bluuebunny/crossref_metadata_2025_split huggingface dataset:
LONG‐TERM TAXON‐SPECIFIC RESPONSES OF MACROINVERTEBRATES TO DAM REMOVAL IN A MID‐SIZED SWEDISH STREAM
Authors: Renöfält B. M. , Lejon A. G. C. , Jonsson M. , Nilsson C. 
Published: June 2012

ABSTRACTDam removal to restore ecologically impaired rivers is becoming increasingly common. Although the target often is to facilitate fish migration, dam removal has also been assumed to benefit other types of organisms. Because few studies thus far deal with effects of dam removal on stream macroinvertebrates and because results have been equivocal, we investigated both short‐ and longer‐term dam‐removal effects on downstream macroinvertebrate communities. We did this in a before‐and‐after study of the removal of a dam located in a south Swedish stream. We sampled the benthic fauna 6 months before dam removal and both 6 months and 3.5 years after the dam was removed. We compared species composition, taxonomic richness, total densities and densities of macroinvertebrate groups before and after dam removal and between downstream and reference sites. We found that dam removal reduced some macroinvertebrate taxa at the downstream site, but we found no effect on community composition. Although this corroborates results from previous short‐term studies, we also found a reduction of taxonomic richness and that some dam‐removal effects persisted or even increased over time. The most likely explanation for the suppression of benthic macroinvertebrate richness following dam removal is a significantly increased sediment transport from the former reservoir and a subsequent loss of preferred substrates. Our results indicate that adverse dam‐removal effects may be long lasting but taxon specific. We therefore call for longer‐term studies on a variety of organisms to better understand how dam removal may influence downstream macroinvertebrate communities. Copyright © 2012 John Wiley & Sons, Ltd.
Microfoundations of strategic problem formulation
Authors: Baer Markus , Dirks Kurt T. , Nickerson Jackson A. 
Published: June 2012

AbstractBefore a strategy can be developed, the problem it is supposed to address needs to be formulated. We establish the microfoundations of strategic problem formulation by developing a theory that predicts a core set of impediments to formulation that arise when complex, ill‐structured problems are addressed by heterogeneous teams. These impediments fundamentally constrain and narrow problem formulation, thereby limiting solution search and potential value creation. We establish these impediments as a set of design goals, which, if remedied by an appropriately constructed mechanism, can expand problem formulation to be more comprehensive. Finally, we consider how organizations can improve problem formulation by creating a structured process that satisfies the theoretically derived design goals and detail a specific example of this mechanism (collaborative structured inquiry). Copyright © 2012 John Wiley & Sons, Ltd.
Chasing Ghosts: Rumours and Representations of the Export of Chinese Convict Labour to Developing Countries
Authors: Hairong Yan , Sautman Barry 
Published: June 2012

AbstractA recent addition to the global discourse of China's interaction with developing countries has been the claim that the Chinese government exports prison labour to these countries. While no evidence is ever presented to support this claim, it has been widely circulated in international and local media, as well as on the internet. This article examines the origins of the rumour and the mechanisms of its transmission. It shows that while the rumour often originates at the grass roots in developing countries, it is promoted locally and globally by political, economic and media elites with distinct agendas that often involve building support for opposition parties, competition in obtaining contracts, or geo-strategic and ideological rivalry. We analyse the rumour's circulation in light of the larger discourse on China and developing countries, and discuss why Chinese official responses to the claim have proved to be ineffective.
RSeQC: quality control of RNA-seq experiments
Authors: Wang Liguo , Wang Shengqin , Li Wei 
Published: June 2012

Abstract
Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive QC tool to assess RNA-seq quality is sorely needed.
Results: We developed the RSeQC package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM/SAM files containing hundreds of millions of alignments.
Availability and implementation: RSeQC is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://code.google.com/p/rseqc/.
Contact: WL1@bcm.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Ectopic Expression of Rubisco Subunits in Maize Mesophyll Cells Does Not Overcome Barriers to Cell Type-Specific Accumulation
Authors: Wostrikoff Katia , Clark Aimee , Sato Shirley , Clemente Tom , Stern David 
Published: June 2012

