bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Method for an Image‐Analysis‐Based Two‐Dimensional Computational Fluid Dynamics Simulation of Moving Fish
Authors: Garvin Justin W. , Kureksiz Ozge , Breczinski Philip J. , Garvin Mona K. 
Published: February 2012

AbstractStudies involving how fish respond given different flow field conditions are important in understanding phenomena such as fish schooling as well as larger‐scale migrations. Simulating a fish moving under various flow field conditions is a difficult task, however, due to the fact that fish responses are dependent upon the environment. This makes the traditional use of analytical expressions to model the movement of fish bodies intractable. Thus, the main focus of the present study was to establish a method for coupling the use of image‐analysis‐based techniques for determining fish body motion with the use of a computational fluid dynamics (CFD) simulation. In particular, we focused on the simulation of a fish (rainbow trout Oncorhynchus mykiss) swimming behind a D‐section cylinder. This simulation was based on previous experiments that studied how vortices being shed from a blunt body affected fish movement. The individual frames of a video depicting a fish swimming behind a D‐section cylinder were segmented, and the resulting x, y coordinates of the fish's body were supplied to a CFD simulation to capture the fish motion. The CFD simulations were performed by using a k– turbulence model to calculate the flow field. Previous experimental results showed that the fish traversed between the shedding vortices. Our computational results show that the propulsive force is greatest when the shedding vortices pass along the sides of the fish body in order to aid in its movement. Future work entails extending the analysis to three dimensions and including more details in the fish geometry.
Laboratory and Production Scale Disinfection of Salmonid Eggs with Hydrogen Peroxide
Authors: Wagner Eric J , Oplinger Randall W , Bartley Matthew 
Published: February 2012

Abstract
Disinfection tests were conducted on eggs from rainbow trout Oncorhynchus mykiss, cutthroat trout O. clarkii, and brown trout Salmo trutta to evaluate hydrogen peroxide (H2O2) as an egg disinfectant. A daily drip of 500 mg/L hydrogen peroxide for 35 min on eyed brown trout eggs safely led to significantly reduced bacterial abundance relative to untreated controls, but abundance did not differ significantly from that in a formalin treatment (2,000 mg/L for 15 min). Using water-hardened cutthroat trout eggs, hydrogen peroxide concentrations of (1) 10 g/L for 2 min, (2) 10 g/L for 3 min, (3) 15 g/L for 2 min, and (4) 1,000 mg/L for 15 min were compared with two controls (untreated; 100 mg/L iodine). Bacteria were significantly more abundant in the untreated eggs, but abundance did not significantly differ among chemical treatments. In another test, rainbow trout eggs treated the day before hatch with 15 g/L H2O2 for 2 min had significantly higher mortality than the controls. In production-scale tests, 10–15 g/L H2O2 for 2 min was safe for rainbow and cutthroat trout eggs and significantly reduced bacterial abundance relative to that in untreated eggs. Complete disinfection was not achievable with either iodine or hydrogen peroxide. Daily drip treatment with either formalin or hydrogen peroxide significantly reduced bacterial growth and is recommended.
Effects of ferromagnet–molecule chemical bonding on spin injection in an Fe3O4–molecule granular system
Authors: Yue F J , Wang S , Lin L , Ding H F , Wu D 
Published: February 2012

Abstract
Spin injection at the interface of Fe3O4/stearic acid molecule is investigated in a comparative study of Fe3O4 nanoparticles chemically bonded with molecules (ChemNPs) and Fe3O4 nanoparticles with physically absorbed molecules (PhyNPs). The resistance of PhyNPs is two orders of magnitude larger than that of ChemNPs, indicating that the resistance of PhyNPs is dominated by the energy barrier at the Fe3O4–molecule interface. A magnetoresistance of −12% under a field of 5.8 kOe at room temperature is observed in ChemNPs, in sharp contrast to the zero magnetoresistance in PhyNPs, reflecting that the chemical bonding is crucial for spin injection. We attribute this result to the induced magnetic moment in molecules by proximity effect, which is likely the origin of the spin-dependent tunnelling through molecules. In addition, the estimated relatively large spin polarization of ChemNPs suggests electronic hybridization at the interface and improved oxygen stoichiometry of the Fe3O4 surface.
First Report of a New TTKSF Race of Wheat Stem Rust (Puccinia graminis f. sp. tritici) in South Africa and Zimbabwe
Authors: Pretorius Z. A. , Szabo L. J. , Boshoff W. H. P. , Herselman L. , Visser B. 
Published: February 2012

