Miracle-dz/UniFAR-FTUs huggingface dataset:
Control intervention design for preclinical and clinical trials: Consensus-based core recommendations from the third Stroke Recovery and Rehabilitation Roundtable

Control comparator selection is a critical trial design issue. Preclinical and clinical investigators who are doing trials of stroke recovery and rehabilitation interventions must carefully consider the appropriateness and relevance of their chosen control comparator as the benefit of an experimental intervention is established relative to a comparator. Establishing a strong rationale for a selected comparator improves the integrity of the trial and validity of its findings. This Stroke Recovery and Rehabilitation Roundtable (SRRR) taskforce used a graph theory voting system to rank the importance and ease of addressing challenges during control comparator design. “Identifying appropriate type of control” was ranked easy to address and very important, “variability in usual care” was ranked hard to address and of low importance, and “understanding the content of the control and how it differs from the experimental intervention” was ranked very important but not easy to address. The CONtrol DeSIGN (CONSIGN) decision support tool was developed to address the identified challenges and enhance comparator selection, description, and reporting. CONSIGN is a web-based tool inclusive of seven steps that guide the user through control comparator design. The tool was refined through multiple rounds of pilot testing that included more than 130 people working in neurorehabilitation research. Four hypothetical exemplar trials, which span preclinical, mood, aphasia, and motor recovery, demonstrate how the tool can be applied in practice. Six consensus recommendations are defined that span research domains, professional disciplines, and international borders.
The cloud analysis tool APOLLO: Improvements and validations

During its more than 12 years of existence, the AVHRR Processing scheme Over cLouds, Land and Ocean (APOLLO) has been modified and extended. The intention of this paper is to document the present state of APOLLO and to summarize the experiences gained. The scope of the processing scheme is reviewed and the actual state of the daytime and night-time algorithms are presented. The reason for the modifications are discussed. Validations of the modifications are made by comparisons with surface observations. They show agreement to - % of the cloud coverage in 70% of the , 90 000 single comparisons. A consistency check with the International Satellite Cloud Climatology Project (ISCCP) shows the influence of coarse sampling on the ISCCP DX data reliability. APOLLO is now a robust and versatile cloud analysis tool. It is presently used to establish a cloud climatology in Central Europe, based on processing of 15 years of daily Advanced Very High Resolution Radiometer (AVHRR) data.
Hindcasts of equatorial sea surface dynamic height in the Atlantic in 1982–1984

Two different wind data sets of the years 1982–1984 are used to force a linear multimode model of the tropical Atlantic ocean. We describe the variations of the equtorial slope in both cases and investigate the differences between the two runs. The main discrepancy occurs in 1983 for the amplitude of the seasonal signal all along the equator. Model results are also compared with observations (hydrocasts and inverted echo sounders) taken during the Programme Francais Ocean et Climat dans l'Atlantique Equatorial/Seasonal Response of the Equatorial Atlantic (FOCAL/SEQUAL) field experiment (July 1982 through October 1984). The contrast between 1983 and 1984 is well captured by the two runs, especially the abnormal flat topography of the sea surface along the equator in the first 3 months of 1984 due to an unusual basin wide relaxation of the equatorial wind stress. The major discrepancy between model results and observations is found during the up welling periods east of 10°W, but at that time dynamic height measurements are too sparse to give a good description of these events.
DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

Abstract Eukaryotic genome and methylome encode DNA fragments’ propensity to form nucleosome particles. Although the mechanical properties of DNA possibly orchestrate such encoding, the definite link between ‘omics’ and DNA energetics has remained elusive. Here, we bridge the divide by examining the sequence-dependent energetics of highly bent DNA. Molecular dynamics simulations of 42 intact DNA minicircles reveal that each DNA minicircle undergoes inside-out conformational transitions with the most likely configuration uniquely prescribed by the nucleotide sequence and methylation of DNA. The minicircles’ local geometry consists of straight segments connected by sharp bends compressing the DNA’s inward-facing major groove. Such an uneven distribution of the bending stress favors minimum free energy configurations that avoid stiff base pair sequences at inward-facing major grooves. Analysis of the minicircles’ inside-out free energy landscapes yields a discrete worm-like chain model of bent DNA energetics that accurately account for its nucleotide sequence and methylation. Experimentally measuring the dependence of the DNA looping time on the DNA sequence validates the model. When applied to a nucleosome-like DNA configuration, the model quantitatively reproduces yeast and human genomes’ nucleosome occupancy. Further analyses of the genome-wide chromatin structure data suggest that DNA bending energetics is a fundamental determinant of genome architecture.
Reaction textures and metamorphic evolution of sapphirine–spinel-bearing and associated granulites from Diguva Sonaba, Eastern Ghats Mobile Belt, India

