julilili42/papers huggingface dataset:
Inferring task performance and confidence from displays of eye movements
2020-07-13

Summary Eye movements reveal what is at the center of people's attention, which is assumed to coincide with what they are thinking about. Eye‐movement displays (visualizations of a person's fixations superimposed onto the stimulus, for example, as dots or circles) might provide useful information for diagnosing that person's performance. However, making inferences about a person's task performance based on eye‐movement displays requires substantial interpretation. Using graph‐comprehension tasks, we investigated to what extent observers ( N = 46) could make accurate inferences about a performer's multiple‐choice task performance (i.e., chosen answer), confidence, and competence from displays of that person's eye movements. Observers' accuracy when judging which answer the performer chose was above chance level and was higher for displays reflecting confident performance. Observers were also able to infer performers' confidence from the eye‐movement displays; moreover, their own task performance and perceived similarity with the performer affected their judgments of the other's competence.
Identifying disease-causing mutations with privacy protection
2020-07-13

Abstract Motivation The use of genome data for diagnosis and treatment is becoming increasingly common. Researchers need access to as many genomes as possible to interpret the patient genome, to obtain some statistical patterns and to reveal disease–gene relationships. The sensitive information contained in the genome data and the high risk of re-identification increase the privacy and security concerns associated with sharing such data. In this article, we present an approach to identify disease-associated variants and genes while ensuring patient privacy. The proposed method uses secure multi-party computation to find disease-causing mutations under specific inheritance models without sacrificing the privacy of individuals. It discloses only variants or genes obtained as a result of the analysis. Thus, the vast majority of patient data can be kept private. Results Our prototype implementation performs analyses on thousands of genomic data in milliseconds, and the runtime scales logarithmically with the number of patients. We present the first inheritance model (recessive, dominant and compound heterozygous) based privacy-preserving analyses of genomic data to find disease-causing mutations. Furthermore, we re-implement the privacy-preserving methods (MAX, SETDIFF and INTERSECTION) proposed in a previous study. Our MAX, SETDIFF and INTERSECTION implementations are 2.5, 1122 and 341 times faster than the corresponding operations of the state-of-the-art protocol, respectively. Availability and implementation https://gitlab.com/DIFUTURE/privacy-preserving-genomic-diagnosis. Supplementary information Supplementary data are available at Bioinformatics online.
Active fatty acid oxidation defines the cellular response towards reactive oxygen species
2020-07-13

Abstract Endocrine disrupting compounds (EDC) are ubiquitous in the human environment, displaying a highly relevant research topic. The impact of EDC on the differentiation of primitive cells, e.g. in hematopoiesis, is of particular interest. We found profound inhibitory effects of di-2-ethylhexyl phthalate (DEHP) on erythropoiesis and dendropoiesis, mediated via reactive oxygen species (ROS) generation. Neutrophil differentiation, however, was not affected by DEHP. ROS leads to a shift from glycolysis to the pentose phosphate pathway and diminishes ATP generation from glycolysis, ultimately resulting in apoptosis in both cell types. In neutrophils, ATP generation is held constant by active fatty acid oxidation (FAO), rendering these cells highly resistant against ROS. This relationship also holds true in HUVEC and HepG2 cells, also in combination with other organic peroxides. We, therefore, uncover a key mechanism for ROS quenching which further explains the distinct ROS quenching ability of different tissues.
Best Practices for Transparency in Machine Generated Personalization
2020-07-13

Machine generated personalization is increasingly used in online systems. Personalization is intended to provide users with relevant content, products, and solutions that address their respective needs and preferences. However, users are becoming increasingly vulnerable to online manipulation due to algorithmic advancements and lack of transparency. Such manipulation decreases users’ levels of trust, autonomy, and satisfaction concerning the systems with which they interact. Increasing transparency is an important goal for personalization based systems and system designers benefit from guidance in implementing transparency in their systems. In this work we combine insights from technology ethics and computer science to generate a list of transparency best practices for machine generated personalization. We further develop a checklist to be used by designers to evaluate and increase the transparency of their algorithmic systems. Adopting a designer perspective, we apply the checklist to prominent online services and discuss its advantages and shortcomings. We encourage researchers to adopt the checklist and work towards a consensus-based tool for measuring transparency in the personalization community. This is a draft of the paper "Best Practices for Transparency in Machine Generated Personalization" presented at UMAP '20 Adjunct: Adjunct Publication of the 28th ACM Conference on User Modeling, Adaptation and Personalization, July 2020, Pages 23–28, https://doi.org/10.1145/3386392.3397593
The SPHERE infrared survey for exoplanets (SHINE)
2020-07-14

