bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Second Spore Stage Confirmed for Apioplagiostoma populi, the Causal Agent of Bronze Leaf Disease of Populus in Minnesota
Authors: Ostry M. E. , Moore M. J. , Anderson N. A. 
Published: May 2012

Bronze leaf disease (BLD) affects several Populus species in North America but is particularly damaging to hybrids in section Populus (4). BLD, caused by the fungus Apioplagiostoma populi (syn. Plagiostoma populi) described by Cash and Waterman (1), takes its name from the characteristic dark purple to brown pigmentation of infected leaves. A. populi has not been cultured on artificial media either from diseased tissues or cast ascospores. An anamorph has not been conclusively identified but spores from blister-like acervuli on symptomatic leaves have been suggested to function as spermatia (3). In an attempt to describe the imperfect stage of A. populi, collections of diseased leaves of P. alba × sieboldii and P. alba × grandidentata‘Crandon’ growing in a plantation near Rosemount, MN, were made on September 14, 2011 (leaves attached to shoots, rolled inward), October 12, 2011 (leaves attached or on the ground, tightly rolled inward), and November 1, 2011 (most leaves on the ground), and examined in the laboratory for fungal development. Leaf laminae from the September 14 collection were uniformly covered with erumpent, subcuticular blister-like acervuli on the adaxial surface only, containing unicellular, colorless spores ranging in size from 2.2 to 10.0 × 2.0 to 5.0 μm (mean 3.6 × 6.2 μm) (n = 100). Attempts to germinate and obtain cultures from these spores on common artificial media were unsuccessful. On leaves collected October 12, the blister-like acervuli were predominantly empty or releasing spores and immature perithecia of A. populi were present. Leaves collected on November 1 contained immature perithecia but were heavily colonized by surface saprophytic fungi and no intact blister-like acervuli were present. DNA was extracted from bulked samples of spores removed from the blister-like acervuli in leaves from multiple trees collected on September 14 using the DNeasy Plant Mini Kit (Qiagen Sciences, Germantown, MD). The internal transcribed spacer (ITS2) region of rDNA was PCR amplified and sequenced with primers ITS3 and ITS4. BLASTn searches revealed that sequences from three independent bulked samples were homologous (99% identity, 353 of 355 nucleotides) to A. populi from isolated perithecia (GenBank Accession No. GU205341) (2). The inability of the spores to germinate, the timing of their development and release, and the tight, inward roll of infected leaves facilitating their spread across the upper leaf surface suggest that these spores function as spermatia in the life cycle of A. populi and the blister-like acervuli in which they develop are spermogonia. References: (1) E. K. Cash and A. M. Waterman. Mycologia 49:756, 1957. (2) L. M. Kawchuk et al. Plant Disease 94:377, 2010. (3) W. A. Sinclair and H. H. Lyon, Comstock Publishing Associates, Cornell University Press, Ithaca, NY, 2005. (4) J. A. Smith et al. Plant Disease 86:462, 2002.
Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources
Authors: Heyndrickx Ken S. , Vandepoele Klaas 
Published: May 2012

Abstract
A major challenge is to unravel how genes interact and are regulated to exert specific biological functions. The integration of genome-wide functional genomics data, followed by the construction of gene networks, provides a powerful approach to identify functional gene modules. Large-scale expression data, functional gene annotations, experimental protein-protein interactions, and transcription factor-target interactions were integrated to delineate modules in Arabidopsis (Arabidopsis thaliana). The different experimental input data sets showed little overlap, demonstrating the advantage of combining multiple data types to study gene function and regulation. In the set of 1,563 modules covering 13,142 genes, most modules displayed strong coexpression, but functional and cis-regulatory coherence was less prevalent. Highly connected hub genes showed a significant enrichment toward embryo lethality and evidence for cross talk between different biological processes. Comparative analysis revealed that 58% of the modules showed conserved coexpression across multiple plants. Using module-based functional predictions, 5,562 genes were annotated, and an evaluation experiment disclosed that, based on 197 recently experimentally characterized genes, 38.1% of these functions could be inferred through the module context. Examples of confirmed genes of unknown function related to cell wall biogenesis, xylem and phloem pattern formation, cell cycle, hormone stimulus, and circadian rhythm highlight the potential to identify new gene functions. The module-based predictions offer new biological hypotheses for functionally unknown genes in Arabidopsis (1,701 genes) and six other plant species (43,621 genes). Furthermore, the inferred modules provide new insights into the conservation of coexpression and coregulation as well as a starting point for comparative functional annotation.
Agrobacterium tumefaciensTumor Morphology Root Plastid Localization and Preferential Usage of Hydroxylated Prenyl Donor Is Important for Efficient Gall Formation
Authors: Ueda Nanae , Kojima Mikiko , Suzuki Katsunori , Sakakibara Hitoshi 
Published: May 2012

