bluuebunny/crossref_metadata_2025 huggingface dataset:
Home Exercise DVD Promotes Exercise Accuracy by Caregivers of Children and Adolescents With Brachial Plexus Palsy
Authors: Rasmussen Lynnette , Justice Denise , Chang Kate W‐C. , Nelson Virginia S. , Yang Lynda J‐S.
Published: June 2013

Objective

To evaluate the accuracy of home exercise performance by caregivers of children with neonatal brachial plexus palsy (NBPP) who use digital versatile disc (DVD) guidance.

Design

Prospective cohort study.

Setting

Brachial Plexus Clinic at the University of Michigan.

Participants

Seventy‐six adult caregivers of a consecutive cohort of pediatric patients with NBPP.

Methods

Caregivers received the Home Exercise Program for Brachial Plexus Palsy DVD and an initial demonstration of correct hand placement and movement patterns by 1 of 2 occupational therapists. At times A, B, and C (approximately 3, 6, and 12 months), caregiver accuracy in exercise performance at each joint and standard measurements of arm function were recorded.

Main Outcome Measurements

Caregiver accuracy in correct hand placement and movement pattern during exercise performance was evaluated with use of a dichotomy scale (yes/no) at each joint. Active and passive range of motion were assessed as indicators of arm function.

Results

The mean patient age was 38 months, and the median Narakas score was 2. No significant difference in exercise accuracy for all upper extremity joints between the initial evaluation and times A, B, and C or between individual times was observed, except at the shoulder (98.9% initially to 88.3% at time A; P = .0002) and elbow (100% initially to 96.6% at time A; P = .04). Regarding arm function, an increase in active range of motion for shoulder flexion, elbow flexion, forearm supination, wrist extension, and finger flexion was observed during the study period.

Conclusions

Shoulder and elbow exercises may be more complex, requiring more frequent performance review with the caregiver. However, the home exercise DVD may benefit patients with NBPP and their caregivers and may provide an adjunct to formal therapy sessions.
Psychosocial and personality factors and physical measures in lateral epicondylalgia reveal two groups of “tennis elbow” patients, requiring different management
Authors: Garnevall Björn , Rabey Martin , Edman Gunnar
Published: June 2013

Graphical abstract

Isometric low load pain tolerance test position.
Domestic Courts' Contribution to the Development of International Criminal Law: Some Reflections
Authors: van der Wilt Harmen
Published: June 2013

This article seeks to give an impression of the way in which domestic courts are contributing to the development of international criminal law. Have they predominantly followed the case law of international tribunals and, by doing so, have they corroborated those standards? Or have they rather ventured in new directions and, as a consequence, been involved in a creative process, establishing and refining international criminal law?

Four different approaches, reflecting the position of domestic courts vis à vis the standards and case law of international criminal tribunals, are identified and analysed: strict compliance, antagonism, judicial construction, and ‘casuistry’. The author concludes that the most important contribution of domestic courts to the development of international criminal law consists of further interpretation of open-ended norms. While this is obviously inherent in the process of ‘judicial creativity’, the feature is reinforced by the non-hierarchical nature of international criminal law. As a consequence, international criminal tribunals lack the power and authority to impose their interpretation of international criminal law on domestic courts. The risk of fragmentation is mitigated, however, by the nature of criminal law, which requires strict and clear standards, and by the increasing interactions between courts at different levels.
Liberal Democracy and the Problem of Patriarchy
Authors: Richards David AJ
Published: June 2013

This article addresses how and why liberal democratic constitutions, such as the United States, have come to recognise the tension between liberal values of equal liberty and patriarchy in three areas – contraception, abortion, and gay/lesbian sex acts – and to resolve them in the way in which they have: by extending constitutional protection to these activities on the basis of a constitutional right to privacy. The article begins with some historical understanding of the background of the rise of patriarchy, and why the control of sexuality in general, and women's sexuality in particular, was so central to its aims. It then turns to how and why liberal constitutionalism has found these aims to be so problematic as a basis for law.
USING EYE-TRACKING TO INVESTIGATE TOPICS IN L2 ACQUISITION AND L2 PROCESSING
Authors: Roberts Leah , Siyanova-Chanturia Anna
Published: June 2013

Second language (L2) researchers are becoming more interested in both L2 learners’ knowledge of the target language and how that knowledge is put to use during real-time language processing. Researchers are therefore beginning to see the importance of combining traditional L2 research methods with those that capture the moment-by-moment interpretation of the target language, such as eye-tracking. The major benefit of the eye-tracking method is that it can tap into real-time (or online) comprehension processes during the uninterrupted processing of the input, and thus, the data can be compared to those elicited by other, more metalinguistic tasks to offer a broader picture of language acquisition and processing. In this article, we present an overview of the eye-tracking technique and illustrate the method with L2 studies that show how eye-tracking data can be used to (a) investigate language-related topics and (b) inform key debates in the fields of L2 acquisition and L2 processing.
Fundraising, celebrations and classroom rewards are substantial sources of unhealthy foods and beverages on public school campuses
Authors: Caparosa Susan L , Shordon Maggie , Santos Asherlev T , Pomichowski Magdalena E , Dzewaltowski David A , Coleman Karen J
Published: June 2013

Objective

The emphasis in school nutrition policy has been on vending and competitive items. Our study was designed to characterize and quantify the amount and source of other foods and beverages on school campuses.

