bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid multicomponent relaxometry in steady state with correction of magnetization transfer effects
Authors: Liu Fang , Block Walter F. , Kijowski Richard , Samsonov Alexey 
Published: May 2015

PurposeTo study the effects of magnetization transfer (MT) on multicomponent T2 parameters obtained using mcDESPOT in macromolecule‐rich tissues and to propose a new method called mcRISE to correct MT‐induced biases.MethodsThe two‐pool mcDESPOT model was modified by the addition of an exchanging macromolecule proton pool to model the MT effect in cartilage. The mcRISE acquisition scheme was developed to provide sensitivity to all pools. An incremental fitting was applied to estimate MT and relaxometry parameters with minimized coupling. The interaction between MT and relaxometry parameters, efficacy of MT correction, and feasibility of mcRISE in vivo were investigated in simulations and in healthy volunteers.ResultsThe MT effect caused significant errors in multicomponent T1/T2 values and in fast‐relaxing water fraction fF, which is consistent with previous experimental observations. fF increased significantly with macromolecule content if MT was ignored. mcRISE resulted in a multifold reduction of MT biases and yielded decoupled multicomponent T1/T2 relaxometry and quantitative MT parameters.ConclusionmcRISE is an efficient approach for correcting MT biases in multicomponent relaxometry based on steady state sequences. Improved specificity of mcRISE may help to elucidate the sources of the previously described high sensitivity of noncorrected mcDESPOT parameters to disease‐related changes in cartilage and the brain. Magn Reson Med 75:1423–1433, 2016. © 2015 Wiley Periodicals, Inc.
Nanoprobes for enhanced electrochemical DNA sensors
Authors: Zaffino Rosa Letizia , Galan Teresa , Pardo Wilmer Alfonso , Mir Mònica , Samitier Josep 
Published: May 2015

Biosensors, small devices enabling selective bioanalysis because of properly assembled biological recognition molecules, represent the fortuitous results of years of interdisciplinary and complementary investigations in different fields of science. The ultimate role of a biosensor is to provide coupling between the recognition element and the analyte of interest, bringing a quantitative value of its concentrations into a complex sample matrix. They offer many advantages. Among them, portability, low cost with fast response times, and the possibility to operate in situ without the need for sample preparation are certainly the most important. Among biosensors, a large space is occupied by DNA biosensors. Screening genomic DNA is of fundamental importance for the development of new tools available to physicians during the clinical process. Sequencing of individual human genomes, accomplished principally by microarrays with optical detection, is complex and expensive for current clinical protocols. Efforts in research are focused on simplifying and reducing the cost of DNA biosensors. For this purpose, other transduction techniques are under study to make more portable and affordable DNA biosensors. Compared with traditional optical detection tools, electrochemical methods allow the same sensitivity and specificity but are less expensive and less labor intensive. Scalability of electrochemical devices makes it possible to use the advantages introduced by nanosized components. The involvement of nanomaterials and nanostructures with custom‐tailored shapes and properties is expected to rapidly boost the field of electrochemical DNA biosensors and, in general, that of next‐generation sequencing technologies. WIREs Nanomed Nanobiotechnol 2015, 7:817–827. doi: 10.1002/wnan.1344This article is categorized under:

Diagnostic Tools > Biosensing
Diagnostic Tools > Diagnostic Nanodevices
Diagnostic Tools > In Vitro Nanoparticle-Based Sensing
Involving Medical Students in Informed Consent: A Pilot Study
Authors: Chiapponi Costanza , Meyer Frank , Jannasch Olof , Arndt Stephan , Stübs Patrick , Bruns Christiane J. 
Published: May 2015

