external signals to the activation of intracellular signal transduction pathways. Agonist-stimulated guanine nucleotide exchange activity of G-protein-coupled receptors results in the exchange of G-protein-bound GDP to GTP and the dissociation and activation of the complex into Gα-GTP and a Gβγ dimer. In
Dictyostelium
, a basal chemotaxis pathway consisting of heterotrimeric and monomeric G proteins is sufficient for chemotaxis. Symmetry breaking and amplification of chemoattractant sensing occurs between heterotrimeric G protein signaling and Ras activation. In a pull-down screen coupled to mass spectrometry, with Gα proteins as bait, we have identified resistant to inhibitors of cholinesterase 8 (Ric8) as a nonreceptor guanine nucleotide exchange factor for Gα-protein. Ric8 is not essential for the initial activation of heterotrimeric G proteins or Ras by uniform chemoattractant; however, it amplifies Gα signaling, which is essential for Ras-mediated symmetry breaking during chemotaxis and development.
Stoichiometry for drug potentiation of a pentameric ion channel
Authors: daCosta Corrie J. B. , Sine Steven M.
Published: April 2013

Drug modulation of ion channels is a powerful means to alter physiological responses for therapeutic benefit, yet the structural bases of modulation remain poorly understood. Here we study potentiation of nicotinic α7 acetylcholine receptors, which are emerging drug targets in several neurological disorders. α7 receptors are ligand-gated ion channels composed of five identical subunits, each bearing a site for the potentiating drug PNU-120596 (PNU). How the individual subunits contribute to PNU potentiation is not known. Taking advantage of a PNU-resistant mutant, we generated receptors composed of normal and PNU-resistant subunits and tagged one of the subunits with conductance mutations to report subunit stoichiometry. We then used patch clamp recording to monitor PNU potentiation of single α7 receptors with defined stoichiometry in real time. We find that potentiation depends steeply on the number of PNU-resistant subunits and that four, and possibly five, subunits must be sensitive to PNU for potentiation to occur. Thus, by monitoring the activity of every possible subunit combination, our findings predict that at the macroscopic level, PNU potentiation is highly cooperative.
Kelch-like 3 and Cullin 3 regulate electrolyte homeostasis via ubiquitination and degradation of WNK4
Authors: Shibata Shigeru , Zhang Junhui , Puthumana Jeremy , Stone Kathryn L. , Lifton Richard P.
Published: April 2013

Pseudohypoaldosteronism type II (PHAII) is a rare Mendelian syndrome featuring hypertension and hyperkalemia resulting from constitutive renal salt reabsorption and impaired K
+
secretion. Recently, mutations in Kelch-like 3 (KLHL3) and Cullin 3 (CUL3), components of an E3 ubiquitin ligase complex, were found to cause PHAII, suggesting that loss of this complex’s ability to target specific substrates for ubiquitination leads to PHAII. By MS and coimmunoprecipitation, we show that KLHL3 normally binds to WNK1 and WNK4, members of WNK (with no lysine) kinase family that have previously been found mutated in PHAII. We show that this binding leads to ubiquitination, including polyubiquitination, of at least 15 specific sites in WNK4, resulting in reduced WNK4 levels. Dominant disease-causing mutations in KLHL3 and WNK4 both impair WNK4 binding, ubiquitination, and degradation. WNK4 normally induces clearance of the renal outer medullary K
+
channel (ROMK) from the cell surface. We show that WT but not mutant KLHL3 inhibits WNK4-induced reduction of ROMK level. We show that PHAII-causing mutations in WNK4 lead to a marked increase in WNK4 protein levels in the kidney in vivo. These findings demonstrate that CUL3–RING (really interesting new gene) ligases that contain KLHL3 target ubiquitination of WNK4 and thereby regulate WNK4 levels, which in turn regulate levels of ROMK. These findings reveal a specific role of CUL3 and KLHL3 in electrolyte homeostasis and provide a molecular explanation for the effects of disease-causing mutations in both KLHL3 and WNK4.
Resetting translational homeostasis restores myelination in Charcot-Marie-Tooth disease type 1B mice
Authors: D’Antonio Maurizio , Musner Nicolò , Scapin Cristina , Ungaro Daniela , Del Carro Ubaldo , Ron David , Feltri M. Laura , Wrabetz Lawrence
Published: April 2013

