Miracle-dz/UniFAR-FTUs huggingface dataset:
QIN DAWG Validation of Gradient Nonlinearity Bias Correction Workflow for Quantitative Diffusion-Weighted Imaging in Multicenter Trials

Previous research has shown that system-dependent gradient nonlinearity (GNL) introduces a significant spatial bias (nonuniformity) in apparent diffusion coefficient (ADC) maps. Here, the feasibility of centralized retrospective system-specific correction of GNL bias for quantitative diffusion-weighted imaging (DWI) in multi-site clinical trials is demonstrated across diverse scanners independent of the scanned object. Using corrector maps generated from system characterization by ice-water phantom measurement completed in the previous project phase, GNL bias correction was performed for test ADC measurements from an independent DWI phantom (room temperature agar) at two offset locations in the bore. The precomputed three-dimensional GNL correctors were retrospectively applied to test DWI scans by the central analysis site. The correction was blinded to reference DWI of the agar phantom at magnet isocenter where the GNL bias is negligible. The performance was evaluated from changes in ADC region of interest histogram statistics before and after correction with respect to the unbiased reference ADC values provided by sites. Both absolute error and nonuniformity of the ADC map induced by GNL (median, 12%; range, −35% to +10%) were substantially reduced by correction (7-fold in median and 3-fold in range). The residual ADC nonuniformity errors were attributed to measurement noise and other non-GNL sources. Correction of systematic GNL bias resulted in a 2-fold decrease in technical variability across scanners (down to site temperature range). The described validation of GNL bias correction marks progress toward implementation of this technology in multicenter trials that utilize quantitative DWI.
Limpet haemocytes. I. Studies on aggregation and spike formation.

In this paper a promising new spontaneously aggregating system of amoebocytes from the blood of limpets is described. The system has the advantage of being readily available without cell culture and of being operational at room temperature. The blood of the limpet Patella contains 2 types of haemocytes, amoebocytes and macro-phages, the latter accounting for less than 1 % of the cell population. The concentration of cells in suspension varies with the body temperature of the animal, from about 1 x 10 6 cells/ml at 5 °C to 9 x 10 6 cells/ml at 25 °C. Following blood withdrawal the amoebocytes are approximately spherical in shape with superficial convoluted lamellae, but over a period of 5 min develop stout marginal spikes. This development is temperature dependent and independent of divalent cations in the medium. Most interestingly, and apparently associated with the stimulus of blood withdrawal, the cells become spontaneously adhesive and commence an extremely rapid aggregation. With a shaking speed of 700 strokes/min the half time of aggregation varies from 15 s at an initial cell density of 4.7 x 10 6 cells/ml to 60 s at a density of 1.4 x 10 6 cells/ml. The aggregates so formed are very resistant to mechanical dispersion and tight junctions have been observed between aggregated cells in electron micrographs. Complete aggregation requires the presence of divalent cations and another unidentified plasma component. Aggregation will occur at 0 °C but the process is slower and less complete than at 20 °C. It is suggested that aggregation involves the triggering or activation of a pre-synthesized adhesive system and that the adhesiveness per unit area increases with increase in temperature.
A Neural Network Model of Ventriloquism Effect and Aftereffect

Presenting simultaneous but spatially discrepant visual and auditory stimuli induces a perceptual translocation of the sound towards the visual input, the ventriloquism effect. General explanation is that vision tends to dominate over audition because of its higher spatial reliability. The underlying neural mechanisms remain unclear. We address this question via a biologically inspired neural network. The model contains two layers of unimodal visual and auditory neurons, with visual neurons having higher spatial resolution than auditory ones. Neurons within each layer communicate via lateral intra-layer synapses; neurons across layers are connected via inter-layer connections. The network accounts for the ventriloquism effect, ascribing it to a positive feedback between the visual and auditory neurons, triggered by residual auditory activity at the position of the visual stimulus. Main results are: i) the less localized stimulus is strongly biased toward the most localized stimulus and not vice versa; ii) amount of the ventriloquism effect changes with visual-auditory spatial disparity; iii) ventriloquism is a robust behavior of the network with respect to parameter value changes. Moreover, the model implements Hebbian rules for potentiation and depression of lateral synapses, to explain ventriloquism aftereffect (that is, the enduring sound shift after exposure to spatially disparate audio-visual stimuli). By adaptively changing the weights of lateral synapses during cross-modal stimulation, the model produces post-adaptive shifts of auditory localization that agree with in-vivo observations. The model demonstrates that two unimodal layers reciprocally interconnected may explain ventriloquism effect and aftereffect, even without the presence of any convergent multimodal area. The proposed study may provide advancement in understanding neural architecture and mechanisms at the basis of visual-auditory integration in the spatial realm.
Designing A Mixed Methods Study In Primary Care