AbstractIntroductionStudies have reported that patients often sign consent documents without understanding the content. Written paperwork, audio‐visual materials, and decision aids have shown to consistently improve patients’ knowledge. How informed consent should be taken is not properly taught at most universities in Germany.Materials and methodsIn this cross‐sectional study, we investigated how much information about their procedure our patients retain. In particular, it should be elucidated whether an additional conversation between patients and properly prepared medical students shortly before surgery as an adjunct to informed consent can be introduced as a new teaching unit aimed to increase the understanding of surgery by patients and students. Informed consent of all patients had been previously obtained by three surgical residents 1–3 days in advance. All patients had received a copy of their consent form. The same residents developed assessment forms for thyroidectomy, laparoscopic cholecystectomy, umbilical hernia repair, and Lichtenstein procedure for inguinal hernia, respectively, containing 3–4 major common complications (e.g., bile duct injury, hepatic artery injury, stone spillage, and retained stones for laparoscopic cholecystectomy) and briefed the medical students before seeing the patients. Structured one‐to‐one interviews between students (n = 9) and patients (n = 55) based on four different assessment forms were performed and recorded by students. Both patients and students were asked to assess the new teaching unit using a short structured questionnaire.ResultsAlthough 100 % of patients said at the beginning of their interview to have understood and memorized the risks of their imminent procedure, 5.8 % (3/55) were not even able to indicate the correct part of the body where the incision would take place. Only 18.2 % (10/55) of the patients were able to mention 2 or more complications, and 45.3 % (25/55) could not even recall a single one. 96.4 % (53/55) of the patients and 100 % (9/9) of the students taking part in this teaching unit found that this exercise represents a significant improvement of clinical teaching and recommended to introduce this teaching unit as a standard on the normal wards.Conclusion and outlookStudents teaching patients (SteP) appears to be an easy and cost‐efficient tool to improve patients’ education and students’ learning. Students become aware of how difficult it is to explain surgical procedures and complications to patients and patients are better informed about their treatment. We plan to (i) introduce the STeP protocol as a standard teaching project in daily clinical routine and (ii) continue the pilot study to reach representative student and patient numbers for a possible final statement and derived recommendation.
Equilibrium similarity solution of the turbulent transport equation along the centreline of a round jet
Authors: Sadeghi H. , Lavoie P. , Pollard A. 
Published: May 2015

A novel similarity-based form is derived of the transport equation for the second-order velocity structure function of$\langle ({\it\delta}q)^{2}\rangle$along the centreline of a round turbulent jet using an equilibrium similarity analysis. This self-similar equation has the advantage of requiring less extensive measurements to calculate the inhomogeneous (decay and production) terms of the transport equation. It is suggested that the normalised third-order structure function can be uniquely determined when the normalised second-order structure function, the power-law exponent of$\langle q^{2}\rangle$and the decay rate constants of$\langle u^{2}\rangle$and$\langle v^{2}\rangle$are available. In addition, the current analysis demonstrates that the assumption of similarity, combined with an inverse relation between the mean velocity$U$and the streamwise distance$x-x_{0}$from the virtual origin (i.e. $U\propto (x-x_{0})^{-1}$), is sufficient to predict a power-law decay for the turbulence kinetic energy ($\langle q^{2}\rangle \propto (x-x_{0})^{m}$), rather than requiring a power-law decay ($m=-2$) as an additionalad hocassumption. On the basis of the current analysis, it is suggested that the mean kinetic energy dissipation rate,$\langle {\it\epsilon}\rangle$, varies as$(x-x_{0})^{m-2}$. These theoretical results are tested against new experimental data obtained along the centreline of a round turbulent jet as well as previously published data on round jets for$11\,000\leqslant \mathit{Re}_{D}\leqslant 184\,000$over the range$10\leqslant x/D\leqslant 90$. For the present experiments,$\langle q^{2}\rangle$exhibits power-law behaviour with$m=-1.83$. The validity of this solution is confirmed using other experimental data where$\langle q^{2}\rangle$follows a power law with$-1.89\leqslant m\leqslant -1.78$. The present similarity form of the transport equation for$\langle ({\it\delta}q)^{2}\rangle$is also shown to be closely satisfied by the experimental data.
Chasing baboons or attending class: protected areas and childhood education in Uganda
Authors: MACKENZIE CATRINA A. , SENGUPTA RAJA R. , KAOSER RIDHWANA 
Published: May 2015

