Miracle-dz/UniFAR-FTUs huggingface dataset:
Titles versus titles and abstracts for initial screening of articles for systematic reviews

Background: There is no consensus on whether screening titles alone or titles and abstracts together is the preferable strategy for inclusion of articles in a systematic review. Methods: Two methods of screening articles for inclusion in a systematic review were compared: titles first versus titles and abstracts simultaneously. Each citation found in MEDLINE or Embase was reviewed by two physician reviewers for prespecified criteria: the citation included (1) primary data; (2) the exposure of interest; and (3) the outcome of interest. Results: There were 2965 unique citations. The titles first strategy resulted in an immediate rejection of 2558 (86%) of the records after reading the title alone, requiring review of 239 titles and abstracts, and subsequently 176 full text articles. The simultaneous titles and abstracts review led to rejection of 2782 citations (94%) and review of 183 full text articles. Interreviewer agreement to include an article for full text review using the titles-first screening strategy was 89%–94% (kappa = 0.54) and 96%–97% (kappa = 0.56) for titles and abstracts combined. The final systematic review included 13 articles, all of which were identified by both screening strategies (yield 100%, burden 114%). Precision was higher in the titles and abstracts method (7.1% versus 3.2%) but recall was the same (100% versus 100%), leading to a higher F-measure for the titles and abstracts approach (0.1327 versus 0.0619). Conclusion: Screening via a titles-first approach may be more efficient than screening titles and abstracts together.
Automatic SAR and optical images registration method based on improved SIFT

An automatic SAR and optical images registration method based on improved SIFT is proposed in this paper, which is a two-step strategy, from rough to accuracy. The geometry relation of images is first constructed by the geographic information, and images are arranged based on the elevation datum plane to eliminate rotation and resolution differences. Then SIFT features extracted by the dominant direction improved SIFT from two images are matched by SSIM as similar measure according to structure information of the SIFT feature. As rotation difference is eliminated in images of flat area after rough registration, the number of correct matches and correct matching rate can be increased by altering the feature orientation assignment. And then, parallax and angle restrictions are introduced to improve the matching performance by clustering analysis in the angle and parallax domains. Mapping the original matches to the parallax feature space and rotation feature space in sequence, which are established by the custom defined parallax parameters and rotation parameters respectively. Cluster analysis is applied in the parallax feature space and rotation feature space, and the relationship between cluster parameters and matching result is analysed. Owing to the clustering feature, correct matches are retained. Finally, the perspective transform parameters for the registration are obtained by RANSAC algorithm with removing the false matches simultaneously. Experiments show that the algorithm proposed in this paper is effective in the registration of SAR and optical images with large differences.
Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level. Here we developed single-cell full-length transcript sequencing by sampling (FLT-seq), together with the computational pipeline FLAMES to overcome these issues and perform isoform discovery and quantification, splicing analysis and mutation detection in single cells. With FLT-seq and FLAMES, we performed the first comprehensive characterization of the full-length isoform landscape in single cells of different types and species and identified thousands of unannotated isoforms. We found conserved functional modules that were enriched for alternative transcript usage in different cell populations, including ribosome biogenesis and mRNA splicing. Analysis at the transcript-level allowed data integration with scATAC-seq on individual promoters, improved correlation with protein expression data and linked mutations known to confer drug resistance to transcriptome heterogeneity. Our methods reveal previously unseen isoform complexity and provide a better framework for multi-omics data integration.
Upscaling of Fractured Oil Reservoirs Using Homogenization Including Non-equilibrium Capillary Pressure

