bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sentence Comprehension in Postinstitutionalized School-Age Children
Authors: Desmarais Chantal , Roeber Barbara J. , Smith Mary E. , Pollak Seth D. 
Published: December 2011

Purpose
In this study, the authors investigated sentence comprehension and spatial working memory abilities in a sample of internationally adopted, postinstitutionalized (PI) children. The authors compared the performance of these PI children with that of an age-matched group of children living with their birth families. They hypothesized that PI children would perform below clinical threshold on tasks of sentence comprehension and that poor sentence comprehension would be associated with poor performance in working memory.

Method
Twenty-three PI children and 36 comparison children were administered sentence comprehension and spatial memory tasks from standardized assessments.

Results
Some oral sentence comprehension skills and the spatial working memory skills were weaker in the school-age PI children than in the age-matched comparison children. A mediational analysis demonstrated that poor spatial working memory performance partially explains the sentence comprehension differences between the 2 groups.

Conclusion
These findings provide valuable information to better plan early intervention and special education for PI children.
Semantic Deficits in Spanish–English Bilingual Children With Language Impairment
Authors: Sheng Li , Peña Elizabeth D. , Bedore Lisa M. , Fiestas Christine E. 
Published: December 2011

Purpose
To examine the nature and extent of semantic deficits in bilingual children with language impairment (LI).

Method

Thirty-seven Spanish–English bilingual children with LI (ranging from age 7;0 [years;months] to 9;10) and 37 typically developing (TD) age-matched peers generated 3 associations to 12 pairs of translation equivalents in English and Spanish. Responses were coded as paradigmatic (e.g.,
dinner
–
lunch,
cena–desayuno
[
dinner
–
breakfast
]), syntagmatic (e.g.,
delicious
–
pizza,
delicioso
–
frijoles
[
delicious
–
beans
]), and errors (e.g.,
wearing
–
where,
vestirse
–
mal
[
to get dressed–bad
]). A semantic depth score was derived in each language and conceptually by combining children’s performance in both languages.

Results

The LI group achieved significantly lower semantic depth scores than the TD group after controlling for group differences in vocabulary size. Children showed higher conceptual scores than single-language scores. Both groups showed decreases in semantic depth scores across multiple elicitations. Analyses of individual performances indicated that semantic deficits (1
SD
below the TD mean semantic depth score) were manifested in 65% of the children with LI and in 14% of the TD children.

Conclusion
School-age bilingual children with and without LI demonstrated spreading activation of semantic networks. Consistent with the literature on monolingual children with LI, sparsely linked semantic networks characterize a considerable proportion of bilingual children with LI.
The Influence of Stimulus Taste and Chemesthesis on Tongue Movement Timing in Swallowing
Authors: Steele Catriona M. , van Lieshout Pascal H. H. M. , Pelletier Cathy A. 
Published: December 2011

Purpose
To explore the influence of taste and trigeminal irritation (chemesthesis) on durational aspects of tongue movement in liquid swallowing, controlling for the influence of perceived taste intensity.

Method
Electromagnetic midsagittal articulography was used to trace tongue movements during discrete liquid swallowing with 5 liquids: water, 3 moderate concentration tastants without odor (sweet, sour, sweet-sour), and a high concentration of citric acid (sour taste plus chemesthesis). Participants were 33 healthy adults in 2 gender-balanced, age-stratified groups (under/over 50). Perceived taste intensity was measured using the Generalized Labeled Magnitude Scale (Bartoshuk, 2000; Bartoshuk et al., 2004). Tongue movement sequencing and durations of the composite tongue movement envelope and component events (rise phase, location of first movement peak, release phase) were calculated.

Results
No obligate sequence of tongue segment movement was observed. Overall durations and the timing of the first movement peak were significantly longer with water than with the moderate concentration of sweet-sour liquid. Perceived taste intensity did not modulate stimulus effects in a significant way. The expected pattern of shorter movement durations with the high concentration of citric acid was not seen.

