Miracle-dz/UniFAR-FTUs huggingface dataset:
Instrumental variable method for time‐to‐event data using a pseudo‐observation approach

Observational studies are often in peril of unmeasured confounding. Instrumental variable analysis is a method for controlling for unmeasured confounding. As yet, theory on instrumental variable analysis of censored time‐to‐event data is scarce. We propose a pseudo‐observation approach to instrumental variable analysis of the survival function, the restricted mean, and the cumulative incidence function in competing risks with right‐censored data using generalized method of moments estimation. For the purpose of illustrating our proposed method, we study antidepressant exposure in pregnancy and risk of autism spectrum disorder in offspring, and the performance of the method is assessed through simulation studies.
Mountain waves and orographic precipitation in a northern Colorado winter storm

This study characterizes mountain waves and orographic precipitation associated with a winter storm passing over the ∼3.5 km above mean sea level (MSL) Park Range of northern Colorado on 15 December 2010. Observations from an airborne vertically pointing Doppler radar are used to document reflectivity and horizontal and vertical velocity in 13 two‐dimensional vertical planes extending across the Park Range from upstream of the windward slope, over the crest and downstream of the lee slope. The winter storm investigated in this study is associated with a general zonal flow over the western continental USA and significant vertical wind shear between 700 and 500 hPa. A vertically propagating wave forced by the Park Range is most evident above 4 km MSL and associated with relatively wide, upstream‐tilted updraughts and downdraughts located above the Park Range windward and lee slopes, respectively. The Park Range also forces a trapped lee wave that manifests itself as a relatively erect updraught ∼15–20 km east of the crest. Smaller‐scale trapped lee waves forced by terrain upstream of the Park Range are evident below 4 km MSL and associated with rotor circulations composed of relatively narrow updraughts and downdraughts located above the Yampa Valley and the Park Range windward slope. A ∼1 km thick layer of strong vertical shear exists between the mountain waves forced by the Park Range and those forced by upstream terrain. This shear layer exhibits a large vertical displacement over the Park Range, with relatively strong westerly winds plunging to low levels over the lee slope. While precipitation on the Park Range windward slope is generally enhanced for the event, data analysed for this case surprisingly does not show a spatially and temporally consistent correlation between mountain‐wave kinematic structures and orographic precipitation. Transient processes such as wave‐regime interactions may have masked this correlation.
Title : Effects of optical correction method on the magnitude and variability of accommodative response : A test-retest study

response: A test-retest study. Authors: Raimundo Jiménez, PhD; Beatriz Redondo, MS; Leon N. Davies, PhD & Jesús Vera, PhD Affiliations: 1. Department of Optics, University of Granada, Spain. 2. Ophthalmic Research Group, School of Life and Health Sciences, Aston University, Birmingham, UK Corresponding author: Jesús Vera, Department of Optics, Faculty of Science, University of Granada, Campus de la Fuentenueva 2, 18001 Granada, Spain. Tel: +34 95824440675. Fax: +34 958248533. E-mail: jesusvv@correo.ugr. es.
A survey of tropical cirrus particle size and shape using ATSR-2 visible/near-infrared data

The visible (0.55, 0.67 and 0.87 um) and near-infrared (1.6 μm) channels of the Along Track Scanning Radiometer-2 are capable of determining the optical depth and the size of cirrus cloud crystals. An addition, the along track view of the ATSR gives some information on the crystal shape and allows cloud height to be determined. Cloud temperature can be derived from the thermal channels (11 and 12 μm). We briefly describe the retrieval of these cloud properties, using representative ice crystal phase functions assuming hexagonal columns and polycrystals, from the ATSR-2 data. We present results of a preliminary survey of cirrus cloud properties using 35 selected scenes of diverse convective activity from the Western Tropical Pacific. The cloud top temperatures of our survey are consistent with the CEPEX field campaign which measured ice crystal shape and size. The conclusions from this limited study are; 1) polycrystal scattering phase functions adequately explain the ATSR-2 dual-view reflectance measurements in 60-80% cases; the remainder are not well explained by column phase functions, 2) crystal sizes decrease with cloud temperature at a rate of around 1μm per °C to asymptote around 50μm at -80°C, 3) crystal sizes are consistantly independent of cloud optical depth and 4) lapse rates for the lower troposphere lie between dry and wet adiabatics but upper level cloud temperatures often appear 'too high'.
Spatial variability and interdependence of rain event characteristics in the Czech Republic

Rain event characteristics are assessed in a 10‐year (1991–2000) record for 122 stations in the Czech Republic. Individual rain events are identified using the minimum interevent time (mit) concept. For each station, the optimal mit value is estimated by examining the distribution of interevent times. In addition, various mit values are considered to account for the effect of mit on rain event characteristics and their interrelationships.
Thermoluminescence as a function of climate and temperature

