bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adding new dimensions to laser‐scanning fluorescence microscopy
Authors: DE A.K. , GOSWAMI D. 
Published: January 2009

SummaryWe describe a novel method of optical imaging by exploiting simple ideas borrowed from pulsed optics. We show that the use of ultrafast pulsed one‐photon excitation in laser‐scanning fluorescence microscopy dramatically brings together several advantages offered by two widely used present day microscopic techniques, confocal and multi‐photon fluorescence microscopy. The method appears as a novel tool in the context of laser‐scanning fluorescence microscopy by having a ‘built‐in’ 3D spatial resolution.
Self‐calibration method for vision‐guided cell micromanipulation systems
Authors: ZHANG Y.L. , HAN M.L. , SHEE C.Y. , CHIA T.F. , ANG W.T. 
Published: January 2009

SummaryA new self‐calibration method for a piezoelectric actuator‐based vision‐guided cell micromanipulation system is proposed. This method consolidates all the system parameters' uncertainties into a matrix instead of classifying into intrinsic and extrinsic. The position difference of the micromanipulator tip in the image plane between the measured and estimated output which is based on estimations of relevant parameters is assumed to be caused by the matrix. This matrix is estimated by means of collecting several pairs of known input and the corresponding output differences. Matrix standard deviation and gray‐value based matching are applied to identify the output differences. Biological contamination is reduced since a calibration template is not required. This self‐calibration is particularly suitable for cell micromanipulation systems where the micromanipulator is frequently dismounted and mounted.
Analysis of 3D elemental mapping artefacts in biological specimens using Monte Carlo simulation
Authors: SCOTT K. , RITCHIE N.W.M. 
Published: January 2009

SummaryIn this paper, we present Monte Carlo simulation results demonstrating the feasibility of using the focused ion beam based X‐ray microanalysis technique (FIB‐EDS) for the 3D elemental analysis of biological samples. In this study, we used a marine diatomThalassiosira pseudonanaas our model organism and NISTMonte for the Monte Carlo simulations. We explored several beam energies commonly used for the X‐ray microanalysis to examine their effects on the resulting 3D elemental volume of the model organism. We also performed a preliminary study on the sensitivity of X‐ray analysis for detecting nanoparticles in the model. For the conditions considered in this work, we show that the X‐ray mapping performed using the 5 keV beam energy results in 3D elemental distributions that closely reflect the elemental distributions in the original model. At 5 keV, the depth resolution of the X‐ray maps is about 250 nm for the model organism. We also show that the nanoparticles that are 50 nm in diameter or greater are easily located. Although much work is still needed in generating more accurate biological models and simulating experimental conditions relevant to these samples, our results indicate that FIB‐EDS is a promising technique for the 3D elemental analysis of some biological specimens.
Adaptive watershed segmentation of binary particle image
Authors: SUN H.Q. , LUO Y.J. 
Published: January 2009

SummaryOversegmentation is a tough problem in the morphological watershed segmentation of irregular‐shaped binary particles, which is usually caused by spurious minima in the inverse distance transform. The position relationship between two objects is clear, according to the value of overlap parameter defined in the paper, and an adaptive algorithm is presented to depress oversegmentation by building the criterion to merge the spurious local minima. Some particle images are provided to validate the performance of the proposed method.
Defocus convergent beam electron diffraction analysis of dislocations in mullite
Authors: GUSTAFSSON S. , FALK L.K.L. 
Published: January 2009

SummaryBurgers vectors of matrix dislocations in mullite have been determined by the defocus large‐angle convergent beam electron diffraction technique. Vectors of the types [100], [010], [110] and [112] were identified. These Burgers vectors are discussed in relation to the open channels and the oxygen vacancy distribution in the mullite structure. It is suggested that a short‐range ordering of oxygen vacancies may account for a Burgers vector of the type [112].
Drought tolerance in Arabidopsis is controlled by the OCP3 disease resistance regulator
Authors: Ramírez Vicente , Coego Alberto , López Ana , Agorio Astrid , Flors Víctor , Vera Pablo 
Published: January 2009