Seven races have been described in the Ug99 race group of Puccinia graminis f. sp. tritici (2). Ug99-related races previously recorded in South Africa are TTKSF, TTKSP, and PTKST (4). In December 2010, severe stem rust infection of the winter wheat cv. Matlabas was observed for the first time in South Africa. Race analysis using the 20 North American (NA) stem rust differential lines and letter code system classified the race as TTKSF. In comparative infection studies in a greenhouse, cv. Matlabas seedlings were susceptible (infection type [IT] 4) to isolate UVPgt61/1 (TTKSF+) collected from Afrikaskop in the eastern Free State, whereas the cultivar was resistant (IT 1 to 2) to stem rust isolates 2013 (TTKSF), UVPgt55 (TTKSF), UVPgt59 (TTKSP), and UVPgt60 (PTKST). Isolate 2013 represents the original collection of race TTKSF in South Africa (1). In addition to the NA differentials, no variation in the IT range of seedlings of lines with Sr7a, 8b, 12, 13, 14, 16, 18, 19, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 39, 41, 42, 43, 44, Em, R, Tt2, and Satu was observed between UVPgt61/1 and UVPgt55. With the exception of cv. Matlabas, ITs of 106 South African cultivars likewise did not differentiate UVPgt61/1 and UVPgt55. Seedling IT studies were conducted at least twice. Microsatellite analysis (4) showed that all single pustule isolates established from the original Matlabas isolate formed part of the Ug99 group. When characterized with selected single nucleotide polymorphisms (SNPs), all single pustule isolates shared an identical genotype that differed from UVPgt55 (TTKSF), a foreign introduction into South Africa (1,3). SNP genotype analysis suggests that UVPgt61/1 is genetically dissimilar to UVPgt55, as is Zim1009, another TTKSF+ isolate that was collected from Birchenough in Zimbabwe. Studies are underway to determine the identity of the defeated Sr gene in Matlabas and the cultivar has been added to the South African stem rust differential set. TTKSF+ is the eighth race detected in the Ug99 group. Since no other cultivars or advanced lines were found to carry the Matlabas gene, it is unlikely that race TTKSF+ will threaten wheat production in South Africa. However, the occurrence of a new Ug99-related race emphasizes the variability within this internationally important group. References: (1) W. H. P. Boshoff et al. Plant Dis. 86:922, 2002. (2) R. F. Park et al. Euphytica 179:109, 2011. (3) B. Visser et al. Mol. Plant Pathol. 10:213, 2009. (4) B. Visser et al. Euphytica 179:119, 2011.
Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing
Authors: STASSEN JOOST H. M. , SEIDL MICHAEL F. , VERGEER PIM W. J. , NIJMAN ISAÄC J. , SNEL BEREND , CUPPEN EDWIN , VAN DEN ACKERVEKEN GUIDO 
Published: February 2012