The theory of thermoluminescence as a function of temperature was tested by measuring the natural thermoluminescence of samples of limestone collected from several climatic areas. The agreement between the theory and the experimental results is satisfactory. In non-polar regions of the world, with average erosion rates and geothermal gradient, the number of electrons responsible for the 230 degrees C glow-curve peak for calcite is in equilibrium with the average temperature of the hottest month. In polar areas the equilibrium is not reached, as frigid conditions have not existed in the area for the necessary length of time.
Crustal structure and seismotectonics of central Sicily (southern Italy): new constraints from instrumental seismicity

SUMMARY In this paper, we propose a new model of the crustal structure and seismotectonics for central Sicily (southern Italy) through the analysis of the depth distribution and kinematics of the instrumental seismicity, occurring during the period from 1983 to 2010, and its comparison with individual geological structures that may be active in the area. The analysed data set consists of 392 earthquakes with local magnitudes ranging from 1.0 to 4.7. We defined a new, detailed 1-D velocity model to relocate the earthquakes that occurred in central Sicily, and we calculated a Moho depth of 37 km and a mean VP/VS ratio of 1.73. The relocated seismic events are clustered mainly in the area north of Caltanissetta (e.g. Mainland Sicily) and in the northeastern sector (Madonie Mountains) of the study area; only minor and greatly dispersed seismicity is located in the western sector, near Belice, and along the southern coast, between Gela and Sciacca. The relocated hypocentral distribution depicts a bimodal pattern: 50 per cent of the events occur within the upper crust at depths less than ∼16 km, 40 per cent of the events occur within the middle and depth crust, at depths between 16 and 32 km, and the remaining 10 per cent occur at subcrustal depths. The energy release pattern shows a similar depth distribution. On the basis of the kinematic analysis of 38 newly computed focal plane solutions, two major geographically distinct seismotectonic domains are distinguished: the Madonie Mountain domain, with prevalent extensional and extensional-oblique kinematics associated with upper crust Late Pliocene–Quaternary faulting, and the Mainland Sicily domain, with prevalent compressional and compressional-oblique kinematics associated with thrust faulting, at mid to deep crust depth, along the north-dipping Sicilian Basal Thrust (SBT). The stress inversion of the Mainland Sicily focal solutions integrated with neighbouring mechanisms available in the literature highlights a regional homogeneous compressional tensor, with a subhorizontal NNW–SSE-striking σ1 axis. In addition, on the basis of geodetic data, the Mainland Sicily domain may be attributed to the SSE-ward thrusting of the Mainland Sicily block along the SBT plane. Seismogenic shearing along the SBT at mid-crustal depths was responsible for the unexpected Belice 1968 earthquake (Mw 6.1), with evident implications in terms of hazard assessment.
Rapid Identification of X-ray Diffraction Spectra Based on Very Limited Data by Interpretable Convolutional Neural Networks

Large volumes of data from material characterizations call for rapid and automatic data analysis to accelerate materials discovery. Herein, we report a convolutional neural network (CNN) that was trained based on theoretic data and very limited experimental data for fast identification of experimental X-ray diffraction (XRD) spectra of metal-organic frameworks (MOFs). To augment the data for training the model, noise was extracted from experimental spectra and shuffled, then merged with the main peaks that were extracted from theoretical spectra to synthesize new spectra. For the first time, one-to-one material identification was achieved. The optimized model showed the highest identification accuracy of 96.7% for the Top 5 ranking among a dataset of 1012 MOFs. Neighborhood components analysis (NCA) on the experimental XRD spectra shows that the spectra from the same material are clustered in groups in the NCA map. Analysis on the class activation maps of the last CNN layer further discloses the mechanism by which the CNN model successfully identifies individual MOFs from the XRD spectra. This CNN model trained by the data-augmentation technique would not only open numerous potential applications for identifying XRD spectra for different materials, but also pave avenues to autonomously analyze data by other characterization tools such as FTIR, Raman, and NMR.
Predictability of Japan/East Sea (JES) system to uncertain initial/lateral boundary conditions and surface winds

Abstract : Numerical ocean modeling usually composes various initial- and boundary-value problems. It integrates hydrodynamic and thermodynamic equations numerically with atmospheric forcing and boundary conditions (lateral and vertical) from initial states of temperature, salinity and velocity. Past observations, historical datasets and climatological datasets of the ocean have contributed greatly to the knowledge of the data fields of initial condition, atmospheric forcing and boundary conditions. Change in either initial or boundary condition leads to a variety of model solutions. It is necessary to specify realistic initial and boundary conditions to achieve better understanding and prediction of the ocean behavior. However, uncertainty often exists in both initial and boundary conditions. Up to now, most studies on ocean predictability have usually been for one particular type of model input uncertainty within the three types of uncertainty (initial conditions, open boundary conditions, atmospheric forcing function). This thesis investigates the response of ocean model to the three types of model input uncertainty simultaneously using Princeton Ocean Model (POM) implemented for the Japan/East Sea (JES).
Adapting to sea-level rise in the US Southeast: The influence of built infrastructure and biophysical factors on the inundation of coastal areas