SummaryWater scarcity and corresponding abiotic drought stress is one of the most important factors limiting plant performance and yield. In addition, plant productivity is severely compromised worldwide by infection with microbial pathogens. Two of the most prominent pathways responsible for drought tolerance and disease resistance to fungal pathogens in Arabidopsis are those controlled by the phytohormones abscisic acid (ABA) and the oxylipin methyl jasmonate (MeJA), respectively. Here, we report on the functional characterization of OCP3, a transcriptional regulator from the homeodomain (HD) family. The Arabidopsis loss‐of‐function ocp3 mutant exhibits both drought resistance and enhanced disease resistance to necrotrophic fungal pathogens. Double‐mutant analysis revealed that these two resistance phenotypes have different genetic requirements. Whereas drought tolerance in ocp3 is ABA‐dependent but MeJA‐independent, the opposite holds true for the enhanced disease resistance characteristics. These observations lead us to propose a regulatory role of OCP3 in the adaptive responses to these two stresses, functioning as a modulator of independent and specific aspects of the ABA‐ and MeJA‐mediated signal transduction pathways.
The CRABS CLAW ortholog from California poppy (Eschscholzia californica, Papaveraceae), EcCRC, is involved in floral meristem termination, gynoecium differentiation and ovule initiation
Authors: Orashakova Svetlana , Lange Matthias , Lange Sabrina , Wege Stefanie , Becker Annette 
Published: January 2009

SummaryThe Arabidopsis transcription factor CRABS CLAW (CRC) is a major determinant of carpel growth and fusion, and, in concert with other redundantly acting genes, of floral meristem termination. Its rice ortholog, however, has additional functions in specifying carpel organ identity. We were interested in understanding the history of gene function modulation of CRC‐like genes during angiosperm evolution. Here, we report the identification and functional characterization of EcCRC, the Californica poppy (Eschscholzia californica) CRC ortholog. The downregulation of EcCRC by virus‐induced gene silencing (VIGS) produces additional organ whorls that develop exclusively into gynoecia, resulting in a reiteration of the fourth whorl. Additionally, defects in carpel polarity and ovule initiation are apparent, and the observed phenotype is restricted to the gynoecium. Our results further show that the history of CRC‐like genes during angiosperm evolution is characterized by gains of function, independent of duplication processes in this gene subfamily. Moreover, our data indicate that the ancestral angiosperm CRC‐like gene was involved in floral meristem termination and the promotion of abaxial cell fate in the gynoecium, and that in the lineage leading to Arabidopsis, additional genes have been recruited to adopt some of these functions, resulting in a high degree of redundancy.
Norwegian adolescents with asthma are physical active and fit*
Authors: Berntsen S. , Carlsen K. C. L. , Anderssen S. A. , Mowinckel P. , Hageberg R. , Bueso A. K. , Carlsen K.‐H. 
Published: January 2009

Background:  Evidence regarding habitual physical activity levels and aerobic fitness of asthmatic compared to nonasthmatic children and adolescents is contradictory, and it is unclear if low physical activity levels can contribute to asthma development. The present study therefore aimed to determine whether adolescents with asthma have reduced physical activity levels and aerobic fitness, or increased energy intake and body fat compared to controls.Methods:  From the environment and childhood asthma study in Oslo, 174 (13‐ to 14‐year old) adolescents, 95 (66 boys) with and 79 (41 boys) without asthma performed maximal running on a treadmill with oxygen consumption measurement (aerobic fitness) and had the sum of four skinfolds and waist circumference recorded (body fat), followed by wearing an activity monitor and registering diet for four consecutive days. Asthma was defined by at least two of the following three criteria fulfilled: (1) dyspnoea, chest tightness and/or wheezing; (2) a doctor’s diagnosis of asthma; (3) use of asthma medication. Participants with asthma used their regular medications.Results:  Neither aerobic fitness, total energy expenditure nor hours in moderate to very vigorous intensity physical activity during week and weekend differed between adolescents with and without asthma. Energy intake and body fat was similar in both groups.Conclusions:  Total energy expenditure, aerobic fitness and hours in moderate to very vigorous intensity physical activity were not reduced and energy intake and body fat measured with skinfolds not increased among Norwegian adolescents with asthma.
Genetic diversity through life history of Dioon edule Lindley (Zamiaceae, Cycadales)
Authors: Octavio‐Aguilar P. , González‐Astorga J. , Vovides A. P. 
Published: January 2009

