Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Tissue Decomposition of Diffusion MRI Signals via  $\ell _{0}$  Sparse-Group Estimation

Sparse estimation techniques are widely utilized in diffusion magnetic resonance imaging (DMRI). In this paper, we present an algorithm for solving the ℓ0 sparse-group estimation problem and apply it to the tissue signal separation problem in DMRI. Our algorithm solves the ℓ0 problem directly, unlike existing approaches that often seek to solve its relaxed approximations. We include the mathematical proofs showing that the algorithm will converge to a solution satisfying the firstorder optimality condition within a finite number of iterations. We apply this algorithm to DMRI data to tease apart signal contributions from white matter, gray matter, and cerebrospinal fluid with the aim of improving the estimation of the fiber orientation distribution function (FODF). Unlike spherical deconvolution approaches that assume an invariant fiber response function (RF), our approach utilizes an RF group to span the signal subspace of each tissue type, allowing greater flexibility in accounting for possible variations of the RF throughout space and within each voxel. Our ℓ0 algorithm allows for the natural groupings of the RFs to be considered during signal decomposition. Experimental results confirm that our method yields estimates of FODFs and volume fractions of tissue compartments with improved robustness and accuracy. Our ℓ0 algorithm is general and can be applied to sparse estimation problems beyond the scope of this paper.
The economic benefits of health and prevention in a high-income country: the example of Germany

This paper complements the current health policy debate, which is largely confined to the cost aspects of health systems, by considering explicitly the potential economic benefits of investing in health in general and via - chiefly primary - prevention. While concerns about high and rising health care costs are justified, we see a pressing need to also measure the benefits, ultimately enabling a complete economic assessment of the socially optimal level of resources for health. Despite the use of Germany as our point of reference, our approach and findings likely apply to a wider set of European highincome countries. Using new and already existing data, we find that in sheer health terms Germany has a lot to gain from more and better illness prevention. Assuming part of this existing burden can be reduced via effective preventive interventions, we find that the resulting economic benefits - expressed in people's willingness to pay for a reduction in mortality risk - would be substantial. We also gather Germany-specific evidence to suggest that the existing burden of ill health - whether caused by lack of prevention or treatment - negatively impacts a number of important economic outcomes at the individual and macro-economic level. Referring to work carried out in parallel to this project, we find that a number of cost-effective, primary preventive interventions exist to tackle part of the avoidable disease burden. Yet we note a deficit of economic evaluations, in particular in non-clinical interventions - a finding that underlines the role of government in the production of research on specifically non-clinical prevention. In light of the market failures discussed, from an economic perspective the role of government not only consists of research, but also - surprisingly to many - extends to actual interventions to address the health behaviour-related determinants of chronic disease. With the stakes as high and the economic justification for action in place, the case for scaling up preventive efforts in Germany, backed up by solid epidemiological and economic research, is hard to deny.
Brief Report: Long-Term (96-Week) Efficacy and Safety After Switching From Tenofovir Disoproxil Fumarate to Tenofovir Alafenamide in HIV-Infected, Virologically Suppressed Adults

Abstract: In a double-blind, phase 3 trial, 663 HIV-infected, virologically suppressed adults were randomized to switch to tenofovir alafenamide (TAF; n = 333) vs. remain on tenofovir disoproxil fumarate (TDF; n = 330), each coformulated with emtricitabine (FTC), while continuing their third agent (boosted protease inhibitor or unboosted third agent). At week 96, 88.6% on FTC/TAF and 89.1% on FTC/TDF had HIV-1 RNA <50 copies per milliliter [adjusted difference −0.5% (95% confidence interval: −5.3 to 4.4%)]. Proteinuria, albuminuria, proximal renal tubular function, and bone mineral density improved after switching to TAF- from TDF-containing regimens. These longer-term data support FTC/TAF as a safe, well-tolerated, and durable nucleotide reverse transcriptase inhibitor backbone.
Diethylcarbamazine Increases Activation of Voltage-Activated Potassium (SLO-1) Currents in Ascaris suum and Potentiates Effects of Emodepside

