Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Coronavirus-Induced Neuronal Programmed Cell Death 1 is Cyclophilin D-Dependent and Potentially Caspase-Dispensable 2 3 4

29 Human coronaviruses (HCoV) are recognized respiratory pathogens. Some HCoV 30 strains, including HCoV-OC43, can invade the central nervous system where they infect 31 neurons, with unclear consequences. We have previously reported that HCoV-OC43 32 infection of human neurons activates the unfolded protein response and caspase-3, induces 33 cell death, and that the viral spike (S) glycoprotein is involved in the process. We now 34 report underlying mechanisms associated with the induction of programmed cell death 35 (PCD) after infection by reference HCoV-OC43 virus (rOC/ATCC) and a more 36 neurovirulent and cytotoxic HCoV-OC43 variant harboring two point mutations in the S 37 glycoprotein (rOC/US183-241). Even though caspase-3 and caspase-9 were both activated 38 after infection, the use of caspase inhibitors neither reduced nor delayed virus-induced 39 PCD, suggesting that these proteases are not essential in the process. On the other hand, the 40 pro-apoptotic proteins BAX, cytochrome C (CytC) and apoptosis-inducing factor (AIF) 41 were relocalized towards mitochondria, cytosol and nucleus, respectively, after infection 42 by both virus variants. Moreover, LA-N-5 neuronal cells treated with cyclosporin A (CsA), 43 an inhibitor of the mitochondrial permeabilization transition pore (mPTP) or knocked44 down for cyclophilin D (CypD), were completely protected from rOC/ATCC-induced 45 neuronal PCD, underlining the involvement of CypD in the process. On the other hand, 46 CsA and CypD knock-down had moderate effects on rOC/US183-241-induced PCD. In 47 conclusion, our results are consistent with mitochondrial AIF and cyclophilin D being 48 central in HCoV-OC43-induced PCD, while caspases appear not to be essential. 49 50 on July 4, 2017 by gest http/jvi.asm . rg/ D ow nladed fom
Phototrophic and heterotrophic pico- and nanoplankton in anoxic depths of the central Baltic Sea

An unexpected increase of phototrophic and heterotrophic picoand nanoplankton under anoxic conditions was encountered in the central Baltic Sea below 120 m depth in August 1991 and 135 m depth in July 1992, respectively. Cell abundances in anoxic layers were up to 10 times higher for chroococcoid cyanobacteria, 6 to 8 times for phototrophic nanoflagellates and 3 to 4 times for bacteria, as compared to the overlaying aphotic oxic layers. A characteristic ciliate community occurred at the oxic/anoxic interface. Phototrophic organisms of anoxic depths were capable of productivity when reoxygenated and returned into the light. Considerable grazing on bacteria (0.41 to 0.65 d ' ) and chroococcoid cyanobacteria (1.19 to 1.29d-') was revealed by serial dilution experiments. Cyanobacteria showed gross growth rates of 0.85 to 1.33 d' under aphotic/anoxic conditions. The origin of deep-water phototrophic picoand nanoplankton and the existence of a permanent anaerobic microbial food web are discussed. A number of investigations have emphasized the occurrence of procaryotic and eucaryotic picoand nanoplankton in the oxic deep-sea (Hamilton et al. 1968, Fournier 1970, 1971, Silver & Alldredge 1981, Platt et al. 1983, Davis et al. 1985, Silver et al. 1986, Lochte & Turley 1988). Little information exists, however, on picoand nanoplankton in anoxic depths. For nearshore areas, recent investigations revealed distinct populations at the oxic/anoxic interface and in anoxic near-bottom layers (Fenchel et al. 1990). Anoxic conditions are typical for the deep basins of the Baltic Sea (Matthaus 1986). The present paper describes our observations of the occurrenceof phototrophic and heterotrophic picoand nanoplankton in deep anoxic water layers of the Gotland Basin, central Baltic Sea. We discuss whether these unique biotas are of overall significance for the interpretation of the Baltic ecosystem. Material and methods. Data presented were collected during RV 'Alkor' cruises BAMBI '91 and BAMBI '92 (Baltic Microbial Biology Investigation) in August 1991 (8 d drift study) and July 1992 (9 d drift study) in the eastern part of the Gotland Sea, central
Computational Modeling of Moral Decisions