AbstractThe distribution of genetic diversity and structure for three populations of Dioon edule Lindley (Zamiaceae) at Monte Oscuro (MO), El Farallón (EF) and Rancho del Niño (RN) in Veracruz, Mexico was studied using 20 allozyme loci, considering four life history classes: seeds, seedlings, juveniles and adults. The MO population is genetically less diverse than the EF and RN populations. Total and local inbreeding differ significantly between life history classes. An increment of inbreeding among all classes was observed, and genetic differentiation among populations was higher in seeds and seedlings than in juveniles and adults. In terms of percentage of polymorphic loci, the MO seeds showed least (80%), followed by RN (95%) and EF had the highest values (100%), probably because of a reduction in effective population size and habitat fragmentation processes. In this context, the mean effective population size was 23.2 ± 11.3 for all populations. We conclude that seed cohorts in EF and RN represent a reservoir of genetic diversity within these two populations. Also, preservation of adult plants is an essential aspect to consider in management and conservation efforts for populations of Dioon edule in natural conditions.
Identification of the spontaneous 7BS/7RL intergenomic translocation in one F1 multigeneric hybrid from the Triticeae tribe
Authors: Carvalho A. , Martín A. , Heslop‐Harrison J. S. , Guedes‐Pinto H. , Lima‐Brito J. 
Published: January 2009

AbstractThe F1 AABBRHch hybrids studied here were produced by crosses between the Portuguese triticale cultivar ‘Douro’ (AABBRR) and the tritordeum line HT9 (AABBHchHch). Fluorescent in situ hybridization performed with genomic DNA probes genomic in situ hybridization (GISH) from rye and Hordeum chilense allowed the unequivocal parental genomes discrimination in all hybrids. Among 55 plants, one presented a spontaneous wheat–rye translocation which was successfully detected after GISH. Recombinant chromosomes identification was made after reprobe with pTa71 and pSc119.2. Nine rDNA loci were detected by pTa71 and pSc119.2 identified the chromosome arms involved in the translocation, after comparing the observed hybridization patterns with those described by several authors. We identified the spontaneous wheat–rye translocation as being the 7BS/7RL. Many wheat–rye translocations have been found (e.g. 1BL.1RS and 1AL.1RS), but as far as we know, this is the first time that this translocation is reported. We considered it helpful for wheat breeding programmes as it could provide the transference of interesting agronomic characteristics from rye (e.g. leaf rust resistance) to wheat.
Identification and isolation of a new x‐type HMW glutenin subunit 1Dx1.6t gene from Aegilops tauschii
Authors: An X. L. , Li X. H. , Xiong X. J. , Yan Y. M. , Zhang Y. Z. , Gao L. Y. , Wang A. L. , Wang K. , Zeller F. J. , Hsam S. L. K. 
Published: January 2009

AbstractA new x‐type HMW glutenin subunit, designated as 1Dx1.6t from Aegilops tauschii was identified and characterized by SDS‐PAGE and MALDI‐TOF‐MS. This subunit is located between 1Dx2 and 1Dx1.5t and possesses a molecular mass (Mr) of 88565.8 Da. Its complete coding sequence was amplified via allele‐specific PCR (AS‐PCR), and the amplified product was cloned and sequenced. The authenticity of the cloned 1Dx1.6t gene was confirmed by successful expression of its open reading frame in Escherichia coli. The molecular characterization of 1Dx1.6t gene showed that its coding region consisted of 2541 bp encoding a polypeptide of 845 amino acid residues. Sequence comparison to previously characterized 1Dx1.5t subunit which is related to good dough quality of bread wheat indicated that the 1Dx1.6t subunit displayed high homology, but possesses 14 residue substitutions and a nonapeptide insertion. A total of 12 single‐nucleotide polymorphisms (1 per 212 bp) was identified in the 1Dx1.6t allele (11 in repetitive domain and 1 in the C‐terminal domain), which could facilitate the design of AS‐PCR markers.
Liver metastasis of a mucinous colonic carcinoma mimicking a haemangioma in T2‐weighted sequences
Authors: Lacout A , El Hajjam M , Julie C , Lacombe P , Pelage JP 
Published: January 2009

