bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Sleep at Altitude: A Comparison of Therapies
Authors: Rodway George W. , Edsell Mark E. , Wong Bob , Windsor Jeremy S. 
Published: October 2011

Objective This study aimed to compare 3 treatment modalities during sleep at an altitude of 5300 m to identify strategies for reducing the incidence of periodic breathing at high altitude. Methods Fifteen trekkers, with identical ascent profiles and no signs or symptoms of altitude illness, served as subjects. All study participants arrived at 5300 m after a gradual ascent from 1300 m. On their second night at 5300 m, subjects were randomly assigned (with a computer-based random assignment procedure) to 1 of 4 different treatment groups: control ( n = 4); 1 L/min O2 via a demand system during sleep ( n = 3); 1 L/min O2/CO2 mix (1.5% CO2) via a demand system during sleep ( n = 4); or 125 mg acetazolamide 30 minutes before bedtime ( n = 4). Heart rate, respiration rate, blood oxygen saturation, tidal volume, minute volume, and apnea hypopnea index were measured. Results Upon comparing the 4 groups, there were no statistically significant differences between the variables. One-way analysis of variance indicated a trend toward statistical significance for SaO2 between groups (F = 2.9, P = .08), and Tukey Honestly Significant Difference (HSD) post hoc tests indicated a trend in the SaO2 difference between the 1 L/min oxygen and control groups ( P = .07). While 1-way analysis of variance suggested no difference for respiratory rate between groups (F = 2.5, P = .1), Tukey HSD indicated a trend in statistical difference of the respiratory rate between 1 L/min O2 and 1 L/min O2/CO2 mixture ( P = .08). Conclusions These statistical trends found between control and treatment groups indicate that further study is warranted.
Keeping Your Cool: A Case Study of a Female Explorer's Solo North Pole Expedition
Authors: Devonport Tracey J. , Lane Andrew M. , Lloyd Juliette 
Published: October 2011

Objective This study explored stress and coping experiences during a solo expedition to the North Pole using concurrent and retrospective methods. Methods A 47-year-old female explorer, with 12 years of polar experience, completed a daily diary during the expedition. On return, 2 semistructured interviews were completed to identify the challenges and coping efforts perceived as being most pertinent during her expedition. Results Inductive coding identified 4 broad stressors, including environmental conditions, personal challenges, supporting resources, and expedition progress. Conclusions Findings highlight the importance of expedition preparation in establishing coping efficacy in managing the extreme demands placed upon polar explorers. Findings also evidence idiosyncrasies in the choice and application of coping strategies and, thus, highlight the need to avoid generalizations regarding coping outcomes.
Does Animation Amplify the Modality Effect – or is there any Modality Effect at All?
Authors: Schmidt-Weigand Florian 
Published: October 2011

Abstract.This study aimed to examine if the modality effect is amplified by the matter of animation. Visual dynamics are suspected to increase split attention affordances due to a higher salience and transience compared to static visuals. In two experiments students watched an instruction on the formation of lightning while their eye movements were recorded. Both experiments varied text presentation (spoken, written) and visualization format (dynamic, static) in a 2x2 design. Learning outcomes were measured with verbal retention, visual retention, and transfer tests. Experiment 1 (N = 50) revealed a modality effect (i. e. better performance in spoken text groups) for visual retention but not for verbal retention and transfer. Experiment 2 (N = 60) replicated Experiment 1 with a faster presentation pace, expecting faster presentation to enlarge modality effects. In contrast, Experiment 2 revealed no modality effects in learning outcomes. In both experiments participants spent less time viewing visualizations when text was written. Within written text conditions text was read first and gained more visual attention than visualizations. Viewing time did not significantly vary between dynamic and static visualizations. Thus, animation did neither affect viewing behavior nor learning outcome. Moreover, the lack of effects in a standard manipulation of text modality cast doubts on the reliability of modality effects and, hence, on the validity of a general modality principle.
Does the Modality Effect in Multimedia Learning Appear only with Text Containing Spatial Information?
Authors: Schüler Anne , Scheiter Katharina , Gerjets Peter 
Published: October 2011