Diethylcarbamazine is a drug that is used for the treatment of filariasis in humans and animals; it also has effects on intestinal nematodes, but its mechanism of action remains unclear. Emodepside is a resistance-busting anthelmintic approved for treating intestinal parasitic nematodes in animals. The novel mode of action and resistance-breaking properties of emodepside has led to its use against intestinal nematodes of animals, and as a candidate drug for treating filarial parasites. We have previously demonstrated effects of emodepside on SLO-1 K+-like currents in Ascaris suum. Here, we demonstrate that diethylcarbamazine, which has been proposed to work through host mediated effects, has direct effects on a nematode parasite, Ascaris suum. It increases activation of SLO-1 K+ currents and potentiates effects of emodepside. Our results suggest consideration of the combination of emodepside and diethylcarbamazine for therapy, which is predicted to be synergistic. The mode of action of diethylcarbamazine may involve effects on parasite signaling pathways (including nitric oxide) as well as effects mediated by host inflammatory mediators.
ID List Forwarding Free Confidentiality Preserving Data Aggregation for Wireless Sensor Networks

Wireless sensor networks (WSNs) are composed of sensor nodes with limited energy which is difficult to replenish. Data aggregation is considered to help reduce communication overhead with in-network processing, thus minimizing energy consumption and maximizing network lifetime. Meanwhile, it comes with challenges for data confidentiality protection. Many existing confidentiality preserving aggregation protocols have to transfer list of sensors' ID for base station to explicitly tell which sensor nodes have actually provided measurement. However, forwarding a large number of node IDs brings overwhelming extra communication overhead. In this paper, we propose provably secure aggregation scheme perturbation-based efficient confidentiality preserving protocol (PEC2P) that allows efficient aggregation of perturbed data without transferring any ID information. In general, environmental data is confined to a certain range; hence, we utilize this feature and design an algorithm to help powerful base station retrieve the ID of reporting nodes. We analyze the accuracy of PEC2P and conclude that base station can retrieve the sum of environmental data with an overwhelming probability. We also prove that PEC2P is CPA secure by security reduction. Experiment results demonstrate that PEC2P significantly reduces node congestion (especially for the root node) during aggregation process in comparison with the existing protocols.
STAT4-associated natural killer cell tolerance following liver transplantation

Objective Natural killer (NK) cells are important mediators of liver inflammation in chronic liver disease. The aim of this study was to investigate why liver transplants (LTs) are not rejected by NK cells in the absence of human leukocyte antigen (HLA) matching, and to identify a tolerogenic NK cell phenotype. Design Phenotypic and functional analyses on NK cells from 54 LT recipients were performed, and comparisons made with healthy controls. Further investigation was performed using gene expression analysis and donor:recipient HLA typing. Results NK cells from non-HCV LT recipients were hypofunctional, with reduced expression of NKp46 (p<0.05) and NKp30 (p<0.001), reduced cytotoxicity (p<0.001) and interferon (IFN)-γ secretion (p<0.025). There was no segregation of this effect with HLA-C, and these functional changes were not observed in individuals with HCV. Microarray and RT-qPCR analysis demonstrated downregulation of STAT4 in NK cells from LT recipients (p<0.0001). Changes in the expression levels of the transcription factors Helios (p=0.06) and Hobit (p=0.07), which control NKp46 and IFNγ expression, respectively, were also detected. Hypofunctionality of NK cells was associated with impaired STAT4 phosphorylation and downregulation of the STAT4 target microRNA-155. Conversely in HCV-LT NK cell tolerance was reversed, consistent with the more aggressive outcome of LT for HCV. Conclusions LT is associated with transcriptional and functional changes in NK cells, resulting in reduced activation. NK cell tolerance occurs upstream of major histocompatibility complex (MHC) class I mediated education, and is associated with deficient STAT4 phosphorylation. STAT4 therefore represents a potential therapeutic target to induce NK cell tolerance in liver disease.
Molecular serogrouping of Escherichia coli