Design

A cross-sectional observational study was conducted using a specially designed objective nutrition observation system.

Setting

One low-income school district in southern California with six elementary and two middle schools.

Subjects

Data were not collected from individual children. A total of 4033 students, 42 % of whom were Hispanic/Latino, 26 % African American and 21 % non-Hispanic white, were observed across school settings.

Results

Data were collected continuously from 9 January 2008 to 16 June 2010. Healthy foods had, per serving, total energy ≤732 kJ (≤175 kcal), total fat content ≤35 %, total saturated fat ≤10 %, sugar less ≤15 g, sodium <200 mg and trans-fat ≤0·5 g. Healthy beverages were only 100 % juice or water, and unflavoured non-fat, 1 %, 2 % milk and soya or rice milk. The system had high inter-rater reliability (r = 0·78 to 0·99), percentage agreement (83 % to 100 %) and test–retest reliability (r = 0·81 to 0·98). Significantly more unhealthy foods and beverages than healthy items were observed on all campuses (P < 0·001). An average of 1·26 (sd 0·46) items per student per week was found with an average of 0·86 (sd 0·34) unhealthy items per child per week.

Conclusions

There were substantial amounts of unhealthy foods and beverages brought onto campuses for classroom rewards, celebrations and fundraising that should be targeted for intervention.
The science of progress and the progress of science
Authors: Hunter Philip
Published: June 2013

Measuring the true impact of science is a Herculean task. Meta‐science studies are beginning to assess more than just publication metrics to gain a fuller, long‐term view of the value of research.
A cost-effective self-sensing biosensor for detection of biological species at ultralow concentrations
Authors: Faegh Samira , Jalili Nader , Yavuzcetin Ozgur , Nagesha Dattatri , Kumar Rajiv , Sridhar Srinivas
Published: June 2013

Detection of ultrasmall masses and identification of biological molecules have been made possible as a result of advances in nanotechnology. Development of biosensing tools has significantly contributed to high-throughput diagnosis and analytical sensing exploiting high affinity of biomolecules. MicroCantilever (MC)-based detection has emerged as a promising biosensing tool for offering label-free and cost-effective sensing capabilities. One of the main criteria determining the success of each biosensor is the capability of the sensing platform to operate in aqueous media. Although being characterized with high sensitivity and simplicity, MCs do not provide an effective tool for measurement of marker proteins in liquid media due to large hydrodynamic damping and losses in the surrounding liquid. In this study, we describe two approaches to high sensitivity biomolecular detection using piezoelectric microcantilevers. (i) Immobilized Mass Detection in Air using electro-mechanical resonance: a unique self-sensing measurement technique is reported utilizing a self-sensing circuit consisting of a piezoelectric MC to address the mentioned limitation. The capability of the self-sensing measurement technique was first verified by detecting ultrasmall biological masses immobilized over the surface of MC by monitoring the shift in fundamental mechanical resonance frequency of the system in air and comparing it with optical-based measurement. This was further utilized for calibration of mass detection in liquid media. (ii) Immobilized Mass Detection in Liquid using the electrical self-sensing circuit's resonance: Once the capability to detect adsorbed mass was verified, the self-sensing platform was implemented to detect different concentrations of target molecule (glucose in this study) in liquid media by adopting the highly sensitive resonance frequency of the whole circuit instead of the mechanical response of MC. Molecular binding occurring over the surface of MC changes the capacitance of the total interface thus changing the resonance frequency of the circuit. The amount of shift in the measured circuit's resonance frequency provides qualitative and quantitative insight into the amount of target protein concentration. The reported diagnostic platform offers a simple, cost-effective, all-electronics method of detection where the need for any bulky, expensive optical based measurement is eliminated. Utilizing this technique, physiological concentration of glucose as low as 500 nM was measured in liquid media. This sensitivity is significantly higher than what has been previously reported using other mechanical resonance techniques.
Electronic structure of CeO studied by a four-component relativistic configuration interaction method
Authors: Moriyama Hiroko , Tatewaki Hiroshi , Yamamoto Shigeyoshi
Published: June 2013

