bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance of windows multicore systems on threading and MPI
Authors: Qiu Judy , Bae Seung‐Hee
Published: May 2011

We present performance results on a Windows cluster with up to 768 cores using Message Passing Interface (MPI) and two variants of threading—Concurrency and Coordination Runtime (CCR) and Task Parallel Library (TPL). CCR presents a message‐based interface, while TPL allows for loops to be automatically parallelized. MPI is used between the cluster nodes (up to 32) and either threading or MPI for parallelism on the 24 cores of each node. We look at the performance of two significant bioinformatics applications; gene clustering and dimension reduction. We find that the two threading runtimes offer similar performance with MPI outperforming both at low levels of parallelism but threading much better when the grain size (problem size per process/thread) is small. We develop simple models for the performance of the clustering code. Copyright © 2011 John Wiley & Sons, Ltd.
Computational Insights into the Roles of Steric and Electrostatic Interactions in Arsenic Ylide Mediated Aziridination Reactions
Authors: Jaccob Madhavan , Venuvanalingam Ponnambalam
Published: May 2011

DFT calculations have been performed to study the mechanism and diastereoselectivity aspects of aziridination reactions of arsenic ylides. The reactions of three different arsenic ylides, unstabilized (H), semistabilized (Ph) and stabilized (COMe) arsenic ylides, with an imine have been considered. For all three arsenic ylides, the transoid mode of addition is more favoured than the cisoid mode of addition. The inherent stability differences between the addition transition‐state geometries are governed by steric interactions induced by the ylidic substituents and the methyl group of the carbamate and weak C–H···O hydrogen‐bonding interactions. For both the semistabilized and stabilized arsenic ylides, the trans selectivity is determined exclusively by the elimination transition states. The formation of trans‐aziridine is explained on the basis of weak hydrogen‐bonding interactions and steric interactions.
Unmasking low‐abundance peptides from human blood plasma and serum samples by a simple and robust two‐step precipitation/immunoaffinity enrichment method
Authors: Halfinger Bernhard , Sarg Bettina , Amann Arno , Hammerer‐Lercher Angelika , Lindner Herbert H.
Published: May 2011

Proteomic analysis of human plasma and serum for identifying and validating disease‐specific marker proteins and peptides has one major drawback besides its unique advantage as a readily available sample source for diagnostic assays. This disadvantage is represented by the predominance of several high‐ and middle‐abundant proteins, which clearly hamper identification and quantification approaches of potential and validated protein and peptide biomarkers, which are often of very low abundance. During the last decades, a significant number of depletion and enrichment techniques evolved to address these two issues. We present here a cost‐effective and easy‐to‐use strategy for protein depletion comprising a thermal precipitation protocol followed by a two‐step liquid/liquid precipitation as well as using an immunoaffinity chromatography method for the specific enrichment and isolation of the low‐abundance polypeptide N‐terminal pro‐B‐type natriuretic peptide and its precursor proBNP clinically used as biomarkers for the detection of severe human heart failure and related diseases. The applicability of this approach is shown by SDS ‐CGE, SDS‐PAGE, electrochemiluminescence immunoassay and nano‐LC ESI‐MS/MS. Our thermal precipitation protocol followed by a two‐step liquid/liquid precipitation could also serve as a potential depletion technique for the characterization of other low‐abundance peptides and proteins.
Importance of risk communication during and after a nuclear accident
Authors: Perko Tanja
Published: May 2011

Past nuclear accidents highlight communication as one of the most important challenges in emergency management. In the early phase, communication increases awareness and understanding of protective actions and improves the population response. In the medium and long term, risk communication can facilitate the remediation process and the return to normal life. Mass media play a central role in risk communication. The recent nuclear accident in Japan, as expected, induced massive media coverage. Media were employed to communicate with the public during the contamination phase, and they will play the same important role in the clean-up and recovery phases. However, media also have to fulfill the economic aspects of publishing or broadcasting, with the “bad news is good news” slogan that is a well-known phenomenon in journalism. This article addresses the main communication challenges and suggests possible risk communication approaches to adopt in the case of a nuclear accident. Integr Environ Assess Manag 2011;7:388–392. © 2011 SETAC
SPATIAL VARIABILITY OF SOIL PHYSICAL PROPERTIES IN A REGION OF THE LOESS PLATEAU OF PR CHINA SUBJECT TO WIND AND WATER EROSION
Authors: Wang Y. Q. , Shao M. A.
Published: May 2011

