nils-herrmann/clean_scirepeval huggingface dataset:
Coexisting Liquid Phases Underlie Nucleolar Subcompartments
Venue: Cell

The nucleolus and other ribonucleoprotein (RNP) bodies are membrane less organelles that appear to assemble through phase separation of their molecular components. However, many such RNP bodies contain internal subcompartments, and the mechanism of their formation remains unclear. Here, we combine in vivo and in vitro studies, together with computational modeling, to show that subcompartments within the nucleolus represent distinct, coexisting liquid phases. Consistent with their in vivo immiscibility, purified nucleolar proteins phase separate into droplets containing distinct non coalescing phases that are remarkably similar to nucleoli in vivo. This layered droplet organization is caused by differences in the biophysical properties of the phases particularly droplet surface tension which arises from sequence encoded features of their macromolecular components. These results suggest that phase separation can give rise to multilayered liquids that may facilitate sequential RNA processing reactions in a variety of RNP bodies. PAPERCLIP.
Metalenses at visible wavelengths: Diffraction limited focusing and subwavelength resolution imaging
Venue: Science

Multifunction planar optics Specially designed two dimensional (2D) arrays of nanometer scale metallic antennas, or metasurfaces, may allow bulky optical components to be shrunk down to a planar device structure. Khorasaninejad et al. show that arrays of nanoscale fins of TiO can function as high end optical lenses. At just a fraction of the size of optical objectives, such planar devices could turn your phone camera or your contact lens into a compound microscope. Maguid et al. interleaved sparse 2D arrays of metal antennas to get multifunctional behavior from the one planar device structure (see the Perspective by Litchinitser) The enhanced functionality of such designed metasurfaces could be used in sensing applications or to increase the communication capacity of nanophotonic networks. Science, this issue pp. 1190 and 1202; see also p. 1177 A planar metasurface can function as a high end optical lens. Subwavelength resolution imaging requires high numerical aperture (NA) lenses, which are bulky and expensive. Metasurfaces allow the miniaturization of conventional refractive optics into planar structures. We show that high aspect ratio titanium dioxide metasurfaces can be fabricated and designed as metalenses with NA 0.8. Diffraction limited focusing is demonstrated at wavelengths of 405, 532, and 660 nm with corresponding efficiencies of 86, 73, and 66% The metalenses can resolve nanoscale features separated by subwavelength distances and provide magnification as high as 170x, with image qualities comparable to a state of the art commercial objective. Our results firmly establish that metalenses can have widespread applications in laser based microscopy, imaging, and spectroscopy.
Getting (Along) With the Guidelines: Reconciling Patient Autonomy and Quality Improvement Through Shared Decision Making
Venue: Academic medicine journal of the Association of American Medical Colleges

In past decades, stark differences in practice pattern, cost, and outcomes of care across regions with similar health demographics have prompted calls for reform. As health systems answer the growing call for accountability in the form of quality indices, while responding to increased scrutiny on practice variation in the form of pay for performance (P4P) a rift is widening between the system and individual patients. Currently, three areas are inadequately considered by P4P structures based largely on physician adherence to guidelines: diversity of patient values and preferences; time and financial burden of therapy in the context of multimorbidity; and narrow focus on quantitative measures that distract clinicians from providing optimal care. As health care reform efforts place greater emphasis on value for money of care delivered, they provide an opportunity to consider the other "value" the values of each patient and care delivery that aligns with them. The inherent balance of risks and benefits in every treatment, especially those involving chronic conditions, calls for engagement of patients in decision making processes, recognizing the diversity of preferences at the individual level. Shared decision making (SDM) is an attractive option and should be an essential component of quality health care rather than its adjunct. Four interwoven steps toward the meaningful implementation of SDM in clinical practice embedding SDM as a health care quality measure, "real world" evaluation of SDM effectiveness, pursuit of an SDM favorable health system, and patient centered medical education are proposed to bring focus back to the beneficiary of health care accountability, the patient.
Evaluating the impact of visualization of wildfire hazard upon decision making under uncertainty
Venue: Int. J. Geogr. Inf. Sci.

