bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Diagnosis and Management of Auditory Processing Disorder
Authors: Moore David R. 
Published: July 2011

PurposeTo provide a personal perspective on auditory processing disorder (APD), with reference to the recent clinical forum on APD and the needs of clinical speech-language pathologists and audiologists.MethodThe Medical Research Council–Institute of Hearing Research (MRC-IHR) has been engaged in research into APD and auditory learning for 8 years. This commentary is informed by and describes that and other research.ResultsCurrently, APD is ill defined, and training-based interventions appear to have limited effectiveness. However, there remains a huge clinical and caregiver appetite for evidence-based information about children’s listening difficulties and how they might be managed. MRC-IHR research suggests that both the problem and the solution revolve around auditory cognition and, in particular, working memory and attention. Children who are poor listeners tend to have a range of cognitive difficulties. But, results of training studies within and beyond auditory science indicate that training primarily influences sustained attention (focus) rather than more basic sensory detection or discrimination.ConclusionProviding logical and rigorous scientific information on the nature and alleviation of listening difficulties in children should remain a high priority for speech, language, and hearing research. We should be optimistic that collaboration between clinicians and researchers will result in much greater understanding and improved management of listening disorders in the near future.
The Role of the Speech-Language Pathologist in Identifying and Treating Children With Auditory Processing Disorder
Authors: Richard Gail J. 
Published: July 2011

Purpose
A summary of issues regarding auditory processing disorder (APD) is presented, including some of the remaining questions and challenges raised by the articles included in the clinical forum.

Method
Evolution of APD as a diagnostic entity within audiology and speech-language pathology is reviewed. A summary of treatment efficacy results and issues is provided, as well as the continuing dilemma for speech-language pathologists (SLPs) charged with providing treatment for referred APD clients.

Conclusion
The role of the SLP in diagnosing and treating APD remains under discussion, despite lack of efficacy data supporting auditory intervention and questions regarding the clinical relevance and validity of APD.
The Impact of Product Name on Dieters’ and Nondieters’ Food Evaluations and Consumption
Authors: Irmak Caglar , Vallen Beth , Robinson Stefanie Rosen 
Published: July 2011

Abstract
This research explores the impact of merely altering the name of a food on dieters’ and nondieters’ evaluations of the food’s healthfulness and taste, as well as consumption. Four studies demonstrate that when a food is identified by a relatively unhealthy name (e.g., pasta), dieters perceive the item to be less healthful and less tasty than do nondieters. When the identical food is assigned a relatively healthy name (e.g., salad), however, dieting tendency has no effect on product evaluations. This effect, which results in differences in actual food consumption, is explained by nondieters’ insensitivity to food cues as well as dieters’ reliance on cues indicating a lack of healthfulness and tendency to employ heuristic information processing when evaluating foods. These findings contribute to the body of literature that explores both individual and contextual factors that influence food evaluation and consumption.
DECOD: fast and accurate discriminative DNA motif finding
Authors: Huggins Peter , Zhong Shan , Shiff Idit , Beckerman Rachel , Laptenko Oleg , Prives Carol , Schulz Marcel H. , Simon Itamar , Bar-Joseph Ziv 
Published: July 2011

Abstract
Motivation: Motif discovery is now routinely used in high-throughput studies including large-scale sequencing and proteomics. These datasets present new challenges. The first is speed. Many motif discovery methods do not scale well to large datasets. Another issue is identifying discriminative rather than generative motifs. Such discriminative motifs are important for identifying co-factors and for explaining changes in behavior between different conditions.
Results: To address these issues we developed a method for DECOnvolved Discriminative motif discovery (DECOD). DECOD uses a k-mer count table and so its running time is independent of the size of the input set. By deconvolving the k-mers DECOD considers context information without using the sequences directly. DECOD outperforms previous methods both in speed and in accuracy when using simulated and real biological benchmark data. We performed new binding experiments for p53 mutants and used DECOD to identify p53 co-factors, suggesting new mechanisms for p53 activation.
Availability: The source code and binaries for DECOD are available at http://www.sb.cs.cmu.edu/DECOD
Contact: zivbj@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
PDBpaint, a visualization webservice to tag protein structures with sequence annotations
Authors: Fournier David , Andrade-Navarro Miguel A. 
Published: July 2011