P0 glycoprotein is an abundant product of terminal differentiation in myelinating Schwann cells. The mutant P0S63del causes Charcot-Marie-Tooth 1B neuropathy in humans, and a very similar demyelinating neuropathy in transgenic mice. P0S63del is retained in the endoplasmic reticulum of Schwann cells, where it promotes unfolded protein stress and elicits an unfolded protein response (UPR) associated with translational attenuation. Ablation of Chop, a UPR mediator, from S63del mice completely rescues their motor deficit and reduces active demyelination by half. Here, we show that Gadd34 is a detrimental effector of CHOP that reactivates translation too aggressively in myelinating Schwann cells. Genetic or pharmacological limitation of Gadd34 function moderates translational reactivation, improves myelination in S63del nerves, and reduces accumulation of P0S63del in the ER. Resetting translational homeostasis may provide a therapeutic strategy in tissues impaired by misfolded proteins that are synthesized during terminal differentiation.
Reduced divisors and embeddings of tropical curves
Authors: Amini Omid
Published: April 2013

Given a divisor

D
D

on a tropical curve

Γ
\Gamma

, we show that reduced divisors define an integral affine map from the tropical curve to the complete linear system

|

D

|

|D|

. This is done by providing an explicit description of the behavior of reduced divisors under infinitesimal modifications of the base point. We consider the cases where the reduced-divisor map defines an embedding of the curve into the linear system and, in this way, classify all the tropical curves with a very ample canonical divisor. As an application of the reduced-divisor map, we show the existence of Weierstrass points on tropical curves of genus at least two and present a simpler proof of a theorem of Luo on rank-determining sets of points. We also discuss the classical analogue of the (tropical) reduced-divisor map: For a smooth projective curve

C
C

and a divisor

D
D

of non-negative rank on

C
C

, reduced divisors equivalent to

D
D

define a morphism from

C
C

to the complete linear system

|

D

|

|D|

, which is described in terms of Wronskians.
Lower bounds of growth of Hopf algebras
Authors: Wang D.-G. , Zhang J. , Zhuang G.
Published: April 2013

Some lower bounds of GK-dimension of Hopf algebras are given.
Resolvent at low energy III: The spectral measure
Authors: Guillarmou Colin , Hassell Andrew , Sikora Adam
Published: April 2013

Let

M
∘

M^\circ

be a complete noncompact manifold and

g
g

an asymptotically conic Riemaniann metric on

M
∘

M^\circ

, in the sense that

M
∘

M^\circ

compactifies to a manifold with boundary

M
M

in such a way that

g
g

becomes a scattering metric on

M
M

. Let

Δ
\Delta

be the positive Laplacian associated to

g
g

, and

P
=
Δ
+
V

P = \Delta + V

, where

V
V

is a potential function obeying certain conditions. We analyze the asymptotics of the spectral measure
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="d upper E left-parenthesis lamda right-parenthesis equals left-parenthesis lamda slash pi i right-parenthesis left-parenthesis upper R left-parenthesis lamda plus i Baseline 0 right-parenthesis minus upper R left-parenthesis lamda minus i Baseline 0 right-parenthesis right-parenthesis">

d
E
(
λ
)
=
(
λ

/

π
i
)

(

R
(
λ
+
i
0
)
−
R
(
λ
−
i
0
)

)

dE(\lambda ) = (\lambda /\pi i) \big ( R(\lambda +i0) - R(\lambda - i0) \big )

of

P
+

1

/

2

P_+^{1/2}

, where

R
(
λ
)
=
(
P
−

λ
2

)

−
1

R(\lambda ) = (P - \lambda ^2)^{-1}

, as

λ
→
0

\lambda \to 0

, in a manner similar to that done by the second author and Vasy (2001) and by the first two authors (2008, 2009). The main result is that the spectral measure has a simple, ‘conormal-Legendrian’ singularity structure on a space which was introduced in the 2008 work of the first two authors and is obtained from

M
2

×
[
0
,

λ
0

)

M^2 \times [0, \lambda _0)

by blowing up a certain number of boundary faces. We use this to deduce results about the asymptotics of the wave solution operators

cos
⁡
(
t

P
+

)

\cos (t \sqrt {P_+})

and

sin
⁡
(
t

P
+

)

/

P
+

\sin (t \sqrt {P_+})/\sqrt {P_+}

, and the Schrödinger propagator

e

i
t

P
+

e^{itP_+}

, as

t
→
∞

t \to \infty

. In particular, we prove the analogue of Price’s law for odd-dimensional asymptotically conic manifolds.

