Miracle-dz/UniFAR-FTUs huggingface dataset:
s-SMOOTH: Sparsity and Smoothness Enhanced EEG Brain Tomography

EEG source imaging enables us to reconstruct current density in the brain from the electrical measurements with excellent temporal resolution (~ ms). The corresponding EEG inverse problem is an ill-posed one that has infinitely many solutions. This is due to the fact that the number of EEG sensors is usually much smaller than that of the potential dipole locations, as well as noise contamination in the recorded signals. To obtain a unique solution, regularizations can be incorporated to impose additional constraints on the solution. An appropriate choice of regularization is critically important for the reconstruction accuracy of a brain image. In this paper, we propose a novel Sparsity and SMOOthness enhanced brain TomograpHy (s-SMOOTH) method to improve the reconstruction accuracy by integrating two recently proposed regularization techniques: Total Generalized Variation (TGV) regularization and ℓ1−2 regularization. TGV is able to preserve the source edge and recover the spatial distribution of the source intensity with high accuracy. Compared to the relevant total variation (TV) regularization, TGV enhances the smoothness of the image and reduces staircasing artifacts. The traditional TGV defined on a 2D image has been widely used in the image processing field. In order to handle 3D EEG source images, we propose a voxel-based Total Generalized Variation (vTGV) regularization that extends the definition of second-order TGV from 2D planar images to 3D irregular surfaces such as cortex surface. In addition, the ℓ1−2 regularization is utilized to promote sparsity on the current density itself. We demonstrate that ℓ1−2 regularization is able to enhance sparsity and accelerate computations than ℓ1 regularization. The proposed model is solved by an efficient and robust algorithm based on the difference of convex functions algorithm (DCA) and the alternating direction method of multipliers (ADMM). Numerical experiments using synthetic data demonstrate the advantages of the proposed method over other state-of-the-art methods in terms of total reconstruction accuracy, localization accuracy and focalization degree. The application to the source localization of event-related potential data further demonstrates the performance of the proposed method in real-world scenarios.
Recent progress toward understanding biosynthesis of the amylopectin crystal.

Plant starch granules provide the largest percentage of calories in the human diet. Starch consists almost entirely of the Glc homopolymers amylopectin and amylose. Amylopectin is the major contributor to both mass and granule structure. Because of the very basic role that starch plays in our
Food-pics: an image database for experimental research on eating and appetite

Our current environment is characterized by the omnipresence of food cues. The sight and smell of real foods, but also graphically depictions of appetizing foods, can guide our eating behavior, for example, by eliciting food craving and influencing food choice. The relevance of visual food cues on human information processing has been demonstrated by a growing body of studies employing food images across the disciplines of psychology, medicine, and neuroscience. However, currently used food image sets vary considerably across laboratories and image characteristics (contrast, brightness, etc.) and food composition (calories, macronutrients, etc.) are often unspecified. These factors might have contributed to some of the inconsistencies of this research. To remedy this, we developed food-pics, a picture database comprising 568 food images and 315 non-food images along with detailed meta-data. A total of N = 1988 individuals with large variance in age and weight from German speaking countries and North America provided normative ratings of valence, arousal, palatability, desire to eat, recognizability and visual complexity. Furthermore, data on macronutrients (g), energy density (kcal), and physical image characteristics (color composition, contrast, brightness, size, complexity) are provided. The food-pics image database is freely available under the creative commons license with the hope that the set will facilitate standardization and comparability across studies and advance experimental research on the determinants of eating behavior.
Evaluation of jet nebulisers for use with gentamicin solution.