The analysis of the spatial variability of soil properties is important for land management and construction of an ecological environment. The objectives of this study were to investigate the spatial variability of saturated hydraulic conductivity (KS), total porosity (TP), capillary porosity (CP) and bulk density (BD) in relation to land use in a 0·54 km2 watershed on the Loess Plateau. Topsoil samples (0–5 cm) from 154 sites within the watershed were collected and analyzed by classical and geostatistical statistics in the summer of 2009. The results from the classical statistical analyses indicated that TP, CP and BD had low variability whereas KS had high variability with the watershed. Farmland had significantly lower BD and higher TP and CP than grassland, shrubland and woodland (p < 0·05). Geostatistical analyses revealed that the KS semivariogram was best fit by a spherical model, the CP semivariogram was best fit by an exponential model and the TP and BD semivariograms were best fit by Gaussian models. The nugget to sill ratios and fractal dimension values indicated that all four soil properties had strong spatial dependence. Moran's I analysis showed that a 100‐m sampling interval would be adequate for detecting the spatial structure of the four soil physical properties within the watershed. Spatial interpolation maps could provide useful information for precision agriculture practices and ecological management. Copyright © 2011 John Wiley & Sons, Ltd.
Coping and its effect on psychological distress of parents of pediatric cancer patients: a longitudinal prospective study
Authors: Hoekstra‐Weebers Josette E.H.M. , Wijnberg‐Williams Barbara J. , Jaspers Jan P.C. , Kamps Willem A. , van de Wiel Harry B.M.
Published: May 2011

Objective

This prospective 5‐year longitudinal study examined the use of coping styles of fathers and mothers of pediatric cancer patients over time and the prospective effects of coping on distress.

Methods

Psychological distress (General Health Questionnaire) and the use of seven coping styles (Utrecht Coping List: active problem focussing, palliative and passive reaction patterns, avoidance, social support seeking, expression of emotions, and comforting cognition) were assessed in 115 parents shortly after diagnosis, 6 and 12 months, and 5 years later.

Results

At diagnosis, parents' use of coping styles did not differ from the norm population except more frequent use of support seeking. No significant change over time was found in a palliative reaction pattern. Support seeking declined and emotional expression increased linearly, whereas use of the remaining coping styles decreased, followed by an increase. At 5 years, parents' use differed from the norm population only in less use of expression of emotions and comforting cognitions. Initial coping use significantly predicted fathers' future distress at 6 and 12 months but not at 5 years. This was not found for mothers. Changes in coping were significantly associated with both parents' changes in distress only during the first year. Increased passive reaction pattern and social support seeking were the risk factors for mothers. Increased avoidance, a passive reaction pattern, expression of emotions, and decreased active problem focussing formed the risk factors for fathers.

Conclusion

Findings illustrate that coping seems to be a situation‐specific process and that coping predictors vary as a function of parents' gender. Copyright © 2011 John Wiley & Sons, Ltd.
Survivor identity after colorectal cancer: antecedents, prevalence and outcomes
Authors: Chambers Suzanne K. , Baade Peter , Meng Xingqiong , Youl Pip , Aitken Joanne , Dunn Jeff
Published: May 2011

Objective

Cancer survivor identity has become a dominant paradigm in describing people with cancer and in driving the focus of programmes and research in supportive care. This study investigated antecedents of survivor identity adoption and population‐based prevalence.

Methods

A prospective survey of a population‐based sample of 1966 (57% response) patients with colorectal cancer assessed socio‐demographic variables, health behaviours, optimism, benefit finding, cancer threat appraisal, psychological distress and satisfaction with life at 5 months post‐diagnosis as predictors of survivor identity 5 years subsequently. Prevalence of survivor identity at 5 years post‐diagnosis and psychological and lifestyle outcomes (n = 786) were later assessed.

Results

Fifty‐five per cent of people identified as a cancer survivor, 39.4% as a person who had had (or has) cancer, 1.4% as a cancer patient and 1.2% as a cancer victim. People who were older and who reported higher personal growth after diagnosis were more likely to assume a survivor identity at 5 years. At 5 years, survivors had higher benefit finding and better satisfaction with life. Cancer survivors uniquely reported a significant decrease in somatization and acceptance, and increases in satisfaction with life and physical activity over time.

Conclusions

For patients with colorectal cancer, the cancer survivor identity is common but not universal 5 years after diagnosis; and may evolve from looking for benefit after cancer through personal growth. People who adopt a cancer survivor identity report more positive adjustment outcomes after cancer and this has implications for the design of clinical and community support interventions. Copyright © 2011 John Wiley & Sons, Ltd.
The disordering effect of periodically poled nonlinear crystals on parametric down conversion
Authors: Kheradmand Reza , Rezaei Mahdi , Kryuchkyan Gagik , Nemati Majid , Razmi Afshin
Published: May 2011

We have investigated the spectral properties and the multimode structure of joint states of photon pair produced by parametric down conversion in periodically poled nonlinear crystals (PPNC) by adding random length to each domain. We have also analysed the effect of additional random length on the output efficiency by considering two different configurations of PPNC and linear crystals, which we call (+, ‐) (PN) and (+, 0,−, 0) (PZNZ) configuration. In this paper we wish to study the effect of length fluctuations of segments which may occur in the preparation of PPNC in the laboratory. We aim at finding out how much error is reasonable in the process. In order to do this, we added random length to each segment and obtained the relevance between the output intensity and length fluctuations of the crystals.
Nanogap Electrode Fabrication for a Nanoscale Device by Volume‐Expanding Electrochemical Synthesis
Authors: Kim Ju‐Hyun , Moon Hanul , Yoo Seunghyup , Choi Yang‐Kyu
Published: May 2011