Abstract
In maize (Zea mays), Rubisco accumulates in bundle sheath but not mesophyll chloroplasts, but the mechanisms that underlie cell type-specific expression are poorly understood. To explore the coordinated expression of the chloroplast rbcL gene, which encodes the Rubisco large subunit (LS), and the two nuclear RBCS genes, which encode the small subunit (SS), RNA interference was used to reduce RBCS expression. This resulted in Rubisco deficiency and was correlated with translational repression of rbcL. Thus, as in C3 plants, LS synthesis depends on the presence of its assembly partner SS. To test the hypothesis that the previously documented transcriptional repression of RBCS in mesophyll cells is responsible for repressing LS synthesis in mesophyll chloroplasts, a ubiquitin promoter-driven RBCS gene was expressed in both bundle sheath and mesophyll cells. This did not lead to Rubisco accumulation in the mesophyll, suggesting that LS synthesis is impeded even in the presence of ectopic SS expression. To attempt to bypass this putative mechanism, a ubiquitin promoter-driven nuclear version of the rbcL gene was created, encoding an epitope-tagged LS that was expressed in the presence or absence of the Ubi-RBCS construct. Both transgenes were robustly expressed, and the tagged LS was readily incorporated into Rubisco complexes. However, neither immunolocalization nor biochemical approaches revealed significant accumulation of Rubisco in mesophyll cells, suggesting a continuing cell type-specific impairment of its assembly or stability. We conclude that additional cell type-specific factors limit Rubisco expression to bundle sheath chloroplasts.
Does concomitant use of paracetamol potentiate the gastroduodenal mucosal injury associated with aspirin? A prospective, randomised, pilot study
Authors: Boike J. R. , Kao R. , Meyer D. , Markle B. , Rosenberg J. , Niebruegge J. , Stein A. C. , Berkes J. , Goldstein J. L. 
Published: June 2012

SummaryBackgroundParacetamol is commonly prescribed for first‐line symptomatic treatment in patients with osteoarthritis and aspirin is often co‐administered for cardiovascular prophylaxis. It is not known if an interaction exists between aspirin and paracetamol in regards to gastroduodenal mucosal injury.AimTo investigate whether or not co‐administered aspirin with paracetamol results in an increased rate of endoscopic gastroduodenal mucosal injury as compared to either agent alone.MethodsIn this prospective, double‐blind, randomised, three‐arm, placebo‐ and active‐controlled, parallel‐group pilot study healthy adult subjects (18–75 years old) with a normal baseline trans‐nasal oesophagogastroduodenoscopy (TN‐EGD), received oral paracetamol 4000 mg q.d.s. (n = 21), aspirin 325 mg q.d.s. (n = 19) or paracetamol 4000 mg q.d.s. and aspirin 325 mg q.d.s. (n = 20). Upper gastrointestinal mucosal injury was evaluated after 7 days of treatment with TN‐EGD.ResultsThe rate of gastric ulcers in subjects receiving paracetamol (0/21, 0%) alone or aspirin (3/19, 16%) or both (2/20, 10%) was not different. There were, however, significantly more subjects with one or more lesions (erosion or ulcer) per subject in the paracetamol and aspirin (16/20, 80%) treated subjects as compared to the aspirin (8/19, 42%, P < 0.001) or the paracetamol (3/21, 14%, P < 0.01) exposed subjects. The mean number of lesions per subject was also greater (7.9 vs. 0.7, P < 0.01) in those treated with aspirin and paracetamol compared to paracetamol alone.ConclusionsCo‐administration of paracetamol and aspirin was not associated with a significant difference in endoscopic ulcer rates compared to either drug alone. There was a strong signal for increased endoscopic erosions and ulcers in the combined group compared to either aspirin or paracetamol alone.
Functional trait divergence of juveniles and adults of nine Inga species with contrasting soil preference in a tropical rain forest
Authors: Palow Danielle T. , Nolting Kristen , Kitajima Kaoru 
Published: June 2012