Abstract O-antigens present on the surface of Escherichia coli provide antigenic specificity for the strain and are the main components for O-serogroup designation. Serotyping using O-group-specific antisera for the identification of E. coli O-serogroups has been traditionally the gold-standard for distinguishing E. coli strains. Knowledge of the O-group is important for determining pathogenic lineage, classifying E. coli for epidemiological studies, for determining virulence, and for tracing outbreaks of diseases and sources of infection. However, serotyping has limitations, as the antisera generated against each specific O-group may cross-react, many strains are non-typeable, and others can autoagglutinate or be rough (lacking an O-antigen). Currently, the nucleotide sequences are available for most of the 187 designated E. coli O-groups. Public health and other laboratories are considering whole genome sequencing to develop genotypic methods to determine O-groups. These procedures require instrumentation and analysis that may not be accessible and may be cost-prohibitive at this time. In this review, we have identified unique gene sequences within the O-antigen gene clusters and have targeted these genes for identification of O-groups using the polymerase chain reaction. This information can be used to distinguish O-groups by developing other platforms for E. coli diagnostics in the future.
A review on micropumps for drug delivery system

MEMS (Micro Electro Mechanical Systems) based drug delivery systems finds plethora of applications in current biomedical engineering. Advancements in MEMS field supported to achieve up to LOC (Lab-On-Chip) level and also made the processes low cost and low power consuming. This article reviews a number of micropumps used in various drug delivery microsystems. Both mechanical and non-mechanical micropumps are analyzed and different versions of each types of micropumps are mentioned with respect to their working principle.
Interferon sensitivity-determining region of hepatitis C virus influences virus production and interferon signaling

The number of amino acid substitutions in the interferon (IFN) sensitivity-determining region (ISDR) of hepatitis C virus (HCV) NS5A is a strong predictor for the outcome of IFN-based treatment. To assess the involvement of ISDR in the HCV life cycle and to clarify the molecular mechanisms influencing IFN susceptibility, we used recombinant JFH-1 viruses with NS5A of the genotype 1b Con1 strain (JFH1/5ACon1) and with NS5A ISDR containing 7 amino acid substitutions (JFH1/5ACon1/i-7mut), and compared the virus propagation and the induction of interferon-stimulated genes (ISGs). By transfecting RNAs of these strains into HuH-7-derived cells, we found that the efficiency of infectious virus production of JFH1/5ACon1/i-7mut was attenuated compared with JFH1/5ACon1. After transfecting full-length HCV RNA into HepaRG cells, the mRNA expression of ISGs was sufficiently induced by IFN treatment in JFH1/5ACon1/i-7mut-transfected but not in JFH1/5ACon1-transfected cells. These data suggested that the NS5A-mediated inhibition of ISG induction was deteriorated by amino acid substitutions in the ISDR. In conclusion, using recombinant JFH-1 viruses, we demonstrated that HCV NS5A is associated with infectious virus production and the inhibition of IFN signaling, and amino acid substitutions in the NS5A ISDR deteriorate these functions. These observations explain the strain-specific evasion of IFN signaling by HCV.
Small Imaging Depth LIDAR and DCNN-Based Localization for Automated Guided Vehicle †

We present our third prototype sensor and a localization method for Automated Guided Vehicles (AGVs), for which small imaging LIght Detection and Ranging (LIDAR) and fusion-based localization are fundamentally important. Our small imaging LIDAR, named the Single-Photon Avalanche Diode (SPAD) LIDAR, uses a time-of-flight method and SPAD arrays. A SPAD is a highly sensitive photodetector capable of detecting at the single-photon level, and the SPAD LIDAR has two SPAD arrays on the same chip for detection of laser light and environmental light. Therefore, the SPAD LIDAR simultaneously outputs range image data and monocular image data with the same coordinate system and does not require external calibration among outputs. As AGVs travel both indoors and outdoors with vibration, this calibration-less structure is particularly useful for AGV applications. We also introduce a fusion-based localization method, named SPAD DCNN, which uses the SPAD LIDAR and employs a Deep Convolutional Neural Network (DCNN). SPAD DCNN can fuse the outputs of the SPAD LIDAR: range image data, monocular image data and peak intensity image data. The SPAD DCNN has two outputs: the regression result of the position of the SPAD LIDAR and the classification result of the existence of a target to be approached. Our third prototype sensor and the localization method are evaluated in an indoor environment by assuming various AGV trajectories. The results show that the sensor and localization method improve the localization accuracy.
Deep-mapnets : A residual network for 3D environment representation