SummaryWe report the case of a patient with a single liver metastasis of a mucinous colonic carcinoma that mimics a haemangioma in T2‐weighted sequences. Although a very high T2 signal in non‐cystic lesions is highly specific for the diagnostic of haemangioma, the use of gadolinium‐enhancement MRI is recommended. In patients with a history of neoplasia, the diagnosis of benign liver nodules should be made with caution.
Brachytherapy for cancer of the cervix: An Australian and New Zealand survey of current treatment techniques
Authors: Van Dyk S , Byram D , Bernshaw D 
Published: January 2009

SummaryEstablishing guidelines for the practice of brachytherapy throughout Australia and New Zealand is one of the goals of the Australasian Brachytherapy Group. To better appreciate Australasian resources and conditions, the group conducted a survey in early 2005. The aims were to survey current practices, to emphasize variations in practice and to determine the availability of advanced imaging and treatment methods to assess resources. A survey was sent to all Australian and New Zealand radiotherapy departments. The survey requested details of treatment with respect to external beam radiotherapy, brachytherapy, optimization methods, reporting methods, scheduling brachytherapy and access to imaging and methods of work‐up. Thirty‐four departments were contacted with 27 (79%) responses returned. Twenty‐one departments use brachytherapy. Doses and fractionation schedules varied and use of sectional imaging was minimal. Individualized dosimetry is practised in a limited fashion by 60% of the surveyed departments. There is high compliance with International Commission on Radiation Units 38 dose reporting recommendations. All brachytherapy units identified have access to CT and 85% to MRI within the hospital settings. Brachytherapy for cancer of the cervix is, currently, largely based on the Manchester system. The survey did emphasize considerable variation in dose and fractionation schemes between departments. The Australasian Brachytherapy Group subgroup intends to proceed with the process of formulating recommendations for cervix brachytherapy. It is intended that these will cover the use of image‐based planning and treatment, target definition(s), verification of brachytherapy treatments and a uniform dose‐reporting mechanism.
Accrediting radiation technique in a multicentre trial of chemoradiation for pancreatic cancer
Authors: Spry N , Bydder S , Harvey J , Borg M , Ngan S , Millar J , Graham P , Zissiadis Y , Kneebone A , Ebert M 
Published: January 2009

SummaryBefore a multicentre trial of 3‐D conformal radiotherapy to treat cancer of the pancreas, participating clinicians were asked to complete an accreditation exercise. This involved planning two test cases according to the study protocol, then returning hard copies of the plans and dosimetric data for review. Any radiation technique that achieved the specified constraints was allowed. Eighteen treatment plans were assessed. Seven plans were prescribed incorrect doses and two of the planning target volumes did not comply with protocol guidelines. All plans met predefined normal tissue dose constraints. The identified errors were attributable to unforeseen ambiguities in protocol documentation. They were addressed by feedback and corresponding amendments to protocol documentation. Summary radiobiological measures including total weighted normal tissue equivalent uniform dose varied significantly between centres. This accreditation exercise successfully identified significant potential sources of protocol violations, which were then easily corrected. We believe that this process should be applied to all clinical trials involving radiotherapy. Due to the limitations of data analysis with hard‐copy information only, it is recommended that complete planning datasets from treatment‐planning systems be collected through a digital submission process.
Chronic obstructive pulmonary disease and interstitial lung disease in patients with lung cancer
Authors: MIZUNO Satoko , TAKIGUCHI Yuichi , FUJIKAWA Ayako , MOTOORI Ken , TADA Yuji , KUROSU Katsushi , SEKINE Yasuo , YANAGAWA Noriyuki , HIROSHIMA Kenzo , MURAOKA Katsumi , MITSUSHIMA Toru , NIKI Noboru , TANABE Nobuhiro , TATSUMI Koichiro , KURIYAMA Takayuki 
Published: January 2009