We studied the ground and excited states of CeO using the restricted active space CI method in the energy range below 25 000 cm−1. Energy levels are computed to within errors of 2700 cm−1. Electron correlation effects arising from the ionic core composed of Ce 5s, 5p, 4f*, 5d*, and O 2s, 2p spinors play crucial role to CeO spectra, as well as correlation effects of electrons distributed in the valence Ce 4f, 5d, 6s, and 6p spinors. Here, 4f* and 5d* denote spinors expanded to describe electron polarization between Ce and O. A bonding mechanism is proposed for CeO. As the two separate atoms in their ground states, Ce (4f 15d16s2) 1G4 and O (2s22p4) 3P2, approach each other, a CeO2+ core is formed by two-electron transfer from Ce 5d, 6s to O 2p. Inside this ellipsoidal ion, a valence bond between Ce 5p and O 2s and an ionic bond between O 2p and Ce 5p are formed with back-donation through Ce 4f* and 5d*.
Discharge mode transition and hysteresis in inductively coupled plasma
Authors: Lee Hyo-Chang , Kim Dong-Hwan , Chung Chin-Wook
Published: June 2013

Experimental verification of the discharge mode transition and the hysteresis by considering matching circuit is investigated in inductively coupled plasma using measurements of the plasma density and the power absorption to the plasma. At an argon gas pressure of 100 mTorr where the hysteresis loop of the plasma density had been observed in some previous experiments, there is no hysteresis loop against either the input power or the absorbed power delivered via an automatic impedance matching network. At a higher gas pressure of 350 mTorr, however, the hysteresis loop is clearly seen as functions of both the absorbed power and the input power. This result suggests that the observed hysteresis is due to not only the matching effect but also the nonlinearity of the plasma during capacitive (E) to inductive (H) and H to E heating mode transitions.
Characterization of electron mobility in ultrathin body germanium-on-insulator metal-insulator-semiconductor field-effect transistors
Authors: Hyun Lee Choong , Nishimura Tomonori , Tabata Toshiyuki , Zhao DanDan , Nagashio Kosuke , Toriumi Akira
Published: June 2013

We have systematically investigated electron mobility behaviors in germanium-on-insulator (GeOI) metal-oxide-semiconductor field-effect transistors (MOSFETs) with reducing the Ge channel thickness down to 9 nm. 9 nm-thick GeOI n-MOSFETs operated with a reasonable Ion/Ioff ratio of ∼105, but it showed the electron mobility degradation compared with thick GeOI case. To investigate the physical origin of the mobility degradation in ultrathin body (UTB) GeOI n-MOSFETs, the depth profiling of GeOI crystallinity was investigated by Raman spectroscopy. A difference of Ge crystallinity in the front channel from that in back one was discussed to explain the mobility degradation in UTB region.
Theoretical aspects of self-assembly of proteins: A Kirkwood-Buff-theory approach
Authors: Ben-Naim Arieh
Published: June 2013

A new approach to the problem of self-assembly of proteins induced by temperature, pressure, or changes in solute concentration is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. In this article we focus on the pressure and solute effects on the association-dissociation equilibrium. We examine the role of both hydrophobic and hydrophilic effects. We argue that the latter are more important than the former. The solute effect, on the other hand, depends on the preferential solvation of the monomer and the aggregate with respect to solvent and co-solvent molecules. An experimental approach based on model compounds to study these effects is suggested.
Electrical conduction in polyethylene: The role of positive charge and the formation of positive packets
Authors: Lewis T. J. , Llewellyn J. P.
Published: June 2013

A model for positive hole transport in polyethylene is developed which takes particular account of the crystalline-amorphous morphology of the polymer. The significant feature is the employment of super-exchange quantum mechanical tunneling to explain hole transport through the amorphous phase. The consequence is that the hole mobility exhibits a maximum as a function of the electric field, a manifestation of the inverse Marcus effect. It is shown that this feature accounts for the majority of the reported high-field hole transport effects in polyethylene, including packet formation.
Charge transfer processes and ultraviolet induced absorption in Yb:YAG single crystal laser materials
Authors: Rydberg S. , Engholm M.
Published: June 2013

Charge transfer (CT) transitions and UV induced color centers in Yb:YAG single crystals have been investigated. A simultaneous pair formation of a stable Yb2+ ion and a hole related (O−) color center (hole polaron) are observed through a CT-process. Slightly different types of hole related color centers are formed in Yb:YAG crystals containing small levels of iron impurities. Furthermore, excitation spectroscopy on the UV irradiated Yb:YAG samples could confirm an energy transfer process between Yb3+ and Yb2+ ions. The findings are important for an increased knowledge of the physical loss mechanisms observed in Yb-doped laser materials, such as the nonlinear decay process in Yb:YAG crystals as well as the photodarkening phenomenon in Yb-doped fiber lasers.
Neutral-cluster implantation in polymers by computer experiments
Authors: Cardia Roberto , Melis Claudio , Colombo Luciano
Published: June 2013