The ability to localize in the co-ordinate system of a 3D model presents an opportunity for safe trajectory planning. While SLAM-based approaches provide estimates of incremental poses with respect to the first camera frame, they do not provide global localization. With the availability of mobile GPUs like the Nvidia TX1 etc., our method provides a novel, elegant and high performance visual method for model based robot localization. We propose a method to learn an environment representation with deep residual nets for localization in a known 3D model representing a real-world area of 25,000 sq. meters. We use the power of modern GPUs and game engines for rendering training images mimicking a downward looking high flying drone using a photorealistic 3D model. We use these images to drive the learning loop of a 50-layer deep neural network to learn camera positions. We next propose to do data augmentation to accelerate training and to make our trained model robust for cross domain generalization, which has been verified with experiments. We test our trained model with synthetically generated data as well as real data captured from a downward looking drone. It takes about 25 miliseconds of GPU processing to predict camera pose. Unlike previous methods, the proposed method does not do rendering at test time and does independent prediction from a learned environment representation.
Hmgb1 inhibits Klotho expression and malignant phenotype in melanoma cells by activating NF-κB

The molecular and cellular mechanisms behind the involvement of inflammation in melanoma have not been fully elucidated. In this study, knockdown of Hmgb1 expression increased apoptosis, reduced invasion and p-NF-κB expression, but increased Klotho protein level in melanoma tumor cells. The effect of Hmgb1 knockdown was overcome by LPS. Introduction of exogenous Hmgb1 significantly decreased apoptosis, increased invasion, elevated p-NF-κB, but lowered Klotho protein level in melanoma cells. The effect of exogenous Hmgb1 was agonized by NF-κB inhibitor CAPE. Hmgb1 knockdown activated, but exogenous Hmgb1 inactivated, p-IGF1R/p-PI3K p-85/p-Akt/p-mTOR signaling. Knockdown of Klotho gene expression significantly decreased apoptosis, increased invasion in melanoma cells, and inhibited xenograft A375 tumor growth. A significantly high percentage of cells stained positive for p-NF-κB, but negative for Klotho, in melanoma tissues compared to normal and benign skin tissues. The positive p-NF-κB and negative Klotho protein expression correlated with poor prognosis in melanoma patients. Multivariate analysis revealed an independent association between p-NF-κB / Klotho protein level and overall survival. In conclusion, Hmgb1 can inhibit Klotho gene expression and malignant phenotype in melanoma cells through activation of NF-κB signaling.
Unveiling relationships between crime and property in England and Wales via density scale-adjusted metrics and network tools

Scale-adjusted metrics (SAMs) are a significant achievement of the urban scaling hypothesis. SAMs remove the inherent biases of per capita measures computed in the absence of isometric allometries. However, this approach is limited to urban areas, while a large portion of the world’s population still lives outside cities and rural areas dominate land use worldwide. Here, we extend the concept of SAMs to population density scale-adjusted metrics (DSAMs) to reveal relationships among different types of crime and property metrics. Our approach allows all human environments to be considered, avoids problems in the definition of urban areas, and accounts for the heterogeneity of population distributions within urban regions. By combining DSAMs, cross-correlation, and complex network analysis, we find that crime and property types have intricate and hierarchically organized relationships leading to some striking conclusions. Drugs and burglary had uncorrelated DSAMs and, to the extent property transaction values are indicators of affluence, twelve out of fourteen crime metrics showed no evidence of specifically targeting affluence. Burglary and robbery were the most connected in our network analysis and the modular structures suggest an alternative to “zero-tolerance” policies by unveiling the crime and/or property types most likely to affect each other.
VPS9 domain‐containing proteins are essential for autophagy and endocytosis in Pyricularia oryzae