The SpHere INfrared Exoplanet (SHINE) project is a 500-star survey performed with SPHERE on the Very Large Telescope for the purpose of directly detecting new substellar companions and understanding their formation and early evolution. Here we present an initial statistical analysis for a subsample of 150 stars spanning spectral types from B to M that are representative of the full SHINE sample. Our goal is to constrain the frequency of substellar companions with masses between 1 and 75 M Jup and semimajor axes between 5 and 300 au. For this purpose, we adopt detection limits as a function of angular separation from the survey data for all stars converted into mass and projected orbital separation using the BEX-COND-hot evolutionary tracks and known distance to each system. Based on the results obtained for each star and on the 13 detections in the sample, we use a Markov chain Monte Carlo tool to compare our observations to two different types of models. The first is a parametric model based on observational constraints, and the second type are numerical models that combine advanced core accretion and gravitational instability planet population synthesis. Using the parametric model, we show that the frequencies of systems with at least one substellar companion are 23.0 −9.7 +13.5 , 5.8 −2.8 +4.7 , and 12.6 −7.1 +12.9 % for BA, FGK, and M stars, respectively. We also demonstrate that a planet-like formation pathway probably dominates the mass range from 1–75 M Jup for companions around BA stars, while for M dwarfs, brown dwarf binaries dominate detections. In contrast, a combination of binary star-like and planet-like formation is required to best fit the observations for FGK stars. Using our population model and restricting our sample to FGK stars, we derive a frequency of 5.7 −2.8 +3.8 %, consistent with predictions from the parametric model. More generally, the frequency values that we derive are in excellent agreement with values obtained in previous studies.
Tenascin-C Orchestrates an Immune-Suppressive Tumor Microenvironment in Oral Squamous Cell Carcinoma
2020-07-14

Abstract Inherent immune suppression represents a major challenge in the treatment of human cancer. The extracellular matrix molecule tenascin-C promotes cancer by multiple mechanisms, yet the roles of tenascin-C in tumor immunity are incompletely understood. Using a 4NQO-induced oral squamous cell carcinoma (OSCC) model with abundant and absent tenascin-C, we demonstrated that tenascin-C enforced an immune-suppressive lymphoid stroma via CCL21/CCR7 signaling, leading to increased metastatic tumors. Through TLR4, tenascin-C increased expression of CCR7 in CD11c+ myeloid cells. By inducing CCL21 in lymphatic endothelial cells via integrin α9β1 and binding to CCL21, tenascin-C immobilized CD11c+ cells in the stroma. Inversion of the lymph node-to-tumor CCL21 gradient, recruitment of T regulatory cells, high expression of anti-inflammatory cytokines, and matrisomal components were hallmarks of the tenascin-C–instructed lymphoid stroma. Ablation of tenascin-C or CCR7 blockade inhibited the lymphoid immune-suppressive stromal properties, reducing tumor growth, progression, and metastasis. Thus, targeting CCR7 could be relevant in human head and neck tumors, as high tenascin-C expression and an immune-suppressive stroma correlate to poor patient survival.
Pseudogap opening in the two-dimensional Hubbard model: A functional renormalization group analysis
2020-07-14

Using the recently introduced multiloop extension of the functional\\nrenormalization group, we compute the frequency- and momentum-dependent\\nself-energy of the two-dimensional Hubbard model at half filling and weak\\ncoupling. We show that, in the truncated-unity approach for the vertex, it is\\nessential to adopt the Schwinger-Dyson form of the self-energy flow equation in\\norder to capture the pseudogap opening. We provide an analytic understanding of\\nthe key role played by the flow scheme in correctly accounting for the impact\\nof the antiferromagnetic fluctuations. For the resulting pseudogap, we present\\na detailed numerical analysis of its evolution with temperature, interaction\\nstrength, and loop order.\\n
Vibrational Dressing in Kinetically Constrained Rydberg Spin Systems
2020-07-14

