bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating a Multimodal Intervention for Children With Limited Expressive Vocabularies Associated With Autism
Authors: Brady Nancy C. , Storkel Holly L. , Bushnell Paige , Barker R. Michael , Saunders Kate , Daniels Debby , Fleming Kandace 
Published: April 2015

Purpose
This study investigated a new intervention package aimed at increasing expressive word learning by school-age children with autism who have limited expressive vocabularies. This pilot investigation was intended to show proof of concept.

Method
Ten children between the ages of 6 and 10 years participated, with educational diagnoses of autism and limited expressive vocabularies at the outset of the study. A multimodal intervention composed of speech sound practice and augmentative and alternative communication was used to teach individualized vocabulary words that were selected on the basis of initial speech sound repertoires and principles of phonotactic probability and neighborhood density. A multiple-probe design was used to evaluate learning outcomes.

Results
Five children showed gains in spoken-word learning across successive word sets (high responders). Five children did not meet learning criteria (low responders). Comparisons of behaviors measured prior to intervention indicated that high responders had relatively higher skills in receptive language, prelinguistic communication, vocal/verbal imitation, adaptive behavior, and consonant productions.

Conclusions
The intervention package holds promise for improving spoken word productions for some children with autism who have limited expressive vocabularies. Further research is needed to better describe who may most benefit from this approach as well as investigate generalized benefits to untaught contexts and targets.
Synthesis of Fluorinated and Trifluoromethyl-Substituted Alkenes through the Modified Julia Olefination: An Update
Authors: Pfund Emmanuel , Lequeux Thierry , Gueyrard David 
Published: April 2015

The modified Julia olefination is now a powerful tool for the synthesis of a large range of functionalized alkenes. This short review covers the last five years and provides an overview of the synthesis of mono-, difluoro-, and trifluoromethyl-substituted alkenes via the modified Julia olefination focusing on the novel scope of this reaction.1	Introduction2	Monofluoroalkenes2.1	Disubstituted α- and β-Monofluoroalkenes2.2	Bis(trifluoromethyl)phenyl Sulfones2.3	Conjugated Monofluoroalkenes2.4	Intramolecular Julia Olefination2.5	Smiles Rearrangement from Fluorinated Keto Sulfones2.6	Fluoroallylamines2.7	Fluorinated exo-Glycals2.8	Monofluoroalkenes with an α-Stereocenter at the Allylic Position3	1,1-Difluoroalkenes4	Trifluoromethyl-Substituted Alkenes5	Conclusion
Sensing of molecules using quantum dynamics
Authors: Migliore Agostino , Naaman Ron , Beratan David N. 
Published: April 2015

Significance
We explore the viability of using intrinsically quantum phenomena for molecular sensing. We formulate a theory for coherent sensing by combining the full analytical description of electronic relaxation processes with mass diffusion and charge transport models. This theory produces molecular-scale design criteria for sensors with responses rooted in quantum mechanical coherence phenomena. For example, the sensitivity of the detector can increase with decreased coupling between the molecular binding sites and the sensor substrate. Exploiting quantum properties of the analyte and the sensing element (e.g., electronic affinity, polarizability, etc.) enables enhanced discrimination among multiple analytes.
Phase Space Distributions
Authors: Dalton Bryan J. , Jeffers John , Barnett Stephen M. 
Published: April 2015

Abstract
This chapter formally presents the representation of the quantum density operator by phase space distribution functions of phase space variables, leading to expressions for quantum correlation functions in terms of phase space integrals in which phase space variables for each mode—c-numbers for bosons, Grassmann numbers for fermions—replace mode annihilation and creation operators. The emphasis is on double-phase-space normally ordered (positive P type) normalised distribution functions, with distinct phase space variables for annihilation and creation operators; however, symmetrically ordered (Wigner type) distribution functions are also considered, along with unnormalised B distribution functions, which lead to phase space integrals for Fock state populations and coherences. Characteristic functions are first defined and then shown to be related to distribution functions via phase space integrals. The existence and symmetry properties of distribution functions—which are non-unique and non-analytic for bosons—is demonstrated using Bargmann coherent-state projectors.
Intramyocellular and Extramyocellular Lipids Are Associated With Arterial Stiffness
Authors: Hasegawa Natsuki , Kurihara Toshiyuki , Sato Koji , Homma Toshiyuki , Fujie Shumpei , Fujita Satoshi , Sanada Kiyoshi , Hamaoka Takafumi , Iemitsu Motoyuki 
Published: April 2015

BACKGROUND
Obese and overweight patients are at increased risk of arterial stiffness, and visceral, epicardial and hepatic fat accumulation is associated with cardiovascular disease risk. In general, muscular lipids are stored either in interstitial adipose tissue (extramyocellular lipid (EMCL)) or in lipid droplets within muscle cells (intramyocellular lipid (IMCL)). However, the association between IMCL or EMCL content and arterial stiffness remains unclear. This cross-sectional study aimed to clarify this association.