Abstract
Summary: Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded protein's 3D space. Mapping sequence features to known or predicted protein structures is useful when trying to deduce the function of those features and when evaluating sequence or structural predictions. To facilitate this goal, we developed PDBpaint, a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user. The current version of PDBpaint allows the visualization of annotations from Pfam, ARD (detection of HEAT-repeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually.
Availability and Implementation: PDBpaint is accessible at http://cbdm.mdc-berlin.de/~pdbpaint. Code is available from http://sourceforge.net/projects/pdbpaint. The website was implemented in Perl, with all major browsers supported.
Contact: david.fournier@mdc-berlin.de
The Irish Sea data-enhancement project: comparison of self-sampling and national data-collection programmes—results and experiences
Authors: Hoare Deirdre , Graham Norman , Schön Pieter-Jan 
Published: July 2011

Abstract
Hoare, D., Graham, N., and Schön, P-J. 2011. The Irish Sea data-enhancement project: comparison of self-sampling and national data-collection programmes—results and experiences. – ICES Journal of Marine Science, 68: 1778–1784. The Irish Sea Data Enhancement Pilot (ISDEP) was initiated by the UK and Irish fishing sectors, with the objective of improving the precision of commercial catch data (landings and discards) from vessels engaged in demersal trawling in the Irish Sea (ICES Division VIIa). The programme was supported by the Irish and UK Governments and managed by national laboratories. The experience of establishing and managing such a programme, including logistical, data-quality, and participation issues, is discussed. By contrasting with parallel national programmes, it is shown that the new data are robust and have improved precision. Experience has also shown that it is preferable to involve a few vessels in providing frequent samples, but that positive incentives are needed to maintain the participation.
First Report of Soybean Rust Caused by Phakopsora pachyrhizi on Pachyrhizus erosus in the United States
Authors: Delaney M. A. , Sikora E. J. , Delaney D. P. , Palm M. E. , Roscoe J. , Haudenshield J. S. , Hartman G. L. 
Published: July 2011

Soybean rust, caused by the fungus Phakopsora pachyrhizi, was detected on jicama (Pachyrhizus erosus L. Urban) for the first time in the United States in November 2009. The pathogen was observed on leaves of a single, potted jicama plant grown outdoors in a residential area and on leaves of all plants in a 12-m2 demonstration plot located at the Auburn University Teaching Garden in Auburn, AL. Symptoms on the upper leaf surfaces were isolated chlorotic areas near the leaf edges in the lower part of the canopy. The abaxial surface was first observed to exhibit brown lesions and subsequently produced volcano-shaped uredinia. These symptoms are consistent with a rust previously described on jicama in Mexico (1). Representative symptomatic plant tissue was sent to the USDA National Identification Services (Mycology) Laboratory in Beltsville, MD for diagnostic confirmation at both the Urbana, IL lab and the USDA National Plant Germplasm and Biotechnology Laboratory for DNA testing. From an infected leaf, samples of approximately 5 mm2 were excised from a microscopically observed rust lesion and an apparently noninfected area. Total DNA was purified with the FastDNA Spin Kit (MP Biomedicals, Solon, OH) followed by the E.Z.N.A. MicroElute DNA Clean-Up Kit (Omega Bio-tek, Inc, Doraville, GA) per manufacturer's instructions. Detection of P. pachyrhizi and P. meibomiae DNA was achieved by quantitative PCR using the method of Frederick et al. (2) and a DNA standard of previously prepared P. pachyrhizi spores. The observed rust pustule was found to contain P. pachyrhizi DNA in excess of 28,000 genomes, while no P. pachyrhizi DNA was observed from the asymptomatic sample. Both samples were negative for P. meibomiae. The fungal structures present were confirmed to be Phakopsora spp. DNA was extracted from sori aseptically removed from leaves with a Qiagen (Valencia, CA) DNeasy Plant Mini Kit and amplified with primers Ppa1 and NL4. The resulting partial ITS2 and 28S ribosomal RNA sequences were 100% identical to GenBank entry DQ354537 P. pachyrhizi internal transcribed spacer 2 and 28S ribosomal RNA gene, partial sequence. Sequences from jicama from Alabama were deposited in GenBank. Voucher specimens were deposited in the USDA Agricultural Research Service, National Fungus Collection (BPI). To our knowledge, this is the first report of the disease on jicama in the United States. References: (1) A. Cárcamo Rodriguez et al. Plant Dis. 90:1260, 2006. (2) R. D. Frederick et al. Phytopathology 92:217, 2002.
Pediatric Capsule Endoscopy
Authors: Cohen Stanley A. , Ephrath Hagit , Lewis Jeffery D. , Klevens Alan , Bergwerk Ari , Liu Steven , Patel Dinesh , Reed‐Knight Bonney , Stallworth Angela , Wakhisi Tamara , Gold Benjamin D. 
Published: July 2011

