bluuebunny/crossref_metadata_2025_split huggingface dataset:
Balmer-Dominated Shocks: A Concise Review
Authors: Heng Kevin 
Published: March 2010

AbstractA concise and critical review of Balmer-dominated shocks (BDSs) is presented, summarizing the state of theory and observations, including models with/without shock precursors and their synergy with atomic physics. Observations of BDSs in supernova remnants are reviewed on an object-by-object basis. The relevance of BDSs towards understanding the acceleration of cosmic rays in shocks is emphasized. Probable and possible detections of BDSs in astrophysical objects other than supernova remnants, including pulsar wind nebulae and high-redshift galaxies, are described. The case for the continued future of studying BDSs in astrophysics is made, including their relevance towards understanding electron–ion temperature equilibration in collisionless shocks.
psrchive and psrfits: Definition of the Stokes Parameters and Instrumental Basis Conventions
Authors: van Straten W. , Manchester R. N. , Johnston S. , Reynolds J. E. 
Published: March 2010

AbstractThis paper defines the mathematical convention adopted to describe an electromagnetic wave and its polarisation state, as implemented in the psrchive software and represented in the psrfits definition. Contrast is made between the convention that has been widely accepted by pulsar astronomers and the IAU/IEEE definitions of the Stokes parameters. The former is adopted as the PSR/IEEE convention, and a set of useful parameters are presented for describing the differences between the PSR/IEEE standard and the conventions (either implicit or explicit) that form part of the design of observatory instrumentation. To aid in the empirical determination of instrumental convention parameters, well-calibrated average polarisation profiles of PSR J0304+1932 and PSR J0742–2822 are presented at radio wavelengths of approximately 10, 20, and 40 cm.
PanCGHweb: a web tool for genotype calling in pangenome CGH data
Authors: Bayjanov Jumamurat R. , Siezen Roland J. , van Hijum Sacha A. F. T. 
Published: March 2010

Abstract
Summary: A pangenome is the total of genes present in strains of the same species. Pangenome microarrays allow determining the genomic content of bacterial strains more accurately than conventional comparative genome hybridization microarrays. PanCGHweb is the first tool that effectively calls genotype based on pangenome microarray data.
Availability: PanCGHweb, the web tool is accessible from: http://bamics2.cmbi.ru.nl/websoftware/pancgh/
Contact: sacha.vanhijum@nizo.nl
Identification of Quantitative Trait Loci Affecting Grain Fat Content in Rice (Oryza sativa L.)
Authors: Shen Yingyue , Liu Linglong , Jiang Ling , Zhang Yingxing , Liu Xiaolu , Zhai Huqu , Wan Jianmin 
Published: March 2010

ABSTRACTFat content (FC) partially determines rice grain quality. The objective of this study was to identify stably expressed quantitative trait loci (QTL) for FC. A total of 85 inbred lines derived from the backcross between Sasanishiki (japonica, as the recurrent parent) and Habataki (indica) were used to detect QTLs for rice fat content. Seven QTLs (denoted as qFC‐1, qFC‐2, qFC‐3, qFC‐6, qFC‐10, qFC‐11, and qFC‐12) were detected on chromosomes 1, 2, 3, 6 10, 11, and 12, respectively, using inclusive composite interval mapping (ICIM) method. Among them, three major QTLs (qFC‐3, qFC‐6, and qFC‐11) with large effect were further confirmed across two different environments using some chromosome segment substitution lines (CSSLs), where Habataki was used as the donor parent and Sasanishiki as the recurrent parent. Further experiments showed that one of the major QTLs (qFC‐11) could increase fat content, fat index, and grain yield together. To our knowledge, qFC‐11 is a newly detected stable QTL that will provide new opportunities for improving rice fat content through marker‐assisted selection.
The Soybean Stem Growth Habit Gene Dt1 Is an Ortholog of Arabidopsis TERMINAL FLOWER1
Authors: Liu Baohui , Watanabe Satoshi , Uchiyama Tomoo , Kong Fanjiang , Kanazawa Akira , Xia Zhengjun , Nagamatsu Atsushi , Arai Maiko , Yamada Tetsuya , Kitamura Keisuke , Masuta Chikara , Harada Kyuya , Abe Jun 
Published: March 2010