Conclusions
A chemesthetic-taste stimulus of high citric acid did not influence the durations of tongue movements compared with those seen during the swallowing of moderate concentration tastants and water.
Vocabulary and Working Memory in Children Fit With Hearing Aids
Authors: Stiles Derek J. , McGregor Karla K. , Bentler Ruth A. 
Published: December 2011

PurposeTo determine whether children with mild-to-moderately severe sensorineural hearing loss (CHL) present with disturbances in working memory and whether these disturbances relate to the size of their receptive vocabularies.MethodChildren 6 to 9 years of age participated. Aspects of working memory were tapped by articulation rate, forward and backward digit span in the auditory and visual modalities, Corsi span, parent surveys, and a sequential encoding task. Articulation rate, digit spans, and Corsi spans were also administered in low-level broadband noise.ResultsCHL and children with normal hearing (CNH) demonstrated auditory advantage in forward serial recall. CHL demonstrated slower articulation rates than CNH, but similar memory spans. CHL with poor executive function presented with poorer performance on the Corsi span task. The presence of background noise had no effect on performance in either group. CHL presented with significantly smaller receptive vocabularies than their CNH peers. Across groups, receptive vocabulary size was positively correlated with digit span in quiet, Corsi span in noise, and articulation rate.ConclusionsIn the presence of mild-to-moderately severe hearing loss, children demonstrated resilient working memory systems. For all children, working memory and vocabulary were related; that is, children with poorer working memory had smaller vocabulary sizes.
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations
Authors: Chandan Kumar , van Iersel Martijn P. , Aladjem Mirit I. , Kohn Kurt W. , Luna Augustin 
Published: December 2011

Abstract
Purpose: The PathVisio-Validator plugin aims to simplify the task of producing biological pathway diagrams that follow graphical standardized notations, such as Molecular Interaction Maps or the Systems Biology Graphical Notation. This plugin assists in the creation of pathway diagrams by ensuring correct usage of a notation, and thereby reducing ambiguity when diagrams are shared among biologists. Rulesets, needed in the validation process, can be generated for any graphical notation that a developer desires, using either Schematron or Groovy. The plugin also provides support for filtering validation results, validating on a subset of rules, and distinguishing errors and warnings.
Availability: The PathVisio-Validator plugin works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X and Linux. The plugin along with the instructions, example rulesets for Groovy and Schematron, and Java source code can be downloaded at http://pathvisio.org/wiki/PathVisioValidatorHelp. The software is developed under the open-source Apache 2.0 License and is freely available for both commercial and academic use.
Contact: chandankmit@gmail.com; augustin@mail.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
htSeqTools: high-throughput sequencing quality control, processing and visualization in R
Authors: Planet Evarist , Attolini Camille Stephan-Otto , Reina Oscar , Flores Oscar , Rossell David 
Published: December 2011

Abstract
Summary: We provide a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. It includes detection of outliers and biases, inefficient immuno-precipitation and overamplification artifacts, de novo identification of read-rich genomic regions and visualization of the location and coverage of genomic region lists.
Availability: www.bioconductor.org
Contact: david.rossell@irbbarcelona.org
Supplementary information: Supplementary data available at Bioinformatics online.
PIE the search: searching PubMed literature for protein interaction information
Authors: Kim Sun , Kwon Dongseop , Shin Soo-Yong , Wilbur W. John 
Published: December 2011

Abstract
Motivation: Finding protein-protein interaction (PPI) information from literature is challenging but an important issue. However, keyword search in PubMed® is often time consuming because it requires a series of actions that refine keywords and browse search results until it reaches a goal. Due to the rapid growth of biomedical literature, it has become more difficult for biologists and curators to locate PPI information quickly. Therefore, a tool for prioritizing PPI informative articles can be a useful assistant for finding this PPI-relevant information.
Results: PIE (Protein Interaction information Extraction) the search is a web service implementing a competition-winning approach utilizing word and syntactic analyses by machine learning techniques. For easy user access, PIE the search provides a PubMed-like search environment, but the output is the list of articles prioritized by PPI confidence scores. By obtaining PPI-related articles at high rank, researchers can more easily find the up-to-date PPI information, which cannot be found in manually curated PPI databases.
Availability: http://www.ncbi.nlm.nih.gov/IRET/PIE/
Contact: sun.kim@nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Propofol Neurotoxicity Is Mediated by p75 Neurotrophin Receptor Activation
Authors: Pearn Matthew L. , Hu Yue , Niesman Ingrid R. , Patel Hemal H. , Drummond John C. , Roth David M. , Akassoglou Katerina , Patel Piyush M. , Head Brian P. 
Published: December 2011