METHODS
A total of 237 subjects (18–81 years) were enrolled in this study. The IMCL and EMCL contents of the right vastus lateralis muscle were evaluated by proton magnetic resonance spectroscopy. Arterial stiffness was estimated using brachial-ankle pulse wave velocity (baPWV).

RESULTS
There were significant correlations between baPWV and the contents of both IMCL (R = −0.23, P &lt; 0.001) and EMCL (R = 0.53, P &lt; 0.001) in all subjects. The baPWV negatively correlated with IMCL content (R = −0.45, P &lt; 0.001) in females only. In contrast, significant positive correlations were observed between baPWV and EMCL content in both males (R = 0.59, P &lt; 0.001) and females (R = 0.55, P &lt; 0.001). IMCL and EMCL contents contributed independently to baPWV variation after adjustment for age, sex, body mass index, visceral and subcutaneous abdominal fat, upper and lower limb fat, blood pressure, heart rate, and lipid profiles.

CONCLUSION
These results suggest that IMCL and EMCL contents may be a risk factor for arterial stiffness, and this association differed with gender and age.
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics
Authors: Perez-Riverol Yasset , Uszkoreit Julian , Sanchez Aniel , Ternent Tobias , del Toro Noemi , Hermjakob Henning , Vizcaíno Juan Antonio , Wang Rui 
Published: April 2015

Abstract
Summary: The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources. Finally, we present a set of algorithms and tools whose implementation illustrates the simplicity of developing applications using the library.
Availability and implementation: The software is freely available at https://github.com/PRIDE-Utilities/ms-data-core-api.
Supplementary information: Supplementary data are available at Bioinformatics online
Contact: juan@ebi.ac.uk
R-U policy frontiers for health data de-identification
Authors: Xia Weiyi , Heatherly Raymond , Ding Xiaofeng , Li Jiuyong , Malin Bradley A 
Published: April 2015

Abstract
Objective The Health Insurance Portability and Accountability Act Privacy Rule enables healthcare organizations to share de-identified data via two routes. They can either 1) show re-identification risk is small (e.g., via a formal model, such as k-anonymity) with respect to an anticipated recipient or 2) apply a rule-based policy (i.e., Safe Harbor) that enumerates attributes to be altered (e.g., dates to years). The latter is often invoked because it is interpretable, but it fails to tailor protections to the capabilities of the recipient. The paper shows rule-based policies can be mapped to a utility (U) and re-identification risk (R) space, which can be searched for a collection, or frontier, of policies that systematically trade off between these goals.
Methods We extend an algorithm to efficiently compose an R-U frontier using a lattice of policy options. Risk is proportional to the number of patients to which a record corresponds, while utility is proportional to similarity of the original and de-identified distribution. We allow our method to search 20 000 rule-based policies (out of 2700) and compare the resulting frontier with k-anonymous solutions and Safe Harbor using the demographics of 10 U.S. states.
Results The results demonstrate the rule-based frontier 1) consists, on average, of 5000 policies, 2% of which enable better utility with less risk than Safe Harbor and 2) the policies cover a broader spectrum of utility and risk than k-anonymity frontiers.
Conclusions R-U frontiers of de-identification policies can be discovered efficiently, allowing healthcare organizations to tailor protections to anticipated needs and trustworthiness of recipients.
Catalysis: facing the future
Authors: Ball Philip 
Published: April 2015