Abstract
Classical genetic analysis has revealed that the determinate habit of soybean (Glycine max) is controlled by a recessive allele at the determinate stem (Dt1) locus. To dissect the molecular basis of the determinate habit, we isolated two orthologs of pea (Pisum sativum) TERMINAL FLOWER1a, GmTFL1a and GmTFL1b, from the soybean genome. Mapping analysis indicated that GmTFL1b is a candidate for Dt1. Despite their high amino acid identity, the two genes had different transcriptional profiles. GmTFL1b was expressed in the root and shoot apical meristems (SAMs), whereas GmTFL1a was mainly expressed in immature seed. The GmTFL1b transcript accumulated in the SAMs during early vegetative growth in both the determinate and indeterminate lines but thereafter was abruptly lost in the determinate line. Introduction of the genomic region of GmTFL1b from the indeterminate line complemented the stem growth habit in the determinate line: more nodes were produced, and flowering in the terminal raceme was delayed. The identity between Dt1 and GmTFL1b was also confirmed with a virus-induced gene silencing experiment. Taken together, our data suggest that Dt1 encodes the GmTFL1b protein and that the stem growth habit is determined by the variation of this gene. The dt1 allele may condition the determinate habit via the earlier loss in GmTFL1b expression concomitant with floral induction, although it functions normally under the noninductive phase of flowering. An association test of DNA polymorphisms with the stem growth habit among 16 cultivars suggested that a single amino acid substitution in exon 4 determines the fate of the SAM after floral induction.
Assessing the impact of deforestation and climate change on the range size and environmental niche of bird species in the Atlantic forests, Brazil
Authors: Loiselle Bette A. , Graham Catherine H. , Goerck Jaqueline M. , Ribeiro Milton Cezar 
Published: March 2010

AbstractAim  Habitat loss and climate change are two major drivers of biological diversity. Here we quantify how deforestation has already changed, and how future climate scenarios may change, environmental conditions within the highly disturbed Atlantic forests of Brazil. We also examine how environmental conditions have been altered within the range of selected bird species.Location  Atlantic forests of south‐eastern Brazil.Methods  The historical distribution of 21 bird species was estimated using Maxent. After superimposing the present‐day forest cover, we examined the environmental niches hypothesized to be occupied by these birds pre‐ and post‐deforestation using environmental niche factor analysis (ENFA). ENFA was also used to compare conditions in the entire Atlantic forest ecosystem pre‐ and post‐deforestation. The relative influence of land use and climate change on environmental conditions was examined using analysis of similarity and principal components analysis.Results  Deforestation in the region has resulted in a decrease in suitable habitat of between 78% and 93% for the Atlantic forest birds included here. Further, Atlantic forest birds today experience generally wetter and less seasonal forest environments than they did historically. Models of future environmental conditions within forest remnants suggest generally warmer conditions and lower annual variation in rainfall due to greater precipitation in the driest quarter of the year. We found that deforestation resulted in a greater divergence of environmental conditions within Atlantic forests than that predicted by climate change.Main conclusions  The changes in environmental conditions that have occurred with large‐scale deforestation suggest that selective regimes may have shifted and, as a consequence, spatial patterns of intra‐specific variation in morphology, behaviour and genes have probably been altered. Although the observed shifts in available environmental conditions resulting from deforestation are greater than those predicted by climate change, the latter will result in novel environments that exceed temperatures in any present‐day climates and may lead to biotic attrition unless organisms can adapt to these warmer conditions. Conserving intra‐specific diversity over the long term will require considering both how changes in the recent past have influenced contemporary populations and the impact of future environmental change.
Disparities between rural and urban areas for osteoporosis management in the province of Quebec following the Canadian 2002 guidelines publication
Authors: Dagenais Pierre , Vanasse Alain , Courteau Josiane , Orzanco Maria Gabriela , Asghari Shabnam 
Published: March 2010

