bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stepped piezoresistive microcantilever designs for biosensors
Authors: Ansari Mohd Zahid , Cho Chongdu , Urban Gerald 
Published: May 2012

Abstract
The sensitivity of a piezoresistive microcantilever biosensor strongly depends on its ability to convert the surface stress-induced deflections into large resistance change. To improve the sensitivity, we present stepped microcantilever biosensor designs that show significant resistance change compared with commonly used rectangular designs. The cantilever is made of silicon dioxide with a u-shaped silicon piezoresistor. The surface stress-induced deflections, bimorph deflection, fundamental resonant frequency and self-heating properties of the cantilever are studied using the FEM software. The surface stress-induced deflections are compared against the analytical model derived in this work. Results show that stepped designs have better signal-to-noise ratio than the rectangular ones and cantilevers with l/L between 0.5 and 0.75 are better designs for improving sensitivity.
Reciprocity in long pulse duration laser interactions with polymers
Authors: Marchant A L , Snelling H V 
Published: May 2012

Abstract
The laser irradiation of polyimide Kapton HN (PI), polyetheretherketone (PEEK), polyethyleneterephthalate (PET) and polypropylene (PP) by long pulse, radio frequency excited, CO2 laser radiation has been studied. In the pulse duration range 47–757 µs the minimum pulse energy required to damage the surface is found to be independent of exposure time. Hence, the threshold fluence is also independent of pulse duration; the same effect is achieved through the application of long pulses at low irradiance as shorter ones at higher irradiance. The values of these threshold fluences have been found to be 8.15 J cm−2, 5.36 J cm−2, 3.39 J cm−2 and 9.63 J cm−2 for PI, PEEK, PET and PP, respectively. The details of this behaviour have been analysed through calculations of the laser-induced temperature rise and the application of an Eyring-type rate law for the thermal decomposition of polyimide and PEEK and by considering the melting points of PP and PET.
On gas flow effects in 3D edge transport simulations for DIII-D plasmas with resonant magnetic perturbations
Authors: Frerichs H. , Reiter D. , Schmitz O. , Harting D. , Evans T.E. , Feng Y. 
Published: May 2012

Abstract
Pumping of neutral gas and re-fuelling in other locations (e.g. neutral beam injection or gas puffing) are key ingredients in divertor physics. However, these have not been included in previous 3D edge plasma transport simulations with the EMC3–EIRENE code. Including these effects brings the simulations closer to reality and we demonstrate that this has a significant impact on divertor parameters. In particular, we study the impact of the pumping efficiency on ITER similar shape plasmas at the DIII-D tokamak in the presence of resonant magnetic perturbations. Further, we investigate the so-called ‘particle pump-out effect’. We show that in the present transport model and for given pumping and re-fuelling rates, the density at the transition to the core region decreases with increasing perturbation current and also the temperature. The striation patterns in the target particle and heat fluxes are extended into the regular scrape-off layer, which is caused by cross-field transport into a thin layer around the perturbed separatrix.
Screening of resonant magnetic perturbations taking into account a self-consistent electric field
Authors: Kaveeva E. , Rozhansky V. 
Published: May 2012

Abstract
Steady-state screening of resonant magnetic perturbations (RMPs) in a tokamak is analysed taking into account a self-consistent electric field. On the one hand, the self-consistent radial electric field is determined by the balance of the electron radial conductivity in a stochastic magnetic field screened by the plasma and by the neoclassical ion conductivity. On the other hand, the parallel current of electrons, the radial projection of which is balanced by the ion current, determines the screening of RMPs. In this work, the self-consistent electric field and RMP screening are calculated. Two different regimes of screening are found: the ‘ion’ branch which corresponds to the negative radial electric field and the ‘electron’ branch for which the electric field is positive. Predictions of the model are compared with the experimental data and results of the simulation with various codes. The corresponding toroidal rotation and pump-out effect are discussed.
Edge topology and flows in the reversed-field pinch
Authors: Spizzo G. , Agostini M. , Scarin P. , Vianello N. , White R. B. , Cappello S. , Puiatti M. E. , Valisa M. 
Published: May 2012