The paper investigates whether the methods chosen for representing uncertain geographic information aid or impair decision making in the context of wildfire hazard. Through a series of three human subject experiments, utilizing 180 subjects and employing increasingly difficult tasks, this research evaluates the effect of five different visualizations and a text based representation on decision making under uncertainty. Our quantitative experiments focus specifically on the task of decision making under uncertainty, rather than the task of reading levels of uncertainty from the map. To guard against the potential for generosity and risk seeking in decision making under uncertainty, the experimental design uses performance based incentives. The experiments showed that the choice of representation makes little difference to performance in cases where subjects are allowed the time and focus to consider their decisions. However, with the increasing difficulty of time pressure, subjects performed best using a spectral color hue based representation, rather than more carefully designed cartographic representations. Text based and simplified boundary encodings were among the worst performers. The results have implications for the performance of decision making under uncertainty using static maps, especially in the stressful environments surrounding an emergency.
Reconstruction of cohort data via EM algorithm

Usually cross sectional data are used instead of longitudinal data in the study of mortality because the cohort data has not a conclude distribution. Sometimes this choice can be questionable and not correct for the goal of the research. We introduce a new methodology that is useful to estimate the missing deaths and to construct the mortality table for an incomplete cohort. The Estimation Maximization (EM) algorithm is generally employed when there are missing data and we want to compute the maximum likelihood. As model we used a mixture of distributions: one Half Normal ad two Shew Normals. We tested the accuracy of the method comparing the estimate number of deaths obtained from the complete data with the estimates found by using EM algorithm. We employed the bootstrap method to compute the confidence intervals. We discovered that the two sets of measures are very close and the confidence intervals are not far from the true distribution. We applied our method to reconstruct the cohort data for different countries of the Human Mortality Database. We estimated the life expectancy at birth and also its confidence interval using bootstrapping.
Automated Retinal Image Analysis for Evaluation of Focal Hyperpigmentary Changes in Intermediate Age Related Macular Degeneration
Venue: Translational vision science technology

To develop and evaluate a software tool for automated detection of focal hyperpigmentary changes (FHC) in eyes with intermediate age related macular degeneration (AMD) Methods Color fundus (CFP) and autofluorescence (AF) photographs of 33 eyes with FHC of 28 AMD patients (mean age 71 years) from the prospective longitudinal natural history MODIAMD study were included. Fully automated to semiautomated registration of baseline to corresponding follow up images was evaluated. Following the manual circumscription of individual FHC (four different readings by two readers) a machine learning algorithm was evaluated for automatic FHC detection.  The overall pixel distance error for the semiautomated (CFP follow up to CFP baseline: median 5.7; CFP to AF images from the same visit: median 6.5) was larger as compared for the automated image registration (4.5 and 5.7; P 0.001 and P 0.001) The total number of manually circumscribed objects and the corresponding total size varied between 637 to 1163 and 520,848 pixels to 924,860 pixels, respectively. Performance of the learning algorithms showed a sensitivity of 96% at a specificity level of 98% using information from both CFP and AF images and defining small areas of FHC "speckle appearance" as "neutral."  FHC as a high risk feature for progression of AMD to late stages can be automatically assessed at different time points with similar sensitivity and specificity as compared to manual outlining. Upon further development of the research prototype, this approach may be useful both in natural history and interventional large scale studies for a more refined classification and risk assessment of eyes with intermediate AMD. Translational Relevance Automated FHC detection opens the door for a more refined and detailed classification and risk assessment of eyes with intermediate AMD in both natural history and future interventional studies.
Fatty acids, eicosanoids and PPAR gamma.
Venue: European journal of pharmacology

Peroxisome proliferator activated receptor g (PPARg) belongs to the family of nuclear nuclear receptors and is mainly expressed in adipose tissue, hematopoietic cells and the large intestine. Contrary to other nuclear receptors that mainly bind a single specific ligand, there are numerous natural PPARg ligands, in particular fatty acids or their derivatives called eicosanoids. PPARg have pleiotropic functions: (i) glucose and lipid metabolism regulation, (ii) anti inflammatory properties, (iii) oxidative stress inhibition, (iv) improvement of endothelial function. Its role has been mainly studied by the use synthetic agonists. In this review, we will focus on the effects of PPARg mediated through fatty acids and how these have beneficial health properties.
IL 1b, IL 18, and eicosanoids promote neutrophil recruitment to pore induced intracellular traps following pyroptosis
Venue: European journal of immunology

Inflammasomes activate caspase 1, initiating a lytic form of programmed cell death termed pyroptosis, which is an important innate immune defense mechanism against intracellular infections. We recently demonstrated in a mouse infection model of pyroptosis that instead of releasing bacteria into the extracellular space, bacteria remain trapped within the pyroptotic cell corpse, termed the pore induced intracellular trap (PIT) This trapping mediates efferocytosis of the PIT and associated bacteria by neutrophils; bacteria are subsequently killed via neutrophil ROS. Using this pyroptosis model, we now show that the pro inflammatory cytokines IL 1b and IL 18 and inflammatory lipid mediators termed eicosanoids are required for effective clearance of bacteria downstream of pyroptosis. We further show that IL 1b, IL 18, and eicosanoids affect this in part by mediating neutrophil recruitment to the PIT. This is in addition to our prior findings that complement is also important to attract neutrophils. Thus, the PIT initiates a robust and coordinated innate immune response involving multiple mediators that attract neutrophils to efferocytose the PIT and its entrapped bacteria.
Bayesian Multi Task Relationship Learning with Link Structure
Venue: IEEE Trans. Knowl. Data Eng.