Recovery in incompletely water-wet fractured reservoirs can be extremely low. In the laboratory, these systems are often mistaken for oil-wet reservoirs, because imbibition only starts after removal of the oil layer, which originally covers the grains. The long time required to remove the oil film will be referred to as delay time. There are two theories that describe the delay time necessary for removal of an oil film, leading to a capillary pressure that depends on time. One of the theories is developed by Barenblatt et al. and it modifies both the capillary pressure and the relative permeabilities. The other theory is developed by Hassanziadeh et al. and it only deals with the non-equilibrium effect for the capillary pressure. No attempt has yet been made to model non-equilibrium effects in fractured reservoirs for a field-scale problem and this is an innovative aspect of this paper. To examine whether the non-equilibrium effect has any effect on larger-scale problems, we apply homogenization to derive an upscaled model for fractured reservoirs in which the non-equilibrium effects are included. We formulate a fully implicit three-dimensional upscaled numerical model. Furthermore, we develop a computationally efficient numerical approach to solve the upscaled model. We use the simulation to determine the range of delay times for which discernable effects occur in terms of oil recovery. It is shown that at low Peclet numbers, i.e., when the residence time of the fluids in the fracture is long with respect to the imbibition time, incorporation of delay times of the order of few months have no significant effect on the oil recovery. However, when the Peclet number is large, the delay times reduce the rate of oil recovery. We will discuss for which values of the delay time (Barenblatt) and capillary-damping coefficient (Hassanizadeh), equivalent results are obtained. This is the first time that such a comparison is made for a field scale project and it shows that both approached show the importance of taking to account delay effects in the capillary pressure behavior.
Revised nucleotide sequence of the gltP gene, which encodes the proton-glutamate-aspartate transport protein of Escherichia coli K-12

The gene encoding the proton-glutamate carrier (GltP) of Escherichia coli K-12 was sequenced, and the primary structure of the protein was analyzed. The nucleotide sequence was found to differ in several aspects from the previously published sequence (B. Wallace, Y. Yang, J. Hong, and D. Lum, J. Bacteriol. 172:3214-3220, 1990). The corrected open reading frame encodes a protein of 437 (instead of 395) amino acids. Hydropathy analysis predicts 12 membrane-spanning alpha-helical regions. The complementary strand does contain an open reading frame possibly encoding a highly hydrophilic polypeptide of 272 amino acids.
A quantum chemistry background of sickle cell anemia and gaps in antisickling drug development

Sickle cell anemia disease has been a great challenge for the world in the present situation. It occurs only due to the polymerization of sickle hemoglobin (HbS) having Pro-Val-Glu (PVG) typed mutation, while the polymerization does not occur in normal hemoglobin (HbA) having Pro-Glu-Glu (PGG) residues. According to data from the literature, Val-beta6 of Pro-Val-Glu is hydrophobic in nature, which appears to fit into a hydrophobic pocket in the adjacent HbS. After the insertion of Pro-Val-Glu into a hydrophobic pocket on the adjacent HbS, the polymerization is started. This is a questionable point on how the replacement of glutamic acid with valine in HbS makes it more reactive to fit into a hydrophobic pocket on adjacent HbS for polymerization. No data from the literature on the reactivity of HbS for polymerization was found yet. This is the first time that the theoretical calculation was done in both HbA and HbS where they were structurally different. After that, a comparative study between PVG and PGG was done at quantum level for the evaluation of the reactivity to fit into a hydrophobic pocket on adjacent HbS. At a quantum level, it was found that the HOMO-LUMO gap of Pro-Val-Glu was lower than that of Pro-Glu-Glu. According to the data from the literature, the lesser HOMO-LUMO gap promotes the initiation of the polymerization reaction. On the basis of the results, it was also shown how the mutation point (Pro-Val-Glu) in HbS becomes more reactive to polymerization, whereas Pro-Glu-Glu in HbA does not. The computational method developed for the first time will be very helpful not only for molecular biologists but also for computational and medicinal chemists. Additionally, the required modifications based on gaps in anti-sickling drug development are also suggested in the presented article.
Edinburgh Research Explorer Genome-Wide Association Studies, Field Synopses, and the Development of the Knowledge Base on Genetic Variation and Human Diseases

