Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Stress Detection in Working Environments From Smartphones’ Accelerometer Data: A First Step

Increase in workload across many organizations and consequent increase in occupational stress are negatively affecting the health of the workforce. Measuring stress and other human psychological dynamics is difficult due to subjective nature of selfreporting and variability between and within individuals. With the advent of smartphones, it is now possible to monitor diverse aspects of human behavior, including objectively measured behavior related to psychological state and consequently stress. We have used data from the smartphone's built-in accelerometer to detect behavior that correlates with subjects stress levels. Accelerometer sensor was chosen because it raises fewer privacy concerns (e.g., in comparison to location, video, or audio recording), and because its low-power consumption makes it suitable to be embedded in smaller wearable devices, such as fitness trackers. About 30 subjects from two different organizations were provided with smartphones. The study lasted for eight weeks and was conducted in real working environments, with no constraints whatsoever placed upon smartphone usage. The subjects reported their perceived stress levels three times during their working hours. Using combination of statistical models to classify selfreported stress levels, we achieved a maximum overall accuracy of 71% for user-specific models and an accuracy of 60% for the use of similar-users models, relying solely on data from a single accelerometer.
A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns

Protrusion and retraction of lamellipodia are common features of eukaryotic cell motility. As a cell migrates through its extracellular matrix (ECM), lamellipod growth increases cell-ECM contact area and enhances engagement of integrin receptors, locally amplifying ECM input to internal signaling cascades. In contrast, contraction of lamellipodia results in reduced integrin engagement that dampens the level of ECM-induced signaling. These changes in cell shape are both influenced by, and feed back onto ECM signaling. Motivated by experimental observations on melanoma cells lines (1205Lu and SBcl2) migrating on fibronectin (FN) coated topographic substrates (anisotropic post-density arrays), we probe this interplay between intracellular and ECM signaling. Experimentally, cells exhibited one of three lamellipodial dynamics: persistently polarized, random, or oscillatory, with competing lamellipodia oscillating out of phase (Park et al., 2017). Pharmacological treatments, changes in FN density, and substrate topography all affected the fraction of cells exhibiting these behaviours. We use these observations as constraints to test a sequence of hypotheses for how intracellular (GTPase) and ECM signaling jointly regulate lamellipodial dynamics. The models encoding these hypotheses are predicated on mutually antagonistic Rac-Rho signaling, Rac-mediated protrusion (via activation of Arp2/3 actin nucleation) and Rho-mediated contraction (via ROCK phosphorylation of myosin light chain), which are coupled to ECM signaling that is modulated by protrusion/contraction. By testing each model against experimental observations, we identify how the signaling layers interact to generate the diverse range of cell behaviors, and how various molecular perturbations and changes in ECM signaling modulate the fraction of cells exhibiting each. We identify several factors that play distinct but critical roles in generating the observed dynamic: (1) competition between lamellipodia for shared pools of Rac and Rho, (2) activation of RhoA by ECM signaling, and (3) feedback from lamellipodial growth or contraction to cell-ECM contact area and therefore to the ECM signaling level.
Genome rearrangement affects RNA virus adaptability on prostate cancer cells

Gene order is often highly conserved within taxonomic groups, such that organisms with rearranged genomes tend to be less fit than wild type gene orders, and suggesting natural selection favors genome architectures that maximize fitness. But it is unclear whether rearranged genomes hinder adaptability: capacity to evolutionarily improve in a new environment. Negative-sense non-segmented RNA viruses (order Mononegavirales) have specific genome architecture: 3′ UTR – core protein genes – envelope protein genes – RNA-dependent RNA-polymerase gene – 5′ UTR. To test how genome architecture affects RNA virus evolution, we examined vesicular stomatitis virus (VSV) variants with the nucleocapsid (N) gene moved sequentially downstream in the genome. Because RNA polymerase stuttering in VSV replication causes greater mRNA production in upstream genes, N gene translocation toward the 5′ end leads to stepwise decreases in N transcription, viral replication and progeny production, and also impacts the activation of type 1 interferon mediated antiviral responses. We evolved VSV gene-order variants in two prostate cancer cell lines: LNCap cells deficient in innate immune response to viral infection, and PC-3 cells that mount an IFN stimulated anti-viral response to infection. We observed that gene order affects phenotypic adaptability (reproductive growth; viral suppression of immune function), especially on PC-3 cells that strongly select against virus infection. Overall, populations derived from the least-fit ancestor (most-altered N position architecture) adapted fastest, consistent with theory predicting populations with low initial fitness should improve faster in evolutionary time. Also, we observed correlated responses to selection, where viruses improved across both hosts, rather than suffer fitness trade-offs on unselected hosts. Whole genomics revealed multiple mutations in evolved variants, some of which were conserved across selective environments for a given gene order.
Ultimate SLAM? Combining Events, Images, and IMU for Robust Visual SLAM in HDR and High-Speed Scenarios