ABSTRACTBackground and objective:  Although lung cancer is frequently accompanied by COPD and interstitial lung disease (ILD), the precise coincidence of these diseases with lung cancer is not well understood. The objectives of this study were to determine the prevalence of abnormal CT and spirometric findings suggestive of COPD or ILD in a population of patients with untreated lung cancer, and to estimate the lung cancer risk in this population.Methods:  The study population consisted of 256 patients with untreated lung cancer and 947 subjects participating in a CT screening programme for lung cancer. Semi‐quantitative analysis of low attenuation area (LAA), fibrosis and ground glass attenuation (GGA) on CT was performed by scoring. Gender‐ and age‐matched subpopulations, with stratification by smoking status, were compared using the Mantel–Haenszel projection method.Results:  Inter‐observer consistency was excellent for LAA, but not as good for fibrosis or GGA scores. Pooled odds ratios for lung cancer risk using LAA, fibrosis, GGA scores and reduced FEV1/FVC and %VC were 3.63, 5.10, 2.71, 7.17 and 4.73, respectively (P < 0.0001 for all parameters). Multivariate regression analyses confirmed these results.Conclusion:  Abnormal CT and spirometric parameters suggestive of COPD and ILD were strong risk factors for lung cancer, even after adjusting for gender, age and smoking status.
Demonstration of long‐range GABAergic connections distributed throughout the mouse neocortex
Authors: Tomioka Ryohei , Okamoto Keiko , Furuta Takahiro , Fujiyama Fumino , Iwasato Takuji , Yanagawa Yuchio , Obata Kunihiko , Kaneko Takeshi , Tamamaki Nobuaki 
Published: January 2009

Abstractγ‐Aminobutyric acid (GABA)ergic neurons in the neocortex have been mainly regarded as interneurons and thought to provide local interactions. Recently, however, glutamate decarboxylase (GAD) immunocytochemistry combined with retrograde labeling experiments revealed the existence of GABAergic projection neurons in the neocortex. We further studied the network of GABAergic projection neurons in the neocortex by using GAD67‐green fluorescent protein (GFP) knock‐in mice for retrograde labeling and a novel neocortical GABAergic neuron labeling method for axon tracing. Many GFP‐positive neurons were retrogradely labeled after Fast Blue injection into the primary somatosensory, motor and visual cortices. These neurons were labeled not only around the injection site, but also at a long distance from the injection site. Of the retrogradely labeled GABAergic neurons remote from the injection sites, the vast majority (91%) exhibited somatostatin immunoreactivity, and were preferentially distributed in layer II, layer VI and in the white matter. In addition, most of GABAergic projection neurons were positive for neuropeptide Y (82%) and neuronal nitric oxide synthase (71%). We confirmed the long‐range projections by tracing GFP‐labeled GABAergic neurons with axon branches traveled rostro‐caudally and medio‐laterally. Axon branches could be traced up to 2 mm. Some (n = 2 of 4) were shown to cross the areal boundaries. The GABAergic projection neurons preferentially received neocortical inputs. From these results, we conclude that GABAergic projection neurons are distributed throughout the neocortex and are part of a corticocortical network.
Contextual cues associated with nicotine administration increase arc mRNA expression in corticolimbic areas of the rat brain
Authors: Schiltz Craig A. , Kelley Ann E. , Landry Charles F. 
Published: January 2009

AbstractConditioned responses to cues associated with the administration of drugs of misuse are an impediment to continued abstinence for drug‐free addicted individuals. In order to study the neuroanatomical and cellular response of the brain to cues associated with nicotine administration, we conditioned Sprague–Dawley rats to receive an ascending dose regimen of nicotine over 14 days in two distinct non‐home cage environments and assessed expression of the early response gene arc in corticolimbic areas in response to the nicotine‐associated context. All of the rats received the same dose regimen of nicotine. Three days after the last training day, the rats were exposed to the test environment. The rats that had previously received nicotine exhibited increased motor activity compared with the rats that had received saline in the test environment. After 45 min in the test environment, brains were taken for Northern blotting and in situ hybridization analysis, which revealed an increase in levels of activity‐regulated, dendritically localized mRNA for arc in a variety of brain regions (medial and lateral prefrontal cortices, cingulate cortex, primary sensory cortex, sensorimotor cortex, ventral striatum and amygdala). Plasma corticosterone levels were not different between the groups, suggesting that exposure to nicotine cues is insufficient to activate the hypothalamo‐pituitary‐adrenal axis. Given that Arc plays a direct role in neuronal plasticity and memory consolidation, its induction by nicotine‐associated cues in brain regions critical for cognitive and emotional processing suggests that rats may be learning that these cues are no longer necessarily predictive of nicotine administration. Further work will be needed in order to assess the role of arc expression in the extinction of conditioned responses to drug‐paired cues.