A novel nanogap fabrication method using an electrochemical nanopatterning technique is presented. Electrochemical deposition of platinum ions reduces the microgap size to the sub‐50‐nm range due to the self‐limited volume expansion of the electrodes. Additionally, the low crystallinity of platinum reduces the line edge roughness in the electrodes, whereas the high crystallinity of gold increases it. Current compliance, a buffered resistor, and a symmetric deposition strategy are used to achieve high reliability and practicality of nanogap electrodes. As a possible application, an organic thin‐film transistor using the nanogap electrodes is also demonstrated.
Effect of Casting Speed on Slab Broadening in Continuous Casting
Authors: Fu Jian‐Xun , Hwang Wen‐Sing , Li Jing‐She , Yang Shu‐Feng , Hui Zhang
Published: May 2011

A three‐dimensional viscoelastic‐plastic thermal‐mechanical coupled finite element model was based on the basis of the secondary development of commercial software (MSC, Marc software, USA) to simulation the effect of casting speed on slab broadening in the secondary cooling zone. The results show that the ratio of ultimate broadening increased with increasing casting speed for various steel grades, but the change in broadening lagged that in casting speed. When the casting speeds were 1.0 m/min, 1.1 m/min, and 1.2 m/min for Q235 steel, the maximum ratios of ultimate broadening were 1.52%, 1.59%, and 1.81%, respectively, and the average ratios of ultimate broadening at the exit of the caster were 1.00%, 1.27%, and 1.48%, respectively; for SPHC steel, the maximum ratios of ultimate broadening were 1.34%, 1.44%, and 1.69%, respectively, and the average ratios of ultimate broadening at the exit of the caster were 0.64%, 0.76%, and 0.95%, respectively. The simulation results were verified by measurements on an SMS‐Demag continuous caster of Maanshan Iron and Steel Co. Ltd.; the measurement results agree with the simulation results. The mechanism of the effect of casting speed on slab broadening was also analyzed.
Model structures for pro-simplicial presheaves
Authors: Jardine J.F.
Published: May 2011

This paper displays model structures for the category of pro-objects in simplicial presheaves on an arbitrary small Grothendieck site. The first of these is an analogue of the Edwards-Hastings model structure for pro-simplicial sets, in which the cofibrations are monomorphisms and the weak equivalences are specified by comparisons of function complexes. Other model structures are built from the Edwards-Hastings structure by using Bousfield-Friedlander localization techniques. There is, in particular, an n-type structure for pro-simplicial presheaves, and also a model structure in which the map from a pro-object to its Postnikov tower is formally inverted.
Non-spherical bubble dynamics in a compressible liquid. Part 2. Acoustic standing wave
Authors: WANG Q. X. , BLAKE J. R.
Published: May 2011

This paper investigates the behaviour of a non-spherical cavitation bubble in an acoustic standing wave. The study has important applications to sonochemistry and in understanding features of therapeutic ultrasound in the megahertz range, extending our understanding of bubble behaviour in the highly nonlinear regime where jet and toroidal bubble formation may be important. The theory developed herein represents a further development of the material presented in Part 1 of this paper (Wang & Blake,J. Fluid Mech. vol. 659, 2010, pp. 191–224) to a standing wave, including repeated topological changes from a singly to a multiply connected bubble. The fluid mechanics is assumed to be compressible potential flow. Matched asymptotic expansions for an inner and outer flow are performed to second order in terms of a small parameter, the bubble-wall Mach number, leading to weakly compressible flow formulation of the problem. The method allows the development of a computational model for non-spherical bubbles by using a modified boundary-integral method. The computations show that the bubble remains approximately of a spherical shape when the acoustic pressure is small or is initiated at the node or antinode of the acoustic pressure field. When initiated between the node and antinode at higher acoustic pressures, the bubble loses its spherical shape at the end of the collapse phase after only a few oscillations. A high-speed liquid bubble jet forms and is directed towards the node, impacting the opposite bubble surface and penetrating through the bubble to form a toroidal bubble. The bubble first rebounds in a toroidal form but re-combines to a singly connected bubble, expanding continuously and gradually returning to a near spherical shape. These processes are repeated in the next oscillation.
The pragmatic variable: Toward a procedural interpretation
Authors: Terkourafi Marina
Published: May 2011

Labov defined the linguistic variable as “a class of variants which are ordered along a continuous dimension and whose position is determined by an independent linguistic or extralinguistic variable” (1966:15). A precondition for identifying surface forms as variants of a single variable is semantic, or truth-conditional, equivalence. This requirement proves hard to apply beyond (morpho)phonology, and was subsequently relaxed into one of functional equivalence. The focus of this article is pragmatic variation and how we should interpret functional equivalence to account for this. It is proposed that the variants of a pragmatic variable share a common procedural meaning, defined as a set of instructions guiding the inferential phase of utterance interpretation. Recasting the core meaning of pragmatic variables in procedural terms allows us to co-examine alternating forms that may express different referential meanings, remaining true to the spirit of Labov's proposal, who saw linguistic variables as socially motivated clusterings of forms. (Pragmatic variation, functional equivalence, procedural meaning, Relevance Theory)*
Understanding the Romano-British–Early Medieval Transition: A Zooarchaeological Perspective from Wroxeter (Viroconium Cornoviorum)
Authors: Hammon Andy
Published: May 2011