Recently nebulised antibiotics (gentamicin and carbenicillin) have been used successfully to treat respiratory tract infection in patients with cystic fibrosis. No information exists, however, on the choice of nebuliser or the ideal mode of operation with antibiotic solutions, which are often viscous. The aerosol output, droplet size, and nebulisation time were assessed for four common brands of jet nebuliser (Bird, DeVilbiss, Inspiron, and Upmist) used to nebulise 2 ml (80 mg) and 4 ml (160 mg) of gentamicin solution (Garamycin, Kirby-Warrick) at four compressed gas flow rates (6, 8, 10, and 12 1 . min-1). There were considerable variations between the nebulisers, DeVilbiss and Upmist being most efficient in the release of respirable (less than 5 micron diameter) droplets. Droplet size and nebulisation time were inversely proportional to gas flow rate. Aerosol output and nebulisation time were increased by raising the volume fill from 2 to 4 ml, although nebulisation time could still be restricted to 12 minutes or less with DeVilbiss and Upmist at 12 1 . min-1. The output of drug in droplets of below 5 micron diameter ranged from 7.2 (SE 0.4) to 71.4 (4.3) mg, according to the type of nebuliser, flow rate, and volume fill. These studies suggest that for optimal drug delivery 4 ml gentamicin solution should be nebulised either at a fixed flow rate of 10-12 1 . min-1 or with a high flow compressor. Previous unsatisfactory clinical results with antibiotic aerosols may have been due in part to incorrect choice of nebuliser or inappropriate operating conditions, or both.
Conditionally Reprogrammed Normal and Transformed Mouse Mammary Epithelial Cells Display a Progenitor-Cell–Like Phenotype

Mammary epithelial (ME) cells cultured under conventional conditions senesce after several passages. Here, we demonstrate that mouse ME cells isolated from normal mammary glands or from mouse mammary tumor virus (MMTV)-Neu–induced mammary tumors, can be cultured indefinitely as conditionally reprogrammed cells (CRCs) on irradiated fibroblasts in the presence of the Rho kinase inhibitor Y-27632. Cell surface progenitor-associated markers are rapidly induced in normal mouse ME-CRCs relative to ME cells. However, the expression of certain mammary progenitor subpopulations, such as CD49f+ ESA+ CD44+, drops significantly in later passages. Nevertheless, mouse ME-CRCs grown in a three-dimensional extracellular matrix gave rise to mammary acinar structures. ME-CRCs isolated from MMTV-Neu transgenic mouse mammary tumors express high levels of HER2/neu, as well as tumor-initiating cell markers, such as CD44+, CD49f+, and ESA+ (EpCam). These patterns of expression are sustained in later CRC passages. Early and late passage ME-CRCs from MMTV-Neu tumors that were implanted in the mammary fat pads of syngeneic or nude mice developed vascular tumors that metastasized within 6 weeks of transplantation. Importantly, the histopathology of these tumors was indistinguishable from that of the parental tumors that develop in the MMTV-Neu mice. Application of the CRC system to mouse mammary epithelial cells provides an attractive model system to study the genetics and phenotype of normal and transformed mouse epithelium in a defined culture environment and in vivo transplant studies.
Alternatively Spliced Products of the UGT1A Gene Interact with the Enzymatically Active Proteins to Inhibit Glucuronosyltransferase Activity In Vitro

UDP-glucuronosyltransferases (UGTs) are major mediators in conjugative metabolism. Current data suggest that UGTs, which are anchored in the endoplasmic reticulum membrane, can oligomerize with each other and/or with other metabolic enzymes, a process that may influence their enzymatic activities. We demonstrated previously that the UGT1A locus encodes previously unknown isoforms (denoted “i2”), by alternative usage of the terminal exon 5. Although i2 proteins lack transferase activity, we showed that knockdown of endogenous i2 levels enhanced cellular UGT1A-i1 activity. In this study, we explored the potential of multiple active UGT1A_i1 proteins (UGT1A1, UGT1A3, UGT1A4, UGT1A6, UGT1A7, UGT1A8, UGT1A9, and UGT1A10) to interact with all spliced i2s by coimmunoprecipitation. We further studied the functional consequences of coexpressing various combinations of spliced i1s and i2s from highly similar UGTs, namely UGT1A7, UGT1A8, and UGT1A9, based on expression profiles observed in human tissues. The i1 isoform of each UGT1A coimmunoprecipitated its respective i2 homolog as well as all other i2s, indicating that they can form heteromeric complexes. Functional data further support the fact that i2 splice species alter glucuronidation activity of i1s independently of the identity of the i2, although the degree of inhibition varied, suggesting that this phenomenon may occur in tissues expressing such combinations of splice forms. These results provide biochemical evidence to support the inhibitory effect of i2s on multiple active UGT1As, probably through formation of inactive heteromeric assemblies of i1s and inactive i2s. The relative abundance of active/inactive oligomeric complexes may thus determine transferase activity.
Lifted First-Order Probabilistic Inference