AbstractUpon Agrobacterium tumefaciens infection of a host plant, Tumor morphology root (Tmr) a bacterial adenosine phosphate-isopentenyltransferase (IPT), creates a metabolic bypass in the plastid for direct synthesis of trans-zeatin (tZ) with 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate as the prenyl donor. To understand the biological importance of Tmr function for gall formation, we compared Tmr and Trans-zeatin secretion (Tzs) another agrobacterial IPT that functions within the bacterial cell. Although there is no significant difference in their substrate specificities in vitro, ectopic overexpression of Tzs in Arabidopsis (Arabidopsis thaliana) resulted in the accumulation of comparable amounts of tZ- and N 6-(∆2-isopentenyl)adenine (iP)-type cytokinins, whereas overexpression of Tmr resulted exclusively in the accumulation of tZ-type cytokinins. Ectopic expression of Tzs in plant cells yields only small amounts of the polypeptide in plastid-enriched fractions. Obligatory localization of Tzs into Arabidopsis plastid stroma by translational fusions with ferredoxin transit peptide (TP-Tzs) increased the accumulation of both tZ- and iP-type cytokinins. Replacement of tmr on the Ti plasmid with tzs, TP-tzs, or an Arabidopsis plastidic IPT induced the formation of smaller galls than wild-type A. tumefaciens, and they were accompanied by the accumulation of iP-type cytokinins. Tmr is thus specialized for plastid localization and preferential usage of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in vivo and is important for efficient gall formation.
Aurora‐A activation, correlated with hypoxia‐inducible factor‐1α, promotes radiochemoresistance and predicts poor outcome for nasopharyngeal carcinoma
Authors: Wan Xiang‐Bo , Fan Xin‐Juan , Huang Pei‐Yu , Dong Dong , Zhang Yan , Chen Ming‐Yuan , Xiang Jin , Xu Jie , Liu Li , Zhou Wei‐Hua , Lv Yan‐Chun , Wu Xiang‐Yuan , Hong Ming‐Huang , Liu Quentin 
Published: May 2012

Previously, we and others showed that hypoxia‐inducible factor‐1α (HIF‐1α) and transcriptionally upregulated Aurora‐A were required for disease progression in several tumors. Here, we address the clinicopathologic value of Aurora‐A and HIF‐1α in locally advanced nasopharyngeal carcinoma (NPC). Aurora‐A and HIF‐1α expression was semiquantitatively evaluated by immunohistochemistry staining in 144 cases from a randomized controlled trial. Of these patients, 69 received neoadjuvant chemotherapy plus concurrent chemoradiotherapy, and acted as the training set, and 75 cases treated with neoadjuvant chemotherapy plus radiotherapy were used as the testing set to validate the prognostic effect of Aurora‐A and HIF‐1α. We found that Aurora‐A and HIF‐1α were highly expressed in NPC, but were deficient in normal adjacent epithelia. In the testing set, Aurora‐A overexpression predicted a shortened 5‐year overall survival (59.1% vs 82.5%, P = 0.024), progression‐free survival (44.8% vs 79.8%, P = 0.004), and distant metastasis‐free survival (43.0% vs 17.3%, P = 0.016). Multivariate regression analysis confirmed that Aurora‐A was indeed an independent prognostic factor for death, recurrence, and distant metastasis both in the testing set and overall patients. Moreover, a positive correlation between Aurora‐A and HIF‐1α was detected (P = 0.037). Importantly, although HIF‐1α did not show any prognostic effect for patient outcome, the subset with Aurora‐A and HIF‐1α co‐overexpression had the poorest overall, progression‐free, and distant metastasis‐free survival (all P < 0.05). Our results confirmed that Aurora‐A was an independent prognostic factor for NPC. Aurora‐A combined with HIF‐1α refined the risk definition of the patient subset, thus potentially directing locally advanced NPC patients for more selective therapy. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02332.x, 2012)
Phase I study of TAC‐101, an oral synthetic retinoid, in Japanese patients with advanced hepatocellular carcinoma
Authors: Okusaka Takuji , Ueno Hideki , Ikeda Masafumi , Takezako Yoriko , Morizane Chigusa 
Published: May 2012