SUMMARYLettuce downy mildew (Bremia lactucae) is a rapidly adapting oomycete pathogen affecting commercial lettuce cultivation. Oomycetes are known to use a diverse arsenal of secreted proteins (effectors) to manipulate their hosts. Two classes of effector are known to be translocated by the host: the RXLRs and Crinklers. To gain insight into the repertoire of effectors used by B. lactucae to manipulate its host, we performed massively parallel sequencing of cDNA derived from B. lactucae spores and infected lettuce (Lactuca sativa) seedlings. From over 2.3 million 454 GS FLX reads, 59 618 contigs were assembled representing both plant and pathogen transcripts. Of these, 19 663 contigs were determined to be of B. lactucae origin as they matched pathogen genome sequences (SOLiD) that were obtained from >270 million reads of spore‐derived genomic DNA. After correction of cDNA sequencing errors with SOLiD data, translation into protein models and filtering, 16 372 protein models remained, 1023 of which were predicted to be secreted. This secretome included elicitins, necrosis and ethylene‐inducing peptide 1‐like proteins, glucanase inhibitors and lectins, and was enriched in cysteine‐rich proteins. Candidate host‐translocated effectors included 78 protein models with RXLR effector features. In addition, we found indications for an unknown number of Crinkler‐like sequences. Similarity clustering of secreted proteins revealed additional effector candidates. We provide a first look at the transcriptome of B. lactucae and its encoded effector arsenal.
Differential expression of forkhead box M1 and its downstream cyclin‐dependent kinase inhibitors p27kip1 and p21waf1/cip1 in the diagnosis of pulmonary neuroendocrine tumours
Authors: Ha Seung Yeon , Lee Chang Hun , Chang Hee Kyung , Chang Sunhee , Kwon Kun Young , Lee Eun Hee , Roh Mee Sook , Seo Boram 
Published: February 2012

Ha S Y, Lee C H, Chang H K, Chang S, Kwon K Y, Lee E H, Roh M S & Seo B  (2012) Histopathology 60, 731–739 Differential expression of forkhead box M1 and its downstream cyclin‐dependent kinase inhibitors p27kip1 and p21waf1/cip1 in the diagnosis of pulmonary neuroendocrine tumoursAims:  Pulmonary neuroendocrine (NE) tumours represent a spectrum of phenotypically distinct entities with different biological behaviours. Difficulties in classifying these tumours are frequently encountered in clinical practice. Forkhead box M1 (FoxM1) is essential for the development of various cancers and is a proliferation‐specific transcription factor that regulates transcription of cell cycle genes, including cyclin‐dependent kinase inhibitors p27kip1 and p21waf1/cip1. This study was performed to determine the utility of FoxM1, p27kip1 and p21waf1/cip1 as immunomarkers for subtyping pulmonary NE tumours.Methods and results:  FoxM1, p27kip1 and p21waf1/cip1 expression was evaluated by immunohistochemistry in 60 pulmonary NE tumours [19 typical carcinoids (TCs), six atypical carcinoids (ACs), 17 large cell neuroendocrine carcinomas (LCNECs) and 18 small cell lung cancers (SCLCs)]. The frequencies of FoxM1 and p21waf1/cip1 expression were significantly different between TCs and ACs (each P = 0.009), and those of FoxM1 and p27kip1 expression were significantly different between LCNECs and SCLCs (P = 0.012 and P = 0.002, respectively). The combined FoxM1(−)/p21waf1/cip1(−) and FoxM1(+)/p27kip1(high) phenotypes had the best diagnostic accuracy for distinguishing TCs from ACs, and SCLCs from LCNECs, respectively.Conclusions:  FoxM1, p27kip1 and p21waf1/cip1 showed distinct immunoreactivity according to histological subtype, which may be of value as an ancillary test in the differential diagnosis of pulmonary NE tumours.
Increased levels of deleted in malignant brain tumours 1 (DMBT1) in active bacteria‐related appendicitis
Authors: Kaemmerer Elke , Schneider Ursula , Klaus Christina , Plum Patrick , Reinartz Andrea , Adolf Maximilian , Renner Marcus , Wolfs Tim G A M , Kramer Boris W , Wagner Norbert , Mollenhauer Jan , Gassler Nikolaus 
Published: February 2012

