510 research outputs found
Measuring co-authorship and networking-adjusted scientific impact
Appraisal of the scientific impact of researchers, teams and institutions
with productivity and citation metrics has major repercussions. Funding and
promotion of individuals and survival of teams and institutions depend on
publications and citations. In this competitive environment, the number of
authors per paper is increasing and apparently some co-authors don't satisfy
authorship criteria. Listing of individual contributions is still sporadic and
also open to manipulation. Metrics are needed to measure the networking
intensity for a single scientist or group of scientists accounting for patterns
of co-authorship. Here, I define I1 for a single scientist as the number of
authors who appear in at least I1 papers of the specific scientist. For a group
of scientists or institution, In is defined as the number of authors who appear
in at least In papers that bear the affiliation of the group or institution. I1
depends on the number of papers authored Np. The power exponent R of the
relationship between I1 and Np categorizes scientists as solitary (R>2.5),
nuclear (R=2.25-2.5), networked (R=2-2.25), extensively networked (R=1.75-2) or
collaborators (R<1.75). R may be used to adjust for co-authorship networking
the citation impact of a scientist. In similarly provides a simple measure of
the effective networking size to adjust the citation impact of groups or
institutions. Empirical data are provided for single scientists and
institutions for the proposed metrics. Cautious adoption of adjustments for
co-authorship and networking in scientific appraisals may offer incentives for
more accountable co-authorship behaviour in published articles.Comment: 25 pages, 5 figure
Graphene for spintronics: giant Rashba splitting due to hybridization with Au
Graphene in spintronics has so far primarily meant spin current leads of high
performance because the intrinsic spin-orbit coupling of its pi-electrons is
very weak. If a large spin-orbit coupling could be created by a proximity
effect, the material could also form active elements of a spintronic device
such as the Das-Datta spin field-effect transistor, however, metal interfaces
often compromise the band dispersion of massless Dirac fermions. Our
measurements show that Au intercalation at the graphene-Ni interface creates a
giant spin-orbit splitting (~100 meV) in the graphene Dirac cone up to the
Fermi energy. Photoelectron spectroscopy reveals hybridization with Au-5d
states as the source for the giant spin-orbit splitting. An ab initio model of
the system shows a Rashba-split dispersion with the analytically predicted
gapless band topology around the Dirac point of graphene and indicates that a
sharp graphene-Au interface at equilibrium distance will account for only ~10
meV spin-orbit splitting. The ab initio calculations suggest an enhancement due
to Au atoms that get closer to the graphene and do not violate the sublattice
symmetry.Comment: 16 pages (3 figures) + supplementary information 16 pages (14
figures
The Shapes of Cooperatively Rearranging Regions in Glass Forming Liquids
The shapes of cooperatively rearranging regions in glassy liquids change from
being compact at low temperatures to fractal or ``stringy'' as the dynamical
crossover temperature from activated to collisional transport is approached
from below. We present a quantitative microscopic treatment of this change of
morphology within the framework of the random first order transition theory of
glasses. We predict a correlation of the ratio of the dynamical crossover
temperature to the laboratory glass transition temperature, and the heat
capacity discontinuity at the glass transition, Delta C_p. The predicted
correlation agrees with experimental results for the 21 materials compiled by
Novikov and Sokolov.Comment: 9 pages, 6 figure
Gate-tunable black phosphorus spin valve with nanosecond spin lifetimes
Two-dimensional materials offer new opportunities for both fundamental
science and technological applications, by exploiting the electron spin. While
graphene is very promising for spin communication due to its extraordinary
electron mobility, the lack of a band gap restricts its prospects for
semiconducting spin devices such as spin diodes and bipolar spin transistors.
The recent emergence of 2D semiconductors could help overcome this basic
challenge. In this letter we report the first important step towards making 2D
semiconductor spin devices. We have fabricated a spin valve based on ultra-thin
(5 nm) semiconducting black phosphorus (bP), and established fundamental spin
properties of this spin channel material which supports all electrical spin
injection, transport, precession and detection up to room temperature (RT).