Abstract
Edge topology and plasma flow deeply influence transport in the reversed-field pinch as well as in all fusion devices, playing an important role in many practical aspects of plasma performance, such as access to enhanced confinement regimes, the impact on global power balance and operative limits, such as the density limit (Spizzo G. et al 2010 Plasma Phys. Control. Fusion
52 095011).
A central role is played by the edge electric field, which is determined by the ambipolar constraint guaranteeing quasi-neutrality in a sheath next to the plasma wall. Its radial component is experimentally determined in RFX over the whole toroidal angle by means of a diagnostic set measuring edge plasma potential and flow with different techniques (Scarin P. et al 2011 Nucl. Fusion
51 073002). The measured radial electric field is used to construct the potential in the form Φ(ψp, θ, ζ) (ψp radial coordinate, θ, ζ angles), by means of the Hamiltonian guiding-centre code ORBIT. Simulations show that a proper functional form of the potential can balance the differential radial diffusion of electrons and ions subject to m = 0 magnetic island O- and X-points. Electrons spend more time in the X-points of such islands than in O-points; ions have comparatively larger drifts and their radial motion is more uniform over the toroidal angle. The final spatial distribution of Φ(ψp, θ, ζ) results in a complex 3D pattern, with convective cells next to the wall. Generally speaking, an edge topology dominating parallel transport with a given symmetry brings about an edge potential with the same symmetry. This fact helps us to build a first step of a unified picture of the effect of magnetic topology on the Greenwald limit, and, more generally, on flows in the edge of RFPs and tokamaks.
Magnetic barriers and their q95 dependence at DIII-D
Authors: Volpe F.A. , Kessler J. , Ali H. , Evans T.E. , Punjabi A. 
Published: May 2012

Abstract
It is well known that externally generated resonant magnetic perturbations (RMPs) can form islands in the plasma edge. In turn, large overlapping islands generate stochastic fields, which are believed to play a role in the avoidance and suppression of edge localized modes (ELMs) at DIII-D. However, large coalescing islands can also generate, in the middle of these stochastic regions, KAM surfaces effectively acting as ‘barriers’ against field-line dispersion and, indirectly, particle diffusion. It was predicted in Ali and Punjabi (2007 Plasma Phys. Control. Fusion
49 1565–82) that such magnetic barriers can form in piecewise analytic DIII-D plasma equilibria. In this work, the formation of magnetic barriers at DIII-D is corroborated by field-line tracing calculations using experimentally constrained EFIT (Lao et al 1985 Nucl. Fusion
25 1611) DIII-D equilibria perturbed to include the vacuum field from the internal coils utilized in the experiments. According to these calculations, the occurrence and location of magnetic barriers depend on the edge safety factor q
95. It was thus suggested that magnetic barriers might contribute to narrowing the edge stochastic layer and play an indirect role in the RMPs failing to control ELMs for certain values of q
95. The analysis of DIII-D discharges where q
95 was varied, however, does not show anti-correlation between barrier formation and ELM suppression.
OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing
Authors: Das Shreepriya , Vikalo Haris 
Published: May 2012