SUMMARYThe influence of protected areas on childhood education is often assumed to be positive, and integrated conservation and development programmes (ICDPs) typically support childhood education by building schools, providing scholarships and improving education quality, which in turn helps build conservation attitudes. In this paper, the impact of a protected area on childhood education is examined within the broader socioeconomic context of villages bordering Kibale National Park (Uganda). Survey data from households and primary schools indicated ICDPs improved primary school enrolment and education for girls. However, crop raiding by Park-protected animals reduced the probability of boys completing four years of primary education because they were preferentially held back from school to guard crops. Since population growth around protected areas is a threat to conservation, and since extending education for both boys and girls helps reduce birth rates and improve future employment opportunities, helping children attain primary school completion supports both conservation and development objectives. The findings highlight the need to continue supporting childhood education near protected areas; however, additional focus should be placed on boys’ educational attainment, and the need for wildlife authorities, governments and conservation organizations to invest in crop-raiding defences to mitigate crop-raiding losses.
Statistical Study of Beam-Induced Motion of Gold Adatoms by a Scanning TEM
Authors: Zhou Wei , Li Xin , Zhu Guo-zhen 
Published: May 2015

AbstractIn order to achieve reliable structural characterization by transmission electron microscopy, beam-induced structural changes should be clarified for any target material system. As an example, the movement of heavy adatoms on a thin carbon support has been repeatedly reported under the electron beam while the underlying reason for such motion is still in debate. By applying statistical analysis to the group behavior of gold adatoms, we investigated their motion under different beam conditions and detected features corresponding to beam-induced motion, under typical scanning transmission electron microscopy observation conditions. Our results are consistent with the theoretical prediction proposed by Egerton (2013).
Sexual violence in armed conflicts: A violation of international humanitarian law and human rights law
Authors: Gaggioli Gloria 
Published: May 2015

AbstractSexual violence is prevalent in contemporary armed conflicts. International humanitarian law and human rights law absolutely prohibit all forms of sexual violence at all times and against anyone; international criminal law moreover provides for the individual criminal responsibility of sexual crimes' perpetrators. These three bodies of law importantly reinforce each other in this field. The discrepancy between the facts on the ground and the law is a matter of concern that cannot be explained by potential legal gaps or uncertainties. What is needed is to find new ways of improving implementation for existing laws at the domestic and international levels.
Expression of the vault RNA protects cells from undergoing apoptosis
Authors: Amort Melanie , Nachbauer Birgit , Tuzlak Selma , Kieser Arnd , Schepers Aloys , Villunger Andreas , Polacek Norbert 
Published: May 2015

AbstractNon-protein-coding RNAs are a functionally versatile class of transcripts exerting their biological roles on the RNA level. Recently, we demonstrated that the vault complex-associated RNAs (vtRNAs) are significantly upregulated in Epstein–Barr virus (EBV)-infected human B cells. Very little is known about the function(s) of the vtRNAs or the vault complex. Here, we individually express latent EBV-encoded proteins in B cells and identify the latent membrane protein 1 (LMP1) as trigger for vtRNA upregulation. Ectopic expression of vtRNA1-1, but not of the other vtRNA paralogues, results in an improved viral establishment and reduced apoptosis, a function located in the central domain of vtRNA1-1. Knockdown of the major vault protein has no effect on these phenotypes revealing that vtRNA1-1 and not the vault complex contributes to general cell death resistance. This study describes a NF-κB-mediated role of the non-coding vtRNA1-1 in inhibiting both the extrinsic and intrinsic apoptotic pathways.
Post-transcriptional inactivation of matrix metalloproteinase-12 after focal cerebral ischemia attenuates brain damage
Authors: Chelluboina Bharath , Warhekar Aditi , Dillard Matt , Klopfenstein Jeffrey D. , Pinson David M. , Wang David Z. , Veeravalli Krishna Kumar 
Published: May 2015

