bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling
Authors: Coffey David , Diez-Ferrer José Luis , Serrate David , Ciria Miguel , Fuente César de la , Arnaudas José Ignacio 
Published: September 2015

AbstractHigh-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths.
K-factor image deshadowing for three-dimensional fluorescence microscopy
Authors: Ilovitsh Tali , Weiss Aryeh , Meiri Amihai , Ebeling Carl G. , Amiel Aliza , Katz Hila , Mannasse-Green Batya , Zalevsky Zeev 
Published: September 2015

AbstractThe ability to track single fluorescent particles within a three dimensional (3D) cellular environment can provide valuable insights into cellular processes. In this paper, we present a modified nonlinear image decomposition technique called K-factor that reshapes the 3D point spread function (PSF) of an XYZ image stack into a narrow Gaussian profile. The method increases localization accuracy by ~60% with compare to regular Gaussian fitting and improves minimal resolvable distance between overlapping PSFs by ~50%. The algorithm was tested both on simulated data and experimentally.
The Optimized Fabrication of Nanobubbles as Ultrasound Contrast Agents for Tumor Imaging
Authors: Cai Wen Bin , Yang Heng Li , Zhang Jian , Yin Ji Kai , Yang Yi Lin , Yuan Li Jun , Zhang Li , Duan Yun You 
Published: September 2015

AbstractNanobubbles, which have the potential for ultrasonic targeted imaging and treatment in tumors, have been a research focus in recent years. With the current methods, however, the prepared uniformly sized nanobubbles either undergo post-formulation manipulation, such as centrifugation, after the mixture of microbubbles and nanobubbles, or require the addition of amphiphilic surfactants. These processes influence the nanobubble stability, possibly create material waste and complicate the preparation process. In the present work, we directly prepared uniformly sized nanobubbles by modulating the thickness of a phospholipid film without the purification processes or the addition of amphiphilic surfactants. The fabricated nanobubbles from the optimal phospholipid film thickness exhibited optimal physical characteristics, such as uniform bubble size, good stability and low toxicity. We also evaluated the enhanced imaging ability of the nanobubbles both in vitro and in vivo. The in vivo enhancement intensity in the tumor was stronger than that of SonoVue after injection (UCA; 2 min: 162.47 ± 8.94 dB vs. 132.11 ± 5.16 dB, P < 0.01; 5 min: 128.38.47 ± 5.06 dB vs. 68.24 ± 2.07 dB, P < 0.01). Thus, the optimal phospholipid film thickness can lead to nanobubbles that are effective for tumor imaging.
The novel ABC transporter ABCH1 is a potential target for RNAi-based insect pest control and resistance management
Authors: Guo Zhaojiang , Kang Shi , Zhu Xun , Xia Jixing , Wu Qingjun , Wang Shaoli , Xie Wen , Zhang Youjun 
Published: September 2015

AbstractInsect pests cause serious crop damage and develop high-level resistance to chemical insecticides andBacillus thuringiensis(Bt) insecticidal Cry toxins. A new promising approach for controlling them and overcoming this resistance is RNA interference (RNAi). The RNAi-based insect control strategy depends on the selection of suitable target genes. In this study, we cloned and characterized a novel ABC transporter genePxABCH1in diamondback moth,Plutella xylostella(L.). Phylogenetic analysis showed thatPxABCH1is closely related to ABCA and ABCG subfamily members. Spatial-temporal expression detection revealed thatPxABCH1was expressed in all tissues and developmental stages and highest expressed in head and male adult. Midgut sequence variation and expression analyses ofPxABCH1in all the susceptible and Bt-resistantP. xylostellastrains and the functional analysis by sublethal RNAi demonstrated that Cry1Ac resistance was independent of this gene. Silencing ofPxABCH1by a relatively high dose of dsRNA dramatically reduced its expression and resulted in larval and pupal lethal phenotypes in both susceptible and Cry1Ac-resistantP. xylostellastrains. To our knowledge, this study provides the first insight into ABCH1 in lepidopterans and reveals it as an excellent target for RNAi-based insect pest control and resistance management.
Identification of outliers in a genomic scan for selection along environmental gradients in the bamboo locust, Ceracris kiangsu
Authors: Feng Xiao-Jing , Jiang Guo-Fang , Fan Zhou 
Published: September 2015