In future articles, this result on the spectral measure will be used to (i) prove restriction and spectral multiplier estimates on asymptotically conic manifolds, and (ii) prove long-time dispersion and Strichartz estimates for solutions of the Schrödinger equation on

M
M

, provided

M
M

is nontrapping.
Threefold flops via matrix factorization
Authors: Curto Carina , Morrison David
Published: April 2013

The explicit McKay correspondence, as formulated by Gonzalez- Sprinberg and Verdier, associates to each exceptional divisor in the minimal resolution of a rational double point, a matrix factorization of the equation of the rational double point. We study deformations of these matrix factorizations, and show that they exist over an appropriate “partially resolved” deformation space for rational double points of types A and D. As a consequence, all simple flops of lengths 1 and 2 can be described in terms of blowups defined from matrix factorizations. We also formulate conjectures which would extend these results to rational double points of type E and simple flops of length greater than 2.
Modelling heat transfer in heterogeneous media using fractional calculus
Authors: Sierociuk Dominik , Dzieliński Andrzej , Sarwas Grzegorz , Petras Ivo , Podlubny Igor , Skovranek Tomas
Published: April 2013

This paper presents the results of modelling the heat transfer process in heterogeneous media with the assumption that part of the heat flux is dispersed in the air around the beam. The heat transfer process in a solid material (beam) can be described by an integer order partial differential equation. However, in heterogeneous media, it can be described by a sub- or hyperdiffusion equation which results in a fractional order partial differential equation. Taking into consideration that part of the heat flux is dispersed into the neighbouring environment we additionally modify the main relation between heat flux and the temperature, and we obtain in this case the heat transfer equation in a new form. This leads to the transfer function that describes the dependency between the heat flux at the beginning of the beam and the temperature at a given distance. This article also presents the experimental results of modelling real plant in the frequency domain based on the obtained transfer function.
A high-speed algorithm for computation of fractional differentiation and fractional integration
Authors: Fukunaga Masataka , Shimizu Nobuyuki
Published: April 2013

A high-speed algorithm for computing fractional differentiations and fractional integrations in fractional differential equations is proposed. In this algorithm, the stored data are not the function to be differentiated or integrated but the weighted integrals of the function. The intervals of integration for the memory can be increased without loss of accuracy as the computing time-step
n
increases. The computing cost varies as

, as opposed to
n
2
of standard algorithms.
A semi-discrete finite element method for a class of time-fractional diffusion equations
Authors: Sun HongGuang , Chen Wen , Sze K. Y.
Published: April 2013

As fractional diffusion equations can describe the early breakthrough and the heavy-tail decay features observed in anomalous transport of contaminants in groundwater and porous soil, they have been commonly used in the related mathematical descriptions. These models usually involve long-time-range computation, which is a critical obstacle for their application; improvement of computational efficiency is of great significance. In this paper, a semi-discrete method is presented for solving a class of time-fractional diffusion equations that overcome the critical long-time-range computation problem. In the procedure, the spatial domain is discretized by the finite element method, which reduces the fractional diffusion equations to approximate fractional relaxation equations. As analytical solutions exist for the latter equations, the burden arising from long-time-range computation can effectively be minimized. To illustrate its efficiency and simplicity, four examples are presented. In addition, the method is used to solve the time-fractional advection–diffusion equation characterizing the bromide transport process in a fractured granite aquifer. The prediction closely agrees with the experimental data, and the heavy-tail decay of the anomalous transport process is well represented.
A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity
Authors: Zhang Bing , Day Daniel S. , Ho Joshua W. , Song Lingyun , Cao Jingjing , Christodoulou Danos , Seidman Jonathan G. , Crawford Gregory E. , Park Peter J. , Pu William T.
Published: April 2013

Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth factor A (VEGFA), a major regulator of angiogenesis, triggers changes in transcriptional activity of human umbilical vein endothelial cells (HUVECs). Here, we used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to measure genome-wide changes in histone H3 acetylation at lysine 27 (H3K27ac), a marker of active enhancers, in unstimulated HUVECs and HUVECs stimulated with VEGFA for 1, 4, and 12 h. We show that sites with the greatest H3K27ac change upon stimulation were associated tightly with EP300, a histone acetyltransferase. Using the variation of H3K27ac as a novel epigenetic signature, we identified transcriptional regulatory elements that are functionally linked to angiogenesis, participate in rapid VEGFA-stimulated changes in chromatin conformation, and mediate VEGFA-induced transcriptional responses. Dynamic H3K27ac deposition and associated changes in chromatin conformation required EP300 activity instead of altered nucleosome occupancy or changes in DNase I hypersensitivity. EP300 activity was also required for a subset of dynamic H3K27ac sites to loop into proximity of promoters. Our study identified thousands of endothelial, VEGFA-responsive enhancers, demonstrating that an epigenetic signature based on the variation of a chromatin feature is a productive approach to define signal-responsive genomic elements. Further, our study implicates global epigenetic modifications in rapid, signal-responsive transcriptional regulation.
Lift-off protocols for thin films for use in EXAFS experiments
Authors: Decoster S. , Glover C. J. , Johannessen B. , Giulian R. , Sprouster D. J. , Kluth P. , Araujo L. L. , Hussain Z. S. , Schnohr C. , Salama H. , Kremer F. , Temst K. , Vantomme A. , Ridgway M. C.
Published: April 2013

Lift-off protocols for thin films for improved extended X-ray absorption fine structure (EXAFS) measurements are presented. Using wet chemical etching of the substrate or the interlayer between the thin film and the substrate, stand-alone high-quality micrometer-thin films are obtained. Protocols for the single-crystalline semiconductors GeSi, InGaAs, InGaP, InP and GaAs, the amorphous semiconductors GaAs, GeSi and InP and the dielectric materials SiO2and Si3N4are presented. The removal of the substrate and the ability to stack the thin films yield benefits for EXAFS experiments in transmission as well as in fluorescence mode. Several cases are presented where this improved sample preparation procedure results in higher-quality EXAFS data compared with conventional sample preparation methods. This lift-off procedure can also be advantageous for other experimental techniques (e.g.small-angle X-ray scattering) that benefit from removing undesired contributions from the substrate.
Quantifying the effect of habitat availability on species distributions
Authors: Aarts Geert , Fieberg John , Brasseur Sophie , Matthiopoulos Jason
Published: April 2013

If animals moved randomly in space, the use of different habitats would be proportional to their availability. Hence, deviations from proportionality between use and availability are considered the tell‐tale sign of preference. This principle forms the basis for most habitat selection and species distribution models fitted to use‐availability or count data (e.g. MaxEnt and Resource Selection Functions).

Yet, once an essential habitat type is sufficiently abundant to meet an individual's needs, increased availability of this habitat type may lead to a decrease in the use/availability ratio. Accordingly, habitat selection functions may estimate negative coefficients when habitats are superabundant, incorrectly suggesting an apparent avoidance. Furthermore, not accounting for the effects of availability on habitat use may lead to poor predictions, particularly when applied to habitats that differ considerably from those for which data have been collected.

Using simulations, we show that habitat use varies non‐linearly with habitat availability, even when individuals follow simple movement rules to acquire food and avoid risk. The results show that the impact of availability strongly depends on the type of habitat (e.g. whether it is essential or substitutable) and how it interacts with the distribution and availability of other habitats.

We demonstrate the utility of a variety of existing and new methods that enable the influence of habitat availability to be explicitly estimated. Models that allow for non‐linear effects (using b‐spline smoothers) and interactions between environmental covariates defining habitats and measures of their availability were best able to capture simulated patterns of habitat use across a range of environments.

