bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spoken Language Processing Model: Bridging Auditory and Language Processing to Guide Assessment and Intervention
Authors: Medwetsky Larry 
Published: July 2011

PurposeThis article outlines the author’s conceptualization of the key mechanisms that are engaged in the processing of spoken language, referred to as the spoken language processing model. The act of processing what is heard is very complex and involves the successful intertwining of auditory, cognitive, and language mechanisms. Spoken language processing disorders occur when a breakdown in any of these mechanisms impacts an individual’s ability to effectively process and use the information that is heard. The symptoms vary depending on the underlying deficit(s). The primary purpose of this article is to provide the reader with a basic understanding of these mechanisms, and, in turn, enable readers to (a) review the literature concerning processing disorders with discernment and (b) have a foundation for developing a test battery to derive composite profiles of individuals' processing abilities.MethodA review of the literature, overview of the spoken language processing model, and suggested approach to diagnostic assessment are presented.ConclusionSpoken language processing can break down due to a myriad of underlying causes. Central auditory nervous system deficits can impact not only the initial processing of stimuli but possibly the development of effective language skills. On the other hand, deficits in various cognitive and language mechanisms can similarly impact the auditory processing of speech stimuli. Therefore, it is critical to understand how these mechanisms interact and contribute to the processing of speech stimuli.
Auditory Processing Theories of Language Disorders: Past, Present, and Future
Authors: Miller Carol A. 
Published: July 2011

PurposeThe purpose of this article is to provide information that will assist readers in understanding and interpreting research literature on the role of auditory processing in communication disorders.MethodA narrative review was used to summarize and synthesize the literature on auditory processing deficits in children with auditory processing disorder (APD), specific language impairment (SLI), and dyslexia. The history of auditory processing theories of these 3 disorders is described, points of convergence and controversy within and among the different branches of research literature are considered, and the influence of research on practice is discussed. The theoretical and clinical contributions of neurophysiological methods are also reviewed, and suggested approaches for critical reading of the research literature are provided.ConclusionResearch on the role of auditory processing in communication disorders springs from a variety of theoretical perspectives and assumptions, and this variety, combined with controversies over the interpretation of research results, makes it difficult to draw clinical implications from the literature. Neurophysiological research methods are a promising route to better understanding of auditory processing. Progress in theory development and its clinical application is most likely to be made when researchers from different disciplines and theoretical perspectives communicate clearly and combine the strengths of their approaches.
How to Make a 29% Increase Look Bigger: The Unit Effect in Option Comparisons
Authors: Pandelaere Mario , Briers Barbara , Lembregts Christophe 
Published: July 2011

Abstract
Quantitative information can appear in different units (e.g., 7-year warranty = 84-month warranty). This article demonstrates that attribute differences appear larger on scales with a higher number of units; expressing quality information on such an expanded scale makes consumers switch to a higher-quality option. Testifying to its practical importance, expressing the energy content of snacks in kilojoules rather than kilocalories increases the choice of a healthy snack. The unit effect occurs because consumers focus on the number rather than the type of units in which information is expressed (numerosity effect). Therefore, reminding consumers of alternative units in which information can be expressed eliminates the unit effect. Finally, the unit effect moderates relative thinking: consumers are more sensitive to relative attribute differences when the attribute is expressed on expanded scales. The relation with anchoring and implications for temporal discounting and loyalty programs are discussed.
Tokamak plasma edge modelling including the main chamber wall
Authors: Baelmans M. , Börner P. , Dekeyser W. , Reiter D. 
Published: July 2011

Quantifying main chamber wall recycling, erosion and resulting material migration, at least on the basis of known or empirical far scrape-off layer (SOL) processes, is still highly uncertain, despite its relevance for ITER and fusion reactor design studies. This affects, for example, the design problem of first mirror performance of many optical diagnostics in the harsh ITER environment. Poor computational access is not least due to a fundamental technical limitation in apparently all current tokamak edge plasma fluid codes, which implicates a wide computationally unresolved gap between the outermost plasma layer treated in codes and the real vessel wall. We show how the current ITER version of the B2-EIRENE code (SOLPS-4.3) can be extended to cover also this far SOL, on the same footing as the rest of the plasma transport model. We discuss consequences of this new model for estimating plasma power and particle sink terms caused by a fairly realistic wall in ITER based on the conventional Bohm criterion along all plasma–wall interfaces.
Corrections were made to this article on 14 July 2011. The authors have been assigned to the correct affiliations.
A novel signal processing approach for the detection of copy number variations in the human genome
Authors: Stamoulis Catherine , Betensky Rebecca A. 
Published: July 2011