AbstractThis study highlights the possible pathological role of MMP-12 in the context of ischemic stroke. Male rats were subjected to a two-hour middle cerebral artery occlusion (MCAO) procedure. MMP-12 shRNA expressing plasmid formulation was administered to these rats twenty-four hours after reperfusion. The results showed a predominant upregulation of MMP-12 (approximately 47, 58, 143 and 265 folds on days 1, 3, 5, 7 post-ischemia, respectively) in MCAO subjected rats. MMP-12 expression was localized to neurons, oligodendrocytes and microglia, but not astrocytes. Transcriptional inactivation of MMP-12 significantly reduced the infarct size. The percent infarct size was reduced from 62.87 ± 4.13 to 34.67 ± 5.39 after MMP-12 knockdown compared to untreated MCAO subjected rats. Expression of myelin basic protein was increased and activity of MMP-9 was reduced in ischemic rat brains after MMP-12 knockdown. Furthermore, a significant reduction in the extent of apoptosis was noticed after MMP-12 knockdown. TNFα expression in the ipsilateral regions of MCAO-subjected rats was reduced after MMP-12 knockdown in addition to the reduced protein expression of apoptotic molecules that are downstream to TNFα signaling. Specific knockdown of MMP-12 after focal cerebral ischemia offers neuroprotection that could be mediated via reduced MMP-9 activation and myelin degradation as well as inhibition of apoptosis.
Non-volatile Clocked Spin Wave Interconnect for Beyond-CMOS Nanomagnet Pipelines
Authors: Dutta Sourav , Chang Sou-Chi , Kani Nickvash , Nikonov Dmitri E. , Manipatruni Sasikanth , Young Ian A. , Naeemi Azad 
Published: May 2015

AbstractThe possibility of using spin waves for information transmission and processing has been an area of active research due to the unique ability to manipulate the amplitude and phase of the spin waves for building complex logic circuits with less physical resources and low power consumption. Previous proposals on spin wave logic circuits have suggested the idea of utilizing the magneto-electric effect for spin wave amplification and amplitude- or phase-dependent switching of magneto-electric cells. Here, we propose a comprehensive scheme for building a clocked non-volatile spin wave device by introducing a charge-to-spin converter that translates information from electrical domain to spin domain, magneto-electric spin wave repeaters that operate in three different regimes - spin wave transmitter, non-volatile memory and spin wave detector and a novel clocking scheme that ensures sequential transmission of information and non-reciprocity. The proposed device satisfies the five essential requirements for logic application: nonlinearity, amplification, concatenability, feedback prevention and complete set of Boolean operations.
BMP7 and EREG Contribute to the Inductive Potential of Dental Mesenchyme
Authors: Gao Bo , Zhou Xin , Zhou Xuedong , Pi Caixia , Xu Ruoshi , Wan Mian , Yang Jing , Zhou Yue , Liu Chengcheng , Sun Jianxun , Zhang Yan , Zheng Liwei 
Published: May 2015

AbstractOdontogenesis is accomplished by reciprocal signaling between the epithelial and mesenchymal compartments. It is generally accepted that the inductive mesenchyme is capable of inducing the odontogenic commitment of both dental and non-dental epithelial cells. However, the duration of this signal in the developing dental mesenchyme and whether adult dental pulp tissue maintains its inductive capability remain unclear. This study investigated the contribution of growth factors to regulating the inductive potential of the dental mesenchyme. Human oral epithelial cells (OEs) were co-cultured with either human dental mesenchymal/papilla cells (FDPCs) or human dental pulp cells (ADPCs) under 2-dimensional or 3-dimensional conditions. Odontogenic-associated genes and proteins were detected by qPCR and immunofluorescence, respectively and significant differences were observed between the two co-culture systems. The BMP7 and EREG expression levels in FDPCs were significantly higher than in ADPCs, as indicated by human growth factor PCR arrays and immunofluorescence analyses. OEs co-cultured with ADPCs supplemented with BMP7 and EREG expressed ameloblastic differentiation genes. Our study suggests that BMP7 and EREG expression in late bell-stage human dental papilla contributes to the inductive potential of dental mesenchyme. Furthermore, adult dental pulp cells supplemented with these two growth factors re-established the inductive potential of postnatal dental pulp tissue.
Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE
Authors: Najafabadi Hamed S. , Albu Mihai , Hughes Timothy R. 
Published: May 2015

