Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of the EGSIEM GRACE Gravity Fields Using GNSS Coordinate Timeseries and In-Situ Ocean Bottom Pressure Records

Over the 15 years of the Gravity Recovery and Climate Experiment (GRACE) mission, various data processing approaches were developed to derive time-series of global gravity fields based on sensor observations acquired from the two spacecrafts. In this paper, we compare GRACE-based mass anomalies provided by various processing groups against Global Navigation Satellite System (GNSS) station coordinate time-series and in-situ observations of ocean bottom pressure. In addition to the conventional GRACE-based global geopotential models from the main processing centers, we focus particularly on combined gravity field solutions generated within the Horizon2020 project European Gravity Service for Improved Emergency Management (EGSIEM). Although two validation techniques are fully independent from each other, it is demonstrated that they confirm each other to a large extent. Through the validation, we show that the EGSIEM combined long-term monthly solutions are comparable to CSR RL05 and ITSG2016, and better than the other three considered GRACE monthly solutions AIUB RL02, GFZ RL05a, and JPL RL05.1. Depending on the GNSS products, up to 25.6% mean Weighted Root-Mean-Square (WRMS) reduction is obtained when comparing GRACE to the ITRF2014 residuals over 236 GNSS stations. In addition, we also observe remarkable agreement at the annual period between GNSS and GRACE with up to 73% median WRMS reduction when comparing GRACE to the 312 EGSIEM-reprocessed GNSS time series. While the correspondence between GRACE and ocean bottom pressure data is overall much smaller due to lower signal to noise ratio over the oceans than over the continents, up to 50% agreement is found between them in some regions. The results fully confirm the conclusions found using GNSS.
A Sex-Stratified Genome-Wide Association Study of Tuberculosis Using a Multi-Ethnic Genotyping Array

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males as in females. While socio-economic status, behaviour and sex hormones influence the male bias they do not fully account for it. Males have only one copy of the X chromosome, while diploid females are subject to X chromosome inactivation. In addition, the X chromosome codes for many immune-related genes, supporting the hypothesis that X-linked genes could contribute to TB susceptibility in a sex-biased manner. We report the first TB susceptibility genome-wide association study (GWAS) with a specific focus on sex-stratified autosomal analysis and the X chromosome. Individuals from an admixed South African population were genotyped using the Illumina Multi Ethnic Genotyping Array, specifically designed as a suitable platform for diverse and admixed populations. Association testing was done on the autosome and X chromosome in a sex stratified and combined manner. SNP association testing was not statistically significant using a stringent cut-off for significance but revealed likely candidate genes that warrant further investigation. A genome wide interaction analysis detected 16 significant interactions. Finally, the results highlight the importance of sex-stratified analysis as strong sex-specific effects were identified on both the autosome and X chromosome.
Remotely Sensed Single Tree Data Enable the Determination of Habitat Thresholds for the Three-Toed Woodpecker (Picoides tridactylus)

Forest biodiversity conservation requires precise, area-wide information on the abundance and distribution of key habitat structures at multiple spatial scales. We combined airborne laser scanning (ALS) data with color-infrared (CIR) aerial imagery for identifying individual tree characteristics and quantifying multi-scale habitat requirements using the example of the three-toed woodpecker (Picoides tridactylus) (TTW) in the Bavarian Forest National Park (Germany). This bird, a keystone species of boreal and mountainous forests, is highly reliant on bark beetles dwelling in dead or dying trees. While previous studies showed a positive relationship between the TTW presence and the amount of deadwood as a limiting resource, we hypothesized a unimodal response with a negative effect of very high deadwood amounts and tested for effects of substrate quality. Based on 104 woodpecker presence or absence locations, habitat selection was modelled at four spatial scales reflecting different woodpecker home range sizes. The abundance of standing dead trees was the most important predictor, with an increase in the probability of TTW occurrence up to a threshold of 44–50 dead trees per hectare, followed by a decrease in the probability of occurrence. A positive relationship with the deadwood crown size indicated the importance of fresh deadwood. Remote sensing data allowed both an area-wide prediction of species occurrence and the derivation of ecological threshold values for deadwood quality and quantity for more informed conservation management.
Diagnostic and Prognostic Performance of Neurofilaments in ALS