Abstract.The current study tested the assumption that the modality effect in multimedia learning only appears when the text conveys spatial rather than non-spatial information. This assumption is based on findings from working memory research suggesting that the processing of spatial text contents and the execution of eye movements during reading may interfere with each other in visuo-spatial working memory. To test this hypothesis, 80 students were randomly assigned to four groups, resulting from a 2 × 2 design with text modality (spoken vs. written text) and text contents (visual vs. spatial) as between-subject factors. Learning outcomes were measured by means of text and picture recognition. Eye movements were recorded during learning. The results did not confirm the expected interaction between text content and text modality. In addition, the main effect of text modality effect was limited to picture recognition but did not appear for text recognition. This modality effect was mediated by the amount of concentration participants reported to have invested into studying the pictures. These results imply that the often found superiority of spoken text in multimedia learning might simply be due to a better availability of pictorial information instead of an overload of visuo-spatial working memory when processing written text.
Lebensqualität von Kindern in der ­Jugendhilfe: Welchen Einfluss besitzt die psychische Belastetheit der Kinder?
Authors: Büttner Peter , Petermann Franz , Petermann Ulrike , Rücker Stefan 
Published: October 2011

Zusammenfassung. Kinder und Jugendliche in teilstationären Erziehungshilfen erreichen im SDQ zu Beginn einer Maßnahme Werte mit klinischer Bedeutsamkeit (N = 84); rund 25% berichten im ILK zudem eingeschränkte Lebensqualität. Bivariate Korrelationen zeigen deutliche Zusammenhänge zwischen den Skalen und dem Konzept der Lebensqualität. Mit Ausnahme der SDQ-Skalen Hyperaktivität und Verhaltensprobleme mit Gleichaltrigen klären die SDQ-Skalen in der Regressionsanalyse 45% der Varianz auf und erweisen sich damit prädiktiv für die Vorhersage eingeschränkter Lebensqualität. Ob sich das Konzept der Lebensqualität im Kontext der Jugendhilfe zur Qualifizierung der Maßnahmen nutzen lässt, muss sich im Längsschnitt zeigen.
An explicitly correlated local coupled cluster method for calculations of large molecules close to the basis set limit
Authors: Adler Thomas B. , Werner Hans-Joachim 
Published: October 2011

A new explicitly correlated local coupled-cluster method with single and double excitations and a perturbative treatment of triple excitations [DF-LCCSD(T0)-F12x (x = a,b)] is presented. By means of truncating the virtual orbital space to pair-specific local domains (domain approximation) and a simplified treatment of close, weak and distant pairs using LMP2-F12 (pair approximation) the scaling of the computational cost with molecular size is strongly reduced. The basis set incompleteness errors as well as the errors due to the domain approximation are largely eliminated by the explicitly correlated terms. All integrals are computed using efficient density fitting (DF) approximations. The accuracy of the method is investigated for 52 reactions involving medium size molecules. A comparison of DF-LCCSD(T0)-F12x reaction energies with canonical CCSD(T)-F12x calculations shows that the errors introduced by the domain approximation are indeed very small. Care must be taken to keep the errors due to the additional pair approximation equally small, and appropriate distance criteria are recommended. Using these parameters, the root mean square (RMS) deviations of DF-LCCSD(T0)-F12a calculations with triple-ζ basis sets from estimated CCSD(T) complete basis set (CBS) limits and experimental data amount to only 1.5 kJ mol−1 and 2.9 kJ mol−1, respectively. For comparison, the RMS deviation of the CCSD(T)/CBS values from the experimental values amounts to 3.0 kJ mol−1. The potential of the method is demonstrated for five reactions of biochemical or pharmacological interest which include molecules with up to 61 atoms. These calculations show that molecules of this size can now be treated routinely and yield results that are close to the CCSD(T) complete basis set limits.
Fast scaffolding with small independent mixed integer programs
Authors: Salmela Leena , Mäkinen Veli , Välimäki Niko , Ylinen Johannes , Ukkonen Esko 
Published: October 2011