The cognitive processes that give rise to moral decisions have long been the focus of intense study. Here I illustrate how computational approaches to studying moral decision-making can advance this endeavor. Computational methods have traditionally been employed in the domains of perceptual and reward-based learning and decision-making, but until recently had not been applied to the study of moral cognition. Using examples from recent studies I show how computational properties of choices provide can provide novel insights into moral decision-making. I conclude with an exploration of new research avenues that arise from these insights, such as how uncertainty in choice shapes morality, and how moral decision-making can be viewed as a learning process.
Machine Learning Winter 2018 Lecture 7 : Regression

This script reviews optimal design in linear experiments, where the goal is to pick a small number of design points (input data points, or feature vectors) from the space of possible data points so that the underlying model, which relates input variables to output responses, is estimated accurately. The chosen set of input data points makes up one particular design, and the problem of finding an optimal (small) design is of interest in many regression settings. For example, in an experiment there might be substantial cost associated with measuring the response of each trial (input vector). The experimenter could then employ optimal design to estimate the model using as few trials as possible. Another popular use case is in the big data domain, where it might be computationally intractable to perform regression on the entire data set. Optimal design can be used to select a subset of the data that estimates the model efficiently. Also, as is reviewed in the scribe, optimal design has applications in bandit problems, especially linear bandits. This script aims to serve as scribe notes for the seventh lecture of CSE 599, with extensions mainly based on the work of [1].
Modeled effects of an improved building insulation scenario in Europe on air pollution, health and societal costs

Contexte : en Europe, une partie importante de l'energie produite est utilisee pour le chauffage domestique et pour la climatisation. La qualite de l'isolation des bâtiments a ainsi un impact significatif sur la pollution de l'air.Objectifs : modeliser et calculer les effets d'une amelioration importante de l'isolation des bâtiments existants en Europe sur les niveaux de pollution de l'air, sur la sante et sur l'economie.Methodes : l'energie utilisee dans deux scenarios differents a ete comparee entre 2005 et 2020 : un scenario d’un programme de l'isolation des bâtiments existants en Europe et un scenario de statu quo. Les variations des emissions issues de ces deux scenarios ont ete integrees dans un modele de la qualite de l'air (the Comprehensive Air-Quality Model with extensions). Les variations annuelles moyennes des principaux polluants atmospheriques ont ete calculees pour chaque pays. Des donnees venant de l’Organisation Mondiale de la Sante (OMS) et de l'Union Europeenne (UE) sur les populations et sur les impacts des polluants ont ete utilisees pour deduire quels sont les effets sur la sante et l’economie. La qualite de l'air interieur ne faisait pas partie de l’etude.Resultats : avec le programme de l'isolation des bâtiments existants en Europe, les niveaux moyens annuels de la pollution atmospherique particulaire fine (PM2,5) variaient de -0,008 µg/m3 (Finlande) a -0,538 µg/m3 (Belgique). Le nombre moyen d'annees de vie gagne par annee par 100 000 adultes etait de 24,3 (intervalle de confiance 95 % de 0,9 a 54,5). Le nombre total d'annees de vie gagnees chaque annee variait, selon les pays, entre 31 en Finlande a 22 524 en Allemagne. Le nombre total d'annees de vie gagnees etait de 78 678 en Europe. Un total de 7 173 cas de bronchite chronique pourrait etre evite chaque annee. Plusieurs autres effets sur la sante etaient ameliores de facon similaire. Les couts pour la societe s’elevaient a 6,64 milliards d’euros par an.Conclusions : en plus de la reduction des emissions de carbone, un programme de l'isolation des bâtiments existants en Europe aurait des avantages substantiels sur la sante grâce a l’amelioration de la pollution atmospherique. Les effets sur la sante et sur l’economie peuvent contrebalancer de facon significative les couts d'investissement et devraient etre pris en compte lors de l'evaluation des strategies d'attenuation du rechauffement climatique.
What creates a valuable cue? The underestimated importance of a cues diagnostic value over the encoding retrieval match for successful memory retrieval

