bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanorod Surface Plasmon Enhancement of Laser-Induced Ultrafast Demagnetization
Authors: Xu Haitian , Hajisalem Ghazal , Steeves Geoffrey M. , Gordon Reuven , Choi Byoung C. 
Published: October 2015

AbstractUltrafast laser-induced magnetization dynamics in ferromagnetic thin films were measured using a femtosecond Ti:sapphire laser in a pump-probe magneto-optic Kerr effect setup. The effect of plasmon resonance on the transient magnetization was investigated by drop-coating the ferromagnetic films with dimensionally-tuned gold nanorods supporting longitudinal surface plasmon resonance near the central wavelength of the pump laser. With ~4% nanorod areal coverage, we observe a >50% increase in demagnetization signal in nanorod-coated samples at pump fluences on the order of 0.1 mJ/cm2 due to surface plasmon-mediated localized electric-field enhancement, an effect which becomes more significant at higher laser fluences. We were able to qualitatively reproduce the experimental observations using finite-difference time-domain simulations and mean-field theory. This dramatic enhancement of ultrafast laser-induced demagnetization points to possible applications of nanorod-coated thin films in heat-assisted magnetic recording.
Vegetation Greening and Climate Change Promote Multidecadal Rises of Global Land Evapotranspiration
Authors: Zhang Ke , Kimball John S. , Nemani Ramakrishna R. , Running Steven W. , Hong Yang , Gourley Jonathan J. , Yu Zhongbo 
Published: October 2015

AbstractRecent studies showed that anomalous dry conditions and limited moisture supply roughly between 1998 and 2008, especially in the Southern Hemisphere, led to reduced vegetation productivity and ceased growth in land evapotranspiration (ET). However, natural variability of Earth’s climate system can degrade capabilities for identifying climate trends. Here we produced a long-term (1982–2013) remote sensing based land ET record and investigated multidecadal changes in global ET and underlying causes. The ET record shows a significant upward global trend of 0.88 mm yr−2 (P < 0.001) over the 32-year period, mainly driven by vegetation greening (0.018% per year; P < 0.001) and rising atmosphere moisture demand (0.75 mm yr−2; P = 0.016). Our results indicate that reduced ET growth between 1998 and 2008 was an episodic phenomenon, with subsequent recovery of the ET growth rate after 2008. Terrestrial precipitation also shows a positive trend of 0.66 mm yr−2 (P = 0.08) over the same period consistent with expected water cycle intensification, but this trend is lower than coincident increases in evaporative demand and ET, implying a possibility of cumulative water supply constraint to ET. Continuation of these trends will likely exacerbate regional drought-induced disturbances, especially during regional dry climate phases associated with strong El Niño events.
Dynamin-related protein 1 controls the migration and neuronal differentiation of subventricular zone-derived neural progenitor cells
Authors: Kim Hyun Jung , Shaker Mohammed R. , Cho Bongki , Cho Hyo Min , Kim Hyun , Kim Joo Yeon , Sun Woong 
Published: October 2015

AbstractMitochondria are important in many essential cellular functions, including energy production, calcium homeostasis and apoptosis. The organelles are scattered throughout the cytoplasm, but their distribution can be altered in response to local energy demands, such as cell division and neuronal maturation. Mitochondrial distribution is closely associated with mitochondrial fission and blocking the fission-promoting protein dynamin-related protein 1 (Drp1) activity often results in mitochondrial elongation and clustering. In this study, we observed that mitochondria were preferentially localized at the leading process of migratory adult neural stem cells (aNSCs), whereas neuronal differentiating cells transiently exhibited perinuclear condensation of mitochondria. Inhibiting Drp1 activity altered the typical migratory cell morphology into round shapes while the polarized mitochondrial distribution was maintained. With these changes, aNSCs failed to migrate and neuronal differentiation was prevented. Because Drp1 blocking also impaired the mitochondrial membrane potential, we tested whether supplementing with L-carnitine, a compound that restores mitochondrial membrane potential and ATP synthesis, could revert the defects induced by Drp1 inhibition. Interestingly, L-carnitine fully restored the aNSC defects, including cell shrinkage, migration and impaired neuronal differentiation. These results suggest that Drp1 is required for functionally active mitochondria and supplementing with ATP can restore the defects induced by Drp1 suppression.
Dengue virus infection alters post-transcriptional modification of microRNAs in the mosquito vector Aedes aegypti
Authors: Etebari Kayvan , Osei-Amo Solomon , Blomberg Simon Phillip , Asgari Sassan 
Published: October 2015