Background
Propofol exposure to neurons during synaptogenesis results in apoptosis, leading to cognitive dysfunction in adulthood. Previous work from our laboratory showed that isoflurane neurotoxicity occurs through p75 neurotrophin receptor (p75(NTR)) and subsequent cytoskeleton depolymerization. Given that isoflurane and propofol both suppress neuronal activity, we hypothesized that propofol also induces apoptosis in developing neurons through p75(NTR).

Methods
Days in vitro 5-7 neurons were exposed to propofol (3 μM) for 6 h and apoptosis was assessed by cleaved caspase-3 (Cl-Csp3) immunoblot and immunofluorescence microscopy. Primary neurons from p75(NTR-/-) mice or wild-type neurons were treated with propofol, with or without pretreatment with TAT-Pep5 (10 μM, 15 min), a specific p75(NTR) inhibitor. P75(NTR-/-) neurons were transfected for 72 h with a lentiviral vector containing the synapsin-driven p75(NTR) gene (Syn-p75(NTR)) or control vector (Syn-green fluorescent protein) before propofol. To confirm our in vitro findings, wild-type mice and p75(NTR-/-) mice (PND5) were pretreated with either TAT-Pep5 or TAT-ctrl followed by propofol for 6 h.

Results
Neurons exposed to propofol showed a significant increase in Cl-Csp3, an effect attenuated by TAT-Pep5 and hydroxyfasudil. Apoptosis was significantly attenuated in p75(NTR-/-) neurons. In p75(NTR-/-) neurons transfected with Syn-p75(NTR), propofol significantly increased Cl-Csp3 in comparison with Syn-green fluorescent protein-transfected p75(NTR-/-) neurons. Wild-type mice exposed to propofol exhibited increased Cl-Csp3 in the hippocampus, an effect attenuated by TAT-Pep5. By contrast, propofol did not induce apoptosis in p75(NTR-/-) mice.

Conclusion
These results demonstrate that propofol induces apoptosis in developing neurons in vivo and in vitro and implicate a role for p75(NTR) and the downstream effector RhoA kinase.
Additional Value of Upper GI Tract Endoscopy in the Diagnostic Assessment of Childhood IBD
Authors: Hummel Thalia Z. , ten Kate Fiebo J.W. , Reitsma Johannes B. , Benninga Marc A. , Kindermann Angelika 
Published: December 2011

ABSTRACTObjectives:For the choice of treatment in children with inflammatory bowel disease (IBD), it is important to make a distinction between Crohn disease (CD) and ulcerative colitis (UC). To look for pathognomonic features of CD, upper gastrointestinal tract (UGT) endoscopy has become part of the routine evaluation of children with suspected IBD; however, pathological changes can also be found in the UGT in patients with UC. The aims of the present study were to establish the role of UGT involvement in the diagnostic assessment of suspected IBD in children and to detect histopathological changes in the UGT mucosa, which can distinguish CD from non‐CD (UC and non‐IBD).Methods:Biopsies (colon, ileum, duodenum, stomach, esophagus) from children suspected of having IBD who underwent endoscopy between 2003 and 2008 were reassessed by a blinded, expert pathologist. The histological findings of the UGT were compared with the diagnosis based on ileocolonic biopsies and the final diagnosis.Results:In 11% of the children with CD, the diagnosis was based solely on the finding of granulomatous inflammation in the UGT. Focal cryptitis of the duodenum and focally enhanced gastritis were found significantly more frequently in children with CD compared with children with UC and non‐IBD, with a specificity and positive predictive value of 99% and 93% and 87.1% and 78.6%, respectively.Conclusions:Histology on ileocolonic biopsies alone is insufficient for a correct diagnosis of CD or UC in children. UGT endoscopy should, therefore, be performed in the diagnostic assessment of all children suspected of having IBD.
Congenital Hepatic Fibrosis and Autosomal Recessive Polycystic Kidney Disease
Authors: Srinath Arvind , Shneider Benjamin L. 
Published: December 2011