There is a need for biomarkers for amyotrophic lateral sclerosis (ALS), to support the diagnosis of the disease, to predict disease progression and to track disease activity and treatment responses. Over the last decade multiple studies have investigated the potential of neurofilament levels, both in cerebrospinal fluid and blood, as biomarker for ALS. The most widely studied neurofilament subunits are neurofilament light chain (NfL) and phosphorylated neurofilament heavy chain (pNfH). Neurofilament levels are reflecting neuronal injury and therefore potentially of value in ALS and other neurological disorders. In this mini-review, we summarize and discuss the available evidence about neurofilaments as diagnostic and prognostic biomarker for human ALS.
Quality of Life in Patients With a Major Mental Disorder in Singapore

Background: There has been a paradigm shift in mental health service delivery, from a focus on reducing symptoms to a more holistic approach, which considers Quality of Life (QoL). Method: This study aimed to explore prediction of Quality of Life (QoL) in Asian patients with a major mental disorder i.e., depression or schizophrenia in Singapore. In the current study, there were 43 patients (65.1% females) with depression. Their ages ranged from 18 to 65 (M = 44.63, SD = 12.22). The data were combined with the data on patients with schizophrenia, where there were 43 patients (65.1% females) with schizophrenia, their ages ranging from 18 to 65 (M = 44.60, SD = 12.19). Results: The components of QoL were examined i.e., Physical Component Summary (PCS) and Mental Component Summary (MCS). For all patients, social support and age accounted for 17.3% of the variance in PCS, F(2, 83) = 8.66, p < 0.001. For patients with depression, disorder severity, age, and duration of treatment accounted for 48.3% of the variance in PCS, F(3, 39) = 12.15, p < 0.001. For patients with schizophrenia, education (Primary or Lower vs. Post-Secondary or Higher) and emotional coping accounted for 21.3% of the variance in PCS, F(2, 40) = 5.40, p < 0.01. For all patients, self-efficacy and age accounted for 27.0% of the variance in MCS, F(2, 83) = 15.37, p < 0.001. For patients with depression, disorder severity accounted for 45.6% of the variance in MCS, F(1, 41) = 34.33, p < 0.001. For patients with schizophrenia, number of hospitalizations accounted for 18.5% of the variance in MCS, F(1, 41) = 9.29, p < 0.01. Conclusion: The findings were discussed in regards to implications in interventions to enhance QoL of patients with schizophrenia and depression in Singapore.
Integration of Metabolomics and Transcriptomics Reveals the Therapeutic Mechanism Underlying Paeoniflorin for the Treatment of Allergic Asthma

Objectives: Asthma is a chronic airway inflammatory disease, which is characterized by airway remodeling, hyperreactivity and shortness of breath. Paeoniflorin is one of the major active ingredients in Chinese peony, which exerts anti-inflammatory and immune-regulatory effects in multiple diseases. However, it remains unclear whether paeoniflorin treatment can suppress allergic asthma. Methods: In this study, we evaluated the effect of paeoniflorin on lung function and airway inflammation in asthmatic mice. These asthmatic Balb/c mice were first sensitized and constructed through ovalbumin (OVA) motivation. Subsequently, we determined the mechanism of action of paeoniflorin in treating allergic asthma through integrated transcriptomic and metabolomic data sets. Results: Our results demonstrated that many genes and metabolites were regulated in the paeoniflorin-treated mice. Moreover, the potential target proteins of paeoniflorin played important roles in fatty acid metabolism, inflammatory response, oxidative stress and local adhesion. Conclusion: Paeoniflorin has a beneficial effect on asthma, which may be achieved through regulating fatty acid metabolism, inflammatory response and the adhesion pathway at system level.
A Longitudinal Study of Eating Rituals in Patients With Anorexia Nervosa