Abstract The Diguva Sonaba area (Vishakhapatnam district, Andhra Pradesh, South India) represents part of the granulite-facies terrain of the Eastern Ghats Mobile Belt. The Precambrian metamorphic rocks of the area predominantly consist of mafic granulite (±garnet), khondalite, leptynite (±garnet, biotite), charnockite, enderbite, calc-granulite, migmatic gneisses and sapphirine–spinel-bearing granulite. The latter rock type occurs as lenticular bodies in khondalite, leptynite and calc-granulite. Textural relations, such as corroded inclusions of biotite within garnet and orthopyroxene, resorbed hornblende within pyroxenes, and coarse-grained laths of sillimanite, presumably pseudomorphs after kyanite, provide evidence of either an earlier episode of upper-amphibolite-facies metamorphism or they represent relics of the prograde path that led to granulite-facies metamorphism. In the sapphirine–spinel-bearing granulite, osumilite was stable in addition to sapphirine, spinel and quartz during the thermal peak of granulite-facies metamorphism but the assemblage was later replaced by Crd–Opx–Qtz–Kfs-symplectite and a variety of reaction coronas during retrograde overprint. Variable amounts of biotite or biotite+quartz symplectite replaced orthopyroxene, cordierite and Opx–Crd–Kfs–Qtz-symplectite at an even later retrograde stage. Peak metamorphic conditions of c. 1000°C and c. 12 kbar were computed by isopleths of XMg in garnet and XAl in orthopyroxene. The sequence of reactions as deduced from the corona and symplectite assemblages, together with petrogenetic grid and pseudosection modelling, records a clockwise P–T evolution. The P–T path is characteristically T-convex suggesting an isothermal decompression path and reflects rapid uplift followed by cooling of a tectonically thickened crust.
Discovery of a layer of probable impact melt spherules in the Late Archaean Jeerinah Formation, Fortescue Group, Western Australia

Individual layers rich in sand‐sized spherules interpreted as distal ejecta from Late Archaean to Early Palaeoproterozoic impacts have already been reported from three stratigraphic units in the Hamersley Group of Western Australia: the Wittenoom Formation, the Carawine Dolomite, and the Dales Gorge Member of the Brockman Iron Formation. Here we report the occurrence of a similar layer near the top of the Jeerinah Formation, the uppermost unit in the underlying Fortescue Group. This layer, which we informally name the Jeerinah Impact Layer, was deposited ca 2.63 Ga below wave‐base in a marine deep shelf to upper slope environment. As in all other spherule layers, the spherules in the Jeerinah Impact Layer are sand‐sized (up to 0.83 mm across), dominantly spheroidal, and show a mix of crystallisation and devitrification textures internally, indicating they are droplets of former low‐silica silicate melt. The morphologies of some of the crystallites indicate they were originally plagioclase, yet they now consist of K‐feldspar; this, too, is common in all of the other spherule layers. Despite the fact that it is ≤⃒6 mm thick, the Jeerinah Impact Layer pinches and swells laterally and consists of several different subunits internally. This indicates that more than the passive settling of particles in still water was involved in the formation of the Jeerinah Impact Layer, which probably involved traction of coarse sand‐sized grains. Despite its thinness, the Jeerinah Impact Layer still represents a thicker accumulation of spherules than all but the most proximal parts of spherule layers formed by some of the largest Phanerozoic impacts, suggesting the Jeerinah Impact Layer represents a major impact. If the Jeerinah Impact Layer and the other spherule layers in the Hamersley Basin did form by impacts, this also means that ejecta from a minimum of three distinct impacts are preserved with age dates suggesting a recurrence interval similar to the inferred rate of impacts in the Phanerozoic. The discovery of the Jeerinah Impact Layer also reconfirms that basinal successions such as black shale are among the most favourable environments for the preservation of distal layers of impact ejecta. It also raises intriguing questions about stratigraphic correlations in the Hamersley Basin of Western Australia and to another spherule layer discovered recently in the Transvaal Supergroup of South Africa.
Effectiveness of Granular Polyacrylamide to Reduce Soil Erosion During Consecutive Rainstorms in a Calcic Regosol Exposed to Different Fire Conditions