BACKGROUND Mixed methods or multimethod research holds potential for rigorous, methodologically sound investigations in primary care. The objective of this study was to use criteria from the literature to evaluate 5 mixed methods studies in primary care and to advance 3 models useful for designing such investigations. METHODS We first identified criteria from the social and behavioral sciences to analyze mixed methods studies in primary care research. We then used the criteria to evaluate 5 mixed methods investigations published in primary care research journals. RESULTS Of the 5 studies analyzed, 3 included a rationale for mixing based on the need to develop a quantitative instrument from qualitative data or to converge information to best understand the research topic. Quantitative data collection involved structured interviews, observational checklists, and chart audits that were analyzed using descriptive and inferential statistical procedures. Qualitative data consisted of semistructured interviews and field observations that were analyzed using coding to develop themes and categories. The studies showed diverse forms of priority: equal priority, qualitative priority, and quantitative priority. Data collection involved quantitative and qualitative data gathered both concurrently and sequentially. The integration of the quantitative and qualitative data in these studies occurred between data analysis from one phase and data collection from a subsequent phase, while analyzing the data, and when reporting the results. DISCUSSION We recommend instrument-building, triangulation, and data transformation models for mixed methods designs as useful frameworks to add rigor to investigations in primary care. We also discuss the limitations of our study and the need for future research.
Spotlight the Negatives: A Generalized Discriminative Latent Model

Discriminative latent variable models (LVM) are frequently applied to various visual recognition tasks. In these systems the latent (hidden) variables provide a formalism for modeling structured variation of visual features. Conventionally, latent variables are de- fined on the variation of the foreground (positive) class. In this work we augment LVMs to include negative latent variables corresponding to the background class. We formalize the scoring function of such a generalized LVM (GLVM). Then we discuss a framework for learning a model based on the GLVM scoring function. We theoretically showcase how some of the current visual recognition methods can benefit from this generalization. Finally, we experiment on a generalized form of Deformable Part Models with negative latent variables and show significant improvements on two different detection tasks.
A cryptic taxon of Galápagos tortoise in conservation peril

As once boldly stated, ‘bad taxonomy can kill’, highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.
Mechanical properties of recycled polyethylene ecocomposites filled with natural organic fillers

The use of natural organic fillers in addition to postconsumer recycled polymers is getting a growing interest during the last years; this is due to many advantages they can provide in terms of cost, aesthetic properties, environmental impact. In this work, several types of wood flour (differing each other with regard to production source and particle size) were added to a recycled polyethylene coming from films for greenhouses and the effects of filler type, content, and size were investigated. Investigation was then focused on the improvement of mechanical properties, through the addition of polar copolymers (ethylene-co-acrylic acid, ethylene-vinyl acetate) and a maleic anhydride-grafted-grafted polyethylene (Licocene® PE MA 4351 TP), in order to try to overcome the poor adhesion between polar filler particles and nonpolar polymer chains. Investigation was also based on SEM micrographs. An overall positive influence of these additives was observed. Polym. Eng. Sci. 46:1131–1139, 2006. © 2006 Society of Plastics Engineers.
Mechanical sensitivity and the dynamics of evolutionary rate shifts in biomechanical systems

The influence of biophysical relationships on rates of morphological evolution is a cornerstone of evolutionary theory. Mechanical sensitivity—the correlation strength between mechanical output and the system's underlying morphological components—is thought to impact the evolutionary dynamics of form–function relationships, yet has rarely been examined. Here, we compare the evolutionary rates of the mechanical components of the four-bar linkage system in the raptorial appendage of mantis shrimp (Order Stomatopoda). This system's mechanical output (kinematic transmission (KT)) is highly sensitive to variation in its output link, and less sensitive to its input and coupler links. We found that differential mechanical sensitivity is associated with variation in evolutionary rate: KT and the output link exhibit faster rates of evolution than the input and coupler links to which KT is less sensitive. Furthermore, for KT and, to a lesser extent, the output link, rates of evolution were faster in ‘spearing’ stomatopods than ‘smashers’, indicating that mechanical sensitivity may influence trait-dependent diversification. Our results suggest that mechanical sensitivity can impact morphological evolution and guide the process of phenotypic diversification. The connection between mechanical sensitivity and evolutionary rates provides a window into the interaction between physical rules and the evolutionary dynamics of morphological diversification.
Unsupervised discovery of acoustic patterns in bird vocalisations employing DTW and clustering