Inserting a few layers of boron nitride between the ferromagnetic electrodes
and bP alleviates the notorious conductivity mismatch problem and allows
efficient electrical spin injection into an n-type bP. In the non-local spin
valve geometry we measure Hanle spin precession and observe spin relaxation
times as high as 4 ns, with spin relaxation lengths exceeding 6 um. Our
experimental results are in a very good agreement with first-principles
calculations and demonstrate that Elliott-Yafet spin relaxation mechanism is
dominant. We also demonstrate that spin transport in ultra-thin bP depends
strongly on the charge carrier concentration, and can be manipulated by the
electric field effect
The exchangeability of shape
<p>Abstract</p> <p>Background</p> <p>Landmark based geometric morphometrics (GM) allows the quantitative comparison of organismal shapes. When applied to systematics, it is able to score shape changes which often are undetectable by traditional morphological studies and even by classical morphometric approaches. It has thus become a fast and low cost candidate to identify cryptic species. Due to inherent mathematical properties, shape variables derived from one set of coordinates cannot be compared with shape variables derived from another set. Raw coordinates which produce these shape variables could be used for data exchange, however they contain measurement error. The latter may represent a significant obstacle when the objective is to distinguish very similar species.</p> <p>Results</p> <p>We show here that a single user derived dataset produces much less classification error than a multiple one. The question then becomes how to circumvent the lack of exchangeability of shape variables while preserving a single user dataset. A solution to this question could lead to the creation of a relatively fast and inexpensive systematic tool adapted for the recognition of cryptic species.</p> <p>Conclusions</p> <p>To preserve both exchangeability of shape and a single user derived dataset, our suggestion is to create a free access bank of reference images from which one can produce raw coordinates and use them for comparison with external specimens. Thus, we propose an alternative geometric descriptive system that separates 2-D data gathering and analyzes.</p
Lattice Boltzmann simulations of soft matter systems
This article concerns numerical simulations of the dynamics of particles
immersed in a continuum solvent. As prototypical systems, we consider colloidal
dispersions of spherical particles and solutions of uncharged polymers. After a
brief explanation of the concept of hydrodynamic interactions, we give a
general overview over the various simulation methods that have been developed
to cope with the resulting computational problems. We then focus on the
approach we have developed, which couples a system of particles to a lattice
Boltzmann model representing the solvent degrees of freedom. The standard D3Q19
lattice Boltzmann model is derived and explained in depth, followed by a
detailed discussion of complementary methods for the coupling of solvent and
solute. Colloidal dispersions are best described in terms of extended particles
with appropriate boundary conditions at the surfaces, while particles with
internal degrees of freedom are easier to simulate as an arrangement of mass
points with frictional coupling to the solvent. In both cases, particular care
has been taken to simulate thermal fluctuations in a consistent way. The
usefulness of this methodology is illustrated by studies from our own research,
where the dynamics of colloidal and polymeric systems has been investigated in
both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures,
76 page
Does Respondent Driven Sampling Alter the Social Network Composition and Health-Seeking Behaviors of Illicit Drug Users Followed Prospectively?
Respondent driven sampling (RDS) was originally developed to sample and provide peer education to injection drug users at risk for HIV. Based on the premise that drug users' social networks were maintained through sharing rituals, this peer-driven approach to disseminate educational information and reduce risk behaviors capitalizes and expands upon the norms that sustain these relationships. Compared with traditional outreach interventions, peer-driven interventions produce greater reductions in HIV risk behaviors and adoption of safer behaviors over time, however, control and intervention groups are not similarly recruited. As peer-recruitment may alter risk networks and individual risk behaviors over time, such comparison studies are unable to isolate the effect of a peer-delivered intervention. This analysis examines whether RDS recruitment (without an intervention) is associated with changes in health-seeking behaviors and network composition over 6 months. New York City drug users (N = 618) were recruited using targeted street outreach (TSO) and RDS (2006–2009). 329 non-injectors (RDS = 237; TSO = 92) completed baseline and 6-month surveys ascertaining demographic, drug use, and network characteristics. Chi-square and t-tests compared RDS- and TSO-recruited participants on changes in HIV testing and drug treatment utilization and in the proportion of drug using, sex, incarcerated and social support networks over the follow-up period. The sample was 66% male, 24% Hispanic, 69% black, 62% homeless, and the median age was 35. At baseline, the median network size was 3, 86% used crack, 70% used cocaine, 40% used heroin, and in the past 6 months 72% were tested for HIV and 46% were enrolled in drug treatment. There were no significant differences by recruitment strategy with respect to changes in health-seeking behaviors or network composition over 6 months. These findings suggest no association between RDS recruitment and changes in network composition or HIV risk, which supports prior findings from prospective HIV behavioral surveillance and intervention studies