In this paper, we study the multi task learning problem with a new perspective of considering the link structure of data and task relationship modeling simultaneously. In particular, we first introduce the Matrix Gaussian (MG) distribution and Matrix Generalized Inverse Gaussian (MGIG) distribution, then define a Matrix Gaussian Matrix Generalized Inverse Gaussian (MG MGIG) prior. Based on this prior, we propose a novel multi task learning algorithm, the Bayesian Multi task Relationship Learning (BMTRL) algorithm. To incorporate the link structure into the framework of BMTRL, we propose link constraints between samples. Through combining the BMTRL algorithm with the link constraints, we propose the Bayesian Multi task Relationship Learning with Link Constraints (BMTRL LC) algorithm. Further, we apply the manifold theory to provide an extension of BMTRL LC to data with  To make the computation tractable, we simultaneously use a convex optimization method and sampling techniques. In particular, we adopt two stochastic EM algorithms for BMTRL and BMTRL LC, respectively. The experimental results on three real datasets demonstrate the promise of the proposed algorithms.
Deep API learning
Venue: SIGSOFT FSE

Developers often wonder how to implement a certain functionality (e.g. how to parse XML files) using APIs. Obtaining an API usage sequence based on an API related natural language query is very helpful in this regard. Given a query, existing approaches utilize information retrieval models to search for matching API sequences. These approaches treat queries and APIs as bags of words and lack a deep understanding of the semantics of the query. We propose DeepAPI, a deep learning based approach to generate API usage sequences for a given natural language query. Instead of a bag of words assumption, it learns the sequence of words in a query and the sequence of associated APIs. DeepAPI adapts a neural language model named RNN Encoder Decoder. It encodes a word sequence (user query) into a fixed length context vector, and generates an API sequence based on the context vector. We also augment the RNN Encoder Decoder by considering the importance of individual APIs. We empirically evaluate our approach with more than 7 million annotated code snippets collected from GitHub. The results show that our approach generates largely accurate API sequences and outperforms the related approaches.
Politics Among Nations: Revisiting a Classic
Venue: Ethics #x0026; International Affairs

When introducing Politics Among Nations to his readers in the fall of 1948, Hans Morgenthau was explicit about the volume's ultimate purpose. His book was neither "disinterested" nor did it mean to offer "knowledge for its own sake." Rather, the author meant to render both a real and practical service to his fellow countrymen. A series of factors had "completely reversed" the geopolitical status of the United States. It now held a position of predominant power in the world, and hence of foremost responsibility. Therefore, "the understanding of the forces that mold international politics and of the factors that determine its course has become more than an interesting intellectual occupation. It has become a vital necessity."
Trait lasting alteration of the brain default mode network in experienced meditators and the experiential selfhood

Based on the finding in novices that four months of meditation training significantly increases frontal default mode network (DMN) module/subnet synchrony while decreasing left and right posterior DMN modules synchrony, the current study tested the prediction whether experienced meditators (those who are practising meditation intensively for several years) had a change in the DMN "trinity" of modules as a baseline trait characteristic and whether this change is in a similar direction as in the novice trainees who practised meditation for only four months. Comparison of functional connectivity within DMN subnets (measured by electroencephalogram operational synchrony in the three separate DMN modules) between five experienced meditators and 10 naive participants (who were about to start the meditation training) fully support the prediction. Interpretation that links such DMN subnets changes to the three dimensional components of the experiential selfhood was proposed.
Lithospheric structure across the central Tien Shan constrained by gravity anomalies and joint inversions of receiver function and Rayleigh wave dispersion