AbstractRecent discoveries regarding the importance of isomiRs have increased our understanding of the regulatory complexities of the miRNAome. Observed changes in the miRNA profiles in mosquitoes infected with flaviviruses have implicated small RNAs in the interactions between viruses and their vectors. Here we analysed the isomiR profiles of both uninfected and infectedAedes aegyptimosquitoes with the major human pathogen dengue virus (DENV). We found that several specific isomiRs were significantly altered in their abundance patterns in response to DENV infection potentially affecting their target repertoire. Notable among these were isomiR variants which displayed arm-switching. We also demonstrate that modifications to the 3p end of miRNAs are vastly more prevalent than those at the 5p ends. We also observed that in only 45% ofAe. aegyptimiRNAs the most abundant read matches the exact sequence reported in miRBase. Further, we found positive correlations between the number of mature miRNA reads, pre-miRNA length, GC content and secondary structure minimum free energy with the number of isomiRs. The findings presented here provide some evidence that isomiR production is not a random phenomenon and may be important in DENV replication in its vector.
3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography
Authors: Egan C. K. , Jacques S. D. M. , Wilson M. D. , Veale M. C. , Seller P. , Beale A. M. , Pattrick R. A. D. , Withers P. J. , Cernik R. J. 
Published: October 2015

AbstractWe report the development of laboratory based hyperspectral X-ray computed tomography which allows the internal elemental chemistry of an object to be reconstructed and visualised in three dimensions. The method employs a spectroscopic X-ray imaging detector with sufficient energy resolution to distinguish individual elemental absorption edges. Elemental distributions can then be made by K-edge subtraction, or alternatively by voxel-wise spectral fitting to give relative atomic concentrations. We demonstrate its application to two material systems: studying the distribution of catalyst material on porous substrates for industrial scale chemical processing; and mapping of minerals and inclusion phases inside a mineralised ore sample. The method makes use of a standard laboratory X-ray source with measurement times similar to that required for conventional computed tomography.
Multishock Compression Properties of Warm Dense Argon
Authors: Zheng Jun , Chen Qifeng , Yunjun Gu , Li Zhiguo , Shen Zhijun 
Published: October 2015

AbstractWarm dense argon was generated by a shock reverberation technique. The diagnostics of warm dense argon were performed by a multichannel optical pyrometer and a velocity interferometer system. The equations of state in the pressure-density range of 20–150 GPa and 1.9–5.3 g/cm3 from the first- to fourth-shock compression were presented. The single-shock temperatures in the range of 17.2–23.4 kK were obtained from the spectral radiance. Experimental results indicates that multiple shock-compression ratio (ηi = ρi/ρ0) is greatly enhanced from 3.3 to 8.8, where ρ0 is the initial density of argon and ρi (i = 1, 2, 3, 4) is the compressed density from first to fourth shock, respectively. For the relative compression ratio (ηi’ = ρi/ρi-1), an interesting finding is that a turning point occurs at the second shocked states under the conditions of different experiments and ηi’ increases with pressure in lower density regime and reversely decreases with pressure in higher density regime. The evolution of the compression ratio is controlled by the excitation of internal degrees of freedom, which increase the compression and by the interaction effects between particles that reduce it. A temperature-density plot shows that current multishock compression states of argon have distributed into warm dense regime.
CHIP Deutschland: Einfluss eines Lebensstil-Schulungsprogramms zur Primär- und Sekundärprävention von Typ 2 Diabetes auf das Ernährungsverhalten und die Bedeutung sozialkognitiver Variablen
Authors: Tigges C. , Wennehorst K. , Saliger B. , Englert H. 
Published: October 2015