Abstract
Most of the chemical reactions used to produce the molecules and materials that our societies need—for example, in the petrochemical and pharmaceutical industries, the synthesis of plastics and other materials, and the production of foods and drinks—make use of catalysts. These speed up the rate at which atoms and molecules rearrange themselves into new forms, and provide a degree of control over the shape and form of those rearrangements. Catalysts let us drive a chemical reaction in a selected direction, in preference to others that could occur. In this way they turn chemistry from crude cookery into a rational and precise form of molecular engineering. And always we can draw inspiration, and sometimes borrow tricks, from the delicate and precise catalytic processes that occur in nature, where enzymes carry out processes in aqueous solution and at mild temperatures and pressures that often we struggle to achieve with far more extreme conditions—such as the fixation of atmospheric nitrogen into useful forms. It is often claimed that this particular catalytic process—the Haber–Bosch process for converting nitrogen into ammonia, discovered just over a century ago—has, by making possible the synthesis of artificial fertilizers, had a greater effect on humankind than any other single chemical innovation. It is what allows us to feed the world. Yet while nature performs this reaction using soluble molecules (enzymes) as catalysts, the Haber–Bosch process uses powdered iron (plus some additives). The reactions between nitrogen and hydrogen take place on the surface of iron particles: this is so-called heterogeneous catalysis, involving surface chemistry, rather than the homogeneous catalysis of enzyme reactions, in which the catalysts are soluble molecules. Both homogeneous and heterogeneous catalysis are essential to the chemical industries. National Science Review spoke with two of the foremost practitioners of the latter field—Nobel laureate Gerhard Ertl of the Fritz Haber Institute in Berlin, Germany, and Avelino Corma of the Institute of Chemical Technology (ITQ) at the Polytechnic University of Valencia, Spain—about the current status of research in catalysis and prospects for the future.
Mullers Muscle Conjunctival Resection for Treatment of Contact Lens-Associated Ptosis
Authors: Teo Livia , Lagler Christine P. , Mannor Geva , Glass Lora D. , Freitag Suzanne K. 
Published: April 2015

Purpose:
The aim of this study was to look at the surgical outcomes of posterior approach Mullers muscle conjunctival resection surgery for contact lens-related ptosis.

Methods:
This was a retrospective, comparative interventional case series. All patients and controls underwent phenylephrine 10% testing and had a positive response prior to surgical intervention.

Results:
Thirty-one eyelids with ptosis were identified in 20 contact lens wearing patients, which were matched with 27 eyelids in 15 controls. The contact lens wearing patients wore contact lenses for a mean of 20.6 ± 12.1 years. More than half (60%) wore soft contact lenses, as opposed to rigid gas-permeable contact lenses. Preoperative margin-to-reflex distance-1 was lower in patients who wore rigid contact lenses (0.8 ± 0.7 mm) as compared with patients with soft contact lenses (1.7 ± 1.1 mm) (p = 0.01). Surgical success, as defined by margin-to-reflex distance-1 ≥3 mm or symmetry of upper eyelid height (within 1 mm), was achieved in 93.5% in the contact lens group and 92.6% of controls. Postoperative margin-to-reflex distance-1 was significantly higher in the contact lens wearers (3.9 ± 1.3 mm) compared with the controls (3.2 ± 1.1 mm; p = 0.01). There was a significant correlation between the amount of tissue resected intraoperatively and the improvement in margin-to-reflex distance-1 (Pearsons correlation coefficient, r =0.36; p = 0.006). There were no surgical complications of any patients in the study.

Conclusion:
Mullers muscle conjunctival resection surgery is an effective surgical correction for contact lens-associated ptosis. Patients can achieve excellent results with minimal risk of residual ptosis or asymmetry.
Adherence to Endoscopy Biopsy Guidelines for Celiac Disease
Authors: Ofei Sylvia , Boyle Brendan , Ediger Tracy , Hill Ivor 
Published: April 2015

ABSTRACTObjective:Histologic changes in celiac disease (CD) may be patchy or confined to the bulb. Present guidelines recommend obtaining multiple biopsies from the bulb and distal duodenum when evaluating for CD. Adherence to these recommendations among adult gastroenterologists is low. There are no such data for pediatric gastroenterologists. This study compared endoscopic biopsy practices among pediatric gastroenterologists in histologically confirmed patients with CD to those without histologically confirmed CD.Methods:Retrospective review of esophagogastroduodenoscopies (EGDs) during a 13‐month period was performed. Children with histologically confirmed CD and a random sample of age‐matched children without CD were identified. Endoscopy and histology reports were reviewed. The site and number of biopsy samples obtained was recorded. The groups were compared for number of biopsies.Results:A total of 98 children with CD were compared with 103 controls without CD. The number of biopsies obtained in the group with CD was higher than the group without CD (5.9 ± 1.6 vs 3.6 ± 1.2) (P < 0.0001). In children with CD, 80.5% had ≥5 biopsies compared with 11.7% in the group without CD (P < 0.0001). Only 10% of the children in the group with CD had bulb biopsies documented compared with none in the group without CD.Conclusions:Pediatric gastroenterologists at our center generally obtain the recommended number of biopsies in children with histologically confirmed CD but seldom document biopsies from the bulb. In those without histologic evidence of CD, fewer biopsies are obtained with none documented from the bulb. Failure to take the recommended number of biopsies could result in some missed cases of CD.
Influence of Enteral Nutrition on Occurrences of Necrotizing Enterocolitis in Very‐Low‐Birth‐Weight Infants
Authors: Kimak Karine S. , de Castro Antunes Margarida M. , Braga Taciana D. , Brandt Katia G. , de Carvalho Lima Marilia 
Published: April 2015