ABSTRACTBackground and Objective:Because capsule endoscopy (CE) avoids ionizing radiation, deep sedation, and general anesthesia, CE may be valuable in pediatrics. We report a single pediatric center's experience with the use and safety of CE.Methods:In a retrospective review of consecutive CE studies, 284 CE studies were performed in 277 patients with a mean age of 15 (±3.7) years during a 5‐year period. The youngest to swallow the capsule was 4.6 years old. Twenty capsules were placed. Overall, 245 (86%) patients underwent CE for suspected (184, 65%) or confirmed (61, 21%) Crohn disease (CD); 27 (9.5%) anemia or gastrointestinal bleeding; 6 (2%) polyposis; and 4 (1.4%) celiac disease.Results:Positive findings were observed in 205 (72%) of the studies, with 152 (54%) having small bowel findings. Of these, 72 (47%) were diagnostic. Gastric (95, 33%) and colonic (31, 11%) abnormalities were also identified. Five CE studies (1.8%) resulted in retention of the capsule in nonsurgical patients. A patency capsule before CE in 23 patients allowed 19 CE to proceed with only 1 retained capsule. In 65 (21%) patients, the video capsule did not enter the colon before the video's end. Of these, 36 (65%) had significant findings, including 27 (49%) documenting small bowel (SB) CD.Conclusions:CE is useful to diagnose SB disease in children. Even in a study population with a high prevalence of confirmed and suspected CD, the risk of retention remains small. The patency capsule may lessen that risk. CE may identify gastric or colonic disease even when SB lesions are not present.
Effect of a 10‐week Weight Loss Camp on Fatty Liver Disease and Insulin Sensitivity in Obese Danish Children
Authors: Grønbæk Henning , Lange Aksel , Birkebæk Niels H. , Holland‐Fischer Peter , Solvig Jan , Hørlyck Arne , Kristensen Kurt , Rittig Søren , Vilstrup Hendrik 
Published: July 2011