Most probabilistic inference algorithms are specified and processed on a propositional level. In the last decade, many proposals for algorithms accepting first-order specifications have been presented, but in the inference stage they still operate on a mostly propositional representation level. [Poole, 2003] presented a method to perform inference directly on the first-order level, but this method is limited to special cases. In this paperwe present the first exact inference algorithm that operates directly on a first-order level, and that can be applied to any first-order model (specified in a language that generalizes undirected graphical models). Our experiments show superior performance in comparison with propositional exact inference.
Verification of Meso-Zeaxanthin in Fish

Background/Objectives The carotenoids lutein (L), zeaxanthin (Z), and meso-zeaxanthin (MZ) accumulate in the central retina (the macula), where they are collectively known as macular pigment (MP). MP has been shown to enhance visual function in both diseased and non-diseased retinae, and therefore an understanding and confirmation of, the origins of these carotenoids is needed. Studies have shown that L and Z are present in many foodstuffs found in a typical Western diet (e.g. spinach, kale, peppers, yellow corn and eggs). It has been shown that MZ is generated from L in the primate retina and earlier reports suggested that MZ was present in some fish species. Recently, however, one research group reported that MZ is not present in fish and suggested that the earlier reports showing MZ in these marine species were a methodological artefact. The current study was designed to investigate the reason for the contradiction, and test for the presence of MZ in fish and some other foods. Methods Raw fruits, vegetables and fish were extracted for carotenoid analysis by high performance liquid chromatography. Results MZ was not detected in any of the fruits or vegetables tested in our study. However, using retention time matching, absorption spectrum comparison, and sample spiking, we verified the presence of MZ in salmon skin, sardine skin, trout skin and trout flesh. Conclusion This study confirmed the presence MZ in nature, and in the human food chain.
Effects of eight months treatment with graded doses of a growth hormone (GH)-releasing peptide in GH-deficient children.

Stimulation of pituitary GH secretion with administered GHRH can be effective therapy for those GH deficient (GHD) patients whose disorder results from insufficient endogenous GHRH secretion. We have previously shown that most such patients also respond acutely to the GH-releasing peptides (GHRP's), which have a different mechanism of action from GHRH, with release of GH. In this study we tested whether the GH response to a newer GHRP, GHRP-2, would be sustained over time. Six prepubertal children with GHD and growth failure received stepwise increasing s.c. doses of GHRP-2, at 0.3, 1.0, and 3.0 micrograms/kg/day, in successive 2-month treatment periods, with monitoring of overnight 12 h episodic GH secretion and toxicity measures at the end of each period. During a fourth 2-month period, they received 3 micrograms/kg GHRP-2 together with 3 micrograms/kg s.c. GHRH. Serum levels of IGF-I and IGFBP-3 were also measured, and stadiometer height measurements were recorded. GHRP-2 administration produced a dosewise increase in overnight GH secretion. GH profiles showed that the effect of GHRP-2 injections was relatively brief, with little effect upon GH secretion later in the night. Serum levels of IGF-I and of IGFBP-3 did not increase. Growth velocity was higher during GHRP-2 treatment than during pretreatment and post-treatment evaluations. There were no side effects or toxicities observed. Thus GHRP-2 is well tolerated and is able to stimulate GH secretion. Formulations or routes of administration that allow for a longer duration of action will likely be needed to use GHRP-2 in therapy.
Pregabalin Reduces the Release of Synaptic Vesicles from Cultured Hippocampal Neurons