AbstractRationale, aims and objectives Clinical guidelines have been seen as a tool for improving management of osteoporosis in order to prevent fragility fractures. However, the impact of guidelines on clinical management of osteoporosis has not been measured. We examined medical investigation and treatment before and after the 2002 Canadian guidelines publication and examined if practice changes were different between rural and urban areas.Methods We conducted a retrospective population‐based observational study using secondary data analysis. Two studied populations were selected; one before, the other after the publication of Canadian practice guidelines. The studied populations consisted of all individuals 65 years or older from Quebec (Canada) for whom a physician claimed a consultation or have been hospitalized for fragility fracture between the two predefined periods.Results There was no significant difference in the rate of bone mineral density testing for women before and after guidelines publication. For men a statistically significant increase was observed but remained very low. A significant increase in bisphosphonates prescribing, but no increased in the reporting of a diagnosis of osteoporosis were observed. A significant reduction of hormonal replacement therapy was seen during the year following guidelines publication. The strongest significant increases were mostly seen in urban regions compared to rural areas.Conclusions Very small changes were observed for diagnostic recognition by physicians, diagnostic testing and some recommended drugs prescribing following guidelines publication. This suggests low guidelines impact on medical practice for osteoporosis in patients suffering fragility fractures.
Barriers to transfer of collaborative recovery training into Australian mental health services: implications for the development of evidence‐based services
Authors: Uppal Shivani , Oades Lindsay G. , Crowe Trevor P. , Deane Frank P. 
Published: March 2010

AbstractRationale  Transfer of training (ToT) is defined as the application of competencies acquired during training into the workplace. Poor ToT to clinical practice in mental health settings has negative implications for evidence‐based service provision.Aims and objectives  This study aimed to explore the variables influencing differences in ToT across mental health settings. Variables of interest included organization type, caseload and several variables related to the opportunity to use training.Method  One hundred and seventy‐three mental health clinicians from community‐based governmental and non‐governmental mental health services in eastern Australia were trained in recovery‐oriented interventions. Measures of ToT included time taken until implementation of intervention protocols, assessed using a clinical audit and a questionnaire survey completed by clinicians to identify barriers to implementation 6 months after training.Results  Approximately 37% of the trained clinicians participating in the study were found to be implementing training protocols in clinical practice. In addition, the average time taken to implement the protocols was 5.6 months following training. The most frequently cited barriers were institutional constraints. Higher caseloads and more frequent client contact were related to a higher level of ToT.Conclusion  ToT can be difficult to achieve in clinical practice. Greater facilitation of ToT may be achieved through better integration of the new ideology and protocols, regular monitoring of progress, staff incentives and examination of external attributions by clinicians of their responsibility to transfer training.
Is the right to information fulfilled in an emergency department? Patients' perceptions of the care provided
Authors: Perez‐Carceles Maria D. , Gironda Jose L. , Osuna Eduardo , Falcon Maria , Luna Aurelio 
Published: March 2010

AbstractRationale, aims and objective  In an emergency department (ED), the effective exchange of information between patients and health care providers is recognized as being critically important to patient care. The aims of this study were to evaluate the extent to which the right to information is fulfilled in the ED, to ascertain the degree of patient satisfaction with the attention received and to evaluate the relation between satisfaction and the information received, waiting time and seriousness of the emergency.Methods  This is a cross‐sectional survey that involved 300 patients who consulted an ED during a period of 3 months. The data were obtained by means of a self‐administered validated questionnaire: sociodemographic characteristics, variables related with the treatment received and overall satisfaction were obtained. Medical records were also analysed.Results  The percentages of patients who received information about the reason for a complementary test, discomfort and complications were: 90.4%, 68.3% and 37%, respectively. In all, 98.3% claimed to have understood diagnosis, but when their written answers were analysed only 37.7% were exactly correlated. The percentages of patients who received information about posology, duration and side effects on medication were: 89.9%, 85.7% and 53%, respectively. Overall, 66% of the patients considered the attention they received as ‘good’ or ‘excellent’. There is a statistically significant relation between patient perceptions of received information and overall satisfaction of care and perceived waiting time.Conclusion  Providing the patients with information in all phases of the care process, giving the opportunity to ask questions, resolving doubts and providing legible and easily understood discharge instructions all contribute to increasing patient satisfaction in ED.
Using a <670> zone axis for convergent beam electron diffraction measurements of lattice strain in strained silicon
Authors: DIERCKS D.R. , KAUFMAN M.J. , IRWIN R.B. , JAIN A. , ROBERTSON L. , WEIJTMANS J.W. , WISE R. 
Published: March 2010