Preclinical models have shown that TAC‐101 (4‐[3,5‐bis(trimethylsilyl) benzamide] benzoic acid), an oral synthetic retinoid, has antitumor activity in hepatocellular carcinoma (HCC). We conducted a phase I study in Japanese patients with advanced HCC to examine the pharmacokinetics, recommended dose, safety, and efficacy of TAC‐101. The administered dose of TAC‐101 was 10 mg/day in four patients (level 1), 20 mg/day in six (level 2), and 30 mg/day in three (level 3). There was no dose‐limiting toxicity at level 1. Only one patient each had dose‐limiting toxicity at level 2 (grade 2 fatigue, recovery requiring eight or more consecutive days of rest) and at level 3 (grade 3 splenic vein thrombosis). Level 3 (30 mg/day) was considered the maximum tolerated dose and 20 mg/day the recommended dose by a panel of medical experts, placing maximum emphasis on safety. The most frequent adverse events were fatigue, headache, and dermal symptoms such as rash. Pharmacokinetic parameters in Japanese patients with HCC were similar to those in patients in the United States, most of whom were Caucasian. Although no patient had a complete or partial response, the disease control rate was 38.5%. In conclusion, the recommended dose of TAC‐101 for patients with HCC is 20 mg/day. TAC‐101 had an acceptable toxicity profile, warranting further evaluation in clinical trials. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02334.x, 2012)
Timing of Xunhua and Guide basin development and growth of the northeastern Tibetan Plateau, China
Authors: Liu Shaofeng , Zhang Guowei , Pan Feng , Zhang Huiping , Wang Ping , Wang Kai , Wang Yan 
Published: May 2012

AbstractThe Xunhua, Guide and Tongren intermontane basin system in the NE Tibetan Plateau, situated near the Xining basin to the N and the Linxia basin to the E, is bounded by thrust fault‐controlled ranges. These include to the N, the Riyue Shan, Laji Shan and Jishi Shan ranges, and to the S the northern West Qinling Shan (NWQ). An integrated study of the structural geology, sedimentology and provenance of the Cenozoic Xunhua and Guide basins provides a detailed record of the growth of the NE Tibetan Plateau since the early Eocene. The Xining Group (ca. 52–21 Ma) is interpreted as consisting of unified foreland basin deposits which were controlled by the bounding thrust belt of the NWQ. The Xunhua, Guide and Xining subbasins were interconnected prior to later uplift and damming by the Laji Shan and Jishi Shan ranges. Their sediment source, the NWQ, is constrained by strong unidirectional paleocurrent trends towards the N, a northward fining lithology, distinct and recognizable clast types and detrital zircon ages. Collectively, formation of this mountain–basin system indicates that the Tibetan Plateau expanded into the NWQ at a time roughly coinciding with Eocene to earliest Miocene continental collision between India and Eurasia. The Guide Group (ca. 21–1.8 Ma) is inferred to have been deposited in the separate Xunhua, Guide and Tongren broken foreland basins. Each basin was filled by locally sourced alluvial fans, braided streams and deltaic‐lacustrine systems. Structural, paleogeographic, paleocurrent and provenance data indicate that thrust faulting in the NWQ stepped northward to the Laji Shan from ca. 21 to 16 Ma. This northward shift was accompanied by E–W shortening related to nearly N–S‐striking thrust faulting in Jishi Shan after 11–13 Ma. A lower Pleistocene conglomerate (1.8–1.7 Ma) was deposited by a through‐flowing river system in the overfilled and connected Guide and Xunhua basins following the termination of thrust activity. All of the basin–mountain zones developed along the Tibetan Plateau's NE margin since Indian–Tibetan continental collision may have been driven by collision‐induced basal drag of old slab remnants in the manner of N‐dipping and flat‐slab subduction, and their subsequent sinking into the deep mantle.
Novel dual inhibitors of vascular endothelial growth factor and VEGFR2 receptor
Authors: Nguyen Jennifer P. , Frost Chelsea D. , Lane Meghan L. , Skelton IV William P. , Skelton Michelle , Vesely David L. 
Published: May 2012