Pregabalin [S-[+]-3-isobutylGABA or (S)-3-(aminomethyl)-5-methylhexanoic acid, Lyrica] is an anticonvulsant and analgesic medication that is both structurally and pharmacologically related to gabapentin (Neurontin; Pfizer Inc., New York, NY). Previous studies have shown that pregabalin reduces the release of neurotransmitters in several in vitro preparations, although the molecular details of these effects are less clear. The present study was performed using living cultured rat hippocampal neurons with the synaptic vesicle fluorescent dye probe FM4-64 to determine details of the action of pregabalin to reduce neurotransmitter release. Our results indicate that pregabalin treatment, at concentrations that are therapeutically relevant, slightly but significantly reduces the emptying of neurotransmitter vesicles from presynaptic sites in living neurons. Dye release is reduced in both glutamic acid decarboxylase (GAD)-immunoreactive and GAD-negative (presumed glutamatergic) synaptic terminals. Furthermore, both calcium-dependent release and hyperosmotic (calcium-independent) dye release are reduced by pregabalin. The effects of pregabalin on dye release are masked in the presence of l-isoleucine, consistent with the fact that both of these compounds have a high binding affinity to the calcium channel α2-δ protein. The effect of pregabalin is not apparent in the presence of an N-methyl-d-aspartate (NMDA) antagonist [D(-)-2-amino-5-phosphonopentanoic acid], suggesting that pregabalin action depends on NMDA receptor activation. Finally, the action of pregabalin on dye release is most apparent before and early during a train of electrical stimuli when vesicle release preferentially involves the readily releasable pool.
Selected missense mutations impair frataxin processing in Friedreich ataxia

Frataxin (FXN) is a highly conserved mitochondrial protein. Reduced FXN levels cause Friedreich ataxia, a recessive neurodegenerative disease. Typical patients carry GAA repeat expansions on both alleles, while a subgroup of patients carry a missense mutation on one allele and a GAA repeat expansion on the other. Here, we report that selected disease‐related FXN missense mutations impair FXN localization, interaction with mitochondria processing peptidase, and processing.
Monitoring Deforestation at Sub-Annual Scales as Extreme Events in Landsat Data Cubes

Current methods for monitoring deforestation from satellite data at sub-annual scales require pixel time series to have many historical observations in the reference period to model normal forest dynamics before detecting deforestation. However, in some areas, pixel time series often do not have many historical observations. Detecting deforestation at a pixel with scarce historical observations can be improved by complementing the pixel time series with spatial context information. In this work, we propose a data-driven space-time change detection method that detects deforestation events at sub-annual scales in data cubes of satellite image time series. First we spatially normalised observations in the local space-time data cube to reduce seasonality. Subsequently, we detected deforestation by assessing whether a newly acquired observation in the monitoring period is an extreme when compared against spatially normalised values in a local space-time data cube defined over reference period. We demonstrated our method at two sites, a dry tropical Bolivian forest and a humid tropical Brazilian forest, by varying the spatial and temporal extent of data cube. We emulated a “near real-time” monitoring scenario, implying that observations in the monitoring period were sequentially rather than simultaneously assessed for deforestation. Using Landsat normalised difference vegetation index (NDVI) time series, we achieved a median temporal detection delay of less than three observations, a producer’s accuracy above 70%, a user’s accuracy above 65%, and an overall accuracy above 80% at both sites, even when the reference period of the data cube only contained one year of data. Our results also show that large percentile thresholds (e.g., 5th percentile) achieve higher producer’s accuracy and shorter temporal detection delay, whereas smaller percentiles (e.g., 0.1 percentile) achieve higher user’s accuracy, but longer temporal detection delay. The method is data-driven, not based on statistical assumption on the data distribution, and can be applied on different forest types. However, it may face challenges in mixed forests where, for example, deciduous and evergreen forests coexist within short distances. A pixel to be assessed for deforestation should have a minimum of three temporal observations, the first of which must be known to represent forest. Such short time series allow rapid deployment of newly launched sensors (e.g., Sentinel-2) for detecting deforestation events at sub-annual scales.
Optimal path planning based on annular space decomposition for AUVs operating in a variable environment