SummaryConvergent beam electron diffraction patterns of silicon from the gate channel region of a complementary metal‐oxide‐semiconductor transistor with recessed Si.82Ge.18 stressors were analysed using three zone axes: <230>, <340> and <670>. Values measured using these axes were compared with each other with regards to strain along the [] and the [001] directions. It was demonstrated that strain measurements made using all three axes showed reasonable agreement with each other: an increase in the [] compressive strain and a switch from compressive to tensile strain in the [001] with decreasing distance below the gate. It was also observed that the strain calculations using the <230> axis had the lowest uncertainty whereas the <670> axis allowed for measurements closest to the gate due to the improved lateral resolution at that tilt angle.
Microstructural characterization of laser surface melted AISI M2 tool steel
Authors: ARIAS J. , CABEZA M. , CASTRO G. , FEIJOO I. , MERINO P. , PENA G. 
Published: March 2010

SummaryWe describe the microstructure of Nd:YAG continuous wave laser surface melted high‐speed steel, namely AISI M2, treated with different laser scanning speeds and beam diameters on its surface. Microstructural characterization of the remelted surface layer was performed using light optical and scanning electron microscopy and X‐ray diffraction. The combination of the three techniques provided new insights into the substantial changes induced by laser surface melting of the steel surface layer. The advantage of the method is that it avoids the difficult and tedious work of preparing samples of this hard material for transmission electron microscopy, which is the technique normally used to study these fine microstructures. A melted zone with a dendritic structure and a partially melted zone with a heterogeneous cellular structure were observed. M2C carbides with different morphologies were identified in the resolidified surface layer after laser melting.
An automated and highly efficient method for counting and measuring fluorescent foci in rod‐shaped bacteria
Authors: NIELSEN H. J. , HANSEN F. G. 
Published: March 2010

SummaryDirect measurements of cells from photo micrographs are becoming increasingly used when investigating the position and/or distribution of chromosomal loci in bacteria. In general, these measurements have been done manually, and without clear definition of how they are made. Here we present a procedure for standardizing the measurement of cell properties from phase contrast images. Furthermore, we present a program using these standardized methods that can measure the intracellular positions of fluorescent foci in bacterial cells faster and with more precision than manual measurement.
Characterization of dilute species within CVD‐grown silicon nanowires doped using trimethylboron: protected lift‐out specimen preparation for atom probe tomography
Authors: PROSA T. J. , ALVIS R. , TSAKALAKOS L. , SMENTKOWSKI V. S. 
Published: March 2010

SummaryThree‐dimensional quantitative compositional analysis of nanowires is a challenge for standard techniques such as secondary ion mass spectrometry because of specimen size and geometry considerations; however, it is precisely the size and geometry of nanowires that makes them attractive candidates for analysis via atom probe tomography. The resulting boron composition of various trimethylboron vapour–liquid–solid grown silicon nanowires were measured both with time‐of‐flight secondary ion mass spectrometry and pulsed‐laser atom probe tomography. Both characterization techniques yielded similar results for relative composition. Specialized specimen preparation for pulsed‐laser atom probe tomography was utilized and is described in detail whereby individual silicon nanowires are first protected, then lifted out, trimmed, and finally wet etched to remove the protective layer for subsequent three‐dimensional analysis.
Primary neuroblastoma in the skin of an adult shih tzu dog
Authors: Michishita Masaki , Momozawa Yuki , Oizumi Takuya , Ohkusu‐Tsukada Kozo , Takahashi Kimimasa 
Published: March 2010