The aim of this study is to investigate the importance of a diagnostic cue over the mere contextual overlap between encoding and retrieval in successful retention. A cued recognition test was conducted to investigate the power of a contextual cues diagnostic value in successful retrieval of memories. Participants were presented with word pairs together with a picture background in three different conditions, (1) baseline, containing no contextual overlap thus no contextual retrieval cues (2) non-diagnostic, with the context being associated with several word pairs and (3) diagnostic, with the context only being associated with one target word. The participants were asked to focus on the word pairs, making the contextual cue task irrelevant. The presented hypothesis assumes a higher accuracy for the diagnostic condition in relation to other conditions. Results showed a significantly higher level of recognition accuracy for the diagnostic condition in relation to the baseline condition and the non-diagnostic condition, supporting the hypothesis. The results provide additional support to the importance of a cues diagnostic value, while at the same time using contextual cues rather than semantic cues, which has not been done before.
Glycosphingolipids in HIV/AIDS: The Potential Therapeutic Application

It has been 30 years since the original description of acquired immunodeficiency syndrome (AIDS) was first reported (Gottlieb et al., 1981). Since this initial discovery, human immunodeficiency virus (HIV) and HIV pathogenesis ranks near the top as one of the most studied human diseases in the history of medical science. Unfortunately, we are no closer now than we were back in the early 1980s at finding a cure. Although there has been significant progress in treatment, there continues to be an increase in the numbers of infected people and those dying from AIDS throughout the world. Current dogma says that HIV type 1 (HIV-1) is the most common HIV virus and that it infects immune cells called helper T-cells. HIV can also infect other cells involved in the immune response such as monocytes, macrophages and dendritic cells. The virus has an envelope that mediates its tropism for immune cells. The viral envelope protein gp120 first recognizes and binds to the CD4 molecule located on the cell-surface of CD4+ helper T-cells (Dalgleish et al., 1984). Although researchers insisted for over a decade that CD4 was the only cellular receptor required for HIV to infect cells, some in the research community were sceptical and aware from clinical and laboratory findings that something else must be required for HIV infection. Indeed, in 1996 it was discovered that CD4 does not act alone. Another family of cell-surface receptors, the chemokine receptors, were shown to be required, in conjunction with CD4, for successful infection with HIV-1 (Feng et al., 1996, Alkhatib et al., 1996). These receptors are important for the tropism of the virus. Thus, the CXCR4 chemokine receptor, directs infection of T cells by T cell-tropic HIV-1, whereas the CCR5 and CCR3 chemokine receptors are responsible for infection of monocytes with monocyte-tropic HIV-1 virions. However, as more studies were undertaken, it became clear that many other chemokine receptors could support HIV-1 infection and that the tropism was directed more to the chemokine co-receptor than to the cell type. Thus, HIV viruses that require CXCR4 are now known as X4 HIV-1 while virus that recognizes CCR5, or other members of this family of chemokine receptor, are now known as R5 HIV-1. (Dragic et al., 1996, Littman, 1998). Thus, the current paradigm for
Thermal Barrier Coating Life Prediction Model Development