Abstract
Motivation: Assembling genomes from short read data has become increasingly popular, but the problem remains computationally challenging especially for larger genomes. We study the scaffolding phase of sequence assembly where preassembled contigs are ordered based on mate pair data.
Results: We present MIP Scaffolder that divides the scaffolding problem into smaller subproblems and solves these with mixed integer programming. The scaffolding problem can be represented as a graph and the biconnected components of this graph can be solved independently. We present a technique for restricting the size of these subproblems so that they can be solved accurately with mixed integer programming. We compare MIP Scaffolder to two state of the art methods, SOPRA and SSPACE. MIP Scaffolder is fast and produces better or as good scaffolds as its competitors on large genomes.
Availability: The source code of MIP Scaffolder is freely available at http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/.
Contact: leena.salmela@cs.helsinki.fi
An assessment of substitution scores for protein profile–profile comparison
Authors: Ye Xugang , Wang Guoli , Altschul Stephen F. 
Published: October 2011

Abstract
Motivation: Pairwise protein sequence alignments are generally evaluated using scores defined as the sum of substitution scores for aligning amino acids to one another, and gap scores for aligning runs of amino acids in one sequence to null characters inserted into the other. Protein profiles may be abstracted from multiple alignments of protein sequences, and substitution and gap scores have been generalized to the alignment of such profiles either to single sequences or to other profiles. Although there is widespread agreement on the general form substitution scores should take for profile-sequence alignment, little consensus has been reached on how best to construct profile–profile substitution scores, and a large number of these scoring systems have been proposed. Here, we assess a variety of such substitution scores. For this evaluation, given a gold standard set of multiple alignments, we calculate the probability that a profile column yields a higher substitution score when aligned to a related than to an unrelated column. We also generalize this measure to sets of two or three adjacent columns. This simple approach has the advantages that it does not depend primarily upon the gold-standard alignment columns with the weakest empirical support, and that it does not need to fit gap and offset costs for use with each substitution score studied.
Results: A simple symmetrization of mean profile-sequence scores usually performed the best. These were followed closely by several specific scoring systems constructed using a variety of rationales.
Contact: altschul@ncbi.nlm.nih.gov
Supplementary Information: Supplementary data are available at Bioinformatics online.
Extraction of data deposition statements from the literature: a method for automatically tracking research results
Authors: Névéol Aurélie , Wilbur W. John , Lu Zhiyong 
Published: October 2011

Abstract
Motivation: Research in the biomedical domain can have a major impact through open sharing of the data produced. For this reason, it is important to be able to identify instances of data production and deposition for potential re-use. Herein, we report on the automatic identification of data deposition statements in research articles.
Results: We apply machine learning algorithms to sentences extracted from full-text articles in PubMed Central in order to automatically determine whether a given article contains a data deposition statement, and retrieve the specific statements. With an Support Vector Machine classifier using conditional random field determined deposition features, articles containing deposition statements are correctly identified with 81% F-measure. An error analysis shows that almost half of the articles classified as containing a deposition statement by our method but not by the gold standard do indeed contain a deposition statement. In addition, our system was used to process articles in PubMed Central, predicting that a total of 52 932 articles report data deposition, many of which are not currently included in the Secondary Source Identifier [si] field for MEDLINE citations.
Availability: All annotated datasets described in this study are freely available from the NLM/NCBI website at http://www.ncbi.nlm.nih.gov/CBBresearch/Fellows/Neveol/DepositionDataSets.zip
Contact: aurelie.neveol@nih.gov; john.wilbur@nih.gov; zhiyong.lu@nih.gov
Supplementary Information: Supplementary data are available at Bioinformatics online.
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
Authors: Wainreb Gilad , Wolf Lior , Ashkenazy Haim , Dehouck Yves , Ben-Tal Nir 
Published: October 2011

