cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Is the energy density of the ground state of the sine-Gordon model unbounded from below for beta^2 > 8 pi ?
Creators: name: Faber, M.
name: Ivanov, A. N.
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We discuss Coleman's theorem concerning the energy density of the ground state of the sine-Gordon model proved in Phys. Rev. D 11, 2088 (1975). According to this theorem the energy density of the ground state of the sine-Gordon model should be unbounded from below for coupling constants beta^2 > 8 pi. The consequence of this theorem would be the non-existence of the quantum ground state of the sine-Gordon model for beta^2 > 8 pi. We show that the energy density of the ground state in the sine-Gordon model is bounded from below even for beta^2 > 8 pi. This result is discussed in relation to Coleman's theorem (Comm. Math. Phys. 31, 259 (1973)), particle mass spectra and soliton-soliton scattering in the sine-Gordon model.
description: 22 pages, Latex, no figures, revised according to the version accepted for publication in Journal of Physics A
Additional file 2 of Evaluation of multi-level barriers and facilitators in a large diabetic retinopathy screening program in federally qualified health centers: a qualitative study
Creators: name: De Carvalho, Ana Bastos
name: S. Lee Ware
name: Belcher, Tamara
name: Franceska Mehmeti
name: Higgins, Eric B.
name: Sprang, Rob
name: Williams, Cody
name: Studts, Jamie L.
name: Studts, Christina R.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 2. Supplementary methods.
The Impact of Price Regulations on Farm-Retail Price Transmission: The Case of Fluid Milk
Creators: name: Rabinowitz, Adam
name: Liu, Yizao
name: Chen, Xuan
name: Rabinowitz, Adam
name: Liu, Yizao
name: Chen, Xuan
Publisher: name: Unknown
Year: 2016
Subjects: subject: Agribusiness
subject: Agricultural and Food Policy
subject: asymmetry
subject: dairy policy
subject: price transmission
subject: retail pricing

description: This article analyzes the impact of federal and state milk pricing regulations on cost past through in the U.S. fluid milk market. Producer pricing in the fluid milk market is regulated by federal and/or state milk marketing regulations while the retailer price is influenced in some geographic locations by state regulations ranging from minimum to maximum pricing policies. The regulation either aims to support local dairy farmers or protect consumers from price gouging, either of which could also affect the response of retail milk prices to farm price changes. We use monthly state-level retail milk pricing data across the US from 2006 to 2011 to estimate the nonreversible function of farm-retail price transmission using the Houck (1977) procedure. Specifically, our model includes increasing and decreasing accumulated farm price changes with an expansion to include interaction terms of pricing regulations. This modeling approach allows us to explore the influences of price regulations on the farm-retail price transmission. The results indicate that pricing regulations have a significant influence on price transmission, regardless of the type of regulation. Minimum price laws have the strongest mitigation power of the asymmetries in farm-retail price transmission, while a maximum price law has an amplifying effect.
Soybean Profitability Comparisons of “Automatic Applications” Versus “Treating as Needed” Approaches for Insect and Disease Control
Creators: name: Stark, C. Robert
name: Lorenz, Gus
name: Faske, Travis
name: Spurlock, Terry
name: Seiter, Nick
name: Studebaker, Glenn
name: Stark, C. Robert
name: Lorenz, Gus
name: Faske, Travis
name: Spurlock, Terry
name: Seiter, Nick
name: Studebaker, Glenn
Publisher: name: Unknown
Year: 2016
Subjects: subject: Farm Management
subject: soybean
subject: partial budget
subject: threshold
subject: treated-as-needed
subject: automatic application