Event cameras are bioinspired vision sensors that output pixel-level brightness changes instead of standard intensity frames. These cameras do not suffer from motion blur and have a very high dynamic range, which enables them to provide reliable visual information during high-speed motions or in scenes characterized by high dynamic range. However, event cameras output only little information when the amount of motion is limited, such as in the case of almost still motion. Conversely, standard cameras provide instant and rich information about the environment most of the time (in low-speed and good lighting scenarios), but they fail severely in case of fast motions, or difficult lighting such as high dynamic range or low light scenes. In this letter, we present the first state estimation pipeline that leverages the complementary advantages of these two sensors by fusing in a tightly coupled manner events, standard frames, and inertial measurements. We show on the publicly available Event Camera Dataset that our hybrid pipeline leads to an accuracy improvement of 130% over event-only pipelines, and 85% over standard-frames-only visual-inertial systems, while still being computationally tractable. Furthermore, we use our pipeline to demonstrate—to the best of our knowledge—the first autonomous quadrotor flight using an event camera for state estimation, unlocking flight scenarios that were not reachable with traditional visual-inertial odometry, such as low-light environments and high dynamic range scenes. Videos of the experiments: http://rpg.ifi. uzh.ch/ultimateslam.html
Transient Scuffing of Candidate Diesel Engine Materials at Temperatures up to 600 o C

This milestone report summarizes the general characteristics of scuffing damage to solid surfaces, then describes transient effects on scuffing observed during oscillating sliding wear tests of candidate material pairs for high-temperature diesel engine applications, like waste-gate bushings in exhaust gas recirculation (EGR) systems. It is shown that oxidation and the formation of wear particle layers influence the friction of such components. In the case of metallic materials in cylindrical contacts where there is a generous clearance, debris layers can form which reduce the torque over time. For ceramic combinations, the opposite effect is observed. Here, the accumulation of wear debris leads to an increase in the turning torque. High-temperature transient scuffing behavior is considered in terms of a series of stages in which the composition and morphology of the contact is changing. These changes are used to explain the behavior of 11 material pairs consisting of stainless steels, Ni-based alloys, Co-based alloys, and structural ceramics.
Evaluating quality indicators of tertiary care hospitals for trauma care in Japan

Objective This study examined the associations between trauma mortality and quality of care indicators currently used in Japan. Design This is a retrospective two-level discrete-time survival analysis. Quality indicators were derived from the 2012-2013 annual hospital survey conducted by the Ministry of Health, Labour and Welfare. Trauma mortality data were derived from the Japan Trauma Data Bank for the period of April 2012 to March 2013. Setting Tertiary care centers designated as emergency and critical care centers (ECCCs) in Japan. Participants The analysis included 12 378 patients aged ≥15 years with blunt trauma and an Injury Severity Score ≥9, registered to the data bank from 91 ECCCs. Intervention Quality of care indicators examined in the annual hospital survey. Main Outcome Measures Deaths within 30 days. Results Of the 12 378 patients, 660 (5%) died within 30 days. Higher indicator score was significantly associated with lower mortality risk (hazard ratio [HR] for the second, third and fourth quartiles vs. lowest quartile 0.61, 0.55 and 0.52, respectively). Factors significantly associated with lower mortality risk were, higher patient volume (HR for the highest vs. lowest quartile, 0.74), director's qualification as specialist (HR 0.57) or consultant (HR 0.58), review of patient arrival process (HR 0.68), triage functions (HR 0.69), availability of psychiatrists (HR 0.75) and operating room being ready 24-h (HR 0.81). Conclusions The study identified certain indicators associated with trauma patient mortality. Further refinement of indicators is required to specifically identify what needs changing.
miEAA: microRNA enrichment analysis and annotation