Eur J Clin Invest 2012; 42 (10): 1061–1067AbstractBackground  Vascular endothelial growth factor (VEGF) helps control tumour growth via causing new capillaries growth in tumours. Four cardiac hormones [i.e. vessel dilator, long‐acting natriuretic peptide (LANP), kaliuretic peptide (KP) and atrial natriuretic peptide (ANP)] that eliminate up to up to 86% of human small‐cell lung cancers growing in mice were investigated for their effects on VEGF and the VEGFR2/KDR/Flk‐1 receptor. The VEGFR2 receptor is the main receptor mediating VEGF’s cancer‐enhancing effects.Materials and Methods  Four cardiac hormones were evaluated for their ability to decrease VEGF/VEGFR2 measured by ELISAs in three human cancer cell lines.Results  Vessel dilator, LANP, KP and ANP, over a concentration range of 100 pM to 10 μM, maximally decreased the VEGFR2 receptor in human pancreatic adenocarcinoma cells by 48%, 49%, 74% and 83%. Vessel dilator, LANP, KP and ANP decreased the VEGFR2 receptor by 77%, 89%, 88% and 67% in human small‐cell lung cancer cells and by 48%, 92%, 64% and 71% in human prostate cancer cells. These results were confirmed with the cardiac hormones also decreasing the VEGFR2 receptor measured by Western blots. VEGF itself in pancreatic carcinoma cells was decreased by 42%, 58%, 36% and 40% by vessel dilator, LANP, KP and ANP. VEGF levels were decreased 25%, 23%, 17% and 23% in small‐cell lung cancer cells and decreased by 24%, 20%, 23% and 24% in prostate cancer cells by vessel dilator, LANP, KP and ANP.Conclusion  Four cardiac hormones are the first dual inhibitors of VEGF and the VEGFR2/KDR/Flk‐1 receptor.
Clinical information transfer and data capture in the acute myocardial infarction pathway: an observational study
Authors: Kesavan Sujatha , Kelay Tanika , Collins Ruth E. , Cox Benita , Bello Fernando , Kneebone Roger L. , Sevdalis Nick 
Published: May 2012

AbstractRationale, aims and objectives  Acute myocardial infarctions (MIs) or heart attacks are the result of a complete or an incomplete occlusion of the lumen of the coronary artery with a thrombus. Prompt diagnosis and early coronary intervention results in maximum myocardial salvage, hence time to treat is of the essence. Adequate, accurate and complete information is vital during the early stages of admission of an MI patient and can impact significantly on the quality and safety of patient care. This study aimed to record how clinical information between different clinical teams during the journey of a patient in the MI care pathway is captured and to review the flow of information within this care pathway.Method  A prospective, descriptive, structured observational study to assess (i) current clinical information systems (CIS) utilization and (ii) real‐time information availability within an acute cardiac care setting was carried out. Completeness and availability of patient information capture across four key stages of the MI care pathway were assessed prospectively.Results  Thirteen separate information systems were utilized during the four phases of the MI pathway. Observations revealed fragmented CIS utilization, with users accessing an average of six systems to gain a complete set of patient information. Data capture was found to vary between each pathway stage and in both patient cohort risk groupings. The highest level of information completeness (100%) was observed only in the discharge stage of the MI care pathway. The lowest level of information completeness (58%) was observed in the admission stage.Conclusion  The study highlights fragmentation, CIS duplication, and discrepancies in the current clinical information capture and data transfer across the MI care pathway in an acute cardiac care setting. The development of an integrated and user‐friendly electronic data capture and transfer system would reduce duplication and would facilitate efficient and complete information provision at the point of care.
Study protocol for a pilot study to explore the determinants of knowledge use in a medical education context
Authors: Reeves Scott , Leslie Karen , Baker Lindsay , Egan‐Lee Eileen , Légaré France , Silver Ivan , Rosenfield Jay , Hodges Brian , Curran Vernon , Armson Heather , Kitto Simon 
Published: May 2012