ABSTRACTObjectives:The published natural history of congenital hepatic fibrosis (CHF) was examined to inform clinical decision making in autosomal recessive polycystic kidney disease (ARPKD).Methods:A systematic literature search of the data on CHF, ARPKD, Caroli disease, Caroli syndrome, and type V choledochal cyst was performed to extract data related to portal hypertension, infection, malignancy, mortality, and transplantation.Results:Information related to 1230 patients with CHF was extracted from 155 articles. Median and mean age at diagnosis were 2 and 11.2 years, respectively. Median and mean time followed after diagnosis were 5.0 and 7.5 years, respectively (range 0–38 years). Sequelae of portal hypertension (n = 409), cholangitis (n = 152), and malignancy (n = 21) were noted. The nature of the portal hypertension was similar to that in other pediatric conditions (164 with varices, 74 bleeding varices, 81 underwent portosystemic shunting). Documented cholangitis was fatal in 3 of 23 children who were infected after renal transplantation. Twenty‐one patients developed hepatobiliary cancer, with the majority having cholangiocarcinoma (n = 19). Cholangiocarcinoma (CCA) was predominant in individuals older than 40 years with either Caroli syndrome or isolated CHF, not ARPKD (median and mean age at CCA diagnosis were 70.3 and 60.1 years, respectively; range 33–75 years). There was a relative paucity of data on combined liver‐kidney transplantation.Conclusions:Clinical decision making in ARPKD should reflect an understanding of the potential issues emanating from CHF. Accepted pediatric specific approaches to portal hypertension are warranted but must take into consideration the stage of renal insufficiency and potential plans for renal transplantation. Cholangitis is a major issue and necessitates anticipatory guidance and awareness. CCA, although a dreaded complication, does not appear to be a major issue during childhood. The indications for liver and combined liver‐kidney transplantation are controversial and warrant further analysis.
Socioenvironmental Factors Associated With Constipation in Hong Kong Children and Rome III Criteria
Authors: Tam Yuk H. , Li Albert M. , So Hung K. , Shit Kam Y. , Pang Kristine K. , Wong Yuen S. , Tsui Siu Y. , Mou Jennifer W. , Chan Kin W. , Lee Kim H. 
Published: December 2011

ABSTRACTObjective:Data regarding the prevalence of constipation in the general population of Asian children using internationally standardized definitions are scarce. Environmental factors surrounding a child's day to day living may trigger or perpetuate constipation and encourage postponement of defecation.Methods:A territory‐wide cross‐sectional questionnaire survey was conducted in 2318 Hong Kong Chinese elementary school students. Constipation was defined by pediatric Rome III criteria.Results:The mean age of the children was 9 ± 1.9 years; 51% were boys. Two hundred eighty‐two children (12.2%, 95% confidence interval [CI] 10.9%–13.5%) were found to have constipation. Children ages 6 to 7 years had the highest prevalence (16.8%, 95% CI 13.8%–19.8%). There was no difference in prevalence between boys and girls (11.6% vs 12.3%; P > 0.05) and between obese and nonobese children (11.5% vs 11.1%; P > 0.05). In univariate analysis, constipation was found to be significantly more prevalent among those children who lived with neither parent, had inadequate company of parents at home, refused to pass bowel movements in school, spent long hours doing homework, had inadequate sleep, and had decreased fiber intake and frequent consumption of fast food (P < 0.05). Multivariate analysis identified refusal to pass bowel movements in school toilets (odds ratio [OR] 1.97, 95% CI 1.42%–2.74%), having dinner with one/both parents <50% of time (OR 1.52, 95% CI 1.01%–2.31%), nighttime sleep <7 hours (OR 1.87, 95% CI 1.04%–3.33%), and frequent consumption of fast food (OR 1.14, 95% CI 1.03%–1.26%) to be independent factors associated with constipation.Conclusions:Socioenvironmental factors are associated with childhood constipation, and bringing them to the awareness of the public may help prevent or stop the progression of childhood constipation at its early stages.
Selective Inhibition of Clade A Phosphatases Type 2C by PYR/PYL/RCAR Abscisic Acid Receptors
Authors: Antoni Regina , Gonzalez-Guzman Miguel , Rodriguez Lesia , Rodrigues Americo , Pizzio Gaston A. , Rodriguez Pedro L. 
Published: December 2011