Genome-wide association studies (GWAS) have led to a rapid increase in available data on common genetic variants and phenotypes and numerous discoveries of new loci associated with susceptibility to common complex diseases. IntegratingtheevidencefromGWASandcandidategenestudiesdependsonconcertedeffortsindataproduction,online publication,databasedevelopment
Variations on principal components and subspace projection for remote hyperspectral classification

This paper discusses recently developed algorithms for the classification of pixels in hyperspectral images, used in conjunction with a library of hyperspectral hemispherical reflectance data measured in the laboratory and partitioned into usable classes of materials. The algorithms are based upon functions of the principal components of the class covariances and the corresponding null spaces, and the underlying measures used in the classification statistics are similar to Mahalanobis distances. The algorithms can be used as stand-alone processing or combined with spatial and temporal algorithms n a higher level system of hyperspectral image processing. The nature of the classification algorithms and the database will be discussed, with particular attention being paid to issues specific to this approach. The basic performance of the classifier algorithms will be demonstrated using modified laboratory data. The applicability of orthogonal subspace projection methods to problems inherent in remote sensing using hyperspectral invisible and IR data will be emphasized, while specifically dealing with the compensation for inaccuracies in necessary estimates of atmospheric attenuation and target temperature. Preliminary results of classification of field collected hyperspectral data will also be presented, and ongoing and future work in hyperspectral classification described.
Expected spatial distribution of low-energy protons precipitated in the auroral zones

A Monte Carlo method was used to compute the latitudinal dispersion in the auroral zone of 5- to 20-kev protons injected on a magnetic field line with equatorial pitch angles less than 3°. Neutral hydrogen atoms resulting from charge exchange at altitudes of 300–500 km were found to travel large distances across field lines. An isotropic injection pitch angle distribution results in precipitation of protons and hydrogen atoms in the atmosphere over an area as wide as 600 km. The associated auroral Balmer α emission is also expected to originate in a region several hundred kilometers wide. The mechanism described here seems adequate to account for the diffuseness of observed auroral hydrogen emission.
Modelling human movement in cholera spreading along fluvial systems

We propose an important extension of a previously studied, spatially explicit and hydrology‐driven, model of cholera spreading. Our reformulation concerns the role of different modelizations of human movement on the overall dynamics of the epidemics, which were previously expressed synthetically by bacterial diffusion. The system is composed of three compartments: susceptible and infected components, Vibrio cholerae dispersion and reaction dynamics. The underlying spatial framework is based on a reaction‐diffusion scheme, which is applied, for simplicity, to ecological corridors modelled as one‐dimensional lattices mimicking river reaches. In this geometry, we are able to predict important features of disease propagation, like the analytical evaluation of the spreading celerity of travelling fronts of epidemics. The explicit mechanism of human movement presented here leads to a comparison with previous approaches, revealing notable differences in how cholera spreads in space and time along the system. Studying human movement allows the analysis of specific quantities useful to policy makers and epidemiologists, such as the value of human diffusion which can generate upstream propagation of the disease. A robust relationship among key parameters, which links together diffusion mechanism, drift speed and resulting epidemic intensity, is also shown. Copyright © 2010 John Wiley & Sons, Ltd.
The Mediterranean Diet and Incidence of Hypertension The Seguimiento Universidad de Navarra ( SUN ) Study

The Mediterranean diet is receiving increasing attention in cardiovascular epidemiology. The association of adherence to the Mediterranean diet with the incidence of hypertension was evaluated among 9,408 men and women enrolled in a dynamic Spanish prospective cohort study during 1999–2005. Dietary intake was assessed at baseline with a validated semiquantitative food frequency questionnaire, and a 9-point Mediterranean diet score was constructed. During a median follow-up period of 4.2 years (range, 1.9–7.9), 501 incident cases of hypertension were identified. After adjustment for major hypertension risk factors and nutritional covariates, adherence to the Mediterranean diet was not associated with hypertension (the hazard ratio was 1.10 (95% confidence interval (CI): 0.81, 1.41) for moderate adherence and 1.12 (95% CI: 0.79, 1.60) for high adherence). However, it was associated with reduced changes in mean levels of systolic blood pressure (moderate adherence, 2.4 mm Hg (95% CI: 4.0, 0.8); high adherence, 3.1 mm Hg (95% CI: 5.4, 0.8)) and diastolic blood pressure (moderate adherence, 1.3 mmHg (95%CI: 2.5, 0.1); high adherence, 1.9 mmHg (95%CI: 3.6, 0.1)) after 6 years of follow-up. These results suggest that adhering to a Mediterranean-type diet could contribute to the prevention of age-related changes in blood pressure.
Influence of vegetation on streambank hydraulics

