jimnoneill/paper-to-field-training huggingface dataset:
GEE-Assisted Forward Regression for Spatial Latent Variable Models

Field: Mathematics (Physical Sciences)

Multivariate spatial data, where multiple responses are recorded at a set of spatial locations, are widely collected in many disciplines. One common approach for analyzing such data is spatial generalized linear latent variable models (spatial GLLVMs), where the latent variables are used to model both the spatial correlation between locations and correlations between responses. However, inference such as variable selection for spatial GLLVMs is computationally demanding, as the marginal likelihood involves a high-dimensional and often intractable integral. To overcome this, we propose to use spatial generalized estimating equations (GEEs) to perform fast, GEE-assisted forward regression for spatial GLLVMs. Focusing on counts and nonnegative continuous responses, we use spatial GEEs to build a forward solution path by choosing the candidate variable which maximizes a score statistic at each point on the path. A model is then selected from this path based on a modified score information criterion. The proposed approach is computationally efficient, relying only on GEEs which are quick to update, coupled with a novel theoretical result linking the coefficients from spatial GEEs to that of spatial GLLVMs. We show that the proposed approach can asymptotically identify all truly important nonzero predictors in the underlying spatial GLLVM. Simulations demonstrate that, when the data are generated from a sparse spatial GLLVM, GEE-assisted forward regression performs well at recovering this sparsity, while taking only a fraction of the computation time required to fit just a single (saturated) spatial GLLVM. Supplementary materials for this article are available online.
Nucleotide sequence of the gamma chain gene of rat fibrinogen: conserved intronic sequences

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Journal Article Nucleotide sequence of the gamma chain gene of rat fibrinogen: conserved intronic sequences Get access John G. Morgan, John G. Morgan Search for other works by this author on: Oxford Academic PubMed Google Scholar Nikki J. Holbrook, Nikki J. Holbrook 1Laboratory of Molecular Genetics, Gerontology Research Center4940 Eastern Avenue, Baltimore, MD 21224, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Gerald R. Crabtree Gerald R. Crabtree Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 15, Issue 6, 25 March 1987, Pages 2774–2776, https://doi.org/10.1093/nar/15.6.2774 Published: 25 March 1987 Article history Received: 20 February 1987 Published: 25 March 1987
Highly variable salinity conditions at the Early Permian Mangrullo Formation (northeastern Uruguay): effects on the biota

Field: Earth and Planetary Sciences (Physical Sciences)

The shales, mudstones and limestones of the Mangrullo Formation (Early Permian, northeastern Uruguay) were deposited in a water body which progressively closed its connection with the open sea, producing a gradual restriction of the basin and an increasing of the salinity by evaporation under arid conditions. This unit contains a peculiar biota, characterized by its low diversity and great abundance, attributes that became particularly evident at the time of highest restriction, when mesosaurs and pygocephalomorph crustaceans colonized the basin. At that time, a system of hypersaline lagoons could have been established, which is coherent with ecological, morphological and geological evidence. The increasing salinity could strongly affect the biota at the base of the unit, which probably lived under brackish to freshwater conditions. Thus, fishes, mollusks, conchostracans and bioturbating organisms become totally absent, just before the first mesosaurs appear. An extremely low diverse community dominated by two or at most three species joining mesosaurs, pygocephalomorphs, and the ichnofossil Chondrites (the "mesosaur community") substituted the fish-dominated biota. Mesosaurs and pygocephalomorphs developed adaptive structures (e.g., salt glands and marsupial chambers) to favor osmoregulation in such specialized environments. Evaporitic gypsum crystals around the fossils suggest seasonal drying, that along with evidence of nearest volcanic activity could have affected the components of the mesosaur community. They become extinct before a new fish-dominated biota appears at the upper mudstones of the unit, suggesting a reestablishment of the connection with the open sea.
The Contributions of CA1, CA2, and CA3 to Hippocampal Coding for Temporal and Spatial Context

Field: Neuroscience (Life Sciences)