Zusammenfassung
Hintergrund: Eine Ernährungsweise mit moderater Fett- und hoher Ballaststoffzufuhr kann das metabolische Risiko bei Diabetikern senken. Die Studie untersucht, ob sich das Ernährungsverhalten der Probanden durch ein intensives Lebensstil-Schulungsprogramm verbessert und welche sozial-kognitiven Variablen als Einflussfaktoren für die Änderung des Ernährungsverhaltens und einer möglichen Gewichtsreduktion identifiziert werden können.
Patienten und Methoden: Es wurden Probanden mit manifestem Diabetes oder einem erhöhten Erkrankungsrisiko eingeschlossen (Intervention: N=43; Kontrolle: N=40). Der Studienzeitraum umfasste die Interventionsphase mit einem einführenden, individuellen Coaching, einem 8-wöchigen intensiven Lebensstilprogramm und einem persönlichen Abschlusscoaching sowie eine anschließende 10-monatige Follow-Up-Phase. Neben anthropometrischen, Vital- und Laborparametern (z. B. Gewicht, HbA1c, FINDRISK) wurden die HAPA-Verhaltensstadien (Unentschiedene, Vorbereitende, Aktive), die Ergebniserwartung, Handlungsplanung und Selbstwirksamkeit in Bezug auf das Ernährungsverhalten erfasst.
Ergebnisse: Das Gewicht reduzierte sich durch die Intervention. Ernährungsverhalten, Selbstwirksamkeit, Handlungsplanung und Ergebniserwartung verbesserten sich in der Interventions-, nicht aber in der Kontrollgruppe. In der Interventionsgruppe wurde ein Zusammenhang zwischen der Selbstwirksamkeit nach 8 Wochen und der Gewichtsreduktion verzeichnet.
Diskussion: Die Ergebnisse zeigen, dass das Risikoprofil der Probanden durch die Intervention verbessert werden konnte. Insbesondere eine gesteigerte Selbstwirksamkeit scheint die Etablierung präventiver Verhaltensweisen beim T2D zu unterstützen.
Schlussfolgerung: Lebensstilcoachings zur langfristigen Verhaltensänderung sollten sich stärker auf die Volitionsphase konzentrieren und die Selbstwirksamkeit der Teilnehmer stärken.
Type I IFN induces protein ISGylation to enhance cytokine expression and augments colonic inflammation
Authors: Fan Jun-Bao , Miyauchi-Ishida Sayuri , Arimoto Kei-ichiro , Liu Dan , Yan Ming , Liu Chang-Wei , Győrffy Balázs , Zhang Dong-Er 
Published: October 2015

Significance
This study demonstrates that the formation of covalent conjugates of IFN-stimulated gene 15 (ISG15) to many cellular proteins, a process known as “protein ISGylation,” exacerbates experimental colitis and colitis-associated cancer in mouse models. Additional mechanistic studies uncovered a previously unidentified regulation of macrophage activity by protein ISGylation through the ubiquitin proteasome system–reactive oxygen species–p38 axis. Using available gene-expression data, we show that higher expression of ubiquitin-activating enzyme E1 homolog is significantly correlated with worse survival in human patients with colorectal cancer. Thus, our work identified, for the first time to our knowledge, an important role of protein ISGylation in regulating colonic inflammation and its related malignant progression.
Molecular pathways for defect annihilation in directed self-assembly
Authors: Hur Su-Mi , Thapar Vikram , Ramírez-Hernández Abelardo , Khaira Gurdaman , Segal-Peretz Tamar , Rincon-Delgadillo Paulina A. , Li Weihua , Müller Marcus , Nealey Paul F. , de Pablo Juan J. 
Published: October 2015