AbstractA subcutaneous mass arising in the right gluteal area of an 11‐year‐old female shih tzu dog was surgically excised. Histologically, the mass was composed of small round or ovoid neoplastic cells that were arranged in nests of various sizes. The neoplastic cells generally had hyperchromatic nuclei and scanty eosinophilic cytoplasm, and were surrounded by a pale pink fibrillar area. Immunohistochemically, the neoplastic cells were positive for vimentin, S‐100 protein, neurone‐specific enolase and synaptophysin, but negative for cytokeratin, neurofilament protein, glial fibrillary acidic protein and chromogranin A. On ultrastructural observation, aggregates of thin cytoplasmic processes were frequently seen among the neoplastic cells. Based on these features, the tumour was diagnosed as a neuroblastoma. To the authors’ knowledge, this is the first description of a neuroblastoma originating from the skin in an adult dog.
Reproductive biology of Echinopsis terscheckii (Cactaceae): the role of nocturnal and diurnal pollinators
Authors: Ortega‐Baes P. , Saravia M. , Sühring S. , Godínez‐Alvarez H. , Zamar M. 
Published: March 2010

AbstractThe aim of this study was to analyse the reproductive biology of Echinopsis terscheckii, a species endemic to northwest Argentina that has nocturnal flowers. We expected that this species had a generalised pollination system, with moths and diurnal visitors as the primary pollinators. To test this, we studied the floral biology, breeding system and floral visitors of this species and the effectiveness of nocturnal and diurnal visitors. Floral biology was defined based on floral morphology, floral cycle and nectar production of the flowers. The breeding system and relative contributions of diurnal and nocturnal visitors to fruit and seed set were analysed through field experiments. E. terscheckii flowers opened at sunset and closed the following day. The peak of nectar production occurred at midnight. Flowers were determined to be self‐incompatible. Moths, bees and birds were identified as floral visitors. Moths were the most frequent visitors at night, whereas bees were the most frequent visitors during the day. Fruit production by diurnal pollinators was less than that by nocturnal pollinators; among all floral visitors, moths were the most effective pollinators. We have demonstrated for the first time that moths are the primary pollinators of columnar cacti of the genus Echinopsis. Our results suggest that moths might be important pollinators of columnar cactus species with nocturnal flowers in the extra‐tropical deserts of South America.
Song Learning in Wild and Domesticated Strains of White‐Rumped Munia,Lonchura striata, Compared by Cross‐Fostering Procedures: Domestication Increases Song Variability by Decreasing Strain‐Specific Bias
Authors: Takahasi Miki , Okanoya Kazuo 
Published: March 2010

AbstractSong diversity results from the interactions between natural selection, sexual selection, and individual learning. To understand song diversity, all three factors must be considered collectively, not separately. Bengalese Finches were domesticated about 250 yr ago. Their courtship songs have become different from their ancestor, the White‐rumped Munia. Bengalese Finches sing songs with complex note‐to‐note transition patterns and with acoustically diverse song notes while White‐rumped Munias sing songs with fixed note sequence and mostly broad band song notes. Bengalese Finches were selected for domestication based on their good parenting ability, not their songs, but this artificial selection has nonetheless affected their songs. To test whether divergence occurred not only in the song phenotypes but also in the genetic basis for predisposition of strain specific song learning, we conducted a cross‐fostering experiment between Bengalese Finches and White‐rumped Munias. In both strains, song learning was affected by rearing condition: the acoustical feature and transition patterns followed those of the foster fathers. However, the accuracy of song learning differed between the wild and the domesticated strains: sharing of song note between sons and tutors in Finches was not very accurate regardless of the tutor, while Munias were highly accurate in copying Munia songs but often omitted song elements from Finch fathers. These results suggest that White‐rumped Munias are strongly constrained to learn their own strain’s song, and that this constraint was relaxed in the Bengalese Finch by domestication.