Pyricularia oryzae is the causal pathogen of rice blast disease. Autophagy has been shown to play important roles in P. oryzae development and plant infection. The P. oryzae endosomal system is highly dynamic and has been shown to be associated with conidiogenesis and pathogenicity as well. To date, the crosstalk between autophagy and endocytosis has not been explored in P. oryzae. Here, we identified three P. oryzae VPS9 domain-containing proteins, PoVps9, PoMuk1 and PoVrl1. We found that PoVps9 and PoMuk1 are localized to vesicles and are each co-localized with PoVps21, a recognized marker of early endosomes. Deletion of PoVPS9 resulted in severe defects in endocytosis and autophagosome degradation and impaired the localization of PoVps21 to endosomes. Additionally, deletion of the PoMUK1 gene in the ΔPovps9 mutant background exhibited more severe defects in development, autophagy and endocytosis compared with the ΔPovps9 mutant. Pull-down assay showed that PoVps9 interacts with PoVps21, PoRab11 and PoRab1, which have been verified to participate in endocytosis. Furthermore, yeast two-hybrid and co-immunoprecipitation assays confirmed that PoVps9 directly interacts with the GDP form of PoVps21. Thus, PoVps9 is a key protein involved in autophagy and in endocytosis.
The Distribution and Morphological Characteristics of Cholinergic Cells in the Brain of Monotremes as Revealed by ChAT Immunohistochemistry

The present study employs choline acetyltransferase (ChAT) immunohistochemistry to identify the cholinergic neuronal population in the central nervous system of the monotremes. Two of the three extant species of monotreme were studied: the platypus (Ornithorhynchus anatinus) and the short-beaked echidna (Tachyglossus aculeatus). The distribution of cholinergic cells in the brain of these two species was virtually identical. Distinct groups of cholinergic cells were observed in the striatum, basal forebrain, habenula, pontomesencephalon, cranial nerve motor nuclei, and spinal cord. In contrast to other tetrapods studied with this technique, we failed to find evidence for cholinergic cells in the hypothalamus, the parabigeminal nucleus (or nucleus isthmus), or the cerebral cortex. The lack of hypothalamic cholinergic neurons creates a hiatus in the continuous antero-posterior aggregation of cholinergic neurons seen in other tetrapods. This hiatus might be functionally related to the phenomenology of monotreme sleep and to the ontogeny of sleep in mammals, as juvenile placental mammals exhibit a similar combination of sleep elements to that found in adult monotremes.
Highly transparent and writable wood all-cellulose hybrid nanostructured paper

Paper, as an inexpensive substrate for flexible electronics and energy devices, has garnered great attention because of its abundance, biodegradability, renewability and sustainability. However, the intrinsic opacity and higher roughness of regular paper greatly restricts further applications. One promising method is to use cellulose nanofibers (CNs) to fabricate nanopaper with a high optical transmittance and excellent smoothness, but there are still some challenges facing nanopaper substrates, such as high-energy consumption to extract nanofibers and the time-consuming process to prepare nanopaper. We design a bilayer hybrid paper using unbeaten wood fibers and CNs with a papermaking technique, which achieves a high optical transmittance and superior smoothness while remaining less expensive than nanopaper and useful as a writable surface. The first transparent paper touchscreen with an excellent anti-glare effect in bright environments is demonstrated using our novel transparent and conductive hybrid paper as the flexible electrode.
Neu-NoC: A high-efficient interconnection network for accelerated neuromorphic systems

A modern neuromorphic acceleration system could consist of hundreds of accelerators, which are often organized through a network-on-chip (NoC). Although the overall computing ability is greatly promoted by a large number of the accelerators, the power consumption and average delay of the NoC itself becomes prominent. In this paper, we first analyze the characteristics of the data traffic in neuromorphic acceleration systems and the bottleneck of the popular NoC designs adopted in such systems. We then propose Neu-NoC — a high-efficient interconnection network to reduce the redundant data traffic in neuromorphic acceleration systems and explore the data transfer ability between adjacent layers. A sophisticated neural network aware mapping algorithm and a multicast transmission scheme are designed to alleviate data traffic congestions without increasing the average transmission distance. Finally, we explore the sparsity characteristics of fully-connected NNs. Simulation results show that compared to the most widely-used Mesh NoC design, Neu-NoC can substantially reduce the average data latency by 28.5% and the energy consumption by 39.2% in accelerated neuromorphic systems.