AbstractIdentification of loci under divergent selection is a key step in understanding the evolutionary process because those loci are responsible for the genetic variations that affect fitness in different environments. Understanding how environmental forces give rise to adaptive genetic variation is a challenge in pest control. Here, we performed an amplified fragment length polymorphism (AFLP) genome scan in populations of the bamboo locust, Ceracris kiangsu, to search for candidate loci that are influenced by selection along an environmental gradient in southern China. In outlier locus detection, loci that demonstrate significantly higher or lower among-population genetic differentiation than expected under neutrality are identified as outliers. We used several outlier detection methods to study the features of C. kiangsu, including method DFDIST, BayeScan and logistic regression. A total of 97 outlier loci were detected in the C. kiangsu genome with very high statistical supports. Moreover, the results suggested that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, humidity and sunshine. These findings illustrate that divergent selection and potential local adaptation are prevalent in locusts despite seemingly high levels of gene flow. Thus, we propose that native environments in each population may induce divergent natural selection.
Intermediates in the cation reactions in solution probed by an in situ surface enhanced Raman scattering method
Authors: Tan Chih-Shan , Chen Hung-Ying , Chen Hsueh-Szu , Gwo Shangjr , Chen Lih-Juann 
Published: September 2015

AbstractFor chemical reactions in liquid state, such as catalysis, understanding of dynamical changes is conducive to practical applications. Solvation of copper salts in aqueous solution has implications for life, the environment and industry. In an ongoing research, the question arises that why the color of aqueous CuCl2 solution changes with solution concentration? In this work, we have developed a convenient and efficient in situ surface enhanced Raman scattering technique to probe the presence of many intermediates, some of them are responsible for color change, in crystallization of aqueous copper chloride solution. The versatility of the novel technique was confirmed in the identification of five intermediates states in the transition from CdS to MoS2 nanowires in solution. The facile in situ method is expected to be widely applicable in probing intermediate states in a variety of chemical reactions in solution.
Modelling the effects of variation in reproductive traits on fish population resilience
Authors: Le Bris Arnault , Pershing Andrew J. , Hernandez Christina M. , Mills Katherine E. , Sherwood Graham D. 
Published: September 2015

Abstract
Preserving larger fish is often advocated as a conservation measure to help fish populations buffer environmental variation and fishing pressure. The rationale is that several size- and age-dependent reproductive traits confer a higher reproductive value to larger fish. The effects of variation in these reproductive traits on the dynamics of populations under various fishing patterns are however seldom evaluated. In this study, we develop a simulation model to evaluate how variation in three reproductive traits (fecundity–mass, hatching probability, and batch spawning) impacts the capacity of a fish population to withstand and recover from high fishing pressure. Biological functions of the model were calibrated based on the Gulf of Maine Atlantic cod stock, which is currently experiencing its lowest biomass level ever estimated. Results showed that variation in the shape of the fecundity–mass relationship had the most substantial impact on population resistance and recovery. Batch spawning and variation in hatching probability had limited impacts. Furthermore, results showed that preserving larger fish by imposing a slot fishery increased the resistance of the population to high fishing pressure, because it helped preserve the population reproductive potential determined by the high fecundity of large fish. The slot fishery, however, impeded population recovery, because it distributed the fishing pressure on intermediate-size classes which potential for biomass growth is maximal. This study underlines the importance of using precise size-dependent fecundity estimates when evaluating the productivity and sustainability of fisheries, as well as the importance of identifying priority among the components of population resilience (e.g. resistance or recovery) before implementing size-selective harvest strategies.
Does integrating nonurgent, clinically significant radiology alerts within the electronic health record impact closed-loop communication and follow-up?
Authors: O’Connor Stacy D , Dalal Anuj K , Sahni V Anik , Lacson Ronilda , Khorasani Ramin 
Published: September 2015

Abstract
Objective To assess whether integrating critical result management software—Alert Notification of Critical Results (ANCR)—with an electronic health record (EHR)-based results management application impacts closed-loop communication and follow-up of nonurgent, clinically significant radiology results by primary care providers (PCPs).
Materials and Methods This institutional review board-approved study was conducted at a large academic medical center. Postintervention, PCPs could acknowledge nonurgent, clinically significant ANCR-generated alerts (“alerts”) within ANCR or the EHR. Primary outcome was the proportion of alerts acknowledged via EHR over a 24-month postintervention. Chart abstractions for a random sample of alerts 12 months preintervention and 24 months postintervention were reviewed, and the follow-up rate of actionable alerts (eg, performing follow-up imaging, administering antibiotics) was estimated. Pre- and postintervention rates were compared using the Fisher exact test. Postintervention follow-up rate was compared for EHR-acknowledged alerts vs ANCR.
Results Five thousand nine hundred and thirty-one alerts were acknowledged by 171 PCPs, with 100% acknowledgement (consistent with expected ANCR functionality). PCPs acknowledged 16% (688 of 4428) of postintervention alerts in the EHR, with the remaining in ANCR. Follow-up was documented for 85 of 90 (94%; 95% CI, 88%-98%) preintervention and 79 of 84 (94%; 95% CI, 87%-97%) postintervention alerts ( P &gt; .99). Postintervention, 11 of 14 (79%; 95% CI, 52%-92%) alerts were acknowledged via EHR and 68 of 70 (97%; 95% CI, 90%-99%) in ANCR had follow-up ( P = .03).
Conclusions Integrating ANCR and EHR provides an additional workflow for acknowledging nonurgent, clinically significant results without significant change in rates of closed-loop communication or follow-up of alerts.
What do we know about developing patient portals? a systematic literature review
Authors: Otte-Trojel Terese , de Bont Antoinette , Rundall Thomas G , van de Klundert Joris 
Published: September 2015