Shear wave velocity structure across the central Tien Shan orogeny was generated by jointly inverting Rayleigh wave phase and group velocity with teleseismic P wave receiver functions at 40 broadband seismic stations. The inferred seismic structure was validated by forward modeling of the complete Bouguer anomaly data. The joint inversion result reveals larger crust thicknesses beneath the Kokshaal ~68 72 km) and Kyrgyz ranges ~62 64 km) while other units have crustal thicknesses between 48 and 58 km. A fast velocity layer (Vs 3.6 3.9 km/s) in the upper crust is found in some seismic stations within the Kazakh Shield. Our models show the presence of high velocity and density layers in the lowermost crust throughout the region, consistent with the presence of mafic/ultramafic lithologies. The large crustal thickness is associated with a thickened mafic layer in the lower crust, indicating that the thickened crust may be partly caused by magmatic underplating. The low velocity and density anomaly in the middle crust, and low upper mantle velocity observed in our model beneath the middle Tien Shan reflect the presence of partial melt in the crust due to the intrusion of hot mantle material. The lack of correlation between Moho depth and topography, together with the gravity results, suggests that the topographic compensation in the central Tien Shan is not confined to the crust. This requires significant support from the mantle to account for the relative high elevation of the middle Tien Shan.
Etica y bioetica en los profesionales de enfermeria

El estudio de la moral forma parte actualmente de una ciencia particular, la etica, la cual integra las ciencias sociales, es decir, aquellas que se ocupan de estudiar las relaciones establecidas entre los hombres en el proceso de produccion, reproduccion y distribucion de su vida material, relaciones que no se limitan, por supuesto, a las relaciones puramente economicas, sino que abarcan todas las relaciones sociales y materiales: produccion de bienes, lucha con la naturaleza, consumo, vida familiar, vida social, etc. La enfermeria ha ido desarrollando el contenido de su funcion a traves de la historia, como lo han hecho la medicina y otras profesiones, por lo que su historia puede dar razones de esta evolucion, que se ha hecho irreversible para convertirse en una profesion sin perder la originalidad de su esencia: el cuidado. Los conceptos eticos aplicados a la enfermeria revisten la responsabilidad de la misma y como tal se refieren a mantener y restaurar la salud, evitar las enfermedades, aliviar el sufrimiento y contribuir a la rehabilitacion del enfermo. Con este trabajo de revision se exponen algunos aspectos relacionados con la etica y la bioetica en la actuacion del profesional de enfermeria. Se concluye que la enfermeria desarrolla las acciones propias de la profesion bajo principios de calidad, eficiencia, eficacia, equidad y respeto al ser humano, haciendo uso de los valores eticos y morales en todos los actos profesionales, con lo que contribuye al mejoramiento de la salud y calidad de vida de la poblacion en general.
Recency Bounded Verification of Dynamic Database Driven Systems
Venue: PODS

We propose a formalism to model database driven systems, called database manipulating systems (DMS) The actions of a (DMS) modify the current instance of a relational database by adding new elements into the database, deleting tuples from the relations and adding tuples to the relations. The elements which are modified by an action are chosen by (full) first order queries. (DMS) is a highly expressive model and can be thought of as a succinct representation of an infinite state relational transition system, in line with similar models proposed in the literature. We propose monadic second order logic (MSO FO) to reason about sequences of database instances appearing along a run. Unsurprisingly, the linear time model checking problem of (DMS) against (MSO FO) is undecidable. Towards decidability, we propose under approximate model checking of (DMS) where the under approximation parameter is the "bound on recency" In a k recency bounded run, only the most recent k elements in the current active domain may be modified by an action. More runs can be verified by increasing the bound on recency. Our main result shows that recency bounded model checking of (DMS) against (MSO FO) is decidable, by a reduction to the satisfiability problem of MSO over nested words.
Bad Call: Technology's Attack on Referees and Umpires and How to Fix It

How technologies can get it wrong in sports, and what the consequences are?referees undermined, fans heartbroken, and the illusion of perfect accuracy maintained.Good call or bad call, referees and umpires have always had the final say in sports. Bad calls are more visible: plays are televised backward and forward and in slow motion. New technologies?the Hawk Eye system used in tennis and cricket, for example, and the goal line technology used in English football?introduced to correct bad calls sometimes get it right and sometimes get it wrong, but always undermine the authority of referees and umpires.  Call looks at the technologies used to make refereeing decisions in sports, analyzes them in action, and explains the consequences.Used well, technologies can help referees reach the right decision and deliver justice for fans: a fair match in which the best team wins. Used poorly, however, decision making technologies pass off statements of probability as perfect accuracy and perpetuate a mythology of infallibility. The authors re analyze three seasons of play in English Premier League football, and discover that goal line technology was irrelevant; so many crucial wrong decisions were made that different teams should have won the Premiership, advanced to the Champions League, and been relegated. Simple video replay could have prevented most of these bad calls. (Major League baseball learned this lesson, introducing expanded replay after a bad call cost Detroit Tigers pitcher Armando Galarraga a perfect game.)What matters in sports is not computer generated projections of ball position but what is seen by the human eye?reconciling what the sports fan sees and what the game official sees.