Background: Eating rituals are any problematic behaviors involving food. They are usually observed in patients with anorexia nervosa, but research into these behaviors and their role in treatment outcomes is lacking. Objective: We set out to assess the presence of eating rituals in patients with anorexia nervosa treated by means of intensive enhanced cognitive behavioral therapy (ICBT-E), in addition to their change over time and role as potential predictors of treatment outcome. Materials and Methods: Ninety adult female inpatients with anorexia nervosa were recruited. The Participants’ body mass index (BMI), and scores for Starvation Symptoms Inventory (SSI), Eating Disorder Examination (EDE), and Brief Symptom Inventory (BSI) were recorded, and a purpose-designed 9-item checklist of eating rituals was completed by trained dieticians during assisted eating – an integral part of the ICBT-E. The Structured Clinical Interview for DSM-IV was used at admission to identify the presence of coexisting axis I psychiatric disorders. All other tests were administered at baseline (admission), the end of treatment and 6-month follow-up. BMI, EDE, and BSI were also re-administered after 4 weeks of treatment in order to examine how refeeding affects these variables. Results: We found a correlation at baseline between eating rituals and both general and eating-disorder psychopathology scores. Eating rituals were also associated with the presence of at least one comorbid anxiety disorder. ICBT-E treatment was associated with a significant reduction in eating rituals, as well as a significant increase in BMI and improved eating-disorder and general psychopathology. However, our most relevant finding was that neither baseline eating ritual scores nor their change during treatment was associated with either BMI or general or eating-disorder psychopathology scores taken at either the end of therapy or at 6-month follow-up. Conclusion: Neither the presence of nor change in eating rituals influence treatment outcomes in patients with anorexia nervosa.
Framework for a Perceptive Mobile Network Using Joint Communication and Radar Sensing

In this paper, we develop a framework for a novel perceptive mobile/cellular network that integrates radar sensing function into the mobile communication network. We propose a unified system platform that enables downlink and uplink sensing, sharing the same transmitted signals with communications. We aim to tackle the fundamental sensing parameter estimation problem in perceptive mobile networks, by addressing two key challenges associated with sophisticated mobile signals and rich multipath in mobile networks. To extract sensing parameters from orthogonal frequency division multiple access and spatial division multiple access communication signals, we propose two approaches to formulate it to problems that can be solved by compressive sensing techniques. Most sensing algorithms have limits on the number of multipath signals for their inputs. To reduce the multipath signals, as well as removing unwanted clutter signals, we propose a background subtraction method based on simple recursive computation, and provide a closed-form expression for performance characterization. The effectiveness of these methods is validated in simulations.
RepChain: A Reputation-Based Secure, Fast, and High Incentive Blockchain System via Sharding

In today’s blockchain system, designing a secure and high throughput blockchain on par with a centralized payment system is a difficult task. Sharding is one of the most worthwhile emerging technologies for improving the system throughput while maintain high-security level. However, previous sharding-related designs have two main limitations. First, the security and throughput of their random-based sharding system are not high enough as they did not leverage the heterogeneity among validators. Second, to design an incentive mechanism that promotes cooperation could incur a huge overhead on their system. In this article, we propose RepChain, a reputation-based secure and fast blockchain system via sharding, which also provides high incentive to stimulate node cooperation. RepChain utilizes reputation to explicitly characterize the heterogeneity among the validators and lay the foundation for the incentive mechanism. We propose a new double-chain architecture—a transaction chain and a reputation chain. For the transaction chain, an efficient Raft-based synchronous consensus has been presented. For the reputation chain, the synchronous Byzantine fault tolerance consensus that combines collective signing has been utilized to prevent the attack on both reputation score and the related transaction blocks. It supports a high throughput transaction chain with moderate generation speed. Moreover, we propose a reputation-based sharding and leader selection scheme. To analyze the security of RepChain, we propose a recursive formula to calculate the epoch security within only $\mathcal {O}(km^{2})$ time. Furthermore, we implement and evaluate RepChain on the Amazon Web Service platform. The results show our solution can enhance both throughout and security level of the existing sharding-based blockchain system.
The information-theoretic value of unlabeled data in semi-supervised learning