Abstract
Motivation: Human genomic variability occurs at different scales, from single nucleotide polymorphisms (SNPs) to large DNA segments. Copy number variations (CNVs) represent a significant part of our genetic heterogeneity and have also been associated with many diseases and disorders. Short, localized CNVs, which may play an important role in human disease, may be undetectable in noisy genomic data. Therefore, robust methodologies are needed for their detection. Furthermore, for meaningful identification of pathological CNVs, estimation of normal allelic aberrations is necessary.
Results: We developed a signal processing-based methodology for sequence denoising followed by pattern matching, to increase SNR in genomic data and improve CNV detection. We applied this signal-decomposition-matched filtering (SDMF) methodology to 429 normal genomic sequences, and compared detected CNVs to those in the Database of Genomic Variants. SDMF successfully detected a significant number of previously identified CNVs with frequencies of occurrence ≥10%, as well as unreported short CNVs. Its performance was also compared to circular binary segmentation (CBS). through simulations. SDMF had a significantly lower false detection rate and was significantly faster than CBS, an important advantage for handling large datasets generated with high-resolution arrays. By focusing on improving SNR (instead of the robustness of the detection algorithm), SDMF is a very promising methodology for identifying CNVs at all genomic spatial scales.
Availability: The data are available at http://tcga-data.nci.nih.gov/tcga/ The software and list of analyzed sequence IDs are available at http://www.hsph.harvard.edu/~betensky/ A Matlab code for Empirical Mode Decomposition may be found at: http://www.clear.rice.edu/elec301/Projects02/empiricalMode/code.html
Contact: caterina@mit.edu
RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
Authors: Hu Qian-Nan , Deng Zhe , Hu Huanan , Cao Dong−Sheng , Liang Yi−Zeng 
Published: July 2011

Abstract
Summary: Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism.
Availability: RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder.
Contact: qnhu@whu.edu.cn
First Report of Phytophthora nicotianae on Bulb Onion in the United States
Authors: French J. M. , Stamler R. A. , Randall J. J. , Goldberg N. P. 
Published: July 2011

Phytophthora nicotianae (synonym P. parasitica) Breda de Haan was isolated from recently harvested onion bulbs (Allium cepa) in cold storage from a commercial field in southern New Mexico. Deteriorating, water-soaked tissue from the center of four bulbs was plated onto water agar and incubated at room temperature. After 72 h, cultures of Phytophthora (identified by the presence of coenocytic hyphae and papillate sporangia) were isolated and transferred to V8 agar amended with ampicillin (250 mg/liter), rifampicin (10 mg/liter), and pimaricin (0.2% wt/vol). Isolates were identified as P. nicotianae based on morphological characteristics and DNA analysis. Sporangia were sharply papilliate, noncaducous, and ovoid to spherical. The average sporangium size was 45.9 × 39.9 μm with a length-to-width ratio of 1.15. Clamydospores, both terminal and intercalary, were spherical to ovoid and averaged 37.2 × 35.2 μm (2). PCR from whole-cell extracts was performed on four cultured isolates from the infected onion tissue using previously described primers ITS4 and ITS6, which amplify the 5.8S rDNA and ITS1 and ITS2 internal transcribed spacers (1,4). A band of approximately 890 bp was amplified and directly sequenced (GenBank Accession No. HQ398876). A BLAST search of the NCBI total nucleotide collection revealed a 100% similarity to multiple P. nicotianae isolates previously sequenced (1). To confirm the pathogenicity of the isolates, onion seedlings were inoculated with 25 ml of P. nicotionae zoospore solution (15,000 zoospores/ml). Necrosis of leaf tissue and seedling death was observed 5 days postinoculation. P. nicotianae was reisolated from the infected onion seedlings and the ITS region was sequenced to confirm its identity. P. nicotianae was previously reported in bulb onion from Australia, Taiwan (Formosa), and Zimbabwe (Rhodesia) (2). P. nicotianae was reported on bunching onions (A. fistulosum) in Hawaii in 1989 (3). Onions are an important crop in New Mexico with a total production value of 47 million dollars in 2008 (NM Agriculture Statistics 2008). This discovery of a potentially significant postharvest disease poses a threat to the onion industry in New Mexico. To our knowledge, this is the first report of P. nicotianae in bulb onion in the United States and the first report of P. nicotianae in New Mexico on any crop. References: (1) D. E. L. Cooke and J. M. Duncan. Mycol. Res. 101:667, 1997. (2) D. C. Erwin and O. K. Ribeiro. Page 56 in: Phytophthora Diseases Worldwide. The American Phytopathological Society, St Paul, MN, 1996. (3) R. D. Raabe et al. Information Text Series No. 22. University of Hawaii. Hawaii Inst. Trop. Agric. Human Resources, 1981. (4) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, 1990.
First Report of Phaeoacremonium mortoniae Associated with Grapevine Decline in Iran
Authors: Mohammadi H. 
Published: July 2011