Fire severity varies widely among and within wildfires. The objective of this work was to test the effectiveness of granular polyacrylamide (PAM) to reduce erosion in a Calcic Regosol exposed to different fire conditions. Three treatments were selected representing disturbances that coexist after a wildfire: unburned, low‐moderate severity direct fire, and prolonged heating under moderate temperature [heated (HT)]. Granular PAM was spread on the surface of disturbed samples at two rates: (i) 0 (control) and (ii) 50 kg ha−1. Additional application rates of 25 and 100 kg ha−1 were tested in HT. Three 80‐mm rainstorms were applied with an intensity of 47 mm h−1, separated by drying periods. PAM reduced soil loss in all storms in unburned and direct fire, although runoff increased during the first storm due to increased runoff viscosity. In the highly stable HT, soil loss was reduced only with an application rate of 100 kg ha−1 and after a drying period. In many cases, granular PAM could be effective to reduce post‐fire erosion. In soils with high structural stability, a PAM dose should be selected to find a right balance between its stabilising effect on soil structure and its effect increasing runoff during the first storm. Copyright © 2015 John Wiley & Sons, Ltd.
Measurement of treatment compliance using a medical device for glaucoma patients associated with intraocular pressure control: a survey

Objective: To identify and characterize treatment compliance profiles of glaucoma patients and evaluate the association with intraocular pressure (IOP). Methods: A computerized device (Travalert ® ) that recorded daily instillation times and eye-drop counts was given for 3 months. Patients were declared compliant when at least 2 drops were instilled per day. Compliance rates were calculated for weekdays and weekends, separately, over 8 consecutive weeks. A principal components analysis (PCA) was followed by an ascendant hierarchical classification (AHC) to identify compliance groups. Results: 140 patients were recruited (mean age 65.5 years; 51.8% female) of whom 83.6% had primary open-angle glaucoma with mean IOP 23.9 mmHg before Travalert ® use. 60.7% were treated with DuoTrav ® (travoprost timolol fixed combination) and 39.3% with travoprost. The PCA identified two axes (compliance and treatment weeks). The AHC identified 3 compliance groups: ‘high’ (56.6%, approx. 80% compliance), ‘medium’ (21.2%, approx. 50% compliance), and ‘low’ (22.1%, approx. 20% compliance). Demographics and glaucoma parameters did not predict low compliance. Final mean IOP was 16.1 mmHg, but higher in the low compliance group (17.7 mmHg, P = 0.02). Conclusions: Compliance measurement by a medical device showed compliance rates , 80% by 50% (approx.) of patients, significantly impacting IOP control. No demographic or glaucoma variable was associated with low compliance.
Nonlinear Waves and Coherent Vortex Structures in Barotropic β-plane Jets

Abstract We examine the nonlinear evolution of barotropic β-plane jets on a periodic domain with a pseudospectral. A calculation of the linear growth rate yields an infected U-shaped curve on the β versus k0 plane which separates regions of stability and instability. This curve aids in clarifying the morphology of the nonlinear structures which evolve from monochromatic small-amplitude perturbations of wavenumber k0. At very small or zero β, we recover and further quantify previously obtained results, including formation of: dipolar vortex structures or bound pools of opposite-signed vortex regions at small k0; staggered streets isolated vortex pools at intermediate k0; and “cat-eyes” or staggered connected pools of vorticity at large but still unstable k0. As β is increased, the jet exhibits quite different evolutionary patterns. At low k0, where the laminar jet may be stable, we find a multistage instability. First, neutrally stable long-wavelength modes of small amplitude interact nonlinearly to produc.
Evidence Implicating Blood-Brain Barrier Impairment in the Pathogenesis of Acquired Epilepsy following Acute Organophosphate Intoxication