Abstract
Motivation: Next-generation DNA sequencing platforms are becoming increasingly cost-effective and capable of providing enormous number of reads in a relatively short time. However, their accuracy and read lengths are still lagging behind those of conventional Sanger sequencing method. Performance of next-generation sequencing platforms is fundamentally limited by various imperfections in the sequencing-by-synthesis and signal acquisition processes. This drives the search for accurate, scalable and computationally tractable base calling algorithms capable of accounting for such imperfections.
Results: Relying on a statistical model of the sequencing-by-synthesis process and signal acquisition procedure, we develop a computationally efficient base calling method for Illumina's sequencing technology (specifically, Genome Analyzer II platform). Parameters of the model are estimated via a fast unsupervised online learning scheme, which uses the generalized expectation–maximization algorithm and requires only 3 s of running time per tile (on an Intel i7 machine @3.07GHz, single core)—a three orders of magnitude speed-up over existing parametric model-based methods. To minimize the latency between the end of the sequencing run and the generation of the base calling reports, we develop a fast online scalable decoding algorithm, which requires only 9 s/tile and achieves significantly lower error rates than the Illumina's base calling software. Moreover, it is demonstrated that the proposed online parameter estimation scheme efficiently computes tile-dependent parameters, which can thereafter be provided to the base calling algorithm, resulting in significant improvements over previously developed base calling methods for the considered platform in terms of performance, time/complexity and latency.
Availability: A C code implementation of our algorithm can be downloaded from http://www.cerc.utexas.edu/OnlineCall/
Contact: hvikalo@ece.utexas.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly
Authors: Li Heng 
Published: May 2012

AbstractMotivation: Eugene Myers in his string graph paper suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs.Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the unitigs against a reference genome. By applying the method on 35-fold human resequencing data, we showed that in comparison to the standard pipeline, our approach yields similar accuracy for SNP calling and better results for INDEL calling. It has higher sensitivity than other de novo assembly based methods for variant calling. Our work suggests that variant calling with de novo assembly can be a beneficial complement to the standard variant calling pipeline for whole-genome resequencing. In the methodological aspects, we propose FMD-index for forward–backward extension of DNA sequences, a fast algorithm for finding all super-maximal exact matches and one-pass construction of unitigs from an FMD-index.Availability: http://github.com/lh3/fermiContact: hengli@broadinstitute.org
First Report of Iris yellow spot virus Infecting Onion in Pennsylvania
Authors: Hoepting C. A. , Fuchs M. F. 
Published: May 2012

Iris yellow spot virus (IYSV; genus Tospovirus; family Bunyaviridae) is an economically important pathogen of onion. It is vectored by onion thrips (Thrips tabaci Lindeman) and causes widespread disease of onion in all major onion growing states in the western United States (1). In the eastern United States, IYSV was first reported in Georgia in 2004 (4) and then in New York in 2006 (2). In mid-July of 2010, symptomatic onion (Allium cepa) plants (cv. Candy) were found in New Holland, Pennsylvania, in Lancaster County on a small, diversified commercial farm (40.06°N, 76.06°W). Bleached, elongated lesions with tapered ends occurred on middle-aged leaves on approximately 30% of the 13,760 plants in an area approximately one tenth of an acre. Leaf tissue from five symptomatic plants tested positive for IYSV in a double-antibody sandwich (DAS)-ELISA with IYSV-specific serological reagents from Agdia Inc. (Elkhart, IN). A reverse transcription (RT)-PCR assay was used to verify the presence of IYSV in a subset of symptomatic leaf samples that reacted to IYSV antibodies in DAS-ELISA. Primers specific to the nucleocapsid (N) gene of IYSV (5′-ACTCACCAATGTCTTCAAC-3′ and 5′-GGCTTCCTCTGGTAAGTGC-3′) were used to characterize a 402-bp fragment (3). The resulting amplicons were ligated in TOPO TA cloning vector (Invitrogen, Carlsbad, CA) and two clones of each isolate were sequenced in both directions. Sequence analysis showed a consensus sequence for the partial N gene of the five IYSV isolates from Pennsylvania (GenBank Accession No. JQ952568) and an 87 to 100% nucleotide sequence identity with other IYSV N gene sequences that are available in GenBank. The highest nucleotide sequence identity (100%) was with an IYSV isolate from Texas (GenBank Accession No. DQ658242) and the lowest was with an isolate from India (GenBank Accession No. EU310291). To our knowledge, this is the first report of IYSV infection of onion in Pennsylvania. This finding confirms further spread of the virus within North America. Further study is warranted to determine the impact of IYSV on the Pennsylvania onion industry and to determine viable management strategies, if necessary. References: (1) D. H. Gent et al. Plant Dis. 88:446, 2004 (2) C. A. Hoepting et al. Plant Dis. 91:327, 2007 (3) C. L. Hsu et al. Plant Dis. 95:735-743. (4) S. W. Mullis et al. Plant Dis. 88: 1285, 2004.
First Report of Elm Yellows Subgroup 16SrV-B Phytoplasma Infecting Chinese Tulip Tree in China
Authors: Li Z. Y. , Dong Z. P. , Hao Z. M. , Dong J. G. 
Published: May 2012