Memories for autobiographical events contain information not only about what happened, but also about when and where. The hippocampus is known to be critical for organizing autobiographical memories, yet little is known about how the temporal context of a memory is represented there, especially on the timescale of hours to days. We sought to elucidate the coding mechanisms used by the hippocampus to represent the spatio-temporal context of events. In our experimental paradigm, rats performed random foraging tasks twice a day for several days, as we conducted electrophysiological recordings in three subregions of the hippocampus, CA1, CA2, and CA3. By recording from the same cells for 30 or more hours, we were able to evaluate the impact of passing time on the representation of identical events in each of these subregions. We performed these experiments within two distinct arenas, allowing us to explore coding for spatial context in addition to temporal context. We found that the population of cells in CA3 showed robust coding for spatial context that was very stable for a period of at least 30 hours. Conversely, neuronal ensembles in CA2 were highly variable on the time scale of hours to days, with the change in time overshadowing change with spatial context. Finally, CA1, which receives input from each of these regions, showed a gradual change with time while also coding strongly for spatial context. These findings correspond well with theoretical predictions that time- stamped memories may be generated by combining a stable content signal with a time-varying temporal context signal. We thus propose that CA2 provides temporal context information to CA1, while CA3 provides stable information about space and spatial context, allowing CA1 to represent both types of information simultaneously
Soil Nutrients and Traditional Agriculture on Young Volcanic Soils on Ta’ū, American Samoa

Field: Agricultural and Biological Sciences (Life Sciences)

Soils and agriculture are inextricably linked, in the past as well as today. How and where people developed agriculture based on soil and landscape properties has not been well developed in the Pacific. Pacific Islands, which often represent nicely organized gradients of substrate age, rainfall, and soil type, represent excellent study systems to understand this interaction between people and soils. Agriculture in Polynesia has been mostly subsistence, in the past and, in many islands, still today. While some agricultural forms have received intensive study, others still lack information and knowledge, particularly those that experienced abandonment following European contact. This is the case of extensive rainfed agricultural systems in the Manu’a islands of American Samoa. To understand prehistoric agricultural systems, we sampled along transects that crossed through intensive agriculture infrastructure in the upland of Fiti’uta on Ta’ū island. Soils were analyzed for several soil fertility properties that have been proposed as indicators of Polynesian agricultural intensification in related systems seen in Hawaii and Rapa Nui. Surveys of remnant economic plants were conducted along the same transects. Data suggest that the previously identified soil fertility indicators aligned well with the agricultural infrastructure on Ta’ū except for exchangeable calcium, which was significantly more depleted than other intensified agriculture in the Pacific. The soil fertility results also correlated well with the vegetation agricultural survey, specifically with the younger Ta’ū soils.
ALLELOPATHIC EFFECT OF AROMATIC AND MEDICINAL PLANTS ON TRIPLEUROSPERMUM INODORUM (L.) C.H. SCHULTZ

Field: Agricultural and Biological Sciences (Life Sciences)

The aim of the study was to evaluate the effect of six cultivated and wild aromatic and medicinal plants, basil (Ocimum basilicum L.), chamomile (Matricaria chamomilla L.), common mallow (Malva sylvestris L.), greater celandine (Chelidonium majus L.), lemon balm (Melissa officinalis L.) and lovage (Levisticum officinale Koch), on germination and growth of weed species scentless mayweed (Tripleurospermum inodorum (L.) C.H. Schultz). In total four experiments were conducted to assess the allelopathic potential of seed and plant aboveground biomass: I) seed cogermination in Petri dishes, II) seed cogermination in pots with soil, III) water extracts in Petri dishes and IV) plant residues in pots with soil. Weed seed germination was significantly reduced for 32.2% with lovage seeds in Petri dishes. In the pots with soil, seed allelopathic potential was less pronounced. The application of extracts from fresh plant biomass in concentrations of 5 and 10% reduced germination and growth of weed, with the extracts from chamomile and common mallow having the highest inhibitory effect. The extracts from dry plant biomass of basil, chamomile, common mallow, greater celandine and lovage in higher concentration completely (100%) inhibited germination and weed seedling growth. On average, the extracts from dry plant biomass had higher inhibitory effect. Reduction in weed seed emergence and growth was recorded when dry plant residues in rates of 10 and 20 g/kg were incorporated in the soil. Lovage and greater celandine residues exhibited the highest allelopathic effect.
Understanding and Inference1

Field: Arts and Humanities (Social Sciences)