In July 2009, a survey was conducted in individually owned rooted vineyards in Iran to determine fungal pathogens associated with grapevine decline. Symptoms of grapevine decline such as slow dieback, stunted growth, small chlorotic leaves, and reduced foliage were observed on 7-year-old grapevines (cv. Askari) in Bavanat (Fars Province, southwestern Iran). Internal wood symptoms such as black spots and dark brown-to-black vascular streaking were observed in cross and longitudinal sections of stems and trunks. Wood samples were collected from symptomatic trunks and cordons. The bark of each fragment was removed and 10 thin cross sections (2 to 3 mm thick) were cut from symptomatic vascular tissue of the samples. These disks were immersed in 1.5% sodium hypochlorite solution for 4 min, washed thrice with sterile distilled water, and plated onto malt extract agar (MEA) supplemented with 100 mg liter–1 of streptomycin sulfate. Plates were incubated at 25°C in darkness. All colonies were transferred to potato dextrose agar (PDA) and incubated at 25°C. Five isolates of a Phaeoacremonium sp. were obtained. Single-spore isolates were transferred to PDA, MEA, and oatmeal agar (OA) media and incubated at 25°C for 8 to 16 days in the dark (2). Colonies reached a radius of 9.5 to 12 mm after 8 days of incubation. Colonies were flat and yellowish white on PDA and OA and white-to-pale gray after 16 days of incubation on MEA. Conidiophores were short and unbranched, 14 to 38.5 (23.5) μm long, and often ending in a single terminal phialide. Phialides were terminal or lateral and mostly monophialidic. Conidia were hyaline, oblong to ellipsoidal or reniform, 2 to 6.5 (4.9) μm long, and 1.1 to 1.7 (1.4) μm wide. On the basis of these characteristics, the isolates were identified as Phaeoacremonium mortoniae (1,2). Additionally, identity of the PMH1 isolate was confirmed by sequencing a fragment of the -tubulin gene with primers T1 and Bt2b (GenBank Accession No. JF831449). The sequence of this isolate was identical to the sequence of P. mortoniae (GenBank Accession No. HM116767). Pathogenicity tests were conducted on 2-month-old grapevine seedlings of cv. Askari by watering the roots with 25 ml of a conidial suspension (107 conidia ml–1) harvested from 21-day-old cultures grown on MEA. Controls were inoculated with 25 ml of sterile distilled water. Fifteen replicates were used for each isolate with an equal number of noninoculated plants. All plants were grown under greenhouse conditions (25 to 30°C). Two months after inoculation, inoculated seedlings showed reduced growth, chlorotic leaves, epinasty, severe defoliation, and finally wilting, while control seedlings remained healthy. The fungus was reisolated from internal tissues of the stems of inoculated seedlings. To my knowledge, this is the first report of P. mortoniae causing grapevine decline in Iran. References: (1) M. Groenewald et al. Mycol. Res. 105:651, 2001. (2) L. Mostert et al. Stud. Mycol. 54:1, 2006.
Rice Ethylene-Response AP2/ERF Factor OsEATB Restricts Internode Elongation by Down-Regulating a Gibberellin Biosynthetic Gene
Authors: Qi Weiwei , Sun Fan , Wang Qianjie , Chen Mingluan , Huang Yunqing , Feng Yu-Qi , Luo Xiaojin , Yang Jinshui 
Published: July 2011