The earth` s global mean surface air temperature has increased by 0.5{degrees}C over the past 100 years. This warming trend has occurred concurrently with increases in the concentration and number of greenhouse gases in the atmosphere. These gases may cause this trend to accelerate in the future and result in a net increase in the earth`s global mean surface air temperature of 1.5 to 4.5{degrees}C by the year 2100. An increase of this magnitude could cause sea surface temperatures to increase would cause sea levels to rise -from thermal expansion of the sea, and the addition of melt waters from alpine glaciers and continental ice sheets. To allow for the cost-effective analysis of the impacts that sea-level rise may have on the US Southeast, a method is needed that will allow sites that are potentially at risk to be identified for study. Previously, no objective method was available to identify such sites. This project addresses this problem by using a geographic data base with information on both physical and climatological factors to identify coastal areas of the US Southeast that are at risk to inundation or accelerated erosion due to sea-level rise. The following six areas were selected for furthermore » study from the many identified as being at high risk: Galveston, Texas; Caminada Pass, Louisiana; Bradenton Beach, Florida; Daytona Beach, Florida; McClellanville, South Carolina; and Nags Head, North Carolina. For each study area the amount of land, by land use type, in danger from inundation from three sea-level-rise scenarios was calculated. The calculated values were based on elevation alone. « less
Scaling of infiltration behavior in dissimilar porous materials

Microscopic characteristic lengths, as used in the theory of similar porous media, were obtained from measurements of hydraulic conductivity at saturation, of soil-water pressure at half saturation, and of the integral of hydraulic conductivity with soil-water pressure, for dissimilar materials with a wide range of particle sizes and shapes. The ratio of the microscopic characteristic lengths obtained in these three ways showed little variation between materials. Dimensionless variables defined in terms of them were used to scale experimental results with packed columns of the materials for vertical downward infiltration, for horizontal infiltration, and for vertical upward capillary rise. The scaled results for all materials were in agreement and fitted theoretically derived relationships for the three situations.
Petrofabrics of high‐pressure rocks exhumed at the slab‐mantle interface from the “point of no return” in a subduction zone (Sivrihisar, Turkey)

The highest pressure recorded by metamorphic rocks exhumed from oceanic subduction zones is ~2.5 GPa, corresponding to the maximum decoupling depth (MDD) (80 ± 10 km) identified in active subduction zones; beyond the MDD (the “point of no return”) exhumation is unlikely. The Sivrihisar massif (Turkey) is a coherent terrane of lawsonite eclogite and blueschist facies rocks in which assemblages and fabrics record P‐T‐fluid‐deformation conditions during exhumation from ~80 to 45 km. Crystallographic fabrics and other features of high‐pressure metasedimentary and metabasaltic rocks record transitions during exhumation. In quartzite, microstructures and crystallographic fabrics record deformation in the dislocation creep regime, including dynamic recrystallization during decompression, and a transition from prism slip to activation of rhomb and basal slip that may be related to a decrease in water fugacity during decompression (~2.5 to ~1.5 GPa). Phengite, lawsonite, and omphacite or glaucophane in quartzite and metabasalt remained stable during deformation, and omphacite developed an L‐type crystallographic fabric. In marble, aragonite developed columnar textures with strong crystallographic fabrics that persisted during partial to complete dynamic recrystallization that was likely achieved in the stability field of aragonite (P > ~1.2 GPa). Results of kinematic vorticity analysis based on lawsonite shape fabrics are consistent with shear criteria in quartzite and metabasalt and indicate a large component of coaxial deformation in the exhuming channel beneath a simple shear dominated interface. This large coaxial component may have multiplied the exhuming power of the subduction channel and forced deeply subducted rocks to flow back from the point of no return.
Sendai virus recruits cellular villin to remodel actin cytoskeleton during fusion with hepatocytes

ETOC: Proteomic approaches identified villin to be a key modulator of Sendai virus–induced membrane fusion. We found that villin influences actin dynamics and that this influence, in turn, promotes membrane mixing through active participation of Sendai viral envelope glycoproteins. Modulation of villin in host cells also results in a discernible effect on the entry and egress of progeny virus.
Components of Sigma B Regulon in Listeria monocytogenes That Contribute to Acid and Salt Tolerance

