531 research outputs found
CONSISE statement on the reporting of Seroepidemiologic Studies for influenza (ROSES-I statement): an extension of the STROBE statement
published_or_final_versio
Quantum spin liquid states in the two dimensional kagome antiferromagnets, ZnxCu4-x(OD)6Cl2
A three-dimensional system of interacting spins typically develops static
long-range order when it is cooled. If the spins are quantum (S = 1/2),
however, novel quantum paramagnetic states may appear. The most highly sought
state among them is the resonating valence bond (RVB) state in which every pair
of neighboring quantum spins form entangled spin singlets (valence bonds) and
the singlets are quantum mechanically resonating amongst all the possible
highly degenerate pairing states. Here we provide experimental evidence for
such quantum paramagnetic states existing in frustrated antiferromagnets,
ZnxCu4-x(OD)6Cl2, where the S = 1/2 magnetic Cu2+ moments form layers of a
two-dimensional kagome lattice. We find that in Cu4(OD)6Cl2, where distorted
kagome planes are weakly coupled to each other, a dispersionless excitation
mode appears in the magnetic excitation spectrum below ~ 20 K, whose
characteristics resemble those of quantum spin singlets in a solid state, known
as a valence bond solid (VBS), that breaks translational symmetry. Doping
nonmagnetic Zn2+ ions reduces the distortion of the kagome lattice, and weakens
the interplane coupling but also dilutes the magnetic occupancy of the kagome
lattice. The VBS state is suppressed and for ZnCu3(OD)6Cl2 where the kagome
planes are undistorted and 90% occupied by the Cu2+ ions, the low energy spin
fluctuations in the spin liquid phase become featureless
Fail-safe optimization of viscous dampers for seismic retrofitting
This paper presents a new optimization approach for designing minimum-cost
fail-safe distributions of fluid viscous dampers for seismic retrofitting.
Failure is modeled as either complete damage of the dampers or partial
degradation of the dampers' properties. In general, this leads to optimization
problems with large number of constraints. Thus, the use of a working-set
optimization algorithm is proposed. The main idea is to solve a sequence of
relaxed optimization sub-problems with a small sub-set of all constraints. The
algorithm terminates once a solution of a sub-problem is found that satisfies
all the constraints of the problem. The retrofitting cost is minimized with
constraints on the inter-story drifts at the peripheries of frame structures.
The structures considered are subjected to a realistic ensemble of ground
motions, and their response is evaluated with time-history analyses. The
transient optimization problem is efficiently solved with a gradient-based
sequential linear programming algorithm. The gradients of the response
functions are calculated with a consistent adjoint sensitivity analysis
procedure. Promising results attained for 3-D irregular frames are presented
and discussed. The numerical results highlight the fact that the optimized
layout and size of the dampers can change significantly even for moderate
levels of damage
Topology by Design in Magnetic nano-Materials: Artificial Spin Ice
Artificial Spin Ices are two dimensional arrays of magnetic, interacting
nano-structures whose geometry can be chosen at will, and whose elementary
degrees of freedom can be characterized directly. They were introduced at first
to study frustration in a controllable setting, to mimic the behavior of spin
ice rare earth pyrochlores, but at more useful temperature and field ranges and
with direct characterization, and to provide practical implementation to
celebrated, exactly solvable models of statistical mechanics previously devised
to gain an understanding of degenerate ensembles with residual entropy. With
the evolution of nano--fabrication and of experimental protocols it is now
possible to characterize the material in real-time, real-space, and to realize
virtually any geometry, for direct control over the collective dynamics. This
has recently opened a path toward the deliberate design of novel, exotic
states, not found in natural materials, and often characterized by topological
properties. Without any pretense of exhaustiveness, we will provide an
introduction to the material, the early works, and then, by reporting on more
recent results, we will proceed to describe the new direction, which includes
the design of desired topological states and their implications to kinetics.Comment: 29 pages, 13 figures, 116 references, Book Chapte
OptiJ: Open-source optical projection tomography of large organ samples
The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi
Small but crucial : the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans
Peer reviewedPublisher PD
Polarons and confinement of electronic motion to two dimensions in a layered transition metal oxide
A very remarkable feature of the layered transition metal oxides (TMOs),
whose most famous members are the high-temperature superconductors (HTSs), is
that even though they are prepared as bulk three-dimensional single crystals,
they display hugely anisotropic electrical and optical properties, seeming to
be insulating perpendicular to the layers and metallic within them. This is the
phenomenon of confinement, a concept at odds with the conventional theory of
solids and recognized as due to magnetic and electron-lattice interactions in