We quantify the separation between the numbers of labeled examples required to learn in two settings: Settings with and without the knowledge of the distribution of the unlabeled data. More specifically, we prove a separation by $\Theta(\log n)$ multiplicative factor for the class of projections over the Boolean hypercube of dimension $n$. We prove that there is no separation for the class of all functions on domain of any size. Learning with the knowledge of the distribution (a.k.a. fixed-distribution learning) can be viewed as an idealized scenario of semi-supervised learning where the number of unlabeled data points is so great that the unlabeled distribution is known exactly. For this reason, we call the separation the value of unlabeled data.
Conditional Domain Adaptation GANs for Biomedical Image Segmentation

Due to visual differences in biomedical image datasets acquired using distinct digitization techniques, Transfer Learning is an important step for improving the generalization capabilities of Neural Networks in this area. Despite succeeding in classification tasks, most Domain Adaptation strategies face serious limitations in segmentation. Therefore, improving on previous Image Translation networks, we propose a Domain Adaptation method for biomedical image segmentation based on adversarial networks that can learn from both unlabeled and labeled data. Our experimental procedure compares our method using several domains, datasets, segmentation tasks and baselines, performing quantitative and qualitative comparisons of the proposed method with baselines. The proposed method shows consistently better results than the baselines in scarce label scenarios, often achieving Jaccard values greater than 0.9 and adequate segmentation quality in most tasks and datasets.
Certainty-Driven Consistency Loss for Semi-supervised Learning

The recently proposed semi-supervised learning methods exploit consistency loss between different predictions under random perturbations. Typically, a student model is trained to predict consistently with the targets generated by a noisy teacher. However, they ignore the fact that not all training data provide meaningful and reliable information in terms of consistency. For misclassified data, blindly minimizing the consistency loss around them can hinder learning. In this paper, we propose a novel certainty-driven consistency loss (CCL) to dynamically select data samples that have relatively low uncertainty. Specifically, we measure the variance or entropy of multiple predictions under random augmentations and dropout as an estimation of uncertainty. Then, we introduce two approaches, i.e. Filtering CCL and Temperature CCL to guide the student learn more meaningful and certain/reliable targets, and hence improve the quality of the gradients backpropagated to the student. Experiments demonstrate the advantages of the proposed method over the state-of-the-art semi-supervised deep learning methods on three benchmark datasets: SVHN, CIFAR10, and CIFAR100. Our method also shows robustness to noisy labels.
Boolean matrix factorization meets consecutive ones property

Boolean matrix factorization is a natural and a popular technique for summarizing binary matrices. In this paper, we study a problem of Boolean matrix factorization where we additionally require that the factor matrices have consecutive ones property (OBMF). A major application of this optimization problem comes from graph visualization: standard techniques for visualizing graphs are circular or linear layout, where nodes are ordered in circle or on a line. A common problem with visualizing graphs is clutter due to too many edges. The standard approach to deal with this is to bundle edges together and represent them as ribbon. We also show that we can use OBMF for edge bundling combined with circular or linear layout techniques. We demonstrate that not only this problem is NP-hard but we cannot have a polynomial-time algorithm that yields a multiplicative approximation guarantee (unless P = NP). On the positive side, we develop a greedy algorithm where at each step we look for the best 1-rank factorization. Since even obtaining 1-rank factorization is NP-hard, we propose an iterative algorithm where we fix one side and and find the other, reverse the roles, and repeat. We show that this step can be done in linear time using pq-trees. We also extend the problem to cyclic ones property and symmetric factorizations. Our experiments show that our algorithms find high-quality factorizations and scale well.
Deep learning-based electroencephalography analysis: a systematic review