This paper presents a method for an unsupervised discovery of acoustic patterns in bird vocalisations recorded in real world natural environments. The proposed method employs sinusoidal detection to provide frequency tracks which are used as features to characterise bird tonal vocalisations. A variant of dynamic time warping, capable of searching for multiple partial matchings, is used to segment the data based on these frequency track sequences. Agglomerative hierarchical clustering approach is then employed to cluster recurring segments. Evaluations are performed on audio recordings provided by the Borror Laboratory of Bioacoustics. The obtained results indicate that structurally distinct stereotyped acoustic units can be determined.
Potential Involvement of Snail Members in Neuronal Survival and Astrocytic Migration during the Gecko Spinal Cord Regeneration

Certain regenerative vertebrates such as fish, amphibians and reptiles are capable of regenerating spinal cord after injury. Most neurons of spinal cord will survive from the injury and regrow axons to repair circuits with an absence of glial scar formation. However, the underlying mechanisms of neuronal anti-apoptosis and glia-related responses have not been fully clarified during the regenerative process. Gecko has becoming an inspiring model to address spinal cord regeneration in amniotes. In the present study, we investigated the regulatory roles of Snail family members, the important transcriptional factors involved in both triggering of the cell migration and cell survival, during the spontaneous spinal cord regeneration. Both Snail1 and Snail3 have been shown to promote neuronal survival and astrocytic migration via anti-apoptotic and GTPases signaling following gecko tail amputation. Transforming growth factor-beta (TGFβ), together with other cytokines were involved in inducing expression of Snail protein. Our data indicate a conserved function of Snail proteins in embryonic development and tissue regeneration, which may provide clues for CNS repair in the mammals.
Outcome Measures in Interventional Trials for Prevention or Treatment of Venous Thrombosis in the Pediatric Population

Determining clinically relevant outcomes are one of the key issues in the design of clinical trials. Recently, a working group from the Perinatal and Pediatric Subcommittee of the Scientific and Standardization Committee of the International Society of Thrombosis and Haemostasis published a position article defining outcomes in interventional trials for prevention and treatment of deep vein thrombosis (DVT) in children. For these studies the primary efficacy outcomes are DVT and the primary safety outcomes are bleeding. The exact definitions for these outcomes are included in this review article. This article expands on these recommendations by summarizing and reviewing the current literature in pediatric anticoagulation studies; discussing the relationship of choice of outcomes to specific clinical trial design; providing a more detailed discussion on the rationale for the defined outcomes in pediatric anticoagulation trials, as well as a detailed examination of secondary and tertiary outcomes. With a growing interest in multicenter, multinational pediatric anticoagulation clinical trials, establishment of standardized outcome measures that are applied uniformly over all studies is critically important. Agreement from the international academic community on these outcomes is an important step in assuring well-designed clinical trials, which are implemented to optimize the prevention and treatment of DVT in children.
Merging Markov and DCT features for multi-class JPEG steganalysis

Blind steganalysis based on classifying feature vectors derived from images is becoming increasingly more powerful. For steganalysis of JPEG images, features derived directly in the embedding domain from DCT coefficients appear to achieve the best performance (e.g., the DCT features10 and Markov features21). The goal of this paper is to construct a new multi-class JPEG steganalyzer with markedly improved performance. We do so first by extending the 23 DCT feature set,10 then applying calibration to the Markov features described in21 and reducing their dimension. The resulting feature sets are merged, producing a 274-dimensional feature vector. The new feature set is then used to construct a Support Vector Machine multi-classifier capable of assigning stego images to six popular steganographic algorithms-F5,22 OutGuess,18 Model Based Steganography without ,19 and with20 deblocking, JP Hide&Seek,1 and Steghide.14 Comparing to our previous work on multi-classification,11, 12 the new feature set provides significantly more reliable results.
Re-Evaluation of PD-1 Expression by T Cells as a Marker for Immune Exhaustion during SIV Infection