AbstractRationale, aims and objectives  While the science of knowledge translation (KT) has been growing steadily for the past decade in relation to understanding processes and actions which are embedded within clinical practice settings, little is known about how empirical knowledge is used within the medical education system. Despite an increase of research in this domain, we know very little about the contribution of this evidence in the development of medical students into effective physicians. This pilot study aims to: provide a synthesis of the evidence for educational strategies within medical education; explore the perceptions and experiences of faculty in undergraduate (UG) medical education in relation to their use of evidence in their educational practices; and illuminate how medical education evidence is formally integrated into a UG medical curriculum.Method  The study will involve three phases. First, a scoping review of the medical education research literature will be undertaken to generate insight into the evidence available for curriculum development, teaching and assessment activities within this domain. Second, a content analysis of undergraduate courses at the University of Toronto will be undertaken to generate an additional insight into the extent that medical education research has been formally integrated into the UG curriculum for medical students at the University. Finally, a purposeful sample of 30–40 medical education leaders from a single large university, selected as it aims to deliver a rigorous research‐oriented medical curriculum, will be interviewed to understand how they use the available evidence in their education practices.Discussion  This study will lay the grounds to generate initial data into the determinants of knowledge use in a medical education context. In doing so, the findings will also inform the development of a larger, pan‐Canadian study at medical schools that will generate a comprehensive account of the processes and challenges related to KT within an educational context. This larger study will also begin to explore the relevance of the Knowledge‐to‐Action model to a medical education context.
Paediatric nutrition risk scores in clinical practice: children with inflammatory bowel disease
Authors: Wiskin A. E. , Owens D. R. , Cornelius V. R. , Wootton S. A. , Beattie R. M. 
Published: May 2012

How to cite this article
Wiskin A.E., Owens D.R., Cornelius V.R., Wootton S.A. & Beattie R.M. (2012) Paediatric nutrition risk scores in clinical practice: children with inflammatory bowel disease. J Hum Nutr Diet. 25, 319–322AbstractBackground:  There has been increasing interest in the use of nutrition risk assessment tools in paediatrics to identify those who need nutrition support. Four non‐disease specific screening tools have been developed, although there is a paucity of data on their application in clinical practice and the degree of inter‐tool agreement.Methods:  The concurrent validity of four nutrition screening tools [Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP), Screening Tool for Risk On Nutritional status and Growth (STRONGkids), Paediatric Yorkhill Malnutrition Score (PYMS) and Simple Paediatric Nutrition Risk Score (PNRS)] was examined in 46 children with inflammatory bowel disease. Degree of malnutrition was determined by anthropometry alone using World Health Organization International Classification of Diseases (ICD‐10) criteria.Results:  There was good agreement between STAMP, STRONGkids and PNRS (kappa > 0.6) but there was only modest agreement between PYMS and the other scores (kappa = 0.3). No children scored low risk with STAMP, STRONGkids or PNRS; however, 23 children scored low risk with PYMS. There was no agreement between the risk tools and the degree of malnutrition based on anthropometric data (kappa < 0.1). Three children had anthropometry consistent with malnutrition and these were all scored high risk. Four children had body mass index SD scores < −2, one of which was scored at low nutrition risk.Conclusions:  The relevance of nutrition screening tools for children with chronic disease is unclear. In addition, there is the potential to under recognise nutritional impairment (and therefore nutritional risk) in children with inflammatory bowel disease.
Reconstruction of paternal genotypes over multiple breeding seasons reveals male green turtles do not breed annually
Authors: WRIGHT LUCY I. , FULLER WAYNE J. , GODLEY BRENDAN J. , McGOWAN ANDREW , TREGENZA TOM , BRODERICK ANNETTE C. 
Published: May 2012

AbstractFor species of conservation concern, knowledge of key life‐history and demographic components, such as the number and sex ratio of breeding adults, is essential for accurate assessments of population viability. Species with temperature‐dependent sex determination can produce heavily biased primary sex ratios, and there is concern that adult sex ratios may be similarly skewed or will become so as a result of climate warming. Prediction and mitigation of such impacts are difficult when life‐history information is lacking. In marine turtles, owing to the difficultly in observing males at sea, the breeding interval of males is unknown. It has been suggested that male breeding periodicity may be shorter than that of females, which could help to compensate for generally female‐biased sex ratios. Here we outline how the use of molecular‐based paternity analysis has allowed us, for the first time, to assess the breeding interval of male marine turtles across multiple breeding seasons. In our study rookery of green turtles (Chelonia mydas), 97% of males were assigned offspring in only one breeding season within the 3‐year study period, strongly suggesting that male breeding intervals are frequently longer than 1 year at this site. Our results also reveal a sex ratio of breeding adults of at least 1.3 males to each female. This study illustrates the utility of molecular‐based parentage inference using reconstruction of parental genotypes as a method for monitoring the number and sex ratio of breeders in species where direct observations or capture are difficult.