A methodology is established to predict thermal barrier coating life in a environment similar to that experienced by gas turbine airfoils. Experiments were conducted to determine failure modes of the thermal barrier coating. Analytical studies were employed to derive a life prediction model. A review of experimental and flight service components as well as laboratory post evaluations indicates that the predominant mode of TBC failure involves thermomechanical spallation of the ceramic coating layer. This ceramic spallation involves the formation of a dominant crack in the ceramic coating parallel to and closely adjacent to the topologically complex metal ceramic interface. This mechanical failure mode clearly is influenced by thermal exposure effects as shown in experiments conducted to study thermal pre-exposure and thermal cycle-rate effects. The preliminary life prediction model developed focuses on the two major damage modes identified in the critical experiments tasks. The first of these involves a mechanical driving force, resulting from cyclic strains and stresses caused by thermally induced and externally imposed mechanical loads. The second is an environmental driving force based on experimental results, and is believed to be related to bond coat oxidation. It is also believed that the growth of this oxide scale influences the intensity of the mechanical driving force.
Simultaneous retrieval of water vapour, temperature and cirrus clouds properties from measurements of far infrared spectral radiance over the Antarctic Plateau

Abstract. The possibility separating the contributions of the atmospheric state and ice clouds by using spectral infrared measurements is a fundamental step to quantifying the cloud effect in climate models. A simultaneous retrieval of cloud and atmospheric parameters from infrared wideband spectra will allow the disentanglement of the spectral interference between these variables. In this paper, we describe the development of a code for the simultaneous retrieval of atmospheric state and ice cloud parameters, and its application to the analysis of the spectral measurements acquired by the Radiation Explorer in the Far Infrared – Prototype for Applications and Development (REFIR-PAD) spectroradiometer, which has been in operation at Concordia Station on the Antarctic Plateau since 2012. The code performs the retrieval with a computational time that is comparable with the instrument acquisition time. Water vapour and temperature profiles and the cloud optical and microphysical properties, such as the generalised effective diameter and the ice water path, are retrieved by exploiting the 230–980 cm−1 spectral band. To simulate atmospheric radiative transfer, the Line-By-Line Radiative Transfer Model (LBLRTM) has been integrated with a specifically developed subroutine based on the δ-Eddington two-stream approximation, whereas the single-scattering properties of cirrus clouds have been derived from a database for hexagonal column habits. In order to detect ice clouds, a backscattering and depolarisation lidar, co-located with REFIR-PAD has been used, allowing us to infer the position and the cloud thickness to be used in the retrieval. A climatology of the vertical profiles of water vapour and temperature has been performed by using the daily radiosounding available at the station at 12:00 UTC. The climatology has been used to build an a priori profile correlation to constrain the fitting procedure. An optimal estimation method with the Levenberg–Marquardt approach has been used to perform the retrieval. In most cases, the retrieved humidity and temperature profiles show a good agreement with the radiosoundings, demonstrating that the simultaneous retrieval of the atmospheric state is not biased by the presence of cirrus clouds. Finally, the retrieved cloud parameters allow us to study the relationships between cloud temperature and optical depth and between effective particle diameter and ice water content. These relationships are similar to the statistical correlations measured on the Antarctic coast at Dumont d'Urville and in the Arctic region.
How Companies Learn Your Secrets

Pole has a master’s degree in statistics and another in economics, and has been obsessed with the intersection of data and human behavior most of his life. His parents were teachers in North Dakota, and while other kids were going to 4-H, Pole was doing algebra and writing computer programs. “The stereotype of a math nerd is true,” he told me when I spoke with him last year. “I kind of like going out and evangelizing analytics. ”
DOES NUTRITION LABELING LEAD TO HEALTHIER EATING

Nutrient labeling is found to significantly affect consumer purchase behavior; some evidence that consumers may act as if they hold nutrient (or health risk) budgets is found. Providing nutrient information may allow consumers to more easily switch consumption away from "unhealthy" products in those food categories where differences in other quality characteristics (e.g., taste) are relatively small between the more and less "healthy" products, toward "unhealthy" products in categories where differences may be relatively large (i.e., a "substitution effect"). If this substitution effect is large, nutrient labeling may not change the overall consumption of "unhealthy" nutrients and thus may not lead to significant changes in health risk.
Conceptual model uncertainty in groundwater modeling: Combining generalized likelihood uncertainty estimation and Bayesian model averaging