Abstract
Clade A protein phosphatases type 2C (PP2Cs) are negative regulators of abscisic acid (ABA) signaling that are inhibited in an ABA-dependent manner by PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR) intracellular receptors. We provide genetic evidence that a previously uncharacterized member of this PP2C family in Arabidopsis (Arabidopsis thaliana), At5g59220, is a negative regulator of osmotic stress and ABA signaling and that this function was only apparent when double loss-of-function mutants with pp2ca-1/ahg3 were generated. At5g59220-green fluorescent protein and its close relative PP2CA-green fluorescent protein showed a predominant nuclear localization; however, hemagglutinin-tagged versions were also localized to cytosol and microsomal pellets. At5g59220 was selectively inhibited by some PYR/PYL ABA receptors, and close relatives of this PP2C, such as PP2CA/ABA-HYPERSENSITIVE GERMINATION3 (AHG3) and AHG1, showed a contrasting sensitivity to PYR/PYL inhibition. Interestingly, AHG1 was resistant to inhibition by the PYR/PYL receptors tested, which suggests that this seed-specific phosphatase is still able to regulate ABA signaling in the presence of ABA and PYR/PYL receptors and therefore to control the highly active ABA signaling pathway that operates during seed development. Moreover, the differential sensitivity of the phosphatases At5g59220 and PP2CA to inhibition by ABA receptors reveals a functional specialization of PYR/PYL ABA receptors to preferentially inhibit certain PP2Cs.
Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform
Authors: Van Bel Michiel , Proost Sebastian , Wischnitzki Elisabeth , Movahedi Sara , Scheerlinck Christopher , Van de Peer Yves , Vandepoele Klaas 
Published: December 2011

Abstract
With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.
Phloem Ultrastructure and Pressure Flow: Sieve-Element-Occlusion-Related Agglomerations Do Not Affect Translocation
Authors: Froelich Daniel R. , Mullendore Daniel L. , Jensen Kåre H. , Ross-Elliott Tim J. , Anstead James A. , Thompson Gary A. , Pélissier Hélène C. , Knoblauch Michael 
Published: December 2011

AbstractSince the first ultrastructural investigations of sieve tubes in the early 1960s, their structure has been a matter of debate. Because sieve tube structure defines frictional interactions in the tube system, the presence of P protein obstructions shown in many transmission electron micrographs led to a discussion about the mode of phloem transport. At present, it is generally agreed that P protein agglomerations are preparation artifacts due to injury, the lumen of sieve tubes is free of obstructions, and phloem flow is driven by an osmotically generated pressure differential according to Münch's classical hypothesis. Here, we show that the phloem contains a distinctive network of protein filaments. Stable transgenic lines expressing Arabidopsis thaliana Sieve-Element-Occlusion-Related1 (SEOR1)–yellow fluorescent protein fusions show that At SEOR1 meshworks at the margins and clots in the lumen are a general feature of living sieve tubes. Live imaging of phloem flow and flow velocity measurements in individual tubes indicate that At SEOR1 agglomerations do not markedly affect or alter flow. A transmission electron microscopy preparation protocol has been generated showing sieve tube ultrastructure of unprecedented quality. A reconstruction of sieve tube ultrastructure served as basis for tube resistance calculations. The impact of agglomerations on phloem flow is discussed.