In this work, we perform atomistic model potential molecular dynamics simulations by means of state-of-the art force-fields to study the implantation of a single Au nanocluster on a polydimethylsiloxane substrate. All the simulations have been performed on realistic substrate models containing up to ∼4.6 × 106 of atoms having depths up to ∼90 nm and lateral dimensions up to ∼25 nm. We consider both entangled-melt and cross-linked polydimethylsiloxane amorphous structures. We show that even a single cluster impact on the polydimethylsiloxane substrate remarkably changes the polymer local temperature and pressure. Moreover, we observe the presence of craters created on the polymer surface having lateral dimensions comparable to the cluster radius and depths strongly dependent on the implantation energy. Present simulations suggest that the substrate morphology is largely affected by the cluster impact and that most-likely such modifications favour the penetration of the next impinging clusters.
The transfer between electron bulk kinetic energy and thermal energy in collisionless magnetic reconnection
Authors: Lu San , Lu Quanming , Huang Can , Wang Shui
Published: June 2013

By performing two-dimensional particle-in-cell simulations, we investigate the transfer between electron bulk kinetic and electron thermal energy in collisionless magnetic reconnection. In the vicinity of the X line, the electron bulk kinetic energy density is much larger than the electron thermal energy density. The evolution of the electron bulk kinetic energy is mainly determined by the work done by the electric field force and electron pressure gradient force. The work done by the electron gradient pressure force in the vicinity of the X line is changed to the electron enthalpy flux. In the magnetic island, the electron enthalpy flux is transferred to the electron thermal energy due to the compressibility of the plasma in the magnetic island. The compression of the plasma in the magnetic island is the consequence of the electromagnetic force acting on the plasma as the magnetic field lines release their tension after being reconnected. Therefore, we can observe that in the magnetic island the electron thermal energy density is much larger than the electron bulk kinetic energy density.
The influence of intense electric fields on three-dimensional asymmetric magnetic reconnection
Authors: Pritchett P. L.
Published: June 2013

A three-dimensional particle-in-cell simulation of magnetic reconnection in an asymmetric configuration without a guide field and with temperature ratio Ti/Te>1 demonstrates that intense perpendicular electric fields are produced on the low-density side of the current layer where there is a strong gradient in the plasma density. The simulation shows that the 3-D reconnection rate is unaffected by these intense electric fields, that the electron current layer near the X line remains coherent and does not break up, but that localized regions of strong energy dissipation exist along the low-density separatrices. Near the X line the dominant term in the generalized Ohm's law for the reconnection electric field remains the off-diagonal electron pressure gradient ∂Pexy/∂x. On the low-beta separatrix, however, the anomalous drag −⟨δnδEy⟩/⟨n⟩ makes an equally important contribution to that of the pressure gradient to the average Ey field.
Effect of electric field on amorphous silicon thin films during Ni induced lateral crystallization
Authors: Ahn Ji-Su , Kim Deok-Kee , Joo Seung-Ki
Published: June 2013

The microstructure and the crystallization mechanism of amorphous silicon thin films during metal induced lateral crystallization (MILC) under an electric field were investigated. With the applied electric field, the growth rate was enhanced in the anode direction, while it was retarded in the cathode direction. The microstructure of the MILC region under an electric field showed a bi-directional needle network structure, but with an enhanced directionality in the anode direction. The enhanced MILC growth under an electric field was due to the negatively charged Ni-ions, which played a vital role in the 4-step MILC growth mechanism.
Identification of desmostanol as a novel vertebrate sterol in short-beaked echidna secretions
Authors: Harris Rachel L. , Davies Noel W. , Nicol Stewart C.
Published: June 2013

Mass spectra and chromatographic data are presented to support the identification of cholest-24-en-3β-ol (desmostanol) in odorous secretions in Tasmanian short-beaked echidnas. This sterol has previously been described only in marine invertebrates and phytoplankton, and may have a role in chemical communication in the echidna.
Specific leaf area: a predictive model using dried samples
Authors: Torrez Vania , Jørgensen Peter M. , Zanne Amy E.
Published: June 2013

Specific leaf area (SLA; fresh-leaf area/dry mass) describes the amount of leaf area for light capture per unit of biomass invested. The standard protocol is simple; however, it requires recently collected sun-exposed leaves to determine fresh-leaf area, limiting where and which samples can be studied. A protocol to predict SLA for fresh leaves from herbarium-dried leaves was developed from samples collected in a dry forest in Bolivia. Leaf area was measured both fresh and dried on the same leaf samples to generate two general mixed-effects models, varying in their inclusion of the position in the crown where the leaf developed. As a test of the potential generality of the models for other systems, we applied them to samples collected in an oak–hickory forest in Missouri, USA. Both models performed well. A recommended protocol for studies predicting SLA from dry leaves was developed. These predictive models and protocols can extend the temporal, geographic, ecological and taxonomic scope of SLA studies.
Bayesian Estimation of Age and Length at 50% Maturity
Authors: Doll Jason C. , Lauer Thomas E.
Published: June 2013