An appealing aspect of some of the methods we discuss is that the relative influence of availability is not defined a priori, but directly estimated by the model. This feature is likely to improve model prediction, hint at the mechanism of habitat selection, and may signpost habitats that are critical for the organism's fitness.
Being Muslim in South Sudan (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Salomon Noah
Published: April 2013

This guest editorial deals with Muslims in South Sudan after partition.
Privatizing the borders: Human rights and the British visa regime (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Kaneff Deema
Published: April 2013

This paper explores the ‘strengthening’ of UK borders through the privatisation of border controls. It looks at the consequences of shifting activities relating to the management of visa applications from the state to the private sector (transnational corporations), and explores the implications this has in terms of human rights and entitlements.
Guns, anthropology, and cultural relativism: A response to Hugh Gusterson's ‘Making a killing’, AT28(1) (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Hultin Niklas
Published: April 2013

This comment responds to Hugh Gusterson's guest editorial on gun control in the February 2013 issue and applies is to the case of Gambia.
Israel/anthropology: ‘Screaming assembly’ (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Rapport Nigel
Published: April 2013

This book review article is a reflection on anthropology in Israel.
Initiating decision‐making in neurology consultations: ‘recommending’ versus ‘option‐listing’ and the implications for medical authority
Authors: Toerien Merran , Shaw Rebecca , Reuber Markus
Published: April 2013

This article compares two practices for initiating treatment decision‐making, evident in audio‐recorded consultations between a neurologist and 13 patients in two hospital clinics in the UK. We call these ‘recommending’ and ‘option‐listing’. The former entails making a proposal to do something; the latter entails the construction of a list of options. Using conversation analysis (CA), we illustrate each, showing that the distinction between these two practices matters to participants. Our analysis centres on two distinctions between the practices: epistemic differences and differences in the slots each creates for the patient’s response. Considering the implications of our findings for understanding medical authority, we argue that option‐listing – relative to recommending – is a practice whereby clinicians work to relinquish a little of their authority. This article contributes, then, to a growing body of CA work that offers a more nuanced, tempered account of medical authority than is typically portrayed in the sociological literature. We argue that future CA studies should map out the range of ways – in addition to recommending – in which treatment decision‐making is initiated by clinicians. This will allow for further evidence‐based contributions to debates on the related concepts of patient participation, choice, shared decision‐making and medical authority.
Biographical value: towards a conceptualisation of the commodification of illness narratives in contemporary healthcare
Authors: Mazanderani Fadhila , Locock Louise , Powell John
Published: April 2013

Illness narratives play a central role in social studies of health and illness, serving as both a key theoretical focus and a popular research method. Despite this, relatively little work has gone into conceptualising how and why illness narratives – be they in books, websites, television or other media – are commodified in contemporary healthcare and its social environment; namely, how distinctive forms of value are generated in the production, circulation, use and exchange of illness narratives. In this article we propose the notion of biographical value as a first step towards conceptualising the values attributed to illness narratives in this context. Based on a secondary analysis of 37 interviews with people affected by 15 different health conditions in the UK (all of whom have shared their illness experiences across various media) and drawing on understandings of value in research on the bioeconomy and the concept of biovalue in particular, we sketch out how epistemic, ethical and economic forms of value converge and co‐constitute each other in the notion of biographical value and in broader economies of illness experiences.
The family meal panacea: exploring how different aspects of family meal occurrence, meal habits and meal enjoyment relate to young children’s diets
Authors: Skafida Valeria
Published: April 2013

The general consensus in the research to date is that family meals are linked to healthier eating habits in children, compared to not eating with the family. Yet, few studies explore what it is about commensality which leads to better food choices among children. Using a representative Scottish sample of five‐year‐old children, this research explores the extent to which family meal occurrence, meal patterns regarding where, when and with whom children eat and perceived meal enjoyment predict the quality of children’s diets after controlling for indicators of maternal capital that influence both meal rituals and taste preferences. Eating the same food as parents is the aspect of family meals most strongly linked to better diets in children, highlighting the detrimental effect in the rise of ‘children’s food’. Although theoretical and empirical work pointed to the important health advantage in children eating together with parents, the results suggested that eating together was a far less important aspect of family meals. In evaluating the importance of the family meal, this article redirects attention away from issues of form and function towards issues of food choice. Policy implications and the importance for public health to recognise the way eating habits are defined by and reproduce social and cultural capital are discussed.
Detection of possible adulteration in commercial ghee samples using low‐resolution gas chromatography triglyceride profiles
Authors: Amrutha Kala A. L.
Published: April 2013