Quantum spin systems with kinetic constraints have become paradigmatic for exploring collective dynamical behavior in many-body systems. Here we discuss a facilitated spin system which is inspired by recent progress in the realization of Rydberg quantum simulators. This platform allows to control and investigate the interplay between facilitation dynamics and the coupling of spin degrees of freedom to lattice vibrations. Developing a minimal model, we show that this leads to the formation of polaronic quasiparticle excitations which are formed by many-body spin states dressed by phonons. We investigate in detail the properties of these quasiparticles, such as their dispersion relation, effective mass, and the quasiparticle weight. Rydberg lattice quantum simulators are particularly suited for studying this phonon-dressed kinetically constrained dynamics as their exaggerated length scales permit the site-resolved monitoring of spin and phonon degrees of freedom.
Quality assurance of IMRT treatment plans for a 1.5 T MR-linac using a 2D ionization chamber array and a static solid phantom
2020-07-14

MR-guided radiotherapy requires novel quality assurance (QA) methods for intensity-modulated radiotherapy treatment plans (TPs). Here, an optimized method for TPs for a 1.5 T MR-linac was developed and implemented clinically. A static solid phantom and an MR-compatible 2D ionization chamber array were used. The array's response with respect to the incident beam gantry angles was characterized for four different orientations of the array relative to the beam. A lookup table was created identifying the optimum orientation for each gantry angle. For the QA of clinical MR-linac TPs, beams were grouped according to their gantry angles and measured with up to four setups. The method was applied to n = 106 clinical TPs of 54 patients for different tumour entities. Reference plans and plans created in the online adaptive workflow were analysed, using a local 3%/3 mm gamma criterion for dose values larger than 30% of the maximum. Pass rates were averaged over all beam groups. The array's response strongly depends on the beam incidence angle. Optimum angles typically range from -10° to 80° around the phantom setup angle. Consequently, plan verification required up to four setups. For clinical MR-linac TPs, the overall median pass rate was 98.5% (range 88.6%-100%). Pass rates depended on the tumour entity. Median pass rates were for liver metastases stereotactic body radiotherapy 99.2%, prostate cancer 99%, pancreatic cancer 98.9%, lymph node metastases 98.7%, partial breast irradiation (PBI) 98%, head-and-neck cancer 97.7%, rectal cancer 94% and others 96.6%. 85% of plans were accepted straightaway, with pass rates above 95%. A single plan with a pass rate below 90% was subsequently verified with a modified method. Off-axis target volumes, e.g. PBI, were verified successfully using a lateral shift of the phantom. The method is suitable to verify reference and online adapted TPs for a 1.5 T MR-linac, including plans for off-axis target volumes.
A skull of a very large crane from the late Miocene of Southern Germany, with notes on the phylogenetic interrelationships of extant Gruinae
2020-07-14

Abstract We describe a partial skull of a very large crane from the early late Miocene (Tortonian) hominid locality Hammerschmiede in southern Germany, which is the oldest fossil record of the Gruinae (true cranes). The fossil exhibits an unusual preservation in that only the dorsal portions of the neurocranium and beak are preserved. Even though it is, therefore, very fragmentary, two morphological characteristics are striking and of paleobiological significance: its large size and the very long beak. The fossil is from a species the size of the largest extant cranes and represents the earliest record of a large-sized crane in Europe. Overall, the specimen resembles the skull of the extant, very long-beaked Siberian Crane, Leucogeranus leucogeranus , but its affinities within Gruinae cannot be determined owing to the incomplete preservation. Judging from its size, the fossil may possibly belong to the very large “ Grus ” pentelici , which stems from temporally and geographically proximate sites. The long beak of the Hammerschmiede crane conforms to an open freshwater paleohabitat, which prevailed at the locality.
Injury of the Tibial Nutrient Artery Canal during External Fixation for Lower Extremity Fractures: A Computed Tomography Study
2020-07-14