Chinese tulip tree (Liriodendron chinensis) is native to China and is planted all around the country as an ornamental tree. In July of 2011, some Chinese tulip trees with typical phytoplasma symptoms were found in Baoding City, Hebei Province, China. Symptoms included yellowing of leaves, slow decline, little leaves, and death of entire plants. To confirm phytoplasma infection of these plants, total DNA was extracted from 100 mg of fresh leaf midribs collected from leaves of nine symptomatic and eight asymptomatic plants with a plant DNA extract kit (Tiangen, Beijing, China) according to the manufacturer's protocols. Using 16S rRNA phytoplasma universal primer pairs P1/P7 followed by R16F2n/R16R2, a nest PCR was carried out (1,2). The results showed that the phytoplasma was only detected in symptomatic samples by nested PCR, while the asymptomatic were negative. An approximate 1.2-kb specific fragment was obtained from the DNA of nine symptomatic plants, but no product was amplified from the leaves of eight healthy ones. The amplified products were cloned and sequenced. The sequence was deposited in GenBank Data Libraries under Accession No. JQ585925 and shared the highest homology of 99% with Puna chicory flat stem phytoplasma (GenBank Accession No. JN582266), Apricot leaf roll phytoplasma (GenBank Accession No. FJ572660), Jujube witches'-broom phytoplasma (GenBank Accession No. AY197661), and other elm yellows group phytoplasmas by BLAST analysis with that of other phytoplasmas from GenBank. Meanwhile, the sequence data was analyzed by iPhyClassifier software and the result showed that the 16S rDNA F2nR2 fragment was identical (similarity coefficient 1.00) to the reference patterns of 16Sr group V, subgroup B (GenBank Accession No.AB052876) (3). Combining the BLAST analysis in GenBank and the analysis of iPhyClassifier, we classified the phytoplasma causing Chinese tulip tree yellow leaves disease into subgroup 16SrV-B. To our knowledge, this is the first report of the 16SrVB group phytoplasmas infecting Chinese tulip tree in China. References: (1) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) I. M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (3) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
CML42-Mediated Calcium Signaling Coordinates Responses to Spodoptera Herbivory and Abiotic Stresses in Arabidopsis
Authors: Vadassery Jyothilakshmi , Reichelt Michael , Hause Bettina , Gershenzon Jonathan , Boland Wilhelm , Mithöfer Axel 
Published: May 2012

Abstract
In the interaction between Arabidopsis (Arabidopsis thaliana) and the generalist herbivorous insect Spodoptera littoralis, little is known about early events in defense signaling and their link to downstream phytohormone pathways. S. littoralis oral secretions induced both Ca2+ and phytohormone elevation in Arabidopsis. Plant gene expression induced by oral secretions revealed up-regulation of a gene encoding a calmodulin-like protein, CML42. Functional analysis of cml42 plants revealed more resistance to herbivory than in the wild type, because caterpillars gain less weight on the mutant, indicating that CML42 negatively regulates plant defense; cml42 also showed increased aliphatic glucosinolate content and hyperactivated transcript accumulation of the jasmonic acid (JA)-responsive genes VSP2 and Thi2.1 upon herbivory, which might contribute to increased resistance. CML42 up-regulation is negatively regulated by the jasmonate receptor Coronatine Insensitive1 (COI1), as loss of functional COI1 resulted in prolonged CML42 activation. CML42 thus acts as a negative regulator of plant defense by decreasing COI1-mediated JA sensitivity and the expression of JA-responsive genes and is independent of herbivory-induced JA biosynthesis. JA-induced Ca2+ elevation and root growth inhibition were more sensitive in cml42, also indicating higher JA perception. Our results indicate that CML42 acts as a crucial signaling component connecting Ca2+ and JA signaling. CML42 is localized to cytosol and nucleus. CML42 is also involved in abiotic stress responses, as kaempferol glycosides were down-regulated in cml42, and impaired in ultraviolet B resistance. Under drought stress, the level of abscisic acid accumulation was higher in cml42 plants. Thus, CML42 might serve as a Ca2+ sensor having multiple functions in insect herbivory defense and abiotic stress responses.
Suppressive effect of recombinant human thioredoxin on ultraviolet light‐induced inflammation and apoptosis in murine skin
Authors: ONO Ryusuke , MASAKI Taro , DIEN Siphora , YU Xijun , FUKUNAGA Atsushi , YODOI Junji , NISHIGORI Chikako 
Published: May 2012