Fifteen commercial and 22 control samples of ghee were analysed for triglyceride compositions by low‐resolution short capillary column gas chromatography. Control samples of mixed milk and buffalo milks exhibited maxima at C38 and C50. The detection level was found to be 2% in case of beef tallow and coconut oil addition. Vegetable fat and lard addition could be detected at 5% and 6.3%, respectively. A sample survey based on triglyceride profile and standardised (S) values calculation revealed up to 43% branded ghee samples and 87.5% samples of unbranded ghee did not conform to triglyceride profiles of control ghee.
High‐grade vaginal intraepithelial neoplasia: can we be selective about who we treat?
Authors: Ratnavelu N , Patel A , Fisher AD , Galaal K , Cross P , Naik R
Published: April 2013

Objective

To determine the role of conservative management in high‐grade vaginal intraepithelial neoplasia (HG VaIN).

Design

Retrospective observational study.

Setting

Northern Gynaecological Oncology Centre, Gateshead, UK.

Population

A total of 100 women with histologically‐proven HG VaIN.

Methods

Review of patient records from 1995 to 2011.

Main outcome measures

Rates of progression to cancer, treatment remission, and disease recurrence, particularly post‐treatment when vaginoscopy is normal but cytology is abnormal.

Results

Of 100 women referred, 69 underwent initial treatment of whom 47 (68%) went into remission: of these, seven developed a recurrence after a median follow‐up of 29 months (range 15–214 months). Of the 31 women managed conservatively with cytological and vaginoscopic surveillance, no cancers developed after a median follow‐up of 35 months (range 2–230 months). Rate of overall progression to cancer was 3% and all were detected among the initial treatment group after a median of 59 months (range 8–249 months). Post‐treatment, when normal vaginoscopy was accompanied by abnormal cytology, two categories existed. Of 24 cases with low‐grade cytological abnormality, recurrence of HG VaIN occurred in seven (29%) after a median follow‐up of 12 months (range 2–110 months). Of 19 cases with HG cytological abnormality, 15 (79%) developed recurrence at a median follow‐up of 7 months (range 2–21 months), giving a hazard ratio 5.6 (95% confidence interval 2.0–15.5, P = 0.001).

Conclusions

It is possible to select women with HG VaIN for conservative surveillance with excellent results. The majority of women undergoing initial treatment will enter remission. Post‐treatment, if cytological abnormality develops in the presence of normal vaginoscopy, the majority of women will develop histological HG VaIN recurrence.
Profiling the Ginsenosides of Three Ginseng Products by Lc‐Q‐Tof/Ms
Authors: Chu Chu , Xu Shaojing , Li Xingnuo , Yan Jizhong , Liu Li
Published: April 2013

Ginseng is a well‐known herbal medicine that has been gaining increasingly popularity as a potential chemopreventive agent. In traditional Chinese medicine practice, white ginseng (WG), red ginseng (RG), and dali ginseng (DG) are 3 different ginseng‐processed products used for different purposes. Although the morphological appearance and some constituents contained in these ginseng products are similar, their pharmacological activities are significantly different due to the varied types and quantity of ginsenosides in each product. In the present study, a practical method based on rapid liquid chromatography coupled with quadrupole time of flight mass spectrometry (LC‐Q‐TOF/MS) was developed to identify the chemical profiles of ginsenosides in these 3 ginseng products. The results demonstrated that a total of 55, 53, and 43 compounds were unambiguously assigned or tentatively identified in DG, WG, and RG samples, respectively. The featured compounds are mainly malonyl ginsenosides in WG, and decarboxyl products of mal‐ginsenosides and the dehydrated compounds from polar ginsenosides were characteristic in RG, while DG contain some characteristic components present both in WG and RG. We presume that heating processing is the major factor affecting the chemical profile of ginseng products. The difference of chemical information revealed by LC‐Q‐TOF/MS could be used to discriminate the WG, RG, and DG samples.