Kaemmerer E, Schneider U, Klaus C, Plum P, Reinartz A, Adolf M, Renner M, Wolfs T G A M, Kramer B W, Wagner N, Mollenhauer J & Gassler N  (2012) Histopathology 60, 561–569 Increased levels of deleted in malignant brain tumours 1 (DMBT1) in active bacteria‐related appendicitisAims:  Deleted in malignant brain tumours 1 (DMBT1; gp340) is a secreted glycoprotein which is found in the surface lining epithelia of human small and large intestine. DMBT1 is suggested to play a role in enterocyte differentiation and surface protection from intestinal bacteria. The aim of this study was to elucidate DMBT1 expression in bacteria‐related active intestinal inflammation such as appendicitis.Methods and results:  mRNA and protein levels of DMBT1 were analysed in surgical resections of 50 appendices (active inflammation: n = 25). In non‐actively inflamed appendices, inter‐individual differences in basal DMBT1 levels of enterocytes and some non‐epithelial cells were found. In active appendicitis, enterocytic DMBT1 mRNA expression was increased approximately fivefold, which was paralleled by a corresponding increase of cytoplasmic and secreted DMBT1 protein levels. Increased DMBT1 expression was predominant in enterocytes adjacent to erosive lesions or ulcers.Conclusions:  Our data demonstrate that bacteria‐related active inflammation results in a sharp increase of DMBT1 levels in enterocytes. These findings substantiate the view that DMBT1 is of functional relevance for host defence and modulation of the course of intestinal bacteria‐related inflammatory responses.
Seasonal cycles of species diversity and similarity in a tropical butterfly community
Authors: Grøtan Vidar , Lande Russell , Engen Steinar , Sæther Bernt‐Erik , DeVries Phil J. 
Published: February 2012

Summary1. Studies of seasonality in ecological diversity rarely extend over more than a few years, and few studies of seasonal diversity have explicitly investigated the influence of environmental factors on seasonal community composition, especially in tropical communities.2. Our 10 years of monthly sampling in Amazonian Ecuador yielded 20 996 individuals of 137 fruit‐feeding butterfly species. Seasonal cycles of rainfall drive annual cycles in species diversity and community similarity. Undetermined processes operating most strongly during the dry season maintain species diversity and high community similarity across years.3. Seasonal cycles in community diversity and similarity are superimposed on a gradual decline in similarity between community samples on a decadal time‐scale because of long‐term changes in species abundances.4. Monitoring and analysis of changes in community composition over a range of time‐scales can be used to refine models of community dynamics by incorporating environmental factors necessary to predict the ecological impact of future climate change.
Urban–rural differences in the nature and prevalence of mental ill‐health in adults with intellectual disabilities
Authors: Kiani R. , Tyrer F. , Hodgson A. , Berkin N. , Bhaumik S. 
Published: February 2012

AbstractBackground  In the general population there are statistically significant urban–rural differences in the rate of common mental disorders. In people with intellectual disability (ID) no study has attempted to address this issue.Aims  To compare the prevalence of mental illness, autism spectrum disorder (ASD) and behaviour disorder in people with ID living in urban areas with those living in rural areas.Methods  Cross‐sectional study of 2713 individuals registered with an ID service. Participants were assigned to urban or rural groups using the Department for Environment Food and Rural Affairs rural/urban local authority classification for their district. The main outcome variable was a clinical diagnosis of mental illness, ASD and behaviour disorder. Differences between diagnoses of mental illness in urban and rural areas were evaluated using the chi‐squared test for the difference in two independent proportions.Results  No differences were observed between gender, age and level of ID of service users based on their place of residence. But more people from an ethnic minority background were living in urban areas than rural areas. No differences were observed in the overall prevalence of mental illness by place of residence. However, the results showed that ASD was more common in people living in rural areas.Conclusions  We found these results surprising and at odds with the majority of studies carried out in the general population and propose several reasons for the differences found. We believe that the results and further studies in this area will help inform health service provision for those with ID who live in different geographical areas.
Service user involvement in pre‐registration mental health nurse education classroom settings: a review of the literature
Authors: TERRY J. 
Published: February 2012