approved: . Desireé Tullos Proper use of vegetation in streambank bioengineering practices requires a comprehensive understanding of the influence of vegetation density on streambank hydraulics. A series of studies were conducted to investigate the relationship between independent variables vegetation density, bank angle, and discharge and dependent variables channel velocity, resistance, turbulence, and shear stress. Flume experiments were conducted varying vegetation stem density (number of plants/horizontal area) and frontal area (number of leaves/vertical area) on 30° and 15° vegetated bank-toes at three discharge rates. Three sets of 3D velocity measures were collected using an ADV at: 1) 0.6 x depth, 2) near-boundary, and 3) velocity profiles. Resistance parameters for drag coefficient (Cd) and Manning’s n were estimated. Turbulent stress measures based on turbulent kinetic energy and Reynolds stress were used to evaluate boundary shear stress. Tensor fields were visualized to explore vorticity and near-boundary hydraulics. Results demonstrated that as vegetation density increased, water was increasingly redirected from the bank-toe to the main channel, decreasing downstream velocity along the bank-toe by 35-95% and increasing downstream velocity in the main channel by 80-240%. As vegetation density increased and water velocity decreased along the bank-toe, depths increased, surface slope flattened, and an eddy formed downstream of the vegetated patch. Cd increased with increasing vegetation density, and decreasing stem Reynolds number. Estimates of Cd and n were high relative to commonly published values, especially when vegetation density was high. Increasing vegetation density also increased turbulence and shear stress, creating greater opportunity for erosion at sensitive locations along the bottom of the bank-toe and in the main channel. Reynolds stresses also increased under the canopy, resulting in higher shearing forces along the bank-toe, especially on the 30° bank-toe. Differences in results between bank-toe angles were minimal, dominated by the influence of vegetation. Magnitude of results decreased with decreasing discharge, but patterns were similar. Findings suggest planting at higher densities may protect the bank from erosion, but may increase the potential for erosion along the interface between the bank and main channel if unprotected, though further research with natural plant communities is encouraged to confirm findings. © Copyright by Nicole M. Czarnomski June 3, 2010 All Rights Reserved INFLUENCE OF VEGETATION ON STREAMBANK HYDRAULICS
Automatic keyphrase extraction from scientific articles

This paper describes the organization and results of the automatic keyphrase extraction task held at the Workshop on Semantic Evaluation 2010 (SemEval-2010). The keyphrase extraction task was specifically geared towards scientific articles. Systems were automatically evaluated by matching their extracted keyphrases against those assigned by the authors as well as the readers to the same documents. We outline the task, present the overall ranking of the submitted systems, and discuss the improvements to the state-of-the-art in keyphrase extraction.
A novel soil moisture‐based drought severity index (DSI) combining water deficit magnitude and frequency