Fish age and length at 50% maturity are used extensively in the management of exploited fish populations. These parameters are historically estimated using logistic regression models (e.g., frequentist inference) for individual year‐classes and often fail to converge or result in insignificant results when a small sample size is used. The sample‐size problem motivated us to evaluate whether a hierarchical logistic regression model fit using frequentist inference or Bayesian inference, could improve our ability to fit these models. Our objective was to compare Bayesian and frequentist inference for estimating age and length at 50% maturity to determine whether the models produced similar values. To make this evaluation, we used a long‐term data set of Yellow PerchPerca flavescensfrom southern Lake Michigan. Frequentist inference of the year‐class‐specific models resulted in significant results when sample size was sufficiently large, a result that occurred in 76% of the models. The hierarchical model produces estimates of age (or length) at 50% maturity for all year‐classes using both frequentist and Bayesian inference. However, Bayesian inference of the hierarchical model resulted in more precise parameter estimates and provided the complete posterior distribution in one seamless and easy approach, and the computation time was 78% to 83% faster. We suggest that a hierarchical model fit using Bayesian inference of age (or length) at 50% maturity is an improvement over frequentist interference methods by providing more information about the population of interest, particularly when sample sizes are limited.
Political and institutional constraints on structural reforms: interpreting the Italian experience
Authors: Fabbrini Sergio
Published: June 2013

During 2011 Italy reached the verge of a financial default because of its huge public debt. Neither the centre-right nor the centre-left governments that alternated in power in the 2000s were able to introduce the reforms necessary for reducing the debt and promoting growth. The impotence of the government became incompatible with the requirements of the country's continued presence in the eurozone. In November 2011, under the pressure of financial markets and eurozone institutions and leaders, the incumbent centre-right government was obliged to resign, and was substituted by a government composed of technocrats and experts, the Monti government. This lasted until December 2012 and was supported in parliament by a cross-partisan coalition; it was able to introduce some of the structural reforms required, because of the threat of default but also because it did not need to seek the electoral support of powerful constituencies. This article advances an interpretation of the Italian crisis of November 2011, identifying the political and institutional structures and the specific political conditions that fostered a policy stalemate in the country in the 2000s and whose persistence makes the continuation of reforms after the February 2013 elections uncertain.
The role(s) of student voice in 14–19 education policy reform: reflections on consultation and participation
Authors: Elwood Jannette
Published: June 2013

Certain policy areas with considerable impact on young people's educational experiences and achievements, notably assessment and qualifications, do not involve consultation with young people to any meaningful extent. Findings from a national study, which included focus groups with 243
students in the 14–19 phase, are presented with respect to student consultation and participation in such policy areas. A lack of meaningful consultation regarding what students see as 'higher level' policy agendas was found (such as qualifications provision, choice or structure). Students
are therefore 'voiceless' in relation to major qualifications reforms.
Aspirations and an austerity state: young people's hopes and goals for the future
Authors: Rose Jo , Baird Jo-Anne
Published: June 2013

Survey findings from 1701 Year 11 and Year 13 students across 35 English educational institutions are reported, which indicate young people's hopes and goals, and the ways in which their institutions support them in their aspirations. This research adds to the literature empirical findings
using a methodological stance on the study of aspirations that is open to broader perspectives of young people's agendas for their lives. The majority of young people reported high-educational (e.g. university) and career (e.g. a professional or well-paid job) aspirations. Life satisfaction
and developing relationships was also high on the agenda of many young people.
Students' voice, aspirations, and perspectives: international reflections and comparisons
Authors: Hopfenbeck Therese N.
Published: June 2013

The findings in this special issue, gives a strong evidence for students' capacity both to contribute with insight on their own teaching and learning, as well provide suggestions and solutions on how to improve the education system. But the data from the Centre Research Study also indicates
that even if many institutions have systems where they consult students about the changes in education programs, students experience much of it as 'tokenistic' and lacking credibility. This is particularly evident in the cases of assessment and qualification. Compared to Norwegian students,
English students seem to lack real influence of many aspects of their own education.
From why to why not? The conundrum of including learners' perspectives: a response to this Special Issue
Authors: Hayward Louise
Published: June 2013

This commentary explores the conundrum of why learners are not routinely involved in decisions about their own learning. It suggests that engaging learners in their own learning and in the development of education systems is central to the improvement of education. Given the evidence
from this Special Issue that all learners have the potential to engage fully in education systems and processes, the commentary concludes that the question why involve learners should change to ask questions of those who do not involve learners as a matter of course in educational decisions
that impact on both the individual and society.
Negative Emotional Stimuli Reduce Contextual Cueing but not Response Times in Inefficient Search
Authors: Kunar Melina A. , Watson Derrick G. , Cole Louise , Cox Angeline
Published: June 2013