Context. Electroencephalography (EEG) is a complex signal and can require several years of training, as well as advanced signal processing and feature extraction methodologies to be correctly interpreted. Recently, deep learning (DL) has shown great promise in helping make sense of EEG signals due to its capacity to learn good feature representations from raw data. Whether DL truly presents advantages as compared to more traditional EEG processing approaches, however, remains an open question. Objective. In this work, we review 154 papers that apply DL to EEG, published between January 2010 and July 2018, and spanning different application domains such as epilepsy, sleep, brain–computer interfacing, and cognitive and affective monitoring. We extract trends and highlight interesting approaches from this large body of literature in order to inform future research and formulate recommendations. Methods. Major databases spanning the fields of science and engineering were queried to identify relevant studies published in scientific journals, conferences, and electronic preprint repositories. Various data items were extracted for each study pertaining to (1) the data, (2) the preprocessing methodology, (3) the DL design choices, (4) the results, and (5) the reproducibility of the experiments. These items were then analyzed one by one to uncover trends. Results. Our analysis reveals that the amount of EEG data used across studies varies from less than ten minutes to thousands of hours, while the number of samples seen during training by a network varies from a few dozens to several millions, depending on how epochs are extracted. Interestingly, we saw that more than half the studies used publicly available data and that there has also been a clear shift from intra-subject to inter-subject approaches over the last few years. About of the studies used convolutional neural networks (CNNs), while used recurrent neural networks (RNNs), most often with a total of 3–10 layers. Moreover, almost one-half of the studies trained their models on raw or preprocessed EEG time series. Finally, the median gain in accuracy of DL approaches over traditional baselines was across all relevant studies. More importantly, however, we noticed studies often suffer from poor reproducibility: a majority of papers would be hard or impossible to reproduce given the unavailability of their data and code. Significance. To help the community progress and share work more effectively, we provide a list of recommendations for future studies and emphasize the need for more reproducible research. We also make our summary table of DL and EEG papers available and invite authors of published work to contribute to it directly. A planned follow-up to this work will be an online public benchmarking portal listing reproducible results.
The Pareto Record Frontier

For iid $d$-dimensional observations $X^{(1)}, X^{(2)}, \ldots$ with independent Exponential$(1)$ coordinates, consider the boundary (relative to the closed positive orthant), or "frontier", $F_n$ of the closed Pareto record-setting (RS) region \[ \mbox{RS}_n := \{0 \leq x \in {\mathbb R}^d: x \not\prec X^{(i)}\ \mbox{for all $1 \leq i \leq n$}\} \] at time $n$, where $0 \leq x$ means that $0 \leq x_j$ for $1 \leq j \leq d$ and $x \prec y$ means that $x_j < y_j$ for $1 \leq j \leq d$. With $x_+ := \sum_{j = 1}^d x_j$, let \[ F_n^- := \min\{x_+: x \in F_n\} \quad \mbox{and} \quad F_n^+ := \max\{x_+: x \in F_n\}, \] and define the width of $F_n$ as \[ W_n := F_n^+ - F_n^-. \] We describe typical and almost sure behavior of the processes $F^+$, $F^-$, and $W$. In particular, we show that $F^+_n \sim \ln n \sim F^-_n$ almost surely and that $W_n / \ln \ln n$ converges in probability to $d - 1$; and for $d \geq 2$ we show that, almost surely, the set of limit points of the sequence $W_n / \ln \ln n$ is the interval $[d - 1, d]$. We also obtain modifications of our results that are important in connection with efficient simulation of Pareto records. Let $T_m$ denote the time that the $m$th record is set. We show that $F^+_{T_m} \sim (d! m)^{1/d} \sim F^-_{T_m}$ almost surely and that $W_{T_m} / \ln m$ converges in probability to $1 - d^{-1}$; and for $d \geq 2$ we show that, almost surely, the sequence $W_{T_m} / \ln m$ has $\liminf$ equal to $1 - d^{-1}$ and $\limsup$ equal to $1$.