AbstractThioredoxin (TRX) is a small ubiquitous protein, which regulates cellular redox status and scavenges reactive oxygen species. The present study was conducted to investigate the effect of TRX on ultraviolet (UV)‐B‐mediated inflammatory and apoptotic responses. Ear swelling after UV‐B irradiation was significantly reduced in TRX‐transgenic mice compared to wild‐type mice. Administration i.p. of recombinant human TRX also reduced acute skin inflammatory reaction, such as skin erythema and swelling. Histologically, numbers of inflammatory cells including neutrophils and lymphocytes were significantly reduced and the average size of the caliber of blood vessels were also reduced in recombinant human TRX‐injected mice. The number of apoptotic keratinocytes, in terms of sunburn cells, activated‐caspase‐3‐positive cells and terminal deoxynucleotidyl transferase dUTP nick end labeling‐positive cells were all significantly reduced in recombinant human TRX‐injected mice. Immunohistochemical intensity of 8‐hydroxy‐2′‐deoxyguanosine was strikingly reduced in recombinant human TRX‐injected mouse. Western blotting showed that administration of recombinant human TRX attenuated duration of phosphorylation of p38 mitogen‐activated protein kinases and intensity of phosphorylation of c‐Jun N‐terminal kinase in the early phase, which play important roles in inflammatory and apoptotic signaling. Collectively, these findings indicated that recombinant human TRX attenuated inflammatory and apoptotic responses caused by UV‐B. Possible mechanisms for this might be via redox regulation of stress signaling and reduction of reactive oxygen species.
Alcohol consumption and psoriatic risk: A meta‐analysis of case–control studies
Authors: ZHU Kun‐Ju , ZHU Cheng‐Yao , FAN Yi‐Ming 
Published: May 2012

AbstractPsoriasis is one of the most common dermatological disorders. The association between alcohol consumption and psoriasis has been inconsistent among studies. To examine the magnitude of the risk of developing psoriasis for drinking populations compared to those with non‐drinking, and to determine causes of the variation in odds ratios (OR) between various case–control studies, we performed a comprehensive published work search and a meta‐analysis of case–control studies considering prevalence. We did electronic searches on Medline, and searched reports to identify case–control studies of prevalent of psoriasis. We did meta‐analyses of study‐specific incremental estimates to determine the risk of psoriasis associated with drinking. The magnitude of the OR was analyzed by combining 15 case–control studies that matched defined criteria. The variance in OR between studies was explored. The overall OR of psoriasis for drinking persons compared to those with non‐drinking was 1.531 (95% confidence interval [CI] = 1.164–2.014, P = 0.002) and the association remains statistically significant across a number of stratified analyses in European descent subgroup (OR = 1.432, 95% CI = 1.085–1.889, P = 0.011) and also persists in sensitivity analyses performed to assess the potential effect of varying psoriasis outcome definitions. Alcohol consumption is associated with increased risk of psoriasis. These epidemiological observations should inform the exploration of biological mechanisms that link alcohol consumption with psoriasis.