The demise of the Western Roman Empire combined with Germanic migration and influence from Continental Europe had a tumultuous and profound affect on the cultural and social identities of Britain's population. The fifth to seventh centuriesa.d.remain a poorly understood epoch in British history, hence the once traditional ‘Dark Ages’ label. A variety of factors have contributed to this phenomenon, which include the exact nature and timing of the Roman administration's abandonment of Britannia, the precise character and extent of Germanic migration, questionable historical sources, the paucity of physical evidence, and problematic artefact dating. Zooarchaeological analysis can, therefore, aid the elucidation of this period through the development of new perspectives, highlighting the socio-cultural (and economic) processes involved in the emergence of early medieval Britain from Roman Britannia. Large-scale excavations were carried out at the baths basilica of Wroxeter (Shrops.) between 1966 and 1990. The city was the fourth largest urban centre in Roman Britain, and was thecivitas-capital of the Cornovii. The excavations demonstrated how the public buildings of this central insula fell into disuse, prior to the possible construction of a grandiose private residence and complex in the sub-Roman period. It has been postulated that this building represents the palatial complex of atyrannus, or possibly a bishopric of the ‘Western British’ church. Analysis of the resultant animal bone assemblage has provided an opportunity to explore the social and ethnic identity of the site's inhabitants through their dietary habits.
There exists a topologically mixing interval exchange transformation
Authors: CHAIKA JON
Published: May 2011

We prove the existence of a topologically mixing interval exchange transformation and prove that no interval exchange is topologically mixing of all orders.
One train may hide another: anomalous origin of the left coronary artery from the pulmonary artery revealed by supraventricular tachycardia
Authors: Cognet Thomas , Séguéla Pierre-Emmanuel , Acar Philippe
Published: May 2011

We report the case of a 1-month-old boy with an unusual association of supraventricular tachycardia and anomalous origin of the left coronary artery from the pulmonary artery. Although signs of infarction were visible on the first electrocardiogram, the presence of an arrhythmia did not immediately suggest a coronary anomaly. Echocardiography allowed the diagnosis, thus leading to appropriate care.
Association between adiposity indices and cardiometabolic risk factors among adults living in Puerto Rico
Authors: Palacios Cristina , Pérez Cynthia M , Guzmán Manuel , Ortiz Ana P , Ayala Alelí , Suárez Erick
Published: May 2011

Objective

To compare the general adiposity index (BMI) with abdominal obesity indices (waist circumference (WC), waist-to-hip ratio (WHR) and waist-to-height ratio (WHtR)) in order to examine the best predictor of cardiometabolic risk factors among Hispanics living in Puerto Rico.

Design

Secondary analysis of measurements taken from a representative sample of adults. Logistic regression models (prevalence odds ratios (POR)), partial Pearson's correlations (controlling for age and sex) and receiver-operating characteristic (ROC) curves were calculated between indices of obesity (BMI, WC, WHR and WHtR) and blood pressure, HDL cholesterol (HDL-C), LDL cholesterol (LDL-C), total cholesterol (TC):HDL-C, TAG, fasting blood glucose, glycosylated Hb, high-sensitivity C-reactive protein (hs-CRP), fibrinogen, plasminogen activator inhibitor-1 (PAI-1) and an aggregated measure of cardiometabolic risk.

Setting

Household study conducted between 2005 and 2007 in the San Juan Metropolitan Area in Puerto Rico.

Subjects

A representative sample of 858 non-institutionalized adults.

Results

All four obesity indices significantly correlated with the cardiometabolic risk factors. WHtR had the highest POR for high TC:HDL-C, blood pressure, hs-CRP, fibrinogen and PAI-1; WC had the highest POR for low HDL-C and high LDL-C and fasting blood glucose; WHR had the highest POR for overall cardiometabolic risk, TAG and glycosylated Hb. BMI had the lowest POR for most risk factors and smallest ROC curve for overall cardiometabolic risk.

Conclusions

The findings of the study suggest that general adiposity and abdominal adiposity are both associated with cardiometabolic risk in this population, although WC, WHR and WHtR appear to be slightly better predictors than BMI.
Have Anglo-Catholics Lost their Vision for Mission Agencies? An Empirical Enquiry among Newly Ordained Clergy in Britain
Authors: Village Andrew , Francis Leslie J.
Published: May 2011

Attitude toward Christian mission agencies was investigated in a sample of 827 Anglican clergy ordained in the UK from 2002 to 2006. The Scale of Attitude Toward Mission Agencies (SATMA) consisted of six items related to the work that agencies do, and whether clergy wished to engage with this work. It had a high internal consistency reliability (Cronbach's alpha = 0.80). After controlling for theological liberalism or conservatism, attitudes were most positive among evangelicals and least positive among Anglo-Catholics. Both liberal and conservative Anglo-Catholic clergy showed less positive attitudes toward mission agencies than did other clergy.
Transient switch-on/off currents in molecular junctions
Authors: Petrov E. G. , Shevchenko Ye. V. , May V. , Hänggi P.
Published: May 2011