In visual search, previous work has shown that negative stimuli narrow the focus of attention and speed reaction times (RTs). This paper investigates these two effects by first asking whether negative emotional stimuli narrow the focus of attention to reduce the learning of a display context in a contextual cueing task and, second, whether exposure to negative stimuli also reduces RTs in inefficient search tasks. In Experiment 1, participants viewed either negative or neutral images (faces or scenes) prior to a contextual cueing task. In a typical contextual cueing experiment, RTs are reduced if displays are repeated across the experiment compared with novel displays that are not repeated. The results showed that a smaller contextual cueing effect was obtained after participants viewed negative stimuli than when they viewed neutral stimuli. However, in contrast to previous work, overall search RTs were not faster after viewing negative stimuli (Experiments 2 to 4). The findings are discussed in terms of the impact of emotional content on visual processing and the ability to use scene context to help facilitate search.
PiHelper: an open source framework for drug-target and antibody-target data
Authors: Aksoy Bülent Arman , Gao Jianjiong , Dresdner Gideon , Wang Weiqing , Root Alex , Jing Xiaohong , Cerami Ethan , Sander Chris
Published: June 2013

Motivation: The interaction between drugs and their targets, often proteins, and between antibodies and their targets, is important for planning and analyzing investigational and therapeutic interventions in many biological systems. Although drug-target and antibody-target datasets are available in separate databases, they are not publicly available in an integrated bioinformatics resource. As medical therapeutics, especially in cancer, increasingly uses targeted drugs and measures their effects on biomolecular profiles, there is an unmet need for a user-friendly toolset that allows researchers to comprehensively and conveniently access and query information about drugs, antibodies and their targets.

Summary: The PiHelper framework integrates human drug-target and antibody-target associations from publicly available resources to help meet the needs of researchers in systems pharmacology, perturbation biology and proteomics. PiHelper has utilities to (i) import drug- and antibody-target information; (ii) search the associations either programmatically or through a web user interface (UI); (iii) visualize the data interactively in a network; and (iv) export relationships for use in publications or other analysis tools.

Availability: PiHelper is a free software under the GNU Lesser General Public License (LGPL) v3.0. Source code and documentation are at http://bit.ly/pihelper. We plan to coordinate contributions from the community by managing future releases.

Contact:  pihelper@cbio.mskcc.org
Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay
Authors: Hurt Jessica A. , Robertson Alex D. , Burge Christopher B.
Published: June 2013

UPF1 is a DNA/RNA helicase with essential roles in nonsense-mediated mRNA decay (NMD) and embryonic development. How UPF1 regulates target abundance and the relationship between NMD and embryogenesis are not well understood. To explore how NMD shapes the embryonic transcriptome, we integrated genome-wide analyses of UPF1 binding locations, NMD-regulated gene expression, and translation in murine embryonic stem cells (mESCs). We identified over 200 direct UPF1 binding targets using crosslinking/immunoprecipitation-sequencing (CLIP-seq) and revealed a repression pathway that involves 3′ UTR binding by UPF1 and translation but is independent of canonical targeting features involving 3′ UTR length and stop codon placement. Interestingly, NMD targeting of this set of mRNAs occurs in other mouse tissues and is conserved in human. We also show, using ribosome footprint profiling, that actively translated upstream open reading frames (uORFs) are enriched in transcription factor mRNAs and predict mRNA repression by NMD, while poorly translated mRNAs escape repression. Together, our results identify novel NMD determinants and targets and provide context for understanding the impact of UPF1 and NMD on the mESC transcriptome.
Calcium-Dependent and -Independent Stomatal Signaling Network and Compensatory Feedback Control of Stomatal Opening via Ca2+ Sensitivity Priming
Authors: Laanemets Kristiina , Brandt Benjamin , Li Junlin , Merilo Ebe , Wang Yong-Fei , Keshwani Malik M. , Taylor Susan S. , Kollist Hannes , Schroeder Julian I.
Published: June 2013

Guard cells use compensatory feedback controls to adapt to conditions that produce excessively open stomata.
A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals
Authors: Nederlof Igor , van Genderen Eric , Li Yao-Wang , Abrahams Jan Pieter
Published: June 2013

When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e− Å−2), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLMandSCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins.
Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging
Authors: Warren Anna J. , Armour Wes , Axford Danny , Basham Mark , Connolley Thomas , Hall David R. , Horrell Sam , McAuley Katherine E. , Mykhaylyk Vitaliy , Wagner Armin , Evans Gwyndaf
Published: June 2013

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.
Nondestructive and Continuous Monitoring of Oxygen Levels in Modified Atmosphere Packaged Ready‐to‐Eat Mixed Salad Products Using Optical Oxygen Sensors, and Its Effects on Sensory and Microbiological Counts during Storage
Authors: Hempel A. , O'Sullivan M. G. , Papkovsky D. B. , Kerry J. P.
Published: June 2013