Accessible summary
Service user involvement is an important part of pre‐registration nursing programmes, as it can give students the opportunity to learn from users about their experiences of health and illness, but so far there have been limited studies in this area.
This literature review provides an opportunity to explore how service user involvement in classroom settings can impact on student learning, and describes methods of best practice.
Further research is needed to understand the influence of service user involvement on student nurses' clinical practice.
AbstractService user involvement in pre‐registration nurse education is now a requirement, yet little is known about how students engage with users in the classroom, how such initiatives are being evaluated, how service users are prepared themselves to teach students, or the potential influence on clinical practice. The aim of this literature review was to bring together published articles on service user involvement in classroom settings in pre‐registration mental health nurse education programmes, including their evaluations. A comprehensive review of the literature was carried out via computer search engines and the Internet, as well as a hand search of pertinent journals and references. This produced eight papers that fitted the inclusion criteria, comprising four empirical studies and four review articles, which were then reviewed using a seven‐item checklist. The articles revealed a range of teaching and learning strategies had been employed, ranging from exposure to users' personal stories, to students being required to demonstrate awareness of user perspectives in case study presentations, with others involving eLearning and assessment skills initiatives. This review concludes that further longitudinal research is needed to establish the influence of user involvement in the classroom over time.
Factor analysis of the French version of the shorter 12‐item Perception of Aggression Scale (POAS) and of a new modified version of the Overt Aggression Scale (MOAS)
Authors: DE BENEDICTIS L. , DUMAIS A. , STAFFORD M.‐C. , CÔTÉ G. , LESAGE A. 
Published: February 2012

Accessible summary
Staff attitudes to violence by psychiatric patients may have an impact on the therapeutic relationship.
The French versions of the Perception of Aggression Scale and of a new Modified version of the Overt Aggression Scale are two useful tools for evaluating the subjective experience of and attitudes towards inpatient violence.
Future study on the management of inpatient violence may use the French version of these scales to evaluate and monitor psychiatric staff attitudes towards violence and subjective experience of the frequency of inpatient violence.
AbstractPsychiatric staff perceptions of aggression by psychiatric patients may affect the therapeutic relationship between care providers and patients in institutions. Attitudes to and the subjective experience of violence may also differ substantially between members of a single care team. This study seeks to validate the French versions of scales of staff attitudes to and subjective experience of institutional violence: a new, modified version of the Overt Aggression Scale (MOAS) to measure the subjective perception of the frequency of aggression in the ward; and the Perception of Aggression Scale (POAS) to assess attitudes to the expression of violence by psychiatric patients. Frontline staff (n= 362) from eight French‐language psychiatric institutions in the province of Quebec were surveyed. Factor analyses were performed to determine the validity of the French‐language MOAS and POAS. As expected, a four‐factor structure emerged for the MOAS. For the 12‐item POAS, a three‐factor structure was found: (1) ‘Aggression as a dysfunctional/undesirable phenomenon’; (2) ‘Aggression as a positive expression’; and (3) ‘Aggression as a protective measure’. This study supports use of the French MOAS and POAS in assessing staff attitudes to and subjective experience of aggression in future projects to explore the perception and management of inpatient violence.
Life style in persons with functional gastrointestinal disorders – large‐scale internet survey of lifestyle in Japan
Authors: Miwa H. 
Published: February 2012

AbstractBackground  Care of patients with functional gastrointestinal disorders (FGIDs) commonly includes offering guidance on diet, exercise, and other lifestyle factors, but there is little information available on the actual lifestyles of FGID sufferers.Methods  An internet questionnaire survey of 15 000 adult members of the general public in Japan who were screened for functional dyspepsia (FD) and irritable bowel syndrome (IBS) using the Rome III adult FGID questionnaire was conducted.Key Results  The prevalence of FD and IBS was 6.5% and 14.0%, respectively, and 3.0% of the subjects met the criteria for both FD and IBS. The prevalence of both FD and IBS was higher in women than in men. The lifestyles of 2 547 subjects who met the Rome III criteria for FD, IBS, or both were compared with the lifestyles of 1 000 control subjects who did not meet the criteria for FD or the criteria for IBS. Compared to the control subjects, a significantly lower percentage of subjects with FD, IBS, or both exercised frequently, and a significantly higher percentage thought that their sleep was insufficient, ate meals irregularly, did not have an appetite, did not like meat, thought that their vegetable consumption was insufficient, felt stress in their daily lives, and regarded themselves as being highly susceptible to stress.Conclusions & Inferences  Persons with FGIDs are affected by impairment of sleep, eating habits, diet, exercise and other lifestyle factors, and feel excessive stress. This suggests that offering lifestyle guidance to FGID patients may be useful.