Based on the nonequilibrium density matrix theory we put forward a unified description of the transient and the steady state current formation through a molecular junction. It is demonstrated that the current follows the time evolution of the populations of those molecular charged states which participate in the inter-electrode charge transmission. As an example, the formation of switch-on/switch-off currents is analyzed for a junction where the molecule has two active terminal sites. It is shown that just after a sudden voltage switch-on or switch-off, the resulting transient currents can significantly exceed their steady state value. This feature is caused by molecular charging or discharging processes, which are fast compared to those processes responsible for establishing the steady state current in the junction. The largest transient currents appear if the coupling of the molecule to the adjacent electrodes is asymmetric, or if the applied voltage causes a transformation of extended molecular states into localized ones.
Structure and reactivity of pyridine crystal under pressure
Authors: Fanetti Samuele , Citroni Margherita , Bini Roberto
Published: May 2011

In this work we have performed an extensive high pressure study of the condensed phases of pyridine by Raman and IR spectroscopy. We have evidenced three different polymorphs, two crystalline, and one glassy and established the pressure conditions in which they exist as stable or metastable phases by several compression/decompression experiments both on annealed and not annealed samples. Crystallization and phase transitions are found to be kinetically driven. The vibrational spectra are extremely complex due to the low symmetry of the crystals, which implies a large number of crystal components. This complexity required a careful analysis of both IR and Raman data that led to the identification of 20 out of 21 external modes expected for phase II. We did not find any conclusive indication of phase transitions on compressing phase II thus indicating that phase II is likely the stable phase at the onset pressure of the chemical transformation of pyridine. The latter starts at 18 GPa and relevant differences from the well characterized benzene reaction suggest that it is likely driven by crystal defects.
Modulation response of quantum dot nanolight-emitting-diodes exploiting purcell-enhanced spontaneous emission
Authors: Suhr T. , Gregersen N. , Lorke M. , Mørk J.
Published: May 2011

The modulation bandwidth for a quantum dot light-emitting device is calculated using a detailed model for the spontaneous emission including the optical and electronic density-of-states. We show that the Purcell enhancement of the spontaneous emission rate depends critically on the degree of inhomogeneous broadening relative to the cavity linewidth and can improve the modulation speed only within certain parameter regimes.
Modeling statistical variations in high power microwave breakdown
Authors: Krile John T. , Neuber Andreas A.
Published: May 2011

Flashover of high power microwave (HPM) vacuum isolation windows presents a serious design limitation of megawatt class HPM systems. The delay time from HPM radiation incident on the window to flashover development on the atmospheric side is critical. Previously developed modeling efforts have yielded reasonable correlation with experimentally observed average delay times while failing to capture any statistical variations. Simply preseeding the volume with an initial electron density is identified as inadequate to describe the source of initiatory electrons. The process of field assisted electron detachment is examined and shown to be a probable candidate for the initiatory electron generation.
Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein
Authors: Nash Abigail I. , McNulty Reginald , Shillito Mary Elizabeth , Swartz Trevor E. , Bogomolni Roberto A. , Luecke Hartmut , Gardner Kevin H.
Published: May 2011

Light-oxygen-voltage (LOV) domains are blue light-activated signaling modules integral to a wide range of photosensory proteins. Upon illumination, LOV domains form internal protein-flavin adducts that generate conformational changes which control effector function. Here we advance our understanding of LOV regulation with structural, biophysical, and biochemical studies of EL222, a light-regulated DNA-binding protein. The dark-state crystal structure reveals interactions between the EL222 LOV and helix-turn-helix domains that we show inhibit DNA binding. Solution biophysical data indicate that illumination breaks these interactions, freeing the LOV and helix-turn-helix domains of each other. This conformational change has a key functional effect, allowing EL222 to bind DNA in a light-dependent manner. Our data reveal a conserved signaling mechanism among diverse LOV-containing proteins, where light-induced conformational changes trigger activation via a conserved interaction surface.
Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV
Authors: Thiagarajan Viruthachalam , Byrdin Martin , Eker André P. M. , Müller Pavel , Brettel Klaus
Published: May 2011

CPD photolyase uses light to repair cyclobutane pyrimidine dimers (CPDs) formed between adjacent pyrimidines in UV-irradiated DNA. The enzyme harbors an FAD cofactor in fully reduced state (FADH
-
). The CPD repair mechanism involves electron transfer from photoexcited FADH
-
to the CPD, splitting of its intradimer bonds, and electron return to restore catalytically active FADH
-
. The two electron transfer processes occur on time scales of 10
-10
and 10
-9
 s, respectively. Until now, CPD splitting itself has only been poorly characterized by experiments. Using a previously unreported transient absorption setup, we succeeded in monitoring cyclobutane thymine dimer repair in the main UV absorption band of intact thymine at 266 nm. Flavin transitions that overlay DNA-based absorption changes at 266 nm were monitored independently in the visible and subtracted to obtain the true repair kinetics. Restoration of intact thymine showed a short lag and a biexponential rise with time constants of 0.2 and 1.5 ns. We assign these two time constants to splitting of the intradimer bonds (creating one intact thymine and one thymine anion radical T
∘-
) and electron return from T
∘-
to the FAD cofactor with recovery of the second thymine, respectively. Previous model studies and computer simulations yielded various CPD splitting times between < 1 ps and < 100 ns. Our experimental results should serve as a benchmark for future efforts to model enzymatic photorepair. The technique and methods developed here may be applied to monitor other photoreactions involving DNA.
Perception of Relative Depth Interval: Systematic Biases in Perceived Depth
Authors: Harris Julie M. , Chopin Adrien , Zeiner Katharina , Hibbard Paul B.
Published: May 2011