Significance
A molecular model is used to calculate the free energy of formation of ordered and disordered copolymer morphologies. We rely on advanced methodologies to identify the minimum free energy pathways that connect such states of the material. Our predictions for defect formation and annealing are compared with experimental observations. Our results provide a detailed molecular view of isolated block copolymer defects, which measure approximately 5 nm and represent isolated events in large areas. They are true “needles in the hay stack” that can only be studied by concerted molecular simulations and dedicated access to production-level fabrication tools. We show that defect annealing is an activated process, where defects are eliminated by operating near the order−disorder transition.
Predictors of Urine Drug Testing for Patients with Chronic Pain: Results from a National Cohort of U.S. Veterans
Authors: Morasco Benjamin J. , Peters Dawn , Krebs Erin E. , Kovas Anne E. , Hart Kyle , Dobscha Steven K. 
Published: October 2015

Background Urine drug testing (UDT) is recommended for all patients who initiate chronic opioid therapy (COT) for the treatment of chronic pain; however, it is infrequently utilized. Some prior research has identified factors that may predict UDT, but studies have been limited. The purpose of this study is to examine the rate and predictors of UDT among a national sample of patients with chronic pain who had new initiations of COT. Methods Administrative data were examined for all veterans receiving medical care at Department of Veterans Affairs medical facilities who had new initiations of chronic opioid therapy (COT) during fiscal year 2011. Results Nineteen percent of patients who had new initiations of COT for chronic noncancer pain received UDT within 90 days of starting opioids. In adjusted analyses, patient-level factors that predicted increased likelihood of UDT included male gender (risk ratio [RR] = 1.23, 95% confidence interval [CI] = 1.02–1.49), Black race (RR = 1.20, 95% CI = 1.06–1.37), divorced/separated marital status (RR = 1.13, 95% CI = 1.02–1.25), higher pain intensity (RR = 1.03, 95% CI = 1.01–1.05), comorbid substance use disorder (RR = 1.42, 95% CI = 1.27–1.60), posttraumatic stress disorder (PTSD) (RR = 1.14, 95% CI = 1.01–1.29), bipolar disorder or schizophrenia (RR = 1.29, 95% CI = 1.08–1.53), having received UDT prior to initiating opioid therapy (RR = 1.43, 95% CI = 1.26–1.62), and a higher baseline opioid dose (RR = 1.38–1.81, 95% CIs = 1.20–1.58, 1.57–2.09). Age was also associated with UDT, in a nonlinear manner. Several factors were associated with lower likelihood of UDT, including living in a highly rural setting (RR = 0.62, 95% CI = 0.29–0.99), having a VA service–connected disability (RR = 0.85–0.89, 95% CIs = 0.75–0.97, 0.79–0.99), and having a nurse practitioner or physician assistant as one's primary care clinician (RR = 0.72, 95% CI = 0.61–0.85). Conclusions Urine drug testing was conducted with 19% of patients who had new initiations of COT. Factors that predicted UDT were multifaceted and included patient and clinician variables. Multidimensional system-level interventions may be needed to facilitate widespread implementation of UDT.
SIM.EM-S11 : High Value Resistance Comparison
Authors: Castro B I , Sanchez H , Kraft M , Jarrett D 
Published: October 2015

This is a report of the results of the Interamerican Metrology System (SIM) comparison on high resistance values, performed to compare the measurement capabilities of NIST and ICE-LMVE and for establishing the degree of equivalence between those laboratories.
During February 2014, two resistance standards were used as traveling standards for measurements in those countries, with NIST-USA acting as pilot laboratory. Results for five measurement points are presented as errors relative to a comparison reference value together with their uncertainty.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes
Authors: Staples Jeffrey , Ekunwe Lynette , Lange Ethan , Wilson James G. , Nickerson Deborah A. , Below Jennifer E. 
Published: October 2015

Abstract
Summary: PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data. However, when genetic data for individuals within a pedigree are missing, often multiple pedigrees can be reconstructed that fit the data. We report a major expansion of PRIMUS that uses mitochondrial (mtDNA) and non-recombining Y chromosome (NRY) haplotypes to eliminate many pedigree structures that are inconsistent with the genetic data. We demonstrate that discordances in mtDNA and NRY haplotypes substantially reduce the number of potential pedigrees, and often lead to the identification of the correct pedigree.
Availability and Implementation: We have implemented PRIMUS updates in PERL and it is available at primus.gs.washington.edu.
Contact: debnick@uw.edu or jennifer.e.below@uth.tmc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes
Authors: Nabavi Sheida , Schmolze Daniel , Maitituoheti Mayinuer , Malladi Sadhika , Beck Andrew H. 
Published: October 2015