Similar to the development of gene set enrichment and gene regulatory network analysis tools over a decade ago, microRNA enrichment tools are currently gaining importance. Building on our experience with the gene set analysis toolkit GeneTrail, we implemented the miRNA Enrichment Analysis and Annotation tool (miEAA). MiEAA is a web-based application that offers a variety of commonly applied statistical tests such as over-representation analysis and miRNA set enrichment analysis, which is similar to Gene Set Enrichment Analysis. Besides the different statistical tests, miEAA also provides rich functionality in terms of miRNA categories. Altogether, over 14 000 miRNA sets have been added, including pathways, diseases, organs and target genes. Importantly, our tool can be applied for miRNA precursors as well as mature miRNAs. To make the tool as useful as possible we additionally implemented supporting tools such as converters between different miRBase versions and converters from miRNA names to precursor names. We evaluated the performance of miEAA on two sets of miRNAs that are affected in lung adenocarcinomas and have been detected by array analysis. The web-based application is freely accessible at: http://www.ccb. uni-saarland.de/mieaa_tool/.
Quantitative Analysis of Particles Segregation

Segregation is a popular phenomenon. It has considerable effects on material performance. To the author's knowledge, there is still no automated objective quantitative indicator for segregation. In order to full fill this task, segregation of particles is analyzed. Edges of the particles are extracted from the digital picture. Then, the whole picture of particles is splintered to small rectangles with the same shape. Statistical index of the edges in each rectangle is calculated. Accordingly, segregation between the indexes corresponding to the rectangles is evaluated. The results show coincident with subjective evaluated results. Further more, it can be implemented as an automated system, which would facilitate the materials quality control mechanism during production process.
Disgust exposure and explicit emotional appraisal enhance the LPP in response to disgusted facial expressions

ABSTRACT The influence of prior exposure to disgusting imagery and the conscious appraisal of facial expressions were examined in an event-related potential (ERP) experiment. Participants were exposed to either a disgust or a control manipulation and then presented with emotional and neutral expressions. An assessment of the gender of the face was required during half the blocks and an affective assessment of the emotion in the other half. The emotion-related early posterior negativity (EPN) and late positive potential (LPP) ERP components were examined for disgust and neutral stimuli. Results indicated that the EPN was enhanced for disgusted over neutral expressions. Prior disgust exposure modulated the middle phase of the LPP in response to disgusted but not neutral expressions, but only when the emotion of the face was explicitly evaluated. The late LPP was enhanced independently of stimuli when an emotional decision was made. Results demonstrated that exposure to disgusting imagery can affect the subsequent processing of disgusted facial expressions when the emotion is under conscious appraisal.
An energy-efficient dynamic memory address mapping mechanism

DRAM-based main memories are energy-hungry components of modern computer systems. Since accesses to DRAM need a complex protocol, the performance of an address-mapping scheme that decides physical locations of data based on physical addresses has a big impact on energy consumption. To improve the energy efficiency, this paper proposes a mechanism that dynamically selects an appropriate address-mapping scheme under the consideration of a trade-off between performance and power consumption. The mechanism works so as to reduce the energy consumption of the main memory. The evaluation results show that the proposed mechanism can reduce the energy consumption in comparison with conventional address-mapping schemes, which do not change their address mappings.
Onstep repair of inguinal hernias.

Inguinal hernias are a protrusion of the peritoneum through a weakening in the groin in which abdominal content (intestines or fat) can herniate and cause a bulge. Inguinal hernias can be painful and require surgery. Worldwide, approximately 20 million patients are operated each year, with 10,000 in Denmark. The repair of inguinal hernias causes pain and 16% of patients experience chronic pain six months after the standard, open, mesh-based Lichtenstein technique. Therefore, surgeons are trying to improve the techniques by finding new ways of operating. The Onstep method was a new method for the repair of inguinal hernias, presented along with excellent results regarding pain, recurrence and complications. However, the technique had not been tested outside the department of the inventors. The overall aim was to clarify whether the Onstep technique should be implemented on a larger scale outside the departments of the inventors. Six papers are included in this thesis: a systematic review, a protocol article, three reports on the Onstep versus Lichtenstein trial, and finally a focus group interview. The systematic review identified nine different methods of placing a preperitoneal mesh through and open anterior approach. In general, the techniques seem to provide good results regarding pain and discomfort, but more studies are needed. The protocol article describes the randomized, double blinded Onstep versus Lichtenstein study, with focus on the statistical analysis and sample size calculations. Four separate sample size calculations were conducted, making several primary outcomes possible. The three reports of the Onstep versus Lichtenstein study reported on early postoperative outcomes, on chronic pain, and lastly on sexual dysfunction. The overall findings from the trial demonstrated that there were no differences between the Onstep and the Lichtenstein technique regarding early and chronic pain (30 days, six months, and 12 months). However, for the group of patients operated with the Onstep technique, fewer patients experienced pain during sexual activity. The focus group interview was done with experienced surgeons teaching the Onstep technique. They described their experience, thoughts, and concerns regarding teaching the technique. The results from the focus group interview can be used to guide future trainings sessions. In this thesis the Onstep technique has been investigated in comparison with the Lichtenstein technique, but the results have not been as promising as the initial studies from the inventors. However, implementation of the Onstep technique outside the departments of the inventors is unlikely to result in increased risk of complications. Furthermore, the Onstep technique could possibly benefit patients by reducing the risk of pain during sexual activity.
Analog circuits fault diagnosis using multi‐valued Fisher's fuzzy decision tree (MFFDT)