Abstract The chapter challenges the inferentialist account of concept possession on which Boghossian relies in Chapter 2 in his account of the transmission of justification by deductive reasoning. Unorthodox speakers who reject the inferences in alleged possession condition can still have the concept by understanding a word for it. In that sense, the inferences are not analytic. Inferentialist accounts of logical constants, theoretical terms (using the method developed by Frank Ramsey, Rudolf Carnap, and David Lewis), and pejorative expressions such as ‘Boche’ are examined and rejected. It is suggested that epistemological questions cannot be reduced to questions in the theory of thought and meaning.
Scanning electron microscopic study of giant tubule content in bovine dentin

Field: Dentistry (Health Sciences)

Abstract — Incisal segments of unerupted permanent incisors from l/Z‐l l/2‐yr‐old calves were fractnred along an axiomesiodistal plane exposing the organic components within the giant tubule lumina situated in this plane. Along the lining wall of the pulpal vasclurized giant tub & portion, large flattened cells and a few odontoblasts were situated in shallow depressions. Just incisal to the vascular loop numerous cells were seen, both along the giant tubule wall and enclosed within a loosely textured collagsnous matrix. Further incisally, the number and size of the cells decreased, and they were embedded in a compact nnmineraPized collagenous matrix that completely filled out the giant tubule lumina. This matrix consisted of fibrils regularly arranged in separate bundles whose orientation was mainly longitudinal. The initial origins of the giant tubes were filled with coarse Fmhrils being about three times thicker than those of the luminal matrix and those of the circumpulpal dentin proper.
A max-cut approximation using a graph based MBO scheme

Field: Mathematics (Physical Sciences)

© 2019 American Institute of Mathematical Sciences. All rights reserved. The Max-Cut problem is a well known combinatorial optimization problem. In this paper we describe a fast approximation method. Given a graph G, we want to find a cut whose size is maximal among all possible cuts. A cut is a partition of the vertex set of G into two disjoint subsets. For an unweighted graph, the size of the cut is the number of edges that have one vertex on either side of the partition; we also consider a weighted version of the problem where each edge contributes a nonnegative weight to the cut. We introduce the signless Ginzburg–Landau functional and prove that this functional Γ-converges to a Max-Cut objective functional. We approximately minimize this functional using a graph based signless Merriman–Bence–Osher (MBO) scheme, which uses a signless Laplacian. We derive a Lyapunov functional for the iterations of our signless MBO scheme. We show experimentally that on some classes of graphs the resulting algorithm produces more accurate maximum cut approximations than the current state-of-the-art approximation algorithm. One of our methods of minimizing the functional results in an algorithm with a time complexity of O(|E|), where |E| is the total number of edges on G.
St Mary's Collegiate Church, Gowran, Co Kilkenny, interior - blocked chancel arch with reset doorway

Field: Arts and Humanities (Social Sciences)

Photograph by Roger Stalley. Doorway reset in east of nave showing recessed orders of roll-and-fillet arch mouldings, stiff-leaf foliage capitals, chamfered jambs and hood moulding terminating in head carved label stops. Scar of orinigal pointed chancel arch in wall over doorway.
Optimal Management of Complicated Infections in the Pediatric Patient: The Role and Utility of Ceftazidime/Avibactam

Field: Medicine (Health Sciences)

Matteo Bassetti,1,2 Maddalena Peghin,1 Alessio Mesini,3 Elio Castagnola3 1Infectious Diseases Clinic, Department of Medicine University of Udine and Azienda Sanitaria Universitaria Integrata, Udine, Italy; 2Department of Health Sciences, University of Genoa, Genoa, Italy; 3Division of Infectious Diseases, IRCCS Istituto Giannina Gaslini, Genoa, ItalyCorrespondence: Matteo BassettiClinica Malattie Infettive, Azienda Ospedaliera Universitaria Santa Maria Della Misericordia, Piazzale Santa Maria Della Misericordia 15, Udine 33100, ItalyTel +39 0432 559355Fax +39 0432 559360Email matteo.bassetti@asuiud.sanita.fvg.itAbstract: Antimicrobial resistance poses a substantial threat to global public health. The pursuit of new antibiotics has decreased and very few options have been investigated for the treatment of complicated multidrug-resistant Gram-negative (MDR-GN) infections in adult population and even less in pediatric patients. Ceftazidime-avibactam (CAZ-AVI) is novel cephalosporin/β-lactamase inhibitor (BL-BLI) combination with broad antibacterial spectrum. The aim of this review is to describe the current and future role CAZ-AVI in the pediatric population with suspected or confirmed MDR-GN infections.Keywords: pediatric, infections, multidrug-resistant Gram-negative, ceftazidime/avibactam
Analysis of precipitation climatology simulated by high resolution coupled global models over the South America