Abstract
Objective Numerous articles have reported on the development of patient portals, including development problems and solutions. We review these articles to inform future patient portal development efforts and to provide a summary of the evidence base that can guide future research.
Materials and Methods We performed a systematic review of relevant literature to answer 5 questions: (1) What categories of problems related to patient portal development have been defined? (2) What causal factors have been identified by problem analysis and diagnosis? (3) What solutions have been proposed to ameliorate these causal factors? (4) Which proposed solutions have been implemented and in which organizational contexts? (5) Have implemented solutions been evaluated and what learning has been generated? Through searches on PubMed, ScienceDirect and LISTA, we included 109 articles.
Results We identified 5 main problem categories: achieving patient engagement, provider engagement, appropriate data governance, security and interoperability, and a sustainable business model. Further, we identified key factors contributing to these problems as well as solutions proposed to ameliorate them. While about half (45) of the 109 articles proposed solutions, fewer than half of these solutions (18) were implemented, and even fewer (5) were evaluated to generate learning about their effects.
Discussion Few studies systematically report on the patient portal development processes. As a result, the review does not provide an evidence base for portal development.
Conclusion Our findings support a set of recommendations for advancement of the evidence base: future research should build on existing evidence, draw on principles from design sciences conveyed in the problem-solving cycle, and seek to produce evidence within various different organizational contexts.
Medication-indication knowledge bases: a systematic review and critical appraisal
Authors: Salmasian Hojjat , Tran Tran H , Chase Herbert S , Friedman Carol 
Published: September 2015

AbstractObjective Medication-indication information is a key part of the information needed for providing decision support for and promoting appropriate use of medications. However, this information is not readily available to end users, and a lot of the resources only contain this information in unstructured form (free text). A number of public knowledge bases (KBs) containing structured medication-indication information have been developed over the years, but a direct comparison of these resources has not yet been conducted.Material and Methods We conducted a systematic review of the literature to identify all medication-indication KBs and critically appraised these resources in terms of their scope as well as their support for complex indication information.Results We identified 7 KBs containing medication-indication data. They notably differed from each other in terms of their scope, coverage for on- or off-label indications, source of information, and choice of terminologies for representing the knowledge. The majority of KBs had issues with granularity of the indications as well as with representing duration of therapy, primary choice of treatment, and comedications or comorbidities.Discussion and Conclusion This is the first study directly comparing public KBs of medication indications. We identified several gaps in the existing resources, which can motivate future research.
Privacy-Preserving Microbiome Analysis Using Secure Computation
Authors: Wagner Justin , Paulson Joseph N. , Wang Xiao-Shaun , Bhattacharjee Bobby , Corrada Bravo Héctor 
Published: September 2015

AbstractMotivationDeveloping targeted therapeutics and identifying biomarkers relies on large amounts of patient data. Beyond human DNA, researchers now investigate the DNA of micro-organisms inhabiting the human body. An individual’s collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies.ResultsWe augment an existing categorization of genomic-privacy attacks to incorporate microbiome sequencing and provide an implementation of metagenomic analyses using secure computation. Our implementation allows researchers to perform analysis over combined data without revealing individual patient attributes. We implement three metagenomic analyses and perform an evaluation on real datasets for comparative analysis. We use our implementation to simulate sharing data between four policy-domains and measure the increase in significant discoveries. Additionally, we describe an application of our implementation to form patient pools of data to allow drug companies to query against and compensate patients for the analysis.AvailabilityThe software is freely available for download at:http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html
Obstetric consequences of subfertility: a retrospective cohort study
Authors: DoPierala AL , Bhatta S , Raja EA , Bhattacharya S , Bhattacharya S 
Published: September 2015