This paper presents an optimal and efficient path planner based on an annular space decomposition (ASD) scheme for Autonomous Underwater Vehicles (AUVs) operating in turbulent, cluttered and uncertain environments. The proposed scheme decomposes the search space into annular regions, and allows placing one or more control points within each of this region. The trajectory is then generated from this set of control points by using Splines. This arrangement gives more freedom to the placement of the control points, while still restricting the search space to reduce computation time. The ASD scheme has been integrated with both the Genetic Algorithm and the Quantum-behaved Particle Swarm Optimization based path planner and tested to generate an optimal trajectory for an AUV travelling through a turbulent ocean field in the presence of obstacles located with positioning uncertainty. Simulation results show that the resulting approach is able to obtain a more optimized trajectory than the concentric circle constrained method, and has faster convergence speed and use less computation time than the unconstrained full space searching method. Monte Carlo simulations demonstrate the robustness and superiority of the proposed ASD scheme compared with the other two schemes.
Telomere length and LINE1 methylation is associated with chromosomal aberrations in peripheral blood

The frequency of chromosomal aberrations in peripheral blood predicts a probable cancer risk. The individual telomere length and methylation of repetitive elements may be susceptibility factors for chromosomal aberrations. A cohort of healthy Norwegian men (N = 364) recruited during 1980–1999 were analyzed for chromosomal aberrations in phytohemagglutinin‐stimulated lymphocytes from peripheral blood. Chromosome‐type or chromatid‐type aberrations were scored. DNA was extracted from slides cytogenetically analyzed and relative average telomere length and methylation of LINE1 repeats were determined by quantitative polymerase chain reaction and bisulfite pyrosequencing, respectively. Information about individuals with malignant tumors (N = 49) diagnosed after chromosomal aberrations testing until end of 2008 was obtained and two matched controls per case were used in a nested case–control analysis. Shorter relative telomere length and higher methylation of LINE1 were associated with higher frequency of total chromosomal aberrations (β = −0.76, P = 0.022; and β = 0.042, P = 0.048, respectively; age‐adjusted ordinal regression). The telomere length was stronger associated with chromosome‐type (β = −1.00, P = 0.006) than with chromatid‐type aberrations (β = −0.49, P = 0.115). The LINE1 methylation was stronger associated with chromatid‐type (β = 0.062, P = 0.003) than with chromosome‐type aberrations (β = 0.018, P = 0.41). Telomere length [individuals with short telomeres odds ratio (OR) = 0.87, 95% confidence interval (CI) 0.38–2.0], LINE1 (individuals with high methylation OR = 1.04, 95% CI 0.43–2.5) and chromosomal aberrations (individuals with high frequency OR = 1.6, 95% CI 0.63–3.9) at baseline did not predict cancer risk, but the conclusions were hampered by low statistical precision. The results suggest that shorter telomere length and higher LINE1 methylation in peripheral blood lymphocytes are predisposition factors for increased frequency of chromosomal aberrations. © 2012 Wiley Periodicals, Inc.
Using an Enriched TAG Derivation Structure as Basis for Semantics

Most of the proposals for semantics in the Tree Adjoining Grammar (TAG) framework suppose that the derivation tree serves as basis for semantics. However, in some cases the derivation tree does not provide the semantic links one needs. This paper concentrates on one of these cases, namely the analysis of quantiﬁers as adjuncts. The paper proposes to enrich the TAG derivation tree and use the resulting structure as basis for semantics. This allows to deal with quantiﬁers, even in PPs embedded into NPs, such that an adequate semantics with appropriate scope orders is obtained. The enriched derivation structure allows also to treat other cases that are problematic for the assumption that a TAG semantics can be based on the derivation tree.
Measuring the Impacts of Teachers I: Evaluating Bias in Teacher Value-Added Estimates

Are teachersʼ impacts on studentsʼ test scores ("value-added") a good measure of their quality? One reason this question has sparked debate is disagreement about whether value-added (VA) measures provide unbiased estimates of teachersʼ causal impacts on student achievement. We test for bias in VA using previously unobserved parent characteristics and a quasi-experimental design based on changes in teaching staff. Using school district and tax records for more than one million children, we find that VA models which control for a studentʼs prior test scores exhibit little bias in forecasting teachersʼ impacts on student achievement.