Uncertainty assessments in groundwater modeling applications typically attribute all sources of uncertainty to errors in parameters and inputs, neglecting what may be the primary source of uncertainty, namely, errors in the conceptualization of the system. Confining the set of plausible system representations to a single model leads to underdispersive and prone‐to‐bias predictions. In this work, we present a general and flexible approach that combines generalized likelihood uncertainty estimation (GLUE) and Bayesian model averaging (BMA) to assess uncertainty in model predictions that arise from errors in model structure, inputs, and parameters. In a prior analysis, a set of plausible models is selected, and the joint prior input and parameter space is sampled to form potential simulators of the system. For each model, the likelihood measures of acceptable simulators, assigned to them based on their ability to reproduce observed system behavior, are integrated over the joint input and parameter space to obtain the integrated model likelihood. The latter is used to weight the predictions of the respective model in the BMA ensemble predictions. For illustrative purposes, we applied the methodology to a three‐dimensional hypothetical setup. Results showed that predictions of groundwater budget terms varied considerably among competing models; despite this, a set of 16 head observations used for conditioning did not allow differentiating between the models. BMA provided average predictions that were more conservative than individual predictions obtained for individual models. Conceptual model uncertainty contributed up to 30% of the total uncertainty. The results clearly indicate the need to consider alternative conceptualizations to account for model uncertainty.
Title Expression of Siamois and Twin in the blastula Chordin / Noggin signaling center is required for brain formation in Xenopus laevis embryos

Expression of Siamois and Twin in the blastula Chordin/Noggin signaling center is required for brain formation in Xenopus laevis embryos Abstract The blastula Chordin and Noggin expressing (BCNE) center located in the dorsal animal region of the Xenopus blastula embryo contains both prospective anterior neuroectoderm and Spemann organizer precursor cells. Here we show that, contrary to previous reports, the canonical Wnt target homeobox genes, Siamois and Twin function in the BCNE center. Double knockdown of these genes using antisense morpholinos in Xenopus laevis blocked head formation, reduced the expression of the other BCNE center genes, upregulated Bmp4 expression, and nullified hyperdorsalization by lithium chloride. Moreover, gain-and loss-of-function experiments showed that Siamois and Twin expression is repressed by the vegetal transcription factor VegT. We propose that VegT expression causes maternal β-Catenin signals to restrict Siamois and Twin expression to the BCNE region. A two-step inhibition of BMP signals by Siamois and Twin – first by transcriptional repression of BMP4 and then by activation of the expression of the BMP inhibitors Chordin and Noggin-in the BCNE center is required for head formation.
UNUSUAL 29,30Si-RICH SiCs OF MASSIVE STAR ORIGIN FOUND WITHIN GRAPHITES FROM THE MURCHISON METEORITE

Correlated transmission electron microscopy and NanoSIMS isotopic studies have revealed two unusual SiCs with large 29,30Si enrichments within micron-sized graphites from the Murchison meteorite. Such anomalies are rare among the overall SiC population (in ≪0.01% of SiCs yet measured), whereas two of the three SiCs found within graphite show 29,30Si enrichments, in one case as large as 29Si/28Si = (2.28 ± 0.03) × solar and 30Si/28Si = (2.03 ± 0.03)× solar. C-burning and Ne-burning in massive stars (>8 M☉ initial mass) during their post-main-sequence development are the only processes capable of producing sufficiently large 29,30Si enrichments. This material with heavy Si isotopic enrichments from the O/Ne and O/Si layers is later incorporated into carbonaceous stardust, either in ejecta from Type II supernovae or perhaps in the colliding winds of Wolf–Rayet binaries. Although often too small for Si isotopic measurements, four other SiC-containing graphites show other signatures of a massive star origin. Abundance estimates suggest that such unusual SiCs are present within ∼1% of high-density graphites. This abundance can be reconciled with the much lower abundance in the overall SiC population if these unusual SiCs are naturally smaller (∼200 nm or less) than SiCs from other isotopic subgroups and if differential destruction of small unusual SiCs occurs in massive star outflows unless these SiCs are encapsulated in graphite.