Abstract
Plant height is a decisive factor in plant architecture. Rice (Oryza sativa) plants have the potential for rapid internodal elongation, which determines plant height. A large body of physiological research has shown that ethylene and gibberellin are involved in this process. The APETALA2 (AP2)/Ethylene-Responsive Element Binding Factor (ERF) family of transcriptional factors is only present in the plant kingdom. This family has various developmental and physiological functions. A rice AP2/ERF gene, OsEATB (for ERF protein associated with tillering and panicle branching) was cloned from indica rice variety 9311. Bioinformatic analysis suggested that this ERF has a potential new function. Ectopic expression of OsEATB showed that the cross talk between ethylene and gibberellin, which is mediated by OsEATB, might underlie differences in rice internode elongation. Analyses of gene expression demonstrated that OsEATB restricts ethylene-induced enhancement of gibberellin responsiveness during the internode elongation process by down-regulating the gibberellin biosynthetic gene, ent-kaurene synthase A. Plant height is negatively correlated with tiller number, and higher yields are typically obtained from dwarf crops. OsEATB reduces rice plant height and panicle length at maturity, promoting the branching potential of both tillers and spikelets. These are useful traits for breeding high-yielding crops.
Growth Arrest by Trehalose-6-Phosphate: An Astonishing Case of Primary Metabolite Control over Growth by Way of the SnRK1 Signaling Pathway
Authors: Delatte Thierry L. , Sedijani Prapti , Kondou Youichi , Matsui Minami , de Jong Gerhardus J. , Somsen Govert W. , Wiese-Klinkenberg Anika , Primavesi Lucia F. , Paul Matthew J. , Schluepmann Henriette 
Published: July 2011

Abstract
The strong regulation of plant carbon allocation and growth by trehalose metabolism is important for our understanding of the mechanisms that determine growth and yield, with obvious applications in crop improvement. To gain further insight on the growth arrest by trehalose feeding, we first established that starch-deficient seedlings of the plastidic phosphoglucomutase1 mutant were similarly affected as the wild type on trehalose. Starch accumulation in the source cotyledons, therefore, did not cause starvation and consequent growth arrest in the growing zones. We then screened the FOX collection of Arabidopsis (Arabidopsis thaliana) expressing full-length cDNAs for seedling resistance to 100 mm trehalose. Three independent transgenic lines were identified with dominant segregation of the trehalose resistance trait that overexpress the bZIP11 (for basic region/leucine zipper motif) transcription factor. The resistance of these lines to trehalose could not be explained simply through enhanced trehalase activity or through inhibition of bZIP11 translation. Instead, trehalose-6-phosphate (T6P) accumulation was much increased in bZIP11-overexpressing lines, suggesting that these lines may be insensitive to the effects of T6P. T6P is known to inhibit the central stress-integrating kinase SnRK1 (KIN10) activity. We confirmed that this holds true in extracts from seedlings grown on trehalose, then showed that two independent transgenic lines overexpressing KIN10 were insensitive to trehalose. Moreover, the expression of marker genes known to be jointly controlled by SnRK1 activity and bZIP11 was consistent with low SnRK1 or bZIP11 activity in seedlings on trehalose. These results reveal an astonishing case of primary metabolite control over growth by way of the SnRK1 signaling pathway involving T6P, SnRK1, and bZIP11.
Mechanisms of Molecular Mimicry of Plant CLE Peptide Ligands by the Parasitic NematodeGlobodera rostochiensis
Authors: Guo Yongfeng , Ni Jun , Denver Robert , Wang Xiaohong , Clark Steven E. 
Published: July 2011

AbstractNematodes that parasitize plant roots cause huge economic losses and have few mechanisms for control. Many parasitic nematodes infect plants by reprogramming root development to drive the formation of feeding structures. How nematodes take control of plant development is largely unknown. Here, we identify two host factors involved in the function of a receptor ligand mimic, GrCLE1, secreted by the potato cyst nematode Globodera rostochiensis. GrCLE1 is correctly processed to an active form by host plant proteases. Processed GrCLE1 peptides bind directly to the plant CLE receptors CLV2, BAM1, and BAM2. Involvement of these receptors in the ligand-mimicking process is also supported by the fact that the ability of GrCLE1 peptides to alter plant root development in Arabidopsis (Arabidopsis thaliana) is dependent on these receptors. Critically, we also demonstrate that GrCLE1 maturation can be entirely carried out by plant factors and that the availability of CLE processing activity may be essential for successful ligand mimicry.
OsPHF1 Regulates the Plasma Membrane Localization of Low- and High-Affinity Inorganic Phosphate Transporters and Determines Inorganic Phosphate Uptake and Translocation in Rice
Authors: Chen Jieyu , Liu Yu , Ni Jun , Wang Yifeng , Bai Youhuang , Shi Jing , Gan Jian , Wu Zhongchang , Wu Ping 
Published: July 2011