Fault diagnosis of analog circuits is more challenging compared with digital circuits as a result of the parametric deviation and the difficulty in signal discretization. There still lacks effective approaches to realize reliable fault detection and isolation for a comprehensive diagnosis. A new fault diagnosis technique called multi‐valued Fisher's fuzzy decision tree (MFFDT) is proposed in this paper to solve the problem. This technique uses the decision tree as the diagnosis model and incorporates the Fisher's linear discriminant principles. The fuzzification mechanism is devised to discretize the input monitoring data. The proposed MFFDT method is composed of two aspects: decision tree training and real fault diagnosis processes. The former uses the benchmark data to train a decision tree, while the latter sends the monitoring data into the decision tree to generate diagnosis results. The proposed method is validated using simulated data and the real‐time data for an active filter circuit and an audio amplifying circuit. The comparative analysis is also presented to evaluate diagnosis performances. Copyright © 2015 John Wiley & Sons, Ltd.
Clinical Name Entity Recognition using Conditional Random Field with Augmented Features

In this paper, We presents a Chinese medical term recognition system submitted to the competition held by China Conference on Knowledge Graph and Semantic Computing. I compare the performance of Linear Chain Conditional Random Field (CRF) with that of Bi-Directional Long Short Term Memory (LSTM) with Convolutional Neural Network (CNN) and CRF layers performance and find that CRF with augmented features performs best with F1 0.927 on the offline competition dataset using cross-validation. Hence, this system was built by using a conditional random field model with linguistic features such as character identity, N-gram, and external dictionary features.
Enrichment analysis with EpiAnnotator

Motivation: Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user‐friendly way. Results: EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures. Availability and implementation: The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator's web interface is accessible at http://computational‐epigenomics.com/en/epiannotator. Contact: epiannotator@computational‐epigenomics.com
Surveillance Planning With Bézier Curves

This letter concerns surveillance planning for an unmanned aerial vehicle (UAV) that is requested to periodically take snapshots of areas of interest by visiting a given set of waypoint locations in the shortest time possible. The studied problem can be considered as a variant of the combinatorial traveling salesman problem in which trajectories between the waypoints respect the kinematic constraints of the UAV. Contrary to the existing formulation for curvature-constrained vehicles known as the Dubins traveling salesman problem, the herein addressed problem is motivated by planning for multirotor UAVs which are not limited by the minimal required forward velocity and minimal turning radius as the Dubins vehicle, but rather by the maximal speed and acceleration. Moreover, the waypoints to be visited can be at different altitudes, and the addressed problem is to find a fast and smooth trajectory in three-dimensional (3-D) space from which all the areas of interest can be captured. The proposed solution is based on unsupervised learning in which the requested 3-D smooth trajectory is determined as a sequence of Bézier curves in a finite number of learning epochs. The reported results support feasibility of the proposed solution which has also been experimentally verified with a real UAV.
Euler-Poincaré reduction for discrete field theories

In this note, we develop a theory of Euler-Poincare reduction for discrete Lagrangian field theories. We introduce the concept of Euler-Poincare equations for discrete field theories, as well as a natural extension of the Moser-Veselov scheme, and show that both are equivalent. The resulting discrete field equations are interpreted in terms of discrete differential geometry. An application to the theory of discrete harmonic mappings is also briefly discussed.
A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets

Activation-induced deaminase (AID) initiates antibody diversification in germinal center (GC) B cells through the deamination of cytosines on immunoglobulin genes. AID can also target other regions in the genome, triggering mutations or chromosome translocations, with major implications for oncogenic transformation. However, understanding the specificity of AID has proved extremely challenging. We have sequenced at very high depth >1,500 genomic regions from GC B cells and identified 275 genes targeted by AID, including 30 of the previously known 35 AID targets. We have also identified the most highly mutated hotspot for AID activity described to date. Furthermore, integrative analysis of the molecular features of mutated genes coupled to machine learning has produced a powerful predictive tool for AID targets. We also have found that base excision repair and mismatch repair back up each other to faithfully repair AID-induced lesions. Finally, our data establish a novel link between AID mutagenic activity and lymphomagenesis.