The tibial nutrient artery (TNA) is the major diaphyseal artery of the tibia supplying two thirds of the inner osseous cortex. Hence, iatrogenic injury of the TNA endangers the integrity of the tibial blood supply and may compromise fracture healing. The incidence of its injury in the setting of external fixation for lower limb fractures has not been previously investigated. The aim of this study was to evaluate the incidence of TNA injury in the context of external fixation and to characterize the topography of the fixator pins in relation to the TNA canal (TNAC). Patients who underwent external fixation for distal femoral fractures and for tibial (proximal, shaft, and distal) fractures and had a postoperative computed tomography study were retrospectively included. The following parameters were retrieved: 1) Pin characteristics (orientation and cortical position of the pins), 2) The anatomic relationship between the TNAC and external fixation pin (topography above/below and at the level of the TNAC, and the distance between the pin and medial tibial plateau and/or the medial malleolus), and 3) The incidence of TNAC injury (complete/partial disruption of TNA lumen). A total of 105 patients with 214 tibial pins were analyzed. In 27 patients (26%), the TNAC was completely injured by the pins of the external fixator. In 13 patients (12%), the TNAC was partially injured. Of the 214 analyzed pins, 85 pins (40%) were located at the level of the TNAC (the TNAC and the pin are seen on the same axial slice). Most pins that were applied at the level of the TNAC belonged to a knee-bridging external fixator. Of those, ninety-three percent of the pins were anteromedially applied according to published surgical guidelines. Six percent of the pins were applied through the tibial crest and 1% anterolaterally. Of those 85 pins, 42 pins (49%) injured the TNAC at least partially. Based on the analyzed pins and the incidence of partial and complete injury of the TNAC, we observed that the tibial segment at which the tibial nutrient artery is endangered was located approximately (95% CI: 13–15 cm) from the medial tibia plateau and (95% CI: 22–25 cm) from the medial malleolus. Thus, TNAC injury by external fixation pins in the context of lower limb fractures can be considered common. Almost half of the pins applied at the middle third of the tibia injured the TNA, despite adherence to published surgical guidelines for external fixation. When possible, pin application at the middle third of tibia should be avoided to circumvent iatrogenic injury of the TNA and to safeguard tibial blood supply.
Fast and reliable easy-to-use diagnostics for eliminating bilharzia in young children and mothers: An introduction to the freeBILy project
2020-07-14

Schistosoma antigen detection tests have a large potential for schistosomiasis control programs due to their ability to detect active and ongoing Schistosoma infections, their much higher sensitivity compared to microscopical methods, and the possibility to use non-invasive urine samples. Pregnant women and young children could especially benefit from affordable and easy-to-use antigen tests as inclusion of these vulnerable groups in mass drug administration campaigns will always require higher justification hurdles, especially in low to middle endemic regions with a higher proportion of individuals who are not infected and thus unnecessarily exposed to praziquantel. The overall objective of the 'fast and reliable easy-to-use diagnostics for eliminating bilharzia in young children and mothers' (freeBILy, www.freeBILy.eu) project is to thoroughly evaluate the point-of-care circulating cathodic antigen (POC-CCA) and the up-converting phosphor reporter particle, lateral flow circulating anodic antigen (UCP-LF CAA) urine strip tests to diagnose Schistosoma infections in pregnant women and young children and to assess their potential as a schistosomiasis control tool in test-and-treat strategies. The freeBILy project will generate valuable, evidence-based findings on improved tools and test-and-treat strategies to reduce the burden of schistosomiasis in pregnant women and young children.
Nutritional and metabolic regulation of the metabolite dimethylguanidino valeric acid: an early marker of cardiometabolic disease
2020-07-14