Summary1. Community‐wide studies have shown that functional traits of tropical trees vary with soil‐type preference, but few have examined trait diversification among closely related taxa. In this study, we asked how functional traits of adults and saplings within a speciose genus, Inga, differ in relation to their soil‐type preferences.2. We quantified soil‐type preference and functional traits of nine Inga species (Fabaceae) in the wet tropical forest at La Selva Biological Station, Costa Rica, where rich alluvial soil and less fertile residual soil of volcanic origin occur in close proximity.3. From the extensive trail network, we randomly selected 104 trail segments, each 50 m long, along which all Inga individuals >50 cm tall were counted and identified to species. Five and three common species showed significant bias to residual or alluvial soil, respectively, while the remaining one showed no significant bias. For these nine species, we quantified five leaf traits for saplings and adults, as well as wood‐specific gravity (WSG) and three seed traits.4. For both adults and saplings, leaf mass per area (LMA) and lamina density were higher for residual‐soil specialists than fertile alluvial‐soil specialists. The opposite trend was found for nitrogen (N) and phosphorus (P) concentrations in leaves. Lamina thickness did not differ between soil‐type preference groups. All leaf trait values except N concentration increased from saplings to adults, with adults showing larger interspecific variations in trait values than saplings.5. Saplings and adults of the single species found on both soils had trait values intermediate between residual and alluvial‐soil specialists.6. Seed mass and seed N, as well as WSG of adults, were higher in residual‐soil specialists than alluvial‐soil specialists. Higher seed N indicates higher maternal investment of species growing on less fertile soil.7. These differences in traits among closely related species across continuous soils suggest that habitat filtering has contributed to the evolution of seed, juvenile and adult traits within a speciose tropical tree genus.
Communication and coordination during transition of older persons between nursing homes and hospital still in need of improvement
Authors: Kirsebom Marie , Wadensten Barbro , Hedström Mariann 
Published: June 2012

AbstractAimTo investigate registered hospital and nursing home nurses' experiences of coordination and communication within and between care settings when older persons are transferred from nursing homes to hospital and vice versa.BackgroundIt has previously been reported that transfers to hospital from nursing homes and discharge of patients from hospital are surrounded by communication difficulties. However, studies focusing on both hospital and nursing home registered nurses' experiences of communication and coordination within and between nursing homes and hospitals are uncommon.DesignA descriptive study design with a qualitative approach was used.MethodsIn 2008, three focus group discussions were conducted with registered nurses from hospitals and nursing homes (n = 20). Data were analysed using content analysis.ResultsNursing home registered nurses found it difficult to decide whether the older person should be referred to hospital from the nursing home. Hospital registered nurses reported often trying to stop premature discharges or having to carry out the discharge although it had not been fully prepared. Both hospital and nursing home registered nurses suggested increased collaboration to understand each other's work situation better.ConclusionCommunication and coordination among hospital and nursing home registered nurses need to be furthered improved. Registered nurses' coordination and planning in the nursing home are extremely important to future elder care. We recommend that the medical care plan be regularly updated and meticulously followed, the aim being to reduce the risk of inappropriate medical treatment and nursing care and unnecessary transfer and admission to hospital.
Immunohistochemical features of BK virus nephropathy in renal transplant recipients
Authors: Yamanaka Kazuaki , Oka Kazumasa , Nakazawa Shigeaki , Hirai Toshiaki , Kishikawa Hidefumi , Nishimura Kenji , Kyo Masahiro , Ichikawa Yasuji 
Published: June 2012

AbstractBK virus nephropathy (BKVN) is one of the factors that reduces renal graft function after transplantation. However, BKVN and rejection present similar pathological findings, as both are accompanied by cellular infiltration to the interstitium and tubulitis, thus they are difficult to distinguish for diagnosis and medical treatment. In the present study, we examined immunohistochemical pathological features of BKVN in four cases treated in our hospital from 2007 to 2010. Common immunohistological finding is that tubulitis in these cases was primarily EMA and 34βE12‐positive and existed predominantly from the collecting duct to the distal convoluted tubule. The majority of infected cells existed in EMA and 34βE12‐positive tubules, which were also located mainly from the collecting duct to the distal tubule. In addition, a large number of SV40‐positive infected cells were similarly seen. Dylon staining clearly revealed eosinophils. We concluded that the main pathological features of BKVN are the presence of tubulitis and infected cells predominantly from the collecting duct to distal tubule and the appearance of eosinophils.
Reviews on mysterious vascular endothelial cells in renal allografts
Authors: Yamaguchi Yutaka 
Published: June 2012