ABSTRACTBackground and Objective:Childhood nonalcoholic fatty liver disease (NAFLD) associated with insulin resistance and obesity is a growing problem and increases the risk of cirrhosis, type 2 diabetes mellitus, and cardiovascular complications. We examined the effects of a 10‐week “weight loss camp” residency in obese children on the prevalence and degree of NAFLD and insulin sensitivity with 12‐month follow‐up.Methods:At the camp, 117 obese white children (body mass index 28.0 ± 3.6 kg/m2, age 12.1 ± 1.3 years) exercised moderately for 1 hour/day and restricted their energy intake to induce weight loss. NAFLD was diagnosed and graded using ultrasound and transaminasemia. Insulin sensitivity and glucose tolerance were assessed using homeostasis model assessment and oral glucose tolerance test. We performed anthropometric measurements and determined body composition using bioimpedance. Data were collected from 71 of 117 children at entry, after the 10 weeks at the camp, and 12 months after the camp ended.Results:The children showed an average weight loss of 7.1 ± 2.7 kg during the camp. At baseline, 43% had ultrasonographic liver steatosis, 50% elevated transaminases (>25 IU/L), and reduced insulin sensitivity. These abnormalities were mutually related and improved significantly during the camp (P ≤ 0.05). Liver fat improvement was sustained at 12 months. At the 12‐month follow‐up, 17 of 71 (24%) children maintained the body weight.Conclusions:This short‐term diet and exercise program induced weight loss, markedly improved all aspects of the threatening condition of NAFLD, and reduced insulin sensitivity in childhood obesity; 24% of the children maintained weight loss at least until the 12‐month follow‐up.
Significance of Abnormalities in Systems Proximal and Distal to the Obstructed Site of Duodenal Atresia
Authors: Alatas Fatima S. , Masumoto Kouji , Esumi Genshiro , Nagata Kouji , Taguchi Tomoaki 
Published: July 2011

ABSTRACTBackground:Duodenal atresia (DA) is a well‐known neonatal intestinal disease. Even after surgery, the proximal segment can continue to be severely dilated with hypoperistalsis, resulting in intestinal dysmotility problems in later life. No data have been published regarding the morphologic differences between the proximal and distal regions of obstructed sites of the intramural components in DA.Methods:Operative duodenal samples (N = 12) from cases with DA (age 1–3 days) were used. Age‐matched controls (N = 2) were used. All of the specimens were immunohistochemically stained with antibodies to S‐100 protein, α‐smooth muscle actin, and c‐kit protein.Results:At the proximal segments of the obstructed site in DA, the number of neuronal cells decreased in size and number. The circular musculature was moderately to severely hypertrophic. Unusual ectopic smooth muscle bundles were also identified. The innermost layer of the circular musculature was thinner. Interstitial cells of Cajal are decreased, even around the myenteric plexus. All of the staining in the distal segments in DA was similar to the control tissues.Conclusions:Proximal and distal segments in DA differ in the neural cells, musculature, and distributions of the interstitial cells of Cajal. Based on the present study, these morphologic changes may contribute to the onset of postoperative duodenal dysmotility.
Ectopic Expression ofAtJMTinNicotiana attenuata: Creating a Metabolic Sink Has Tissue-Specific Consequences for the Jasmonate Metabolic Network and Silences Downstream Gene Expression
Authors: Stitz Michael , Gase Klaus , Baldwin Ian T. , Gaquerel Emmanuel 
Published: July 2011

AbstractTo create a metabolic sink in the jasmonic acid (JA) pathway, we generated transgenic Nicotiana attenuata lines ectopically expressing Arabidopsis (Arabidopsis thaliana) jasmonic acid O-methyltransferase (35S-jmt) and additionally silenced in other lines the N. attenuata methyl jasmonate esterase (35S-jmt/ir-mje) to reduce the deesterification of methyl jasmonate (MeJA). Basal jasmonate levels did not differ between transgenic and wild-type plants; however, after wounding and elicitation with Manduca sexta oral secretions, the bursts of JA, jasmonoyl-isoleucine (JA-Ile), and their metabolites that are normally observed in the lamina, midvein, and petiole of elicited wild-type leaves were largely absent in both transformants but replaced by a burst of endogenous MeJA that accounted for almost half of the total elicited jasmonate pools. In these plants, MeJA became a metabolic sink that affected the jasmonate metabolic network and its spread to systemic leaves, with major effects on 12-oxo-phytodieonic acid, JA, and hydroxy-JA in petioles and on JA-Ile in laminas. Alterations in the size of jasmonate pools were most obvious in systemic tissues, especially petioles. Expression of threonine deaminase and trypsin proteinase inhibitor, two JA-inducible defense genes, was strongly decreased in both transgenic lines without influencing the expression of JA biosynthesis genes that were uncoupled from the wounding and elicitation with M. sexta oral secretions-elicited JA-Ile gradient in elicited leaves. Taken together, this study provides support for a central role of the vasculature in the propagation of jasmonates and new insights into the versatile spatiotemporal characteristics of the jasmonate metabolic network.
Subfunctionalization of Cellulose Synthases in Seed Coat Epidermal Cells Mediates Secondary Radial Wall Synthesis and Mucilage Attachment
Authors: Mendu Venugopal , Griffiths Jonathan S. , Persson Staffan , Stork Jozsef , Downie A. Bruce , Voiniciuc Cătălin , Haughn George W. , DeBolt Seth 
Published: July 2011