Field: Earth and Planetary Sciences (Physical Sciences)

The results of coupled high resolution global models (CGCMs) over South America are discussed. HiGEM1.2 and HadGEM1.2 simulations, with horizontal resolution of ~90 and 135 km, respectively, are compared. Precipitation estimations from CMAP (Climate Prediction Center—Merged Analysis of Precipitation), CPC (Climate Prediction Center) and GPCP (Global Precipitation Climatology Project) are used for validation. HiGEM1.2 and HadGEM1.2 simulated seasonal mean precipitation spatial patterns similar to the CMAP. The positioning and migration of the Intertropical Convergence Zone and of the Pacific and Atlantic subtropical highs are correctly simulated by the models. In HiGEM1.2 and HadGEM1.2, the intensity and locations of the South Atlantic Convergence Zone are in agreement with the observed dataset. The simulated annual cycles are in phase with estimations of rainfall for most of the six regions considered. An important result is that HiGEM1.2 and HadGEM1.2 eliminate a common problem of coarse resolution CGCMs, which is the simulation of a semiannual cycle of precipitation due to the semiannual solar forcing. Comparatively, the use of high resolution in HiGEM1.2 reduces the dry biases in the central part of Brazil during austral winter and spring and in most part of the year over an oceanic box in eastern Uruguay.
Malate Dehydrogenase of Ox Kidney. Comparison of the Reactivity of Sulfhydryl Groups and their Relationship to Activities of the Mitochondrial and Cytoplasmic Enzymes

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Out of 10 to 11 cysteine residues per mole of kidney mitochondrial malate dehydrogenase, 3 to 4 exhibit time‐dependent reactivity with 5,5′‐dithio‐bis‐(2‐nitrobenzoic acid) (DTNB) at pH 9.5 to 9.8, when incubated over a period of 3 hours. Under the same conditions, 1.5 to 2.0 out of a total of 6 cysteine residues of the cytoplasmic malate dehydrogenase became DTNB‐reactive. The process of unmasking of unreactive thiols is initiated by a relatively rapid (10 min) reaction on one thiol with DTNB. Beyond this initial reaction, DTNB is not required and unmasking of thiol groups proceeds spontaneously in an alkaline medium. Enzymatic activity is unaffected by the reaction of thiol groups with DTNB. Both the rate and the extent of the thiol‐DTNB reaction is greatly increased in the presence of 2 M urea, which by itself has no effect on the availability of thiol groups. Thiol unmasking in the mitochondrial enzyme is completely inhibited by 1 mM NADH (or to a lesser extent by ADP), whereas the cytoplasmic enzyme does not respond to these agents. Enzymatic activity of the cytoplasmic malate dehydrogenase is more resistant than the mitochondrial enzyme to 4 M urea. ADP or NADH tend to stabilize enzymatic activities of both isoenzymes. There is no simple relationship between enzymatic activity and reactive cysteine thiols. The specific effect of NADH (or ADP) on the mitochondrial malate dehydrogenase by preventing thiol liberation, is interpreted as an expression of a specific nucleotide binding site which controls small scale unfolding of the enzyme protein.
Viscosities of binary and ternary liquid mixtures of alkyl benzenes with carbon tetrachloride in cyclohexane

Field: Chemistry (Physical Sciences)

Department of Chemistry, St. Mary's College, Shillong-793 003, India Department of Chemistry, North-Eastern Hill University, Shillong-793 003, India Manuscript received 28 April 1998, revised 1 September 1998. accepted 9 September 1998 The viscosities of ternary mixtures of benzene-carbon tetrachloride, toluene-carbon tetrachloride and o-xylene-carbon tetrachloride in cyclohexanc have been determined at 298.15, 303.15, 308.15 and 313.15 K. The data are analyzed using Frankel model. Viscometric data are used to study the interaction between the weakly interacting systems. The equilibrium constants and other thermodynamic parameters arc reported.
CP-030 25 years of chronic hepatitis C: From discovery to cure. Retrospective analysis of a cohort of patients

Field: Medicine (Health Sciences)

Background

In Portugal, it is estimated that hepatitis C incidence is 1/100 000/year and the prevalence is 1.5% with a diagnostic rate of 30%.