Organophosphate (OP) poisoning can trigger cholinergic crisis, a life-threatening toxidrome that includes seizures and status epilepticus. These acute toxic responses are associated with persistent neuroinflammation and spontaneous recurrent seizures (SRS), also known as acquired epilepsy. Blood-brain barrier (BBB) impairment has recently been proposed as a pathogenic mechanism linking acute OP intoxication to chronic adverse neurologic outcomes. In this review, we briefly describe the cellular and molecular components of the BBB, review evidence of altered BBB integrity following acute OP intoxication, and discuss potential mechanisms by which acute OP intoxication may promote BBB dysfunction. We highlight the complex interplay between neuroinflammation and BBB dysfunction that suggests a positive feedforward interaction. Lastly, we examine research from diverse models and disease states that suggest mechanisms by which loss of BBB integrity may contribute to epileptogenic processes. Collectively, the literature identifies BBB impairment as a convergent mechanism of neurologic disease and justifies further mechanistic research into how acute OP intoxication causes BBB impairment and its role in the pathogenesis of SRS and potentially other long-term neurologic sequelae. Such research is critical for evaluating BBB stabilization as a neuroprotective strategy for mitigating OP-induced epilepsy and possibly seizure disorders of other etiologies. SIGNIFICANCE STATEMENT Clinical and preclinical studies support a link between blood-brain barrier (BBB) dysfunction and epileptogenesis; however, a causal relationship has been difficult to prove. Mechanistic studies to delineate relationships between BBB dysfunction and epilepsy may provide novel insights into BBB stabilization as a neuroprotective strategy for mitigating epilepsy resulting from acute organophosphate (OP) intoxication and non-OP causes and potentially other adverse neurological conditions associated with acute OP intoxication, such as cognitive impairment.
La calidad percibida en el sector de la mensajería; diferencias entre correos y otros operadores

This research has focused on the customer evaluation of perceived quality in the urgent transport service in Spain. Using different statistical procedures, such as ordinal regression, between-groups comparison or multilevel modeling, this study shows how the perceived service quality of the public company “Correos” is lower than several of the main competitors: Seur, Halcourier and Nacex. Despite the investment achieved by this public institution in order to improve service quality, these efforts haven not been reflected in the customer evaluation, at least to the same extent as competitors. Several recommendations for further research are discussed in the final part of the study.
Lateral extension in Sphagnum mires along the southern margin of the boreal region, Western Siberia

Although recent studies have recognized Northern Eurasian ecosystems as an important carbon reservoir, little is known about the forest–peatland interactions in a boreal environment induced by ongoing climatic changes. This study focuses on the evaluation of both the long-term and contemporary trends of land-cover changes and rates of lateral extension of peat-accumulating wetlands toward the adjacent forests, estimated at the southern climatic range of the Sphagnum-dominated mires in Western Siberia. We used the radiocarbon dates and stratigraphy of peat sediments from seven peat cores, analyzed at two types of forest–peatland ecotones, which are located close to each other but differ by topography and composition of their plant communities. The rate of lateral extension was found in a wide range varying from 2.3 to 791.7 cm yr−1. It was observed to be rapid during the initial stage of mire development, but to have slowed down over the last 2000–3000 yr. Our results, therefore, strongly contradict the concept of progressive peat accumulation throughout the late Holocene and contribute to our knowledge about ongoing land-cover change in the natural ecosystems of the Northern hemisphere.
Material update procedure for planar transient flow of ice with evolving anisotropy