AbstractEndothelial cells (ECs) are involved in allograft rejection and are prime targets, but also key players. HLA antigens are the most prominent targets of alloantibodies in transplantation. Alloantibodies against other antigens such as ABO blood group antigens and non‐HLA antigens could also be demonstrated. Alloantibodies undoubtedly cause allograft rejection. Activation of ECs by anti‐EC antibodies and direct antibody‐ or complement mediated EC damage may be suggested. However, the mechanisms underlying acute antibody‐mediated rejection (AAMR) and chronic rejection (CR) remain unclear. In this review, the relationship between vascular endothelium and rejection is discussed mainly from our reports, and the mechanism and pathogenesis of CR are discussed.
Dissociation of tone and vowel processing in Mandarin idioms
Authors: Hu Jiehui , Gao Shan , Ma Weiyi , Yao Dezhong 
Published: June 2012

AbstractUsing event‐related potentials, this study measured the access of suprasegmental (tone) and segmental (vowel) information in spoken word recognition with Mandarin idioms. Participants performed a delayed‐response acceptability task, in which they judged the correctness of the last word of each idiom, which might deviate from the correct word in either tone or vowel. Results showed that, compared with the correct idioms, a larger early negativity appeared only for vowel violation. Additionally, a larger N400 effect was observed for vowel mismatch than tone mismatch. A control experiment revealed that these differences were not due to low‐level physical differences across conditions; instead, they represented the greater constraining power of vowels than tones in the lexical selection and semantic integration of the spoken words. Furthermore, tone violation elicited a more robust late positive component than vowel violation, suggesting different reanalyses of the two types of information. In summary, the current results support a functional dissociation of tone and vowel processing in spoken word recognition.
Morphology Control and Self‐Setting Modification of α‐Calcium Sulfate Hemihydrate Bone Cement by Addition of Ethanol
Authors: Pan Zongyou , Yang Guangyong , Lou Yi , Xue Enxing , Xu Huazi , Miao Xigeng , Liu Jianli , Hu Chunfeng , Huang Qing 
Published: June 2012

The self‐setting behavior of α‐calcium sulfate hemihydrate is highly dependent on its morphology that is tuned through the addition of ethanol into CaCl2 aqueous solutions during a salt solution method. With the increase of the ethanol/water volume ratios, the mean lengths of the formed crystals decreased from 24 to 19 μm, whereas their mean widths increased from 6 to 18 μm. It is also detected that the setting time of α‐CSH paste reduced from 120 ± 12.3 to 17 ± 2.1 min as the crystal morphology evolved from rod‐like to equiaxial.
Dual infection with Pythium insidiosum and Blastomyces dermatitidis in a dog
Authors: Connolly Sara L. , Frank Chad , Thompson Craig A. , Van Alstine William G. , Gelb Hylton , Heng Hock Gan , Klosterman Emily , Kiupel Matti , Grooters Amy M. 
Published: June 2012

AbstractA 4‐year‐old male neutered Labrador Retriever with severe gastrointestinal signs, but no respiratory signs, was diagnosed with multifocal pyogranulomatous gastritis, enteritis, and lymphadenitis with intralesional hyphae and multifocal pyogranulomatous pneumonia with intralesional yeast. Based on cytologic evaluation, histologic examination with special stains, and immunohistochemical analysis of tissues collected antemortem or at necropsy, dual infections with Pythium insidiosum and Blastomyces dermatitidis were detected and are reported for the first time.
Increased plasma cardiac troponin I concentration in lambs with myocarditis
Authors: Karapinar Tolga , Eroksuz Yesari , Beytut Enver , Sozdutmaz Ibrahim , Eroksuz Hatice , Dabak Murat 
Published: June 2012