The objective of this study was to determine the percentage oxygen consumption of fresh, respiring ready‐to‐eat (RTE) mixed leaf salad products (Iceberg salad leaf, Caesar salad leaf, and Italian salad leaf). These were held under different modified atmosphere packaging (MAP) conditions (5% O2, 5% CO2, 90% N2 (MAPC—commercial control), 21% O2, 5% CO2, 74% N2 (MAP 1), 45% O2, 5% CO2, 50% N2 (MAP 2), and 60% O2, 5% CO2, 35% N2 (MAP 3)) and 4 °C for up to 10 d. The quality and shelf‐life stability of all packaged salad products were evaluated using sensory, physiochemical, and microbial assessment. Oxygen levels in all MAP packs were measured on each day of analysis using optical oxygen sensors allowing for nondestructive assessment of packs. Analysis showed that with the exception of control packs, oxygen levels for all MAP treatments decreased by approximately 10% after 7 d of storage. Oxygen levels in control packs were depleted after 7 d of storage. This appears to have had no detrimental effect on either the sensory quality or shelf‐life stability of any of the salad products investigated. Additionally, the presence of higher levels of oxygen in modified atmosphere packs did not significantly improve product quality or shelf‐life stability; however, these additional levels of oxygen were freely available to fresh respiring produce if required. This study shows that the application of optical sensors in MAP packs was successful in nondestructively monitoring oxygen level, or changes in oxygen level, during refrigerated storage of RTE salad products.
Salt Reduction in Vegetable Fermentation: Reality or Desire?
Authors: Bautista‐Gallego J. , Rantsiou K. , Garrido‐Fernández A. , Cocolin L. , Arroyo‐López F. N.
Published: June 2013

NaCl is a widely used chemical in food processing which affects sensory characteristics and safety; in fact, its presence is frequently essential for the proper preservation of the products. Because the intake of high contents of sodium is linked to adverse effects on human health, consumers demand foods with low‐sodium content. A 1st step to reduce the use of salt would imply the proper application of this compound, reducing its levels to those technologically necessary. In addition, different chloride salts have been evaluated as replacers for NaCl, but KCl, CaCl2, and ZnCl2 show the most promising perspectives of use. However, prior to any food reformulation, there is a need for exhaustive research before its application at industrial level. Salt reduction may lead to an increased risk in the survival/ growth of pathogens and may also alter food flavor and cause economic losses. This review deals with the technological, microbiological, sensorial, and health aspects of the potential low‐salt and salt‐substituted vegetable products and how this important segment of the food industry is responding to consumer demand.
RInSp: an r package for the analysis of individual specialization in resource use
Authors: Zaccarelli Nicola , Bolnick Daniel I. , Mancinelli Giorgio
Published: June 2013

In the last decade, an increasing number of papers testifies a renewed interest in the topic of individual specialization in resource use and its implication at higher levels of ecological organization.

We present the package R Individual Specialization (RInSp) for the free open‐source statistical software r. RInSp provides a comprehensive set of classical and recently proposed indices for quantifying the degree of individual specialization using both categorical and continuous resource use data. The package also includes tools for ad hoc Monte Carlo and jackknife resampling procedures for significance testing, plotting and input/output data manipulation.

The use of RInSp is demonstrated by two examples. In addition, the potential of the package to be implemented beyond its original scope for multi‐level quantitative analyses of individual trait variance in natural communities is illustrated.
Acquisition of MDMA self‐administration: pharmacokinetic factors and MDMA‐induced serotonin release
Authors: Bradbury Sarah , Bird Judith , Colussi‐Mas Joyce , Mueller Melanie , Ricaurte George , Schenk Susan
Published: June 2013

The current study aimed to elucidate the role of pharmacokinetic (PK) parameters and neurotransmitter efflux in explaining variability in (±) 3, 4‐methylenedioxymethamphetamine (MDMA) self‐administration in rats. PK profiles of MDMA and its major metabolites were determined after the administration of 1.0 mg/kg MDMA (iv) prior to, and following, the acquisition of MDMA self‐administration. Synaptic levels of 5‐hydroxytryptamine (5HT) and dopamine (DA) in the nucleus accumbens were measured following administration of MDMA (1.0 and 3.0 mg/kg, iv) using in vivo microdialysis and compared for rats that acquired or failed to acquire MDMA self‐administration. Effects of the 5HT neurotoxin, 5,7 dihydroxytryptamine (5, 7‐DHT), on the acquisition of MDMA and cocaine self‐administration were also determined. In keeping with previous findings, approximately 50% of rats failed to meet a criterion for acquisition of MDMA self‐administration. The PK profiles of MDMA and its metabolites did not differ between rats that acquired or failed to acquire MDMA self‐administration. MDMA produced more overflow of 5HT than DA. The MDMA‐induced 5HT overflow was lower in rats that acquired MDMA self‐administration compared with those that did not acquire self‐administration. In contrast, MDMA‐induced DA overflow was comparable for the two groups. Prior 5,7‐DHT lesions reduced tissue levels of 5HT and markedly increased the percentage of rats that acquired MDMA self‐administration and also decreased the latency to acquisition of cocaine self‐administration. These data suggest that 5HT limits the initial sensitivity to the positively reinforcing effects of MDMA and delays the acquisition of reliable self‐administration.
Feeling Safe: A Metasynthesis of the Maternity Care Needs of Women Who Were Sexually Abused in Childhood
Authors: Montgomery Elsa
Published: June 2013