PD-1 expression is generally associated with exhaustion of T cells during chronic viral infections based on the finding that PD-1 expressing cells respond poorly to antigen activation and blockade of PD-1/PD-ligand interaction restores such antigen specific responses in vitro. We tested this hypothesis by examining PD-1 expression on virus-specific CD8 T cells and total T cells in vivo to determine whether PD-1 expression constitutes a reliable marker of immune exhaustion during SIV infection. The expression of PD-1 and Ki67 was monitored longitudinally on T cell subsets in peripheral blood, bone marrow, lymph node and rectal biopsy specimens from rhesus macaques prior to and post infection with pathogenic SIVmac239. During the course of infection, a progressive negative correlation was noted between PD-1 density and Ki67 expression in p11CM+ CD8+ T cells, as seen in other studies. However, for total and memory CD4 and CD8 T cells, a positive correlation was observed between PD-1 and Ki67 expression. Thus, while the levels of non-proliferating PD-1+ p11CM+ CD8 T cells were markedly elevated with progressing infection, such an increase was not seen on total T cells. In addition, total memory PD1+ T cells exhibited higher levels of CCR5 than PD-1− T cells. Interestingly, few PD-1+ CD8+ T cells expressed CCR7 compared to PD-1+ CD4 T cells and PD-1− T cells. In conclusion, overall PD1+ T cells likely represent a particular differentiation stage or trafficking ability rather than exhaustion and in the context of chronic SIV infection, the level of PD-1 expression by T cells does not by itself serve as a reliable marker for immune exhaustion.
Ocean–Cloud–Atmosphere–Land Interactions in the Southeastern Pacific: The VOCALS Program

The present paper describes the Variability of the American Monsoon Systems (VAMOS) Ocean–Cloud–Atmosphere–Land Study (VOCALS), an international research program focused on the improved understanding and modeling of the southeastern Pacific (SEP) climate system on diurnal to interannual time scales. In the framework of the SEP climate, VOCALS has two fundamental objectives: 1) improved simulations by coupled atmosphere–ocean general circulation models (CGCMs), with an emphasis on reducing systematic errors in the region; and 2) improved estimates of the indirect effects of aerosols on low clouds and climate, with an emphasis on the more precise quantification of those effects. VOCALS major scientific activities are outlined, and selected achievements are highlighted. Activities described include monitoring in the region, a large international field campaign (the VOCALS Regional Experiment), and two model assessments. The program has already produced significant advances in the understanding of major issue.
Antisense Suppression of the Small Chloroplast Protein CP12 in Tobacco Alters Carbon Partitioning and Severely Restricts Growth1[W]

The thioredoxin-regulated chloroplast protein CP12 forms a multienzyme complex with the Calvin-Benson cycle enzymes phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). PRK and GAPDH are inactivated when present in this complex, a process shown in vitro to be dependent upon oxidized CP12. The importance of CP12 in vivo in higher plants, however, has not been investigated. Here, antisense suppression of CP12 in tobacco (Nicotiana tabacum) was observed to impact on NAD-induced PRK and GAPDH complex formation but had little effect on enzyme activity. Additionally, only minor changes in photosynthetic carbon fixation were observed. Despite this, antisense plants displayed changes in growth rates and morphology, including dwarfism and reduced apical dominance. The hypothesis that CP12 is essential to separate oxidative pentose phosphate pathway activity from Calvin-Benson cycle activity, as proposed in cyanobacteria, was tested. No evidence was found to support this role in tobacco. Evidence was seen, however, for a restriction to malate valve capacity, with decreases in NADP-malate dehydrogenase activity (but not protein levels) and pyridine nucleotide content. Antisense repression of CP12 also led to significant changes in carbon partitioning, with increased carbon allocation to the cell wall and the organic acids malate and fumarate and decreased allocation to starch and soluble carbohydrates. Severe decreases were also seen in 2-oxoglutarate content, a key indicator of cellular carbon sufficiency. The data presented here indicate that in tobacco, CP12 has a role in redox-mediated regulation of carbon partitioning from the chloroplast and provides strong in vivo evidence that CP12 is required for normal growth and development in plants.
Cognitive dysfunction associated with metabolic syndrome

Metabolic syndrome which includes visceral obesity, elevated triglycerides, elevated fasting blood sugar, high blood pressure and a decrease in high‐density lipoprotein cholesterol levels comprises the most common chronic physical illnesses in modern society. Components of the metabolic syndrome play a role in the pathogenesis of a plethora of medical illnesses. Evidence has emerged highlighting the detrimental effects of metabolic syndrome and its constituent features on the cognitive aspects of neurological function. The precise mechanisms underlying this association are not known but a combination of neuroanatomical changes and neuroendocrine consequences of somatic dysregulation may be relevant. As the population ages and the prevalence of metabolic syndrome increases, it is important that this clinically relevant association be recognized.