the layers which must be overcome at a substantial energy cost if electrons are
to be transferred between layers. The associated energy gap or 'pseudogap' is
particularly obvious in experiments where charge is moved perpendicular to the
planes, most notably scanning tunneling microscopy (STM) and polarized infrared
spectroscopy. Here, using the same experimental tools, we show that there is a
second family of TMOs - the layered manganites La2-2xSr1+2xMn2O7 (LSMO) - with
even more extreme confinement and pseudogap effects. The data, which are the
first to resolve atoms in any metallic manganite, demonstrate quantitatively
that because they are attached to polarons - lattice and spin textures within
the planes -, it is equally difficult to remove carriers from the planes via
vacuum tunneling into a conventional metallic tip, as it is for them to move
between Mn-rich layers within the material itself
Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015
SummaryBackground The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. Methods We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence. We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. We developed a metric that allows comparisons of exposure across risk factors—the summary exposure value. Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk. We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates. We characterised risk exposure in relation to a Socio-demographic Index (SDI). Findings Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period. All risks jointly evaluated in 2015 accounted for 57·8% (95% CI 56·6–58·8) of global deaths and 41·2% (39·8–42·8) of DALYs. In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211·8 million [192·7 million to 231·1 million] global DALYs), smoking (148·6 million [134·2 million to 163·1 million]), high fasting plasma glucose (143·1 million [125·1 million to 163·5 million]), high BMI (120·1 million [83·8 million to 158·4 million]), childhood undernutrition (113·3 million [103·9 million to 123·4 million]), ambient particulate matter (103·1 million [90·8 million to 115·1 million]), high total cholesterol (88·7 million [74·6 million to 105·7 million]), household air pollution (85·6 million [66·7 million to 106·1 million]), alcohol use (85·0 million [77·2 million to 93·0 million]), and diets high in sodium (83·0 million [49·3 million to 127·5 million]). From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines. Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use. Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI. In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015. Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa. Interpretation Declines in some key environmental risks have contributed to declines in critical infectious diseases. Some risks appear to be invariant to SDI. Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining. Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. Funding Bill & Melinda Gates Foundation
Class-modeling analysis reveals T-cell homeostasis disturbances involved in loss of immune control in elite controllers
Despite long-lasting HIV replication control, a significant proportion of elite controller (EC) patients may experience CD4 T-cell loss. Discovering perturbations in immunological parameters could help our understanding of the mechanisms that may be operating in those patients experiencing loss of immunological control.
Methods A case–control study was performed to evaluate if alterations in different T-cell homeostatic parameters can predict CD4 T-cell loss in ECs by comparing data from EC patients showing significant CD4 decline (cases) and EC patients showing stable CD4 counts (controls). The partial least-squares–class modeling (PLS-CM) statistical methodology was employed to discriminate between the two groups of patients, and as a predictive model.
Results
Herein, we show that among T-cell homeostatic alterations, lower levels of naïve and recent thymic emigrant subsets of CD8 cells and higher levels of effector and senescent subsets of CD8 cells as well as higher levels of exhaustion of CD4 cells, measured prior to CD4 T-cell loss, predict the loss of immunological control.
Conclusions
These data indicate that the parameters of T-cell homeostasis may identify those EC patients with a higher proclivity to CD4 T-cell loss. Our results may open new avenues for understanding the mechanisms underlying immunological progression despite HIV replication control, and eventually, for finding a functional cure through immune-based clinical trials.projects RD12/0017/0031, RD16/0025/
0013, and SAF2015-66193-R as part of the Health Research and Development
Strategy, State Plan for Scientific and Technical Research and Innovation (2008–
2011 and 2013–2016) and cofinanced by the Institute of Health Carlos III (ISCIII),
Sub-Directorate General for Research Assessment and Promotion and European
Regional Development Fund. NR is a Miguel Servet investigator from the ISCIII
(CP14/00198), Madrid, Spain. C Restrepo was funded by project RD12/0017/
0031 and is currently funded by project RD16/0025/0013. M García is a
predoctoral student co-funded by grant CP14/00198 and an Intramural
Research Scholarship from Instituto de Investigación Sanitaria-Fundación Jiménez
Díaz (IIS-FJD)
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