Sigma B ( (cid:1) B ) is an alternative sigma factor that controls the transcriptional response to stress in Listeria monocytogenes and is also known to play a role in the virulence of this human pathogen. In the present study we investigated the impact of a sigB deletion on the proteome of L. monocytogenes grown in a chemically deﬁned medium both in the presence and in the absence of osmotic stress (0.5 M NaCl). Two new phenotypes associated with the sigB deletion were identiﬁed using this medium. (i) Unexpectedly, the strain with the (cid:2) sigB deletion was found to grow faster than the parent strain in the growth medium, but only when 0.5 M NaCl was present. This phenomenon was independent of the carbon source provided in the medium. (ii) The (cid:2) sigB mutant was found to have unusual Gram staining properties compared to the parent, suggesting that (cid:1) B contributes to the maintenance of an intact cell wall. A proteomic analysis was performed by two-dimensional gel electrophoresis, using cells growing in the exponential and stationary phases. Overall, Caco-2 loss of Lmo2748 the cell wall in the (cid:2) sigB mutant. two new phenotypes loss clear roles for B in both and low-pH stress and identiﬁed speciﬁc components of the (cid:1) B regulon that contribute to the responses observed.
Model development and comparison to predict softwood and hardwood per cent cover using high and medium spatial resolution imagery

The recent availability of high spatial resolution multispectral scanners provides an opportunity to adapt existing methods and test models to derive spatially explicit forest type and per cent cover information at the Landsat pixel level. A regression modelling methodology was applied for scaling‐up high resolution (IKONOS) to medium spatial resolution satellite imagery (Landsat) to predict softwood and hardwood forest type and density (per cent cover) in a northern Maine study area. Regression relationships (63 different models) were developed and compared. The model variables included vegetation indices and several date (season) combinations of Landsat Enhanced Thematic Mapper Plus (ETM+) imagery (August, September, October and May). A model incorporating all variables from four dates of Landsat ETM+ imagery produced the highest coefficient of variation in predicting both softwood (0.655) and hardwood cover (0.66). The addition of vegetation indices with the six ETM+ reflected bands did not significantly improve or detract from the regression relationships for any of the multi‐date or single date models examined. A two‐date combination of October and May variables provided an acceptable (and arguably more cost‐effective) model as the adjusted R 2 value was 0.645 for softwood and 0.649 for hardwood. A significant result was that all single‐date models produced inferior results with a sharp drop in adjusted R 2, compared with the multi‐date seasonal models. This research has demonstrated that the regression models including multi‐date variables produce good results and can provide spatially explicit forest type and stand structure data that has been difficult or infeasible to obtain from medium spatial resolution imagery using traditional classification methods.
Investigating the Temporal Dynamics of Inter- Organizational Exchange: Patient Transfers among Italian Hospitals

Previous research on interaction behavior among organizations (resource exchange, collaboration, communication) has typically aggregated records of those behaviors over time to constitute a 'network' of organizational relationships. We instead directly study structural-temporal patterns in organizational exchange, focusing on the dynamics of reciprocation. Applying this lens to a community of Italian hospitals during the period 2003-2007, we observe two mechanisms of interorganizational reciprocation: organizational embedding and resource dependence. We flesh out these two mechanisms by showing how they operate in distinct time frames: Dependence operates on contemporaneous exchange structures, whereas embedding develops through longer-term historical patterns. We also show how these processes operate differently in competitive and noncompetitive contexts, operationalized in terms of market differentiation and geographic space. In noncompetitive contexts, we observe both logics of reciprocation, dependence in the short term and embedding over the long term, developing into patterns of generalized exchange in this population. In competitive contexts, we observe neither form of reciprocation and instead observe the microfoundations of status hierarchies in exchange. Since at any time the given structure of relations is all that exists… all influence of the past works through the shape given to those relations by the actions of the past. Memory of course provides a symbolic record of the past, which then reinterprets and reshapes it as a foundation for current action. But in the first instance, social structure is itself the memory of the social process.
454 Life Sciences: Illuminating the future of genome sequencing and personalized medicine

Imagine going to the doctor with a migraine headache and knowing the next day whether your DNA is to blame. Or better yet, imagine knowing whether your DNA encodes a risk for migraines even before a headache strikes. If 454 Life Sciences’ dream is realized, doctors will be able to quickly and inexpensively unlock the mysteries of patients’ genomes, revealing indicators of disease susceptibility and shedding light on the potential efficacy of particular drug regimens. Due to advances in technology made by companies like 454 Life Sciences in Branford, Connecticut, personalized genomic medicine is becoming a reality and is sure to revolutionize not only your doctor’s visits, but also the way society views human health and disease