ObjectiveTo compare the risk of adverse pregnancy outcomes in women with and without subfertility and to investigate whether fertility treatment contributes to the adverse outcomes.DesignRegister‐based retrospective cohort study.SettingAberdeen, ScotlandPopulationThe exposed group included women with subfertility attending Aberdeen Fertility Clinic between 1989 and 2008 and delivering a singleton (n = 3188) or twin (n = 350) at Aberdeen Maternity Hospital between 1992 and 2009. The unexposed cohort included the remainder of women (singleton n = 52443, twin n = 1125) delivering at Aberdeen Maternity Hospital between 1992 and 2009.MethodsThe Aberdeen Fertility Centre database and Aberdeen Maternity and Neonatal Databank were linked using Community Health Index numbers. Regression models were used to calculate risk ratios and 95% confidence intervals adjusting for potential confounders.Main outcome measuresMaternal outcomes including pre‐eclampsia, antepartum haemorrhage, preterm birth, induction of labour; delivery outcomes including operative vaginal delivery, caesarean section; and offspring outcomes including low birthweight, stillbirth and neonatal death.ResultsWomen with a history of subfertility who delivered a singleton were at a higher risk of pre‐eclampsia [adjusted risk ratios (aRR) 1.18, 95% confidence intervals (CI) 1.02–1.37], antepartum haemorrhage (aRR 1.32, 95% CI 1.18–1.47), induction of labour (aRR 1.21, 95% CI 1.11–1.31) and very preterm delivery (<32 weeks) (aRR 1.96, 95% CI 1.53–2.49). Subfertile women delivering twins were at a higher risk of being delivered by emergency caesarean section (aRR 2.14, 95% CI 1.26–3.66). There were no significant differences in adverse outcomes for singleton pregnancies between the treated and untreated subfertile couples.ConclusionSubfertility per se, rather than fertility treatment, was associated with increased risk of adverse outcomes in singleton pregnancies.Tweetable abstractLarge cohort study found higher incidence of adverse outcome in subfertile women having singletons or twins
RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in r
Authors: Boettiger Carl , Chamberlain Scott , Vos Rutger , Lapp Hilmar 
Published: September 2015

Summary

NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the r programming language with easy‐to‐use tools for reading and writing NeXML documents, including rich metadata, in a way that interfaces seamlessly with the extensive library of phylogenetic tools already available in the r ecosystem.

Wherever possible, we designed RNeXML to map NeXML document contents, whose arrangement is influenced by the format's XML Schema definition, to their most intuitive or useful representation in r. To make NeXML's powerful facility for recording semantically rich machine‐readable metadata accessible to r users, we designed a functional programming interface to it that hides the semantic web standards leveraged by NeXML from r users who are unfamiliar with them.

RNeXML can read any NeXML document that validates, and it generates valid NeXML documents from phylogeny and character data in various r representations in use. The metadata programming interface at a basic level aids fulfilling data documentation best practices, and at an advanced level preserves NeXML's nearly limitless extensibility, for which we provide a fully working demonstration. Furthermore, to lower the barriers to sharing well‐documented phylogenetic data, RNeXML has started to integrate with taxonomic metadata augmentation services on the web, and with online repositories for data archiving.

RNeXML allows r's rich ecosystem to read and write data in the NeXML format through an interface that is no more involved than reading or writing data from other, less powerful data formats. It also provides an interface designed to feel familiar to r programmers and to be consistent with recommended practices for r package development, yet that retains the full power for users to add their own custom data and metadata to the phylogenies they work with, without introducing potentially incompatible changes to the exchange standard.
Alterations in energy homeostasis to favour adipose tissue gain: A longitudinal study in healthy pregnant women
Authors: Abeysekera Minoli V. , Morris Jack A. , Davis Gregory K. , O'Sullivan Anthony J. 
Published: September 2015

BackgroundPregnancy is associated with an increase in body fat; however, excessive gestational weight gain predisposes to significant maternal and neonatal morbidity and mortality. It remains unclear whether alterations in energy homeostasis have a major influence on fat storage.AimsTo evaluate longitudinal changes in body composition and energy metabolism in healthy pregnant women.Materials and MethodsBody composition, energy expenditure and energy intake were measured longitudinally in 26 women with singleton pregnancies at 12–14 weeks, 24–26 weeks and 34–36 weeks of gestation. Fat mass (FM) and lean body mass (LBM) were measured using bio‐impedance analysis, total energy expenditure (TEE) using the Sensewear Armband and energy intake through a 3‐day food recall diary.ResultsThroughout pregnancy, all women remained healthy. Body weight increased by 10.8 ± 3.9 kg, from 67.3 ± 14.1 kg to 78.1 ± 13.8 kg from the first to the third trimester (P < 0.001). Body fat percentage increased by 4.5 ± 4.2% (P < 0.001). LBM also increased throughout pregnancy, by 3.9 ± 2.4 kg (P < 0.001). TEE increased significantly from the first to the third trimesters (9514 kJ/day to 10 263 kJ/day; P < 0.05). In contrast, energy expenditure due to physical activity, energy intake and macronutrient intake did not change significantly throughout pregnancy.ConclusionHealthy women increase FM during pregnancy despite slight increases in TEE and no change in energy intake. This suggests that energy storage efficiency improves during pregnancy, which may be related to alterations in gut microbiota and activation of anabolic pathways during pregnancy. Clarifying factors leading to this more efficient fat and energy storing state, and the role of the pregnancy‐related changes in gut microbiota, may be important for managing gestational weight gain.