Abstract
Arabidopsis (Arabidopsis thaliana) epidermal seed coat cells follow a complex developmental program where, following fertilization, cells of the ovule outer integument differentiate into a unique cell type. Two hallmarks of these cells are the production of a doughnut-shaped apoplastic pocket filled with pectinaceous mucilage and the columella, a thick secondary cell wall. Cellulose is thought to be a key component of both these secondary cell wall processes. Here, we investigated the role of cellulose synthase (CESA) subunits CESA2, CESA5, and CESA9 in the seed coat epidermis. We characterized the roles of these CESA proteins in the seed coat by analyzing cell wall composition and morphology in cesa mutant lines. Mutations in any one of these three genes resulted in lower cellulose content, a loss of cell shape uniformity, and reduced radial wall integrity. In addition, we found that attachment of the mucilage halo to the parent seed following extrusion is maintained by cellulose-based connections requiring CESA5. Hence, we show that cellulose fulfills an adhesion role between the extracellular mucilage matrix and the parent cell in seed coat epidermal cells. We propose that mucilage remains attached to the seed coat through interactions between components in the seed mucilage and cellulose. Our data suggest that CESA2 and CESA9 serve in radial wall reinforcement, as does CESA5, but CESA5 also functions in mucilage biosynthesis. These data suggest unique roles for different CESA subunits in one cell type and illustrate a complex role for cellulose biosynthesis in plant developmental biology.
A comprehensive molecular phylogeny of tardigrades—adding genes and taxa to a poorly resolved phylum‐level phylogeny
Authors: Guil Noemí , Giribet Gonzalo 
Published: July 2011

AbstractTardigrades constitute a phylum of miniaturized metazoans with ca. 1030 living species, a fossil record that probably dates back to the Cambrian, and physiological properties that allow them to live in almost any environment known to host life on Earth—they can also survive in space. Despite broad consensus regarding their membership of the superclade Ecdysozoa, the exact position of the phylum remains contested (some analyses suggest onychophorans and arthropods as their closest relatives, while others suggest a relationship to nematodes and nematomorphs) and the internal relationships of the phylum are still poorly understood. In the present study, we present a hypothesis of tardigrade relationships by examining more taxa and more markers than any previously published phylogeny of the group. We generated novel data for three markers (18S rRNA, 28S rRNA, COI) for 42 individuals of 16 carefully identified species, comprising 12 genera and five families from the classes Heterotardigrada and Eutardigrada, and analysed them in conjunction with nearly all data available from GenBank. Our results show certain disagreement with current taxonomy both at higher ranks (families, orders, classes) and at low (generic) taxonomic levels. When studying the sensitivity to outgroup choice, the class Eutardigrada was monophyletic under only one combination of outgroups; all other combinations placed the eutardigrade order Apochela as sister to the class Heterotardigrada. Phylogenetic relationships within the other eutardigrade order, Parachela, were stable to outgroup choice. Eutardigrade superfamilies recently proposed by Sands and collaborators in the order Parachela were tested with the introduction of new sequences from additional genera, and the possible morphological synapomorphies supporting those superfamilies are discussed.© The Will Henning Society 2011.