Given an estimate of the binocular disparity between a pair of points and an estimate of the viewing distance, or knowledge of eye position, it should be possible to obtain an estimate of their depth separation. Here we show that, when points are arranged in different vertical geometric configurations across two intervals, many observers find this task difficult. Those who can do the task tend to perceive the depth interval in one configuration as very different from depth in the other configuration. We explore two plausible explanations for this effect. The first is the tilt of the empirical vertical horopter: Points perceived along an apparently vertical line correspond to a physical line of points tilted backwards in space. Second, the eyes can rotate in response to a particular stimulus. Without compensation for this rotation, biases in depth perception would result. We measured cyclovergence indirectly, using a standard psychophysical task, while observers viewed our depth configuration. Biases predicted from error due either to cyclovergence or to the tilted vertical horopter were not consistent with the depth configuration results. Our data suggest that, even for the simplest scenes, we do not have ready access to metric depth from binocular disparity.
Global defects in collagen secretion in a Mia3/TANGO1 knockout mouse
Authors: Wilson Deanna G. , Phamluong Khanhky , Li Li , Sun Mei , Cao Tim C. , Liu Peter S. , Modrusan Zora , Sandoval Wendy N. , Rangell Linda , Carano Richard A. D. , Peterson Andrew S. , Solloway Mark J.
Published: May 2011

Melanoma inhibitory activity member 3 (MIA3/TANGO1) is an evolutionarily conserved endoplasmic reticulum resident transmembrane protein. Recent in vitro studies have shown that it is required for the loading of collagen VII, but not collagen I, into COPII-coated transport vesicles. In this paper, we show that mice lacking Mia3 are defective for the secretion of numerous collagens, including collagens I, II, III, IV, VII, and IX, from chondrocytes, fibroblasts, endothelial cells, and mural cells. Collagen deposition by these cell types is abnormal, and extracellular matrix composition is compromised. These changes are associated with intracellular accumulation of collagen and the induction of a strong unfolded protein response, primarily within the developing skeleton. Chondrocyte maturation and bone mineralization are severely compromised in Mia3-null embryos, leading to dwarfism and neonatal lethality. Thus, Mia3’s role in protein secretion is much broader than previously realized, and it may, in fact, be required for the efficient secretion of all collagen molecules in higher organisms.
Plünnecke’s Theorem for asymptotic densities
Authors: Jin Renling
Published: May 2011

Plünnecke proved that if

B
⊆

N

B\subseteq \mathbb {N}

is a basis of order

h
>
1

h>1

, i.e.,

σ
(
h
B
)
=
1

\sigma (hB)=1

, then

σ
(
A
+
B
)
⩾
σ
(
A

)

1
−

1
h

\sigma (A+B)\geqslant \sigma (A)^{1-\frac {1}{h}}

, where

A
A

is an arbitrary subset of

N

\mathbb {N}

and

σ
\sigma

represents Shnirel’man density. In this paper we explore whether

σ
\sigma

can be replaced by other asymptotic densities. We show that Plünnecke’s inequality above is true if

σ
\sigma

is replaced by lower asymptotic density

d
_

\underline {d}

or by upper Banach density

B
D

BD

but not by upper asymptotic density

d
¯

\overline {d}

. The result about

d
_

\underline {d}

has some interesting consequences such as the inequality

d
_

(
A
+
P
)
⩾

d
_

(
A

)

2

/

3

\underline {d}(A+P)\geqslant \underline {d}(A)^{2/3}

for any

A
⊆

N

A\subseteq \mathbb {N}

, where

P
P

is the set of all prime numbers, and the inequality

d
_

(
A
+
C
)
⩾

d
_

(
A

)

3

/

4

\underline {d}(A+C)\geqslant \underline {d}(A)^{3/4}

for any

A
⊆

N

A\subseteq \mathbb {N}

, where

C
C

is the set of all cubes of nonnegative integers. The result about

B
D

BD

generalizes Theorem 3 of a 2001 work of the author by reducing the requirement of

B
B

being a piecewise basis to the requirement of

B
B

being an upper Banach basis.
Elder Abuse
Authors: McBride Kate
Published: May 2011

‘Elder abuse is a single or repeated act or lack of appropriate action, occurring within a relationship where there is an expectation of trust which causes harm or distress to an older person’. This article aims to explain the nature of elder abuse, including management which requires a multidisciplinary patient-centred approach.
Central neuropathic pain
Authors: Bowsher David
Published: May 2011

Central neuropathic pain can arise following damage to spinothalamocortical pathways in the spinal cord and brain

Stroke, multiple sclerosis, and spinal cord injury (trauma or disease) are the predominant causes

Central neuropathic pain is wrongly considered a rarity; several tens of thousands of cases exist in the UK and it can develop up to two years after stroke...
Transcutaneous electrical nerve stimulation (TENS) and acupuncture
Authors: Johnson Mark I.
Published: May 2011