Background

The impact of childhood sexual abuse on birth experiences was highlighted 20 years ago in Birth. Subsequent accounts in the midwifery press testify to the emotional trauma that women who were sexually abused as children may suffer during childbirth and the potential for caregivers to make the situation worse. This study synthesizes research on the maternity care experiences of women who were sexually abused in childhood to answer the questions: what do women need during their childbearing experiences and what can health care practitioners do about it?

Methods

A metasynthesis was conducted to integrate the findings of several qualitative studies. The eight eligible studies identified by database searches were closely read, recurring themes were extracted and compared across studies, and core themes were identified by means of an interpretative process of synthesis.

Results

The key themes identified were control, remembering, vulnerability, dissociation, disclosure, and healing. If women were able to retain control and forge positive, trusting relationships with health care professionals, they felt safe and might experience healing in the process. “Safety” requires that women are not reminded of abusive situations. In the absence of control and trusting relationships, maternity care can be experienced as a re‐enactment of abuse.

Conclusions

During their maternity care experience women who were sexually abused in childhood need to “feel safe.” Health care professionals can help them achieve this feeling by seeking to ensure that those experiences do not re‐enact abuse. (BIRTH 40:2 June 2013)
Adolescents' school‐related self‐concept mediates motor skills and psychosocial well‐being
Authors: Viholainen Helena , Aro Tuija , Purtsi Jarno , Tolvanen Asko , Cantell Marja
Published: June 2013

Background

The health benefits of exercise participation and physical activity for mental health and psychosocial well‐being (PSWB) have been shown in several studies. However, one important background factor, that is, motor skills (MSs), has largely been ignored. In addition, most of the existing research focuses on poor MSs, that is, poor MSs are often connected to poorer PSWB. The mechanism linking MSs and PSWB is unclear. However, a preliminary suggestion has been made that self‐worth or self‐perceptions might mediate the association between MSs and PSWB.

Aim

We investigated whether the self‐concepts (SCs) of school‐related physical education (SCPE), reading (SCR), and mathematics (SCM) mediate the relationship between MSs and PSWB in adolescence.

Methods

The study sample consisted of a second‐grade female cohort (N = 327), ranging in age between 12 and 16 (years) in a municipality in Central Finland. PSWB was measured by the Strengths and Difficulties Questionnaire and the school‐related SCs by the SC of ability scale adapted for use in Finland. MSs was assessed by a self‐reported adolescent version of the Developmental Coordination Disorder Questionnaire. Structural mediator modelling was used to test the associations between MSs and PSWB with SC as a mediator.

Results

First, MSs was strongly associated with school‐related SCPE and SCM. However, a mediator role was observed only for SCPE, which weakly mediated peer problems. Second, MSs and PSWB, especially conduct problems, showed a very strong direct association.

Conclusions

The study suggests that MSs is connected to PSWB in adolescent girls. Enhancement of MSs could be a preventive strategy for supporting PSWB in adolescent girls.
Spatial mental representations derived from spatial descriptions: The predicting and mediating roles of spatial preferences, strategies, and abilities
Authors: Meneghetti Chiara , Ronconi Lucia , Pazzaglia Francesca , De Beni Rossana
Published: June 2013

The aim of this research was to investigate how spatial self‐assessments and spatial cognitive abilities jointly influence the construction of mental representations derived from spatial descriptions. Two studies were conducted using the path models approach to test to what extent spatial self‐assessments (Study 1, 194 participants) and the combination of the latter with spatial abilities (Study 2, 206 participants) can be modelled to predict memory for spatial descriptions. In both studies, we recorded spatial representation preferences (distinguishing between survey, route, and landmark‐focused mode) and self‐reported strategies used to memorize descriptions (distinguishing between survey, route, and verbal strategies); in Study 2, we also measured spatial abilities by testing mental rotation (MR) and visuo‐spatial working memory (VSWM). Participants listened to spatial descriptions and then completed recall tasks. In both studies, the final path models showed that spatial preferences influenced spatial recall through the mediation of congruent strategies: that is a survey (route) preference influenced spatial recall mediated by a survey (route) strategy. MR predicted spatial recall, mediated by both VSWM and survey strategy (Study 2). Overall, these findings indicate that spatial preferences (particularly for a survey mode) in association with spatial abilities effectively concur to help form mental representations derived from spatial descriptions.