Abstract
Summary: Current methods for motif discovery from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data often identify non-targeted transcription factor (TF) motifs, and are even further limited when peak sequences are similar due to common ancestry rather than common binding factors. The latter aspect particularly affects a large number of proteins from the Cys2His2 zinc finger (C2H2-ZF) class of TFs, as their binding sites are often dominated by endogenous retroelements that have highly similar sequences. Here, we present recognition code-assisted discovery of regulatory elements (RCADE) for motif discovery from C2H2-ZF ChIP-seq data. RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding preferences of C2H2-ZF proteins. We show that RCADE is able to identify generalizable binding models even from peaks that are exclusively located within the repeat regions of the genome, where state-of-the-art motif finding approaches largely fail.
Availability and implementation: RCADE is available as a webserver and also for download at http://rcade.ccbr.utoronto.ca/.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: t.hughes@utoronto.ca
BFC: correcting Illumina sequencing errors
Authors: Li Heng 
Published: May 2015

Abstract
Summary: BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools. It particularly does well in suppressing systematic sequencing errors, which helps to improve the base accuracy of de novo assemblies.
Availability and implementation: https://github.com/lh3/bfc
Contact: hengli@broadinstitute.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Working over Time: Dynamic Inconsistency in Real Effort Tasks
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Authors: Augenblick Ned , Niederle Muriel , Sprenger Charles 
Published: May 2015

Abstract
Experimental tests of dynamically inconsistent time preferences have largely relied on choices over time-dated monetary rewards. Several recent studies have failed to find the standard patterns of present bias. However, such monetary studies contain often-discussed confounds. In this article, we sidestep these confounds and investigate choices over consumption (real effort) in a longitudinal experiment. We pair this effort study with a companion monetary discounting study. We confirm very limited time inconsistency in monetary choices. However, subjects show considerably more present bias in effort. Furthermore, present bias in the allocation of work has predictive power for demand of a meaningfully binding commitment device. Therefore our findings validate a key implication of models of dynamic inconsistency, with corresponding policy implications.
Effect of 1.5% Topical Diclofenac on Clinical Neuropathic Pain
Authors: Ahmed Shihab U. , Zhang Yi , Chen Lucy , Cohen Abigail , St. Hillary Kristin , Vo Trang , Houghton Mary , Mao Jianren 
Published: May 2015

AbstractAbstract
Using a blinded, placebo-controlled, crossover trial design, lower pain scores were observed after treatment with topical diclofenac. Several secondary endpoints and functional status were unchanged. Topical diclofenac was not associated with complications within the timeframe of the study.

Background:
Neuropathic pain is a condition resulting from injury to the peripheral and/or central nervous system. Despite extensive research over the last several decades, neuropathic pain remains difficult to manage.

Methods:
The authors conducted a randomized, placebo-controlled, double-blinded, and crossover clinical trial to examine the effect of 1.5% topical diclofenac (TD) on neuropathic pain. The authors hypothesized that 1.5% TD would reduce the visual pain score and improve both quantitative sensory testing and functional status in subjects with neuropathic pain. The authors recruited subjects with postherpetic neuralgia and complex regional pain syndrome. The primary outcome was subject’s visual pain score.

Results:
Twenty-eight subjects completed the study (12 male and 16 female) with the mean age of 48.8 yr. After 2 weeks of topical application, subjects in 1.5% TD group showed lower overall visual pain score compared with placebo group (4.9 [1.9] vs. 5.6 [2.1], difference: 0.8; 95% CI, 0.1 to 1.3; P = 0.04) as well as decreased burning pain (2.9 [2.6] vs. 4.3 [2.8], difference, 1.4; 95% CI, 0.2 to 2.6; P = 0.01). There were no statistical differences in constant pain, shooting pain, or hypersensitivity over the painful area between the groups. This self-reported improvement of pain was corroborated by the decreased pain summation detected by quantitative sensory testing. There were no statistically significant changes in functional status in these subjects. There were no complications in both groups.

Conclusion:
The findings indicate that 1.5% TD may serve as an effective treatment option for patients with neuropathic pain from postherpetic neuralgia and complex regional pain syndrome.