TENS and acupuncture are simple and generally safe methods of stimulating peripheral nerves and muscles close to the site of pain in order to modulate nociceptive input to the spinal cord

TENS can be useful for peripheral neuropathic pain and analgesic effects are often felt immediately...
Spinal cord stimulation
Authors: Simpson Brian A.
Published: May 2011

Electricity has been used for centuries to relieve pain but spinal cord stimulation (SCS) came about with the Gate Control Theory in the 1960s

SCS was originally thought simply to close the gate by activating A fibres but its effect is more complex. It is likely that it helps to normalize the dysfunction that manifests as neuropathic pain...
Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice
Authors: Ficklin Stephen P. , Feltus F. Alex
Published: May 2011

One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.
A critical role for FcgammaRIIB in up-regulation of Fas ligand induced by a microbial polysaccharide
Authors: Piccioni M , Monari C , Bevilacqua S , Perito S , Bistoni F , Kozel T R , Vecchiarelli A
Published: May 2011

The microbial capsular polysaccharide glucuronoxylomannan (GXM) from the opportunistic fungus Cryptoccocus neoformans is able to alter the innate and adaptive immune response through multi-faceted mechanisms of immunosuppression. The ability of GXM to dampen the immune response involves the induction of T cell apoptosis, which is dependent on GXM-induced up-regulation of Fas ligand (FasL) on antigen-presenting cells. In this study we elucidate the mechanism exploited by GXM to induce up-regulation of FasL. We demonstrate that (i) the activation of FasL is dependent on GXM interaction with FcgammaRIIB (FcγRIIB); (ii) GXM induces activation of c-Jun NH2-terminal kinase (JNK) and p38 signal transduction pathways via FcγRIIB; (iii) this leads to downstream activation of c-Jun; (iv) JNK and p38 are simultaneously, but independently, activated; (v) FasL up-regulation occurs via JNK and p38 activation; and (vi) apoptosis occurs via FcγRIIB engagement with consequent JNK and p38 activation. Our results highlight a fast track to FasL up-regulation via FcγRIIB, and assign to this receptor a novel anti-inflammatory role that also accounts for induced peripheral tolerance. These results contribute to our understanding of the mechanism of immunosuppression that accompanies cryptococcosis.
Pyrosequencing cut‐off value identifying BRAFV600E mutation in fine needle aspiration samples of thyroid nodules
Authors: Yeo Min‐Kyung , Liang Zhe Long , Oh Taejeong , Moon Youngho , An Sungwhan , Kim Min Kyeong , Kim Koon Soon , Shong Minho , Kim Jin‐Man , Jo Young Suk
Published: May 2011

Context  Recently, tremendous efforts have been made towards the development of sensitive techniques to detect the BRAFV600E mutation in fine needle aspiration biopsy (FNAB) samples. However, newly developed quantitative and semi‐quantitative methods, such as dual‐priming oligonucleotide (DPO)‐based multiplex polymerase chain reaction (PCR), have the potential to generate false‐positive (FP) results.

Objectives  To eliminate the possibility of FP results, we generated a receiver operating characteristic (ROC) curve to investigate the diagnostic accuracy of pyrosequencing using quantitative data.

Design  Cytological diagnoses of 983 thyroid nodules were made according to the Bethesda System 2007. The BRAFV600E mutation was analysed by pyrosequencing, and statistical analyses were performed.

Results  Of the 983 nodules, 902 were adopted to evaluate the diagnostic value of pyrosequencing. The number of pathologically confirmed malignancies was 192, of which 182 were papillary thyroid cancer (PTC). By generating an ROC curve, we defined the optimal cut‐off value of the mutant allele peak as 5·95% (area under the curve, 0·849; sensitivity, 0·55; 1‐specificity, 0). When we applied this selective cut‐off value, the number of PTCs positive for BRAFV600E was 99 (54·4% of the total number of PTCs). With cytology alone, the diagnostic sensitivity and specificity of detecting malignancy were 71·2% and 100%, respectively. Pyrosequencing improved the diagnostic sensitivity from 71·2% to 78·5% (McNemar’s test, P < 0·001), without any change in the diagnostic specificity. When ‘suspicious for malignancy’ was considered a positive cytological outcome, pyrosequencing increased the diagnostic sensitivity of cytology from 95·8% to 96·9%; however, this improvement did not show statistical significance (McNemar’s test, P > 0·05).