A correct identification of drought events over vegetated lands can be achieved by detecting those soil moisture conditions that are both unusually dry compared with the ‘normal’ state and causing severe water stress to the vegetation. In this paper, we propose a novel drought index that accounts for the mutual occurrence of these two conditions by means of a multiplicative approach of a water deficit factor and a dryness probability factor. The former quantifies the actual level of plant water stress, whereas the latter verifies that the current water deficit condition is unusual for the specific site and period. The methodology was tested over Europe between 1995 and 2012 using soil moisture maps simulated by Lisflood, a distributed hydrological precipitation–runoff model. The proposed drought severity index (DSI) demonstrates to be able to detect the main drought events observed over Europe in the last two decades, as well as to provide a reasonable estimation of both extension and magnitude of these events. It also displays an improved adaptability to the range of possible conditions encountered in the experiment as compared with currently available indices based on the sole magnitude or frequency. The results show that, for the analyzed period, the most extended drought events observed over Europe were the ones in Central Europe in 2003 and in southern Europe in 2011/2012, while the events affecting the Iberian Peninsula in 1995 and 2005 and Eastern Europe in 2000 were among the most severe ones. © 2015 European Commission ‐ Joint Research Centre. Hydrological Processes published by John Wiley & Sons Ltd.
Effects of tidal forcing, conductivity gradient, and active seeding on the climatology of equatorial spread F over Kwajalein

Plasma structure in nighttime equatorial F layer, referred to as equatorial spread F (ESF), displays climatology whose seasonal variation depends on longitude. At longitudes where ESF favors equinoxes, times when maxima occur can be predicted in terms of the day of year, when E region sunset is simultaneous in conjugate hemispheres (i.e., “sunset nodes”). Aside from occurrences around equinoxes, there are only three longitudes where ESF also occurs during a solstice; one is the central Pacific region. Here ESF activity is strong during the June solstice, when solar activity is high. To understand this puzzling behavior, ESF climatology over the Kwajalein Atoll was compared with properties of the postsunset rise (PSSR) of the F layer and seeding activity in the troposphere. The key findings are as follows: (1) Maxima in PSSR velocity (VPSSR) are better aligned with equinoxes than with sunset nodes; hence, seasonal pattern of VPSSR, not only sunset nodes, should be included in interpretation of ESF climatology. (2) The source of VPSSR during solstice appears to differ from that during equinoxes. (3) Equinoctial maxima in VPSSR could be related to a semiannual variation in equatorial electrojet strength and its contribution to polarization of the F region dynamo current. (4) Enhanced VPSSR during the June solstice is interpreted in terms of tidal forcing with a wave number of 2. (5) Displacements of maxima in ESF climatology from maxima in VPSSR are shown to be consistent with deep convective activity.
Mathematical Modeling of Rhesus Cytomegalovirus Transplacental Transmission in Seronegative Rhesus Macaques

Approximately 0.7% of infants are born with congenital cytomegalovirus (CMV), making it the most common congenital infection. About 1 in 5 congenitally infected babies will suffer long-term sequelae, including sensorineural deafness, intellectual disability, and epilepsy. CMV infection is highly species-dependent, and the rhesus CMV (RhCMV) infection of rhesus monkey fetuses is the only animal model that replicates essential features of congenital CMV (cCMV) infection in humans, including placental transmission, fetal disease, and fetal loss. Using experimental data from RhCMV seronegative rhesus macaques inoculated with RhCMV in the late first to early second trimesters of pregnancy, we built and calibrated a mathematical model for the placental transmission of CMV. The model was then used to study the effect of the timing of inoculation, maternal immune suppression, and hyper-immune globulin infusion on the risk of placental transmission in the context of primary and reactivated chronic maternal CMV infection.
Probabilistic modelling of water balance at a point: the role of climate, soil and vegetation

The soil moisture dynamics under seasonally fixed conditions are studied at a point. The water balance is described through the representation of rainfall as a marked Poisson process which in turn produces an infiltration into the soil dependent on the existing level of soil moisture. The losses from the soil are due to evapotranspiration and leakage which are also considered dependent on the existing soil moisture. The steady–state probability distributions for soil moisture are then analytically obtained. The analysis of the distribution allows for the assessment of the role of climate, soil and vegetation on soil moisture dynamics. Further hydrologic insight is obtained by studying the various components of an average water balance. The realistic representation of the processes acting at a site and the analytical tractability of the model make it well suited for further analyses which consider the spatial aspect of soil moisture dynamics.