ABSTRACTObjective:The aim of the present study was to investigate the influence of enteral feeding management on occurrences of necrotizing enterocolitis (NEC) in very‐low‐birth‐weight (VLBW) infants.Methods:This was a case‐control study conducted in a sample of 1028 VLBW infants (750 to 1499 g) admitted to a neonatal intensive care unit between January 2003 and May 2008. “Cases” were infants born with VLBW and diagnosed with NEC within the first 30 days of life, and “controls” were VLBW infants who did not develop NEC during this period. Occurrences of NEC were defined using the modified Bell criteria (stage ≥2).Results:Among the 1028 VLBW infants, 55 (5.4%) developed NEC within the first month of life. Logistic regression analysis showed that breast milk given exclusively for <7 days (odds ratio [OR] = 4.02), never achieving full enteral feeding during the first month (OR = 3.50), and parenteral nutrition (OR = 2.70) were factors that increased the chances of NEC occurrence. The use of vasoactive drugs was associated with a lower risk of NEC (OR = 0.15).Conclusions:Breast milk should be recommended as a priority for the enteral nutrition of VLBW infants for no <7 days. Enteral nutrition should start early and progress quickly to achieve full enteral feeding; these procedures may help reduce the occurrence of NEC.
Acute and chronic gregarisation are associated with distinct DNA methylation fingerprints in desert locusts
Authors: Mallon Eamonn B. , Amarasinghe Harindra E. , Ott Swidbert R. 
Published: April 2015

AbstractDesert locusts (Schistocerca gregaria) show a dramatic form of socially induced phenotypic plasticity known as phase polyphenism. In the absence of conspecifics, locusts occur in a shy and cryptic solitarious phase. Crowding with conspecifics drives a behavioural transformation towards gregariousness that occurs within hours and is followed by changes in physiology, colouration and morphology, resulting in the full gregarious phase syndrome. We analysed methylation-sensitive amplified fragment length polymorphisms (MS-AFLP) to compare the effect of acute and chronic crowding on DNA methylation in the central nervous system. We find that crowd-reared and solitary-reared locusts show markedly different neural MS-AFLP fingerprints. However, crowding for a day resulted in neural MS-AFLP fingerprints that were clearly distinct from both crowd-reared and uncrowded solitary-reared locusts. Our results indicate that changes in DNA methylation associated with behavioural gregarisation proceed through intermediate states that are not simply partial realisations of the endpoint states.
Predicting genetic interactions from Boolean models of biological networks
Authors: Calzone Laurence , Barillot Emmanuel , Zinovyev Andrei 
Published: April 2015

AbstractGenetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. We use the probabilistic framework defined in MaBoSS software, based on continuous time Markov chains and stochastic simulations. In addition, we suggest several computational tools for studying the distribution of double mutants in the space of model phenotype probabilities. We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. We classify the obtained interactions according to their class of epistasis, dependence on the chosen initial conditions and phenotype. The use of this methodology for validating mathematical models from experimental data and designing new experiments is discussed.†
Measuring the Landscape of CpG Methylation of Individual Repetitive Elements
Authors: Suzuki Yuta , Korlach Jonas , Turner Stephen W. , Tsukahara Tatsuya , Taniguchi Junko , Qu Wei , Ichikawa Kazuki , Yoshimura Jun , Yurino Hideaki , Takahashi Yuji , Mitsui Jun , Ishiura Hiroyuki , Tsuji Shoji , Takeda Hiroyuki , Morishita Shinichi 
Published: April 2015

ABSTRACTDetermining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it performs long read lengths, and its kinetic information is sensitive to DNA modifications. We propose a novel algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Both the sensitivity and precision of our algorithm were ∼93.7% on CpG site basis for the genome of an inbred medaka (Oryzias latipes) strain within a practical read coverage of ∼30-fold. The method is quantitatively accurate because we observed a high correlation coefficient (R= 0.884) between our method and bisulfite sequencing, and 92.0% of CpG sites were in concordance within 0.25. Using this method, we characterized the landscape of the methylation status of repetitive elements, such as LINEs, in the human genome, thereby revealing the strong correlation between CpG density and unmethylation and detecting unmethylation hot spots of LTRs and LINEs. We could uncover the methylation states for nearly identical active transposons, two novel LINE insertions of identity ∼99% and length 6050 base pairs (bp) in the human genome, and sixteenTol2elements of identity >99.8% and length 4682 bp in the medaka genome.