Abstract
Motivation: Accurate prediction of protein stability is important for understanding the molecular underpinnings of diseases and for the design of new proteins. We introduce a novel approach for the prediction of changes in protein stability that arise from a single-site amino acid substitution; the approach uses available data on mutations occurring in the same position and in other positions. Our algorithm, named Pro-Maya (Protein Mutant stAbilitY Analyzer), combines a collaborative filtering baseline model, Random Forests regression and a diverse set of features. Pro-Maya predicts the stability free energy difference of mutant versus wild type, denoted as ΔΔG.
Results: We evaluated our algorithm extensively using cross-validation on two previously utilized datasets of single amino acid mutations and a (third) validation set. The results indicate that using known ΔΔG values of mutations at the query position improves the accuracy of ΔΔG predictions for other mutations in that position. The accuracy of our predictions in such cases significantly surpasses that of similar methods, achieving, e.g. a Pearson's correlation coefficient of 0.79 and a root mean square error of 0.96 on the validation set. Because Pro-Maya uses a diverse set of features, including predictions using two other methods, it also performs slightly better than other methods in the absence of additional experimental data on the query positions.
Availability: Pro-Maya is freely available via web server at http://bental.tau.ac.il/ProMaya.
Contact: nirb@tauex.tau.ac.il; wolf@cs.tau.ac.il
Supplementary Information: Supplementary data are available at Bioinformatics online.
Use of Enteral Nutrition for the Control of Intestinal Inflammation in Pediatric Crohn Disease
Authors: Critch Jeff , Day Andrew S. , Otley Anthony , King‐Moore Cynthia , Teitelbaum Jonathan E. , Shashidhar Harohalli ,   NASPGHAN IBD Committee
Published: October 2011

ABSTRACTExclusive enteral nutrition is an effective yet often underused therapy for the induction of remission in pediatric Crohn disease. The North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition formed the Enteral Nutrition Working Group to review the use of enteral nutrition therapy in pediatric Crohn disease. The group was composed of 5 pediatric gastroenterologists and 1 pediatric nutritionist, all with an interest and/or expertise in exclusive enteral nutrition. Specific attention was placed upon review of the evidence for efficacy of therapy, assessment of the variations in care, identification of barriers to its widespread use, and compilation of the necessary components for a successful program. The present guideline is intended to aid physicians in developing an enteral nutrition therapy program and potentially promote its use.
No Advantage for Antibiotic Treatment Over Placebo in Blastocystis hominis–positive Children With Recurrent Abdominal Pain
Authors: Heyland Klaas , Friedt Michael , Buehr Patrick , Braegger Christian P. 
Published: October 2011

ABSTRACTObjective:The aim of the study was to investigate whether recurrent abdominal pain (RAP) in Blastocystis hominis–positive children can be treated successfully with trimethoprim‐sulfamethoxazole (TMP/SMX).Methods:From October 2004 to December 2008, all of the patients referred to the Division of Gastroenterology and Nutrition of the University Children's Hospital Zurich because of RAP and detection of B hominis in stool samples as the only pathological finding after a standard workup were offered to participate in the study. Patients were randomly assigned into 2 groups. TMP/SMX or placebo was given for 7 days in a double‐blind, placebo‐controlled manner. Pain index (PI) was measured with a visual analogue scale. Two weeks after completion of treatment, 3 stool samples were collected and patients were followed clinically. If B hominis was still present, metronidazole was given for 7 days.Results:Forty patients were included; 37 finished the study (TMP/SMX n = 20, placebo n = 17). Mean PI declined from 7.1 to 3.6 for all of the patients, with a decrease from 6.9 to 4.1 in the TMP/SMX and 7.4 to 3.0 in the placebo group, irrespective of detection of B hominis after treatment. There was no statistically significant difference in PI reduction between the 2 groups. Metronidazole treatment led to a further PI decline from 3.7 to 1.9. Eradication rates were 35% (TMP/SMX) and 44% (metronidazole), compared with spontaneous clearance of 29% in the placebo group.Conclusions:There is no advantage for TPM/SMX over placebo in the treatment of RAP in B hominis–positive children.
Stool Pattern Changes in Toddlers Consuming a Follow‐on Formula Supplemented With Polydextrose and Galactooligosaccharides
Authors: Ribeiro Tereza C.M. , Costa‐Ribeiro Hugo , Almeida Patricia S. , Pontes Mariana V. , Leite Maria E.Q. , Filadelfo Lais R. , Khoury Jane C. , Bean Judy A. , Mitmesser Susan H. , Vanderhoof Jon A. , Scalabrin Deolinda M.F. 
Published: October 2011