Conclusions  Pyrosequencing is an effective method for detecting the BRAFV600E mutation in FNAB samples. By allowing the optimal cut‐off value to be determined, pyrosequencing improves the diagnostic sensitivity while eliminating the possibility of FP results.
Role of type 2 diabetes mellitus in nonalcoholic fatty liver disease
Authors: Bozzetto L. , Prinster A. , Cocozza S. , Rivellese A. A. , Annuzzi G.
Published: May 2011

Eur J Clin Invest 2011; 41 (12): 1368
Climbers' narratives of mountain spaces above 8000 metres: a social constructivist perspective
Authors: Wilson Geoff A
Published: May 2011

This article analyses narratives used by mountaineers experiencing mountain spaces above 8000 metres. Adopting a social constructivist perspective, the article focuses on published narratives by established mountaineers (focusing on Everest and K2), with the aim of exploring perceived notions of mountain spaces above 8000 metres as psychological and geographical physical and mental thresholds. By discussing specific narratives associated with technological aids (e.g. oxygen masks), summit fever, risk‐taking, the role of guides as important intermediaries for the reinforcement of socially constructed extreme mountain spaces, or the politicisation of mountain spaces through risk perceptions clouded by nationalism, the article argues that narrative constructivism helps us question nature‐society dualisms linked to high mountain spaces, especially by emphasising the artificiality of dehumanised spaces such as the ‘death zone’ above 8000 metres.
Susan Murcott and Pure Home Water: Building a Sustainable Mission–Driven Enterprise in Northern Ghana
Authors: Nelson Teresa , Ingols Cynthia , Christian–Murtie Jennifer , Myers Paul
Published: May 2011

Massachusetts Institute of Technology environmental engineer and social entrepreneur Susan Murcott has worked for more than two decades to deliver clean drinking water to the world's poorest citizens. The stakes are high: polluted water is one of the world's leading causes of disease and death, particularly for children under the age of five. In this case, Murcott launches a new social enterprise in the West African nation of Ghana. The demanding leadership role of the entrepreneur is highlighted as Murcott and her team face many standard start–up challenges around venture mission, market definition, and product pricing and quality within a culturally rich, global setting.
Angel Investors’ and Entrepreneurs’ Intentions to Exit Their Ventures: A Conflict Perspective
Authors: Collewaert Veroniek
Published: May 2011

This study examines the relationships among angel investor–entrepreneur relationship conflicts, task conflicts, and goal conflicts on the one hand and their intentions to exit on the other. I evaluate the hypotheses with survey data from 65 angel investors and 72 entrepreneurs belonging to 54 ventures located in either California or Belgium. Regression analyses indicate that entrepreneurial intentions to exit are higher for entrepreneurs who face more task and goal conflicts. Angel investors’ intentions to exit are only increased when faced with more goal conflicts. Together, these results indicate the importance of taking into account investor–entrepreneur relations when studying their respective exit processes.
The Decision to Exploit Opportunities for Innovation: A Study of High–Tech Small–Business Owners
Authors: de Jong Jeroen P.J.
Published: May 2011

We collected longitudinal data from 160 high–tech small–business owners to analyze if the planned behavior constructs are related to their decision to innovate, as evidenced by their behavior (rather than their intentions to do so). Subjective norms and perceived behavioral control are directly related with innovation exploitation. Attitude towards the opportunity is significant only when respondents perceive both positive subjective norms and being in high control. This multiplicative effect suggests that the planned behavior constructs can be thought of as necessary conditions beneath which business owners are much less likely to exploit identified opportunities. Implications are discussed.
Impact of precision grip tasks on cervical spinal network excitability in humans
Authors: Roche N. , Bussel B. , Maier M. A. , Katz R. , Lindberg P.
Published: May 2011

Non technical summary  Motor skill acquisition may induce modifications of spinal network excitability. We studied the impact of two different precision grip force control tasks on cervical spinal network excitability in healthy subjects. The results show that the nature of the motor task performed has a specific impact on the excitability of these cervical spinal circuits and that presynaptic Ia inhibition may play an important role for acquisition of a new motor task. The results strongly suggest that early motor adaptations induced by a motor task are not only cortical but also spinal in origin.
Dihydrotestosterone stimulates amino acid uptake and the expression of LAT2 in mouse skeletal muscle fibres through an ERK1/2‐dependent mechanism
Authors: Hamdi M. M. , Mutungi G.
Published: May 2011

Non technical summary  In a recent study we showed that dihydrotestosterone (DHT), but not testosterone, increases force production in fast contracting muscles and decreases it in slow contracting ones. These findings led us to suggest that DHT may be a better muscle building hormone than testosterone. In the present study, we have examined the effects of these hormones on amino acid transport in mouse fast and slow contracting skeletal muscle fibre bundles. Our results show that DHT increases protein synthesis and the transport of essential amino acids into fast contracting muscle fibre bundles, whereas testosterone does not. These findings confirm our previous proposition and reinforce our suggestion that DHT may be a better hormone for the treatment of muscle wasting conditions than testosterone.
Inhibition of K+ secretion in the distal nephron in nephrotic syndrome: possible role of albuminuria
Authors: Fila Marc , Brideau Gaëlle , Morla Luciana , Cheval Lydie , Deschênes Georges , Doucet Alain
Published: May 2011

Non‐technical summary  Plasma potassium concentration is a major determinant of muscle contractility and nerve conduction. The maintenance of plasma potassium concentration depends on the ability of kidneys to daily secrete in the urine the exact quantity of potassium ingested in the food. We show that in nephrotic syndrome, a common disease featuring abnormal urinary protein excretion and sodium retention, the membrane protein called ROMK channel responsible for kidney potassium secretion is inhibited. Thus, nephrotic rats are unable to excrete a dietary load of potassium and develop hyperkalaemia. Based on these findings, we would recommend not only a low sodium diet but also a controlled potassium diet for patients with nephrotic syndrome.