Purpose

Evaluation of efficacy, tolerability and costs of NS5A/B polymerase inhibitor regimens in a cohort of hepatitis C patients.

Material and methods

A retrospective observational study. We considered patients who completed treatment with ledipasvir/sofosbuvir (LDV/SOF), sofosbuvir (SOF), daclatasvir/sofosbuvir (DCV/SOF), simepravir/sofosbuvir (SMV/SOF), with or without pegylated interferon/ribavirin.

Results

We identified 145 patients, 40 HIV infected. The main genotype was 1a in 60 patients (41.4%), followed by genotype 3 in 27 patients (18.6%), then genotype 1b in 23 patients (15.9%) and genotype 4 in 19 patients (13.1%). 1 patient had genotype 5a and 15 patients did not have genotype information in their clinical files. 46 patients (31.7%) did not have clinical records regarding fibrosis degree. 50 patients (34.5%) were included with cirrosis (F4), 27 (18.6%) with advanced fibrosis (F3), 15 (10.3%) F2 and 7 patients (4.8%) F1. 93 patients (64.1%) had been previously treated with dual therapy, with an average duration of 6.6 months. 4 of these patients had also received protease inhibitors (2.8%) and due to relapse, were proposed for new treatments. 52 naive patients were included. 124 patients (85.5%) received SOF/LDV for 12 weeks (49 patients) or 24 weeks (96 patients). 18 patients (12.4%) received SOF, 2 patients (1.4%) received SOF/DCV and 1 patient (0.7%) received SOF/SMV. 82 patients (87.2%) had undetectable numbers of copies regarding fast virologic response. 39 patients (26.9%) had undetectable numbers of copies 12 weeks after the end of treatment. Adverse reactions in 69 patients (47.6%) were headache, insomnia, asthenia, dizziness, diarrhoea, gastritis, joint pains, nausea, vomiting, anxiety and irritability. Costs between February and July 2015 were 3 206 956.40€, foreseeing a cost of 7 300 000€.

Conclusion

Recent approved therapeutics allow for a virological response at 4 weeks in most patients with excellent tolerability, unlike previous schemes. We await the results of sustained virological response at 12 weeks. The high cost requires strict compliance with the Clinical Guidance Standards in place and continuous monitoring of the whole process.

References and/or Acknowledgements

DGS-Norma No 011/2012 30/4/2015 (2012) No conflict of interest.
Intertial Frame Dragging in an Acoustic Analogue spacetime

Field: Physics and Astronomy (Physical Sciences)

We report an incipient exploration of the Lense-Thirring precession effect in a rotating \textit{acoustic analogue black hole} spacetime. An exact formula is deduced for the precession frequency of a gyroscope due to inertial frame dragging, close to the ergosphere of a `Draining Bathtub' acoustic spacetime which has been studied extensively for acoustic Hawking radiation of phonons and also for `superresonance'. The formula is verified by embedding the two dimensional spatial (acoustic) geometry into a three dimensional one where the similarity with standard Lense-Thirring precession results within a strong gravity framework is well known. Prospects of experimental detection of this new `fixed-metric' effect in acoustic geometries, are briefly discussed.
OPTIMIZATION OF TISSUE CULTURE MEDIA FOR PROPAGATION OF MARIANNA ROOTSTOCKS

Field: Agricultural and Biological Sciences (Life Sciences)

Marianna rootstock is used predominantly in South Africa for cultivation of plum cultivars. In order to develop an adventitious regeneration system for plant transformations, shoot cultures should been grown in vitro. Initially shoot cultures of Marianna rootstock were propagated on K2 salts, but the cultures declined over time. Therefore, eight different growth media were tested for improved proliferation of the cultures. Two of these eight supported good growth, and they were optimised further. The results showed that the in vitro shoots grew much better when cultivated on MS medium with phloroglucinol or a combination of phloroglucinol and gibberellic acid.