Abstract
Motivation: A major goal of biomedical research is to identify molecular features associated with a biological or clinical class of interest. Differential expression analysis has long been used for this purpose; however, conventional methods perform poorly when applied to data with high within class heterogeneity.
Results: To address this challenge, we developed EMDomics, a new method that uses the Earth mover’s distance to measure the overall difference between the distributions of a gene’s expression in two classes of samples and uses permutations to obtain q-values for each gene. We applied EMDomics to the challenging problem of identifying genes associated with drug resistance in ovarian cancer. We also used simulated data to evaluate the performance of EMDomics, in terms of sensitivity and specificity for identifying differentially expressed gene in classes with high within class heterogeneity. In both the simulated and real biological data, EMDomics outperformed competing approaches for the identification of differentially expressed genes, and EMDomics was significantly more powerful than conventional methods for the identification of drug resistance-associated gene sets. EMDomics represents a new approach for the identification of genes differentially expressed between heterogeneous classes and has utility in a wide range of complex biomedical conditions in which sample classes show within class heterogeneity.
Availability and implementation: The R package is available at http://www.bioconductor.org/packages/release/bioc/html/EMDomics.html
Contact: abeck2@bidmc.harvard.edu
Supplementary information: supplementary data are available at Bioinformatics online.
Gapped sequence alignment using artificial neural networks: application to the MHC class I system
Authors: Andreatta Massimo , Nielsen Morten 
Published: October 2015

AbstractMotivation: Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to peptides of length 8–11 amino acids. On this relatively simple system, we developed a sequence alignment method based on artificial neural networks that allows insertions and deletions in the alignment.Results: We show that prediction methods based on alignments that include insertions and deletions have significantly higher performance than methods trained on peptides of single lengths. Also, we illustrate how the location of deletions can aid the interpretation of the modes of binding of the peptide-MHC, as in the case of long peptides bulging out of the MHC groove or protruding at either terminus. Finally, we demonstrate that the method can learn the length profile of different MHC molecules, and quantified the reduction of the experimental effort required to identify potential epitopes using our prediction algorithm.Availability and implementation: The NetMHC-4.0 method for the prediction of peptide-MHC class I binding affinity using gapped sequence alignment is publicly available at: http://www.cbs.dtu.dk/services/NetMHC-4.0.Contact: mniel@cbs.dtu.dkSupplementary information: Supplementary data are available at Bioinformatics online.
What hat are you wearing? On the multiple roles of fishery scientists in the ICES community
Authors: Dankel Dorothy J. , Stange Kari , Nielsen Kåre Nolde 
Published: October 2015

Abstract
Trends towards a more participatory agenda in policy-relevant science imply that the roles and work tasks of scientists become more multifaceted. In Europe, the increased use of multiannual plans creates a need for fishery scientists to contribute with their expertise in a wide variety of situations. We identify and characterize four roles for scientists as developers , reviewers , judges , and messengers in arenas where management plans are produced and evaluated. Using examples of producing and evaluating management plans for pelagic fish stocks in Europe, we present different scientific roles and how they may intertwine. The examples illustrate that fishery scientists increasingly interact with advisory councils and industry stakeholders when performing roles as developers and messengers. The roles as reviewers and judges are typically affiliated with evaluation processes carried out under the auspices of the marine science and advisory organization International Council for the Exploration of the Sea (ICES). While it may be difficult to separate the roles in practice, we argue that it must be emphasized to be aware of their different requirements to ensure that scientific credibility is not compromised. By asking the question “What hat are you wearing?”, we encourage individual fishery scientists, their employers, and ICES as a network organization of expertise to reflect on roles, affiliations, mandates, and possible consequences of wearing different “hats”.