Abstract
PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (PHF1) is known to regulate the plasma membrane localization of PHT1;1, a high-affinity inorganic phosphate (Pi) transporter in Arabidopsis (Arabidopsis thaliana). OsPHF1, a rice (Oryza sativa) gene homologous to AtPHF1, was isolated and found to regulate the localization of both low- and high-affinity Pi transporters to the plasma membrane. Three OsPHF1 allelic mutants carrying one-point mutations at the fifth WD-repeat motif and two at the transmembrane helix, respectively, showed arsenate resistance and severely reduced Pi accumulation. The data indicate that mutation of OsPHF1 results in the endoplasmic reticulum retention of the low-affinity Pi transporter OsPT2 and high-affinity Pi transporter OsPT8. Mutation of OsPHF1 also reduced Pi accumulation in plants exhibiting excessive shoot Pi accumulation due to the overexpression of OsPHR2. However, the transcript level of OsPHF1 itself is not controlled by OsPHR2. Overexpression of OsPHF1 increased Pi accumulation in both roots and shoots in a solution culture with Pi-supplied condition. These results indicate that the role of OsPHF1 is unique in the localization of both low- and high-affinity Pi transporters on the plasma membrane in rice and determines Pi uptake and translocation in rice. The similar function of PHF1 required to facilitate PHT1 transit through the endoplasmic reticulum between Arabidopsis and rice provides an example of expectations from what one would deduce from sequence comparisons to extend knowledge from Arabidopsis to crops.
GIMEMA AIDA 0493 amended protocol for elderly patients with acute promyelocytic leukaemia. Long‐term results and prognostic factors
Authors: Latagliata Roberto , Breccia Massimo , Fazi Paola , Vignetti Marco , Di Raimondo Francesco , Sborgia Marco , Vincelli Donatella , Candoni Anna , Salvi Flavia , Rupoli Serena , Martinelli Giovanni , Kropp Maria Grazia , Tonso Anna , Venditti Adriano , Melillo Lorella , Cimino Giuseppe , Petti Maria Concetta , Avvisati Giuseppe , Lo‐Coco Francesco , Mandelli Franco ,   for the GIMEMA Acute Leukaemia Working Party
Published: July 2011

SummaryTo reduce toxicity in elderly patients with acute promyelocytic leukaemia, in 1997 the Gruppo Italiano Malattie Ematologiche Dell’Adulto (GIMEMA) started an amended protocol for patients aged >60 years, with the same induction [all‐trans retinoic acid (ATRA) + idarubicin] as in younger patients, followed by a single consolidation course (idarubicin + cytarabine) and maintenance with intermittent ATRA. Among 60 enrolled patients, 54 (90%) achieved haematological remission and six died during induction. Four additional patients died in complete remission (CR) from haemorrhage (2) and infection (2) prior or during consolidation therapy. Eleven patients relapsed at a median time of 17·5 months from CR. The 5‐year overall survival (OS), disease‐free survival (DFS) and cumulative incidence of relapse (CIR) rates were 76·1%, 64·6% and 27·4%, respectively. Univariate analysis identified a performance score (PS) = 2 as the only significant adverse prognostic factor for both OS (P = 0·017) and DFS (P = 0·0003). Male sex had an unfavourable impact on DFS (P = 0·021) and on CIR (P = 0·019), but not on OS (P = 0·234). In multivariate analysis for DFS, only PS = 2 retained prognostic significance (HR = 4·5, P = 0·0083). In conclusion, the amended GIMEMA protocol is effective, with similar relapse rate and inferior toxicity compared to the original AIDA 0493. However, considering the recent availability of effective new agents, a less aggressive approach should be tested in this setting.