Abstract A flow law for polar ice is derived, which takes into account the effect of deformation-induced anisotropy due to hexagonal single-crystal symmetry. Attention is focused on the main effect of crystal-lattice rotation. Existence of a continuous so-called orientation-distribution function ODF, for the crystals is assumed. With its help the microscale constitutive behaviour is transformed to the large-scale. This transformation is simplified by imposing different consistency conditions (CC) due to Voigt-Taylor (VT) and Sachs-Reuss(SR), respectively. Here we take the grain interaction into account by linearly combining the VTand the SR conditions, i.e. by one additional parameter determining the relative weight of the two. A coupled finite-element-finite-volume approach is used to account for fabric evolution at the ice-sheet scale. For different CC, VT and SR, an orientation update is derived for planar flow, which results in only three additional degrees of freedom at each finite-element integration point to account for orthotropic material symmetry. Computations for the GRIP-core data demonstrate that a better fit can be obtained than with VT or SR alone.
Bespoke data augmentation and network construction enable developmental morphological classification on limited microscopy datasets

Deep learning is a powerful tool for image classification, yet training deep learning models often requires large datasets, which are not always available in biological research. Here we use a small dataset to train an accurate classifier by employing data augmentation regimes and Bayesian optimisation. We establish a new staging system for the Hamburger-Hamilton stage 10 chick embryo brain, based on morphology, identifying three sub-stages uncoupled from somite number, the usual metric used to stage chick embryos. Incorporating biologically informed, data-driven preprocessing, we train a deep convolutional neural network to classify our sub-stages. We find that augmenting our images with a combination of rotation, blur, shear, and cutout transformations is effective in training an accurate classifier on a small microscopy dataset. We then apply our approach to an unrelated small microscopy dataset comprising images of limb buds, finding good agreement with the results from brain classification. Through saliency analysis, we ensure that relevant features are being used by our classifier, gain insight into the efficacy of different data augmentations, and identify sub-stage specific features. In summary, we apply biological domain expertise to design effective data augmentation regimes for training a neural network-based image classifier on small, specialised datasets, classifying the developing brains and limbs with up to 90.9% and 94.4% accuracy respectively. These reliable classifiers can inform future experiments.
Accurate staging of chick embryonic tissues via deep learning of salient features

ABSTRACT Recent work shows that the developmental potential of progenitor cells in the HH10 chick brain changes rapidly, accompanied by subtle changes in morphology. This demands increased temporal resolution for studies of the brain at this stage, necessitating precise and unbiased staging. Here, we investigated whether we could train a deep convolutional neural network to sub-stage HH10 chick brains using a small dataset of 151 expertly labelled images. By augmenting our images with biologically informed transformations and data-driven preprocessing steps, we successfully trained a classifier to sub-stage HH10 brains to 87.1% test accuracy. To determine whether our classifier could be generally applied, we re-trained it using images (269) of randomised control and experimental chick wings, and obtained similarly high test accuracy (86.1%). Saliency analyses revealed that biologically relevant features are used for classification. Our strategy enables training of image classifiers for various applications in developmental biology with limited microscopy data.
Depth-focusing analysis using a wavefront-curvature criterion

Depth‐focusing analysis (DFA), a method of refining velocities for prestack depth migration, relies on amplitude buildups at zero offset to determine the extrapolation depths that best focus the migrated data. Unfortunately, seismic energy from dipping interfaces, diffractions, and noise often produce spurious amplitude indications of focusing. To reduce possible ambiguity in the DFA interpretation process, we introduce a new attribute for determining focusing that is relatively independent of amplitude. Our approach is based on estimates of the radius of wavefront curvature. The estimates are derived from normal moveout analysis of nonzero‐offset data saved during migration. By relating steeper moveout to smaller radius of wavefront curvature, focusing is defined by a wavefront curvature of zero radius. Additionally, we show that applying inverse‐radius weights to the amplitude data attenuates nonfocused events due to their large radius of curvature. Using the Marmousi data set, our weighting scheme resu.
The 17 August 1999 Izmit Earthquake

On 17 August 1999, an earthquake of magnitude 7.4 shook northwestern Turkey. Details on the earthquake9s characteristics and effects across northwestern Turkey are provided and are put in the historical context of previous earthquakes in the region. The earthquake was the seventh in a series of earthquakes migrating westwards along the North Anatolian fault since 1939. Information on historical earthquakes, modeling and estimates of the slip rate along the fault indicate that the location and severity of the earthquake should not have come as a surprise.