ABSTRACTHealthy 9‐ to 48‐month‐old children (n = 133) were randomized to receive a cow's‐milk–based follow‐on formula (control) or the same formula with polydextrose and galactooligosaccharides (PDX/GOS) for 108 days. Pediatricians assessed diarrheal disease, stool pattern, acute respiratory infection, systemic antibiotic use, and growth. The 2 groups had similar weight‐for‐length/height z score and similar odds of having diarrheal disease, acute respiratory infection, and systemic antibiotic use; however, PDX/GOS had greater odds of increased defecation than control (P ≤ 0.01). Addition of PDX and GOS to a follow‐on formula was well tolerated and induced a pattern of more frequent and softer stools in toddlers.
YUCCAGenes Are Expressed in Response to Leaf Adaxial-Abaxial Juxtaposition and Are Required for Leaf Margin Development
Authors: Wang Wei , Xu Ben , Wang Hua , Li Jiqin , Huang Hai , Xu Lin 
Published: October 2011

AbstractDuring leaf development, the formation of leaf adaxial-abaxial polarity at the primordium stage is crucial for subsequent leaf expansion. However, little is known about the genetic control from polarity establishment to blade outgrowth. The leaf margin, comprising elongated margin cells and hydathodes, is thought to affect leaf expansion. Here, we show that mutants with defective leaf polarity or with loss of function in the multiple auxin-biosynthetic YUCCA (YUC) genes exhibited a similar abnormal leaf margin and less-expanded leaves. Leaf margins of these mutants contained fewer hydathodes and an increased number of cell patches in which the patterns of epidermal cells resembled those of hydathodes. The previously characterized leaf-abaxialized asymmetric leaves2 (as2) revoluta (rev) and leaf-adaxialized kanadi1 (kan1) kan2 double mutants both produce finger-shaped, hydathode-like protrusions on adaxial and abaxial leaf surfaces, respectively. YUCs are required for formation of the protrusions, as those produced by as2 rev and kan1 kan2 were absent in the yuc1 yuc2 yuc4 triple mutant background. Expressions of YUC1, YUC2, and YUC4 were spatially regulated in the leaf, being associated with hydathodes in wild-type leaves and protrusions on as2 rev and kan1 kan2 leaves. In addition, inhibition of auxin transport by treatment of seedlings with N-(1-naphtyl) phtalamic acid or disruption of the auxin gradient by transforming plants with the 35S:YUC1 construct also blocked leaf margin development. Collectively, our data show that expressions of YUCs in the leaf respond to the adaxial-abaxial juxtaposition, and that the activities of auxin mediate leaf margin development, which subsequently promotes blade outgrowth.
Auxin-Dependent Cell Cycle Reactivation through Transcriptional Regulation ofArabidopsis E2Faby Lateral Organ Boundary Proteins
Authors: Berckmans Barbara , Vassileva Valya , Schmid Stephan P.C. , Maes Sara , Parizot Boris , Naramoto Satoshi , Magyar Zoltan , Kamei Claire Lessa Alvim , Koncz Csaba , Bögre Laszlo , Persiau Geert , De Jaeger Geert , Friml Jiří , Simon Rüdiger , Beeckman Tom , De Veylder Lieven 
Published: October 2011

AbstractMulticellular organisms depend on cell production, cell fate specification, and correct patterning to shape their adult body. In plants, auxin plays a prominent role in the timely coordination of these different cellular processes. A well-studied example is lateral root initiation, in which auxin triggers founder cell specification and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report that the E2Fa transcription factor of Arabidopsis thaliana is an essential component that regulates the asymmetric cell division marking lateral root initiation. Moreover, we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis through E2Fa transcriptional activation, whereas E2Fa expression under control of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation, vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected in auxin signaling and lbd mutants, indicating that the transcriptional induction of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle activation. Our data illustrate how a conserved mechanism driving cell cycle entry has been adapted evolutionarily to connect auxin signaling with control of processes determining plant architecture.