Dimethylguanidino valeric acid (DMGV) is a marker of fatty liver disease, incident coronary artery disease, cardiovascular mortality, and incident diabetes. Recently, it was reported that circulating DMGV levels correlated positively with consumption of sugary beverages and negatively with intake of fruits and vegetables in three Swedish community-based cohorts. Here, we validate these results in the Framingham Heart Study Third Generation Cohort. Furthermore, in mice, diets rich in sucrose or fat significantly increased plasma DMGV concentrations. DMGV is the product of metabolism of asymmetric dimethylarginine (ADMA) by the hepatic enzyme AGXT2. ADMA can also be metabolized to citrulline by the cytoplasmic enzyme DDAH1. We report that a high-sucrose diet induced conversion of ADMA exclusively into DMGV (supporting the relationship with sugary beverage intake in humans), while a high-fat diet promoted conversion of ADMA to both DMGV and citrulline. On the contrary, replacing dietary native starch with high-fiber-resistant starch increased ADMA concentrations and induced its conversion to citrulline, without altering DMGV concentrations. In a cohort of obese nondiabetic adults, circulating DMGV concentrations increased and ADMA levels decreased in those with either liver or muscle insulin resistance. This was similar to changes in DMGV and ADMA concentrations found in mice fed a high-sucrose diet. Sucrose is a disaccharide of glucose and fructose. Compared with glucose, incubation of hepatocytes with fructose significantly increased DMGV production. Overall, we provide a comprehensive picture of the dietary determinants of DMGV levels and association with insulin resistance.
Organic defaults in online‐shopping: Immediate effects but no spillover to similar choices
2020-07-14

Abstract Changing defaults—the preselection that becomes effective without active choice—is becoming a prominent policy tool, after having been proven to be effective in areas as varied as retirement savings, organ donation and product customization. Yet, little is known about how default effects spill over to subsequent similar behaviors. In an online shopping scenario, we found standard default effects on the share of organically produced products in the overall selection of products. These effects did not spill over to subsequent active shopping choices. This was true for defaults that were hard and easy to change (Exp. 1, N = 90), for immediate and delayed subsequent choices (Exp. 2, N = 106) and for self‐selected defaults (Exp. 3, N = 181). These findings suggest that the reach and scalability of default manipulations in policy making may be limited, but also speak against the possibility for negative spillover.
A New FGF21 Analog for the Treatment of Fatty Liver Disease
2020-07-14

Nonalcoholic fatty liver disease (NAFLD) describes a non–alcohol-induced cluster of conditions related to excessive fat stored in the liver. Defined as 5% or more hepatic fat content, NAFLD is prevalent, affecting ∼25% of the general population (1). Approximately 20% of individuals with NAFLD have a more aggressive form of the disease, termed nonalcoholic steatohepatitis (NASH), which is in addition characterized by liver inflammation and extensive scarring (cirrhosis) (1,2). NASH is a growing cause of liver cancer and a leading indication for liver transplantation (2). In addition, NAFLD and NASH are risk factors for chronic kidney disease (3), type 2 diabetes (4), and cardiovascular disease (5). Despite being serious afflictions, NAFLD and in particular NASH face two major headwinds. One, they are difficult to diagnose because they require liver biopsies for conclusive diagnosis. Two, there are currently no approved medications for treatment. Lifestyle intervention to reduce body weight is the primary strategy to manage the disease. However, while reducing caloric intake and increasing physical activity are obvious remedies, such lifestyle modification has very limited efficacy in the long run, with typically no more than 3–4% of weight loss after 4 years (6). With a quickly growing population of patients with NAFLD/NASH (2) and no approved therapies, there is an unmet yet steadily increasing medical need for safe and effective pharmacotherapy. Unfortunately, resembling the quest for the Holy Grail, the development of such a therapy seemed, as of today, a ...
Geomorphology of the upper Mkhomazi River basin, KwaZulu-Natal, South Africa, with emphasis on late Pleistocene colluvial deposits
2020-07-14

We present a 1:50 000 scale geomorphological map of the upper Mkhomazi River basin, located in the foothills of the Drakensberg mountains in KwaZulu-Natal Province, South Africa. The sub-horizontal strata of the Permo-Triassic Beaufort Group forms plateau interfluves with a concave valley slope morphology. Locally, thick sequences of late Pleistocene colluvial deposits and associated buried paleosols (Masotcheni Formation) infill first-order tributary stream valleys and extend across the adjacent lower slopes. Surface runoff processes preferentially incise into the poorly consolidated, highly erodible sediments causing severe gully erosion that is responsible for widespread land degradation and desertification phenomena. The main purpose of this work is to derive a geomorphological map of the study area focussing on the erosional landforms to understand their spatial distribution and their relation to the colluvial deposits. Finally, a local and regional stratigraphic correlation of colluvial deposits and associated buried palaeosol profiles is proposed.