BackgroundCardiac troponin I (cTnI) is a blood biomarker of myocardial injury. A human cTnI assay may be useful for measuring cTnI concentrations in lambs with naturally occurring myocarditis.ObjectiveThe aims of this study were to evaluate the utility of a commercially available human chemiluminescent microparticle cTnI immunoassay for measuring plasma cTnI concentrations in lambs with naturally occurring myocarditis from infection with foot and mouth disease virus (FMDV), and to determine cTnI expression in cardiac muscle of affected lambs.MethodsTen lambs with myocarditis and 10 clinically healthy lambs (control group) were included. Clinical signs, gross and histologic necropsy findings, and immunoreactivity for cTnI in cardiac tissue were evaluated. Plasma cTnI concentration was determined using the commercial human immunoassay system.ResultsAll lambs with myocarditis died within 1 day of clinical signs. Infection with FMDV was confirmed by PCR analysis. Gross cardiac lesions were evident and histologic examination revealed myocarditis. Immunoreactivity for cTnI was absent in cardiac myocytes that were degenerative or necrotic, but was strong in cardiac myocytes from unaffected areas of the myocardium and in all cardiac myocytes of healthy lambs. The geometric mean plasma concentrations of cTnI for lambs in the myocarditis and control groups were 146.78 μg/L (95% confidence interval [CI], 61.90–348.06) and 0.013 μg/L (95% CI, 0.010–0.017), respectively (t‐value 19.27; P < .0001).ConclusionsA commercial human cTnI assay may be used to detect plasma cTnI concentrations in sheep, and cTnI may be used as a blood‐based biomarker of myocarditis in this species.
SU‐B‐BRB‐01: Professional Council Symposium: Practice Standards ‐ Driving Forces, Benefits, Potential Pitfalls
Authors: Halvorsen P , Hevezi J , Pizzutiello R , Pacella M 
Published: June 2012

Recent coverage in the mainstream media has brought significant attention to the uses of ionizing radiation in medicine. This is not a transient concern, however. Many factors are contributing to this trend, in addition to the general public's concern: ASTRO, ACR and AAPM have advocated clear practice guidelines and mandatory accreditation of all clinical programs in imaging and radiation therapy; payers' requirements and/or assumptions about physicist support for billable procedures, including physicist credentials and supervision; ASTRO's White Paper series on patient safety, which have included a significant focus on staffing; and some states' requirements for external audits of clinical programsLearning Objectives:1. Understand the convergence of external factors that are driving the trend toward minimum practice standards, including CMS assumptions about physicist supervision of certain procedures;2. Understand the effect of this trend in imaging, particularly the impact on community clinics and consulting physicists; and3. Understand the impact in radiation oncology, particularly on freestanding and small community centers.4. Understand the AAPM's multi‐faceted approach to ensuring that medical physicists can shape the future of clinical medical physics practice.
TU‐A‐211‐01: ACR MRI Accreditation: Process and Pitfalls
Authors: Price R 
Published: June 2012

ACR MRI accreditation was initiated in 1996. Over the years, the accreditation process and requirements have evolved in order to keep pace with the rapidly changing MRI technology. This presentation will briefly review changes that have been initiated in response to the changing technology along with the evolving changes in the responsibilities of the Medical Physicist for providing advice and support for system performance, quality assurance and safety. Specific differences in the accreditation process between conventional general‐purpose MRI systems and specialty (extremity) systems used for anatomical imaging and systems used for breast imaging will be discussed. Additional requirements that have resulted from the Medicare Improvements for Patients and Providers Act (MIPPA), common reasons for accreditation failure and the anticipated changes and updates to the 2004 ACR MRI Quality Control Manual will also be discussed.Learning Objectives:1. Review the responsibilities of the Medical Physicist in the accreditation process2. Discuss the CMS/MIPPA accreditation requirements as of January 1, 2012.3. Review differences in breast and specialty (extremity) system accreditation4. Discuss common reasons for accreditation failure5. Discuss anticipated changes and updates in the ACR MRI Quality Control Manual