ALG: Automated Genotype Calling of Luminex Assays
Single nucleotide polymorphisms (SNPs) are the most commonly used polymorphic markers in genetics studies. Among the different platforms for SNP genotyping, Luminex is one of the less exploited mainly due to the lack of a robust (semi-automated and replicable) freely available genotype calling software. Here we describe a clustering algorithm that provides automated SNP calls for Luminex genotyping assays. We genotyped 3 SNPs in a cohort of 330 childhood leukemia patients, 200 parents of patient and 325 healthy individuals and used the Automated Luminex Genotyping (ALG) algorithm for SNP calling. ALG genotypes were called twice to test for reproducibility and were compared to sequencing data to test for accuracy. Globally, this analysis demonstrates the accuracy (99.6%) of the method, its reproducibility (99.8%) and the low level of no genotyping calls (3.4%). The high efficiency of the method proves that ALG is a suitable alternative to the current commercial software. ALG is semi-automated, and provides numerical measures of confidence for each SNP called, as well as an effective graphical plot. Moreover ALG can be used either through a graphical user interface, requiring no specific informatics knowledge, or through command line with access to the open source code. The ALG software has been implemented in R and is freely available for non-commercial use either at http://alg.sourceforge.net or by request to [email protected]
Genome-wide enhancer maps link risk variants to disease genes
Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complextraits, each of which could reveal insights into the mechanisms of disease(1). Many ofthe underlying causal variants may affect enhancers(2,3), but we lack accurate maps of enhancers and their target genes to interpret such variants. We recently developed the activity-by-contact (ABC) model to predict which enhancers regulate which genes and validated the model using CRISPR perturbations in several cell types(4). Here we apply this ABC model to create enhancer-gene maps in 131 human cell types and tissues, and use these maps to interpret the functions of GWAS variants. Across 72 diseases and complex traits, ABC links 5,036 GWAS signals to 2,249 unique genes, including a class of 577genesthat appear to influence multiple phenotypes through variants in enhancers that act in different cell types. In inflammatory bowel disease (IBD), causal variants are enriched in predicted enhancers by more than 20-fold in particular cell types such as dendritic cells, and ABC achieves higher precision than other regulatory methods at connecting noncoding variants to target genes. These variant-to-function maps reveal an enhancer that contains an IBD risk variant and that regulates the expression of PPIF to alter the membrane potential of mitochondria in macrophages. Our study reveals principles of genome regulation, identifies genes that affect IBD and provides a resource and generalizable strategy to connect risk variants of common diseases to their molecular and cellular functions.Peer reviewe
The Pioneer Anomaly
Radio-metric Doppler tracking data received from the Pioneer 10 and 11
spacecraft from heliocentric distances of 20-70 AU has consistently indicated
the presence of a small, anomalous, blue-shifted frequency drift uniformly
changing with a rate of ~6 x 10^{-9} Hz/s. Ultimately, the drift was
interpreted as a constant sunward deceleration of each particular spacecraft at
the level of a_P = (8.74 +/- 1.33) x 10^{-10} m/s^2. This apparent violation of
the Newton's gravitational inverse-square law has become known as the Pioneer
anomaly; the nature of this anomaly remains unexplained. In this review, we
summarize the current knowledge of the physical properties of the anomaly and
the conditions that led to its detection and characterization. We review
various mechanisms proposed to explain the anomaly and discuss the current
state of efforts to determine its nature. A comprehensive new investigation of
the anomalous behavior of the two Pioneers has begun recently. The new efforts
rely on the much-extended set of radio-metric Doppler data for both spacecraft
in conjunction with the newly available complete record of their telemetry
files and a large archive of original project documentation. As the new study
is yet to report its findings, this review provides the necessary background
for the new results to appear in the near future. In particular, we provide a
significant amount of information on the design, operations and behavior of the
two Pioneers during their entire missions, including descriptions of various
data formats and techniques used for their navigation and radio-science data
analysis. As most of this information was recovered relatively recently, it was
not used in the previous studies of the Pioneer anomaly, but it is critical for
the new investigation.Comment: 165 pages, 40 figures, 16 tables; accepted for publication in Living
Reviews in Relativit
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