description: Arkansas soybean producers spend significant amounts of money on annual input costs. 2015 UA Division of Agriculture crop enterprise budgets estimated irrigated soybean average operating expenses at $328.75 per acre across Roundup Ready, Liberty Link, and conventional systems. Commodity market price declines, such as have been seen in late 2015, increase the importance of input cost evaluations to maintain profitable returns. This study compares “automatic applications” made on crop phenology versus “treating as needed” systems where applications are made based on scouting for insect and disease thresholds. Seven large block trial locations were initiated in 2015 with five treatments utilizing insecticides, fungicides, combinations of products, and application system approaches. Partial budgeting methodology is employed to estimate economic outcome under each system. Cost, yield, and profitability measures are calculated for each treatment. The agronomic and economic research results will be used to evaluate overall profitability of current state extension recommendations including treatment threshold levels.
Electronic Supplementary Materials from Attractiveness of thermally different, uniformly black targets to horseflies: Tabanus tergestinus prefers sunlit warm shiny dark targets
Creators: name: Horváth, Gábor
name: Pereszlényi, Ádám
name: Tóth, Tímea
name: Polgár, Szabolcs
name: Jánosi, Imre M.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: Calibration of the Thermocamera + Supplementary Results (Reflection-polarization characteristics of the warm and cold barrels, Thermal characteristics of the warm and cold barrels, Schlieren imagery of the warm/cold air next to the warm/cold barrels, Attractiveness of the warm and cold barrels to tabanids) + Supplementary Tables S1, S2, S3 + Supplementary Figures S1, S2, S3, S4
Effect of Regulatory Quality on Wood Pulp Imports by India
Creators: name: Das, Joy
name: Tanger, Shaun
name: Kennedy, P. Lynn
name: Das, Joy
name: Tanger, Shaun
name: Kennedy, P. Lynn
Publisher: name: Unknown
Year: 2016
Subjects: subject: International Relations/Trade
subject: Wood Pulp
subject: Imports
subject: Regulatory Quality
subject: India

description: India is one of the largest importers of wood pulp in the world. The total value of wood pulp imported by India during 2004 was $ 171.9 million, which increased to approximately $744.5 million by 2013. With a population of about 1.2 billion people, the demand for paper and wood pulp is very high in India. Despite this harvesting timber for commercial use has been heavily restricted, therefore India has to import wood pulp to meet its growing domestic market demand. With a large population and limited resource access, India remains an attractive market for global wood pulp exporters. Using a pooled ordinary least squared (POLS) regression model of estimation, the study examines a panel of trade flows during 2009-2013, exploring the influence of Regulatory Quality on the pattern of wood pulp imports by India from 67 exporting countries. The effect of Regulatory Quality and other explanatory variables such as the distance between the exporting country and India, total forest area of exporting country, GDP and population indicators on imports of wood pulp by India is estimated with the help of the above-mentioned model. Moreover, the study also looks into the volume of exports from countries belonging to specific regions such as East Asia and Pacific, Latin America & the Caribbean, Europe & Central Asia, North America, South Asia and Sub-Saharan Africa.
An experiment with denotational semantics
Creators: name: Andrzej, Blikle
Publisher: name: arXiv
Year: 2019
Subjects: subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences
subject: 68N30

description: The paper is devoted to showing how to systematically design a programming language in 'reverse order', i.e. from denotations to syntax. This construction is developed in an algebraic framework consisting of three many-sorted algebras: of denotations, of an abstract syntax and of a concrete syntax. These algebras are constructed in such a way that there is a unique homomorphism from concrete syntax to denotations, which constitutes the denotational semantics of the language. Besides its algebraic framework, the model is set-theoretic, i.e. the denotational domains are just sets, rather than Scott's reflexive domains. The method is illustrated by a layer-by-layer development of a virtual language Lingua: an applicative layer, an imperative layer (with recursive procedures) and an SQL layer where Lingua is regarded as an API (Application Programming Interface) for an SQL engine. The latter is given a denotational semantics as well. The langue is equipped with a strong typing mechanism which covers basic types (numbers, Booleans, etc.), lists, arrays, record and their arbitrary combinations plus SQL-like types: rows, tables and databases. The model of types includes SQL integrity constraints.
description: A preprint of 44 pages. All comments will be highly appreciated. You may contact me on andrzej.blikle@moznainaczej.com.pl
Surgical techniques for repair of abdominal rectus diastasis: a scoping review
Creators: name: Jessen, Majken Lyhne
name: Öberg, Stina
name: Rosenberg, Jacob
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy

description: Rectus diastasis is characterized by widening and laxity of the linea alba, causing the abdominal content to bulge. Rectus diastasis is treated either conservatively with physiotherapy, or surgically, surgical treatment showing especially convincing results. The primary aim of this study was to describe surgical techniques used to correct abdominal rectus diastasis. Secondary, we wished to assess postoperative complications in relation to the various techniques. A systematic scoping review was conducted and reported according to the PRISMA-ScR statement. PubMed, Embase, and Cochrane Library were searched systematically. Studies were included if they described a surgical technique used to repair abdominal rectus diastasis, with or without concomitant ventral hernia. Secondary outcomes were recurrence rate and other complications. A total of 61 studies were included: 46 used an open approach and 15 used a laparoscopic approach for repair of the abdominal rectus diastasis. All the included studies used some sort of plication, but various technical modifications were used. The most common surgical technique was classic low abdominoplasty. The plication was done as either a single or a double layer, most commonly with permanent sutures. There were overall low recurrence rates and other complication rates after both the open and the laparoscopic techniques. We identified many techniques for repair of abdominal rectus diastasis. Recurrence rate and other complication rates were in general low. However, there is a lack of high-level evidence and it is not possible to recommend one method over another. Thus, further randomized controlled trials are needed in this area.
Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches
Creators: name: Jones, Andrew J. Y.
name: Gabriel, Florian
name: Tandale, Aditi
name: Nietlispach, Daniel
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: GPCR
lipids
membrane mimetics
NMR

description: Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
Listroderes apicalis Waterhouse 1841
Creators: name: Morrone, Juan J.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Curculionidae
Listroderes
Listroderes apicalis

description: Listroderes apicalis Waterhouse, 1841
 Listroderes apicalis Waterhouse, 1841: 123 (type locality: Uruguay: Montevideo; type material: S: BMNH).
 Listroderes argentinensis Hustache, 1926: 198 (type locality: Argentina: Buenos Aires; type material: S: MNHN); Kuschel, 1950: 13 (= L. apicalis).
 Host plants. Beta vulgaris L. (Chenopodiaceae), Helianthus annus L. (Asteraceae), and Triticum aestivum L. (Poaceae) (Morrone, 1993d; Lanteri et al., 2002).
 Distribution. Northern and central Argentina, southern Brazil, central Chile (probably introduced), Paraguay, Uruguay, and USA (introduced) (Wibmer and O’Brien, 1986; Morrone, 1993d).
description: Published as part of Morrone, Juan J., 2011, Annotated checklist of the tribe Listroderini (Coleoptera: Curculionidae: Cyclominae) 3119, pp. 1-68 in Zootaxa 3119 (1) on page 28, DOI: 10.11646/zootaxa.3119.1.1, http://zenodo.org/record/5246257
Raising ABV Levels, Alcohol Consumption and Alcohol-Related Motor Vehicle Fatalities in the United States
Creators: name: Yang, Xiaosi
name: Berning, Joshua
name: Yang, Xiaosi
name: Berning, Joshua
Publisher: name: Unknown
Year: 2016
Subjects: subject: Health Economics and Policy
subject: alcohol consumption
subject: fatality
subject: alcohol by volume

description: Over the past 10 years, five states have proposed to raise the alcohol by volume (ABV) limit on beer being sold to promote the beer brewery industry in their states. An increase in ABV limits increases the variety of beer being sold and may change people’s consumption behavior. Such changes could subsequently influence drinking behaviors as well as driving safety in those states. This paper investigates the relationship between the increase in ABV limits and individual alcohol consumption and alcohol-related fatal crashes. We use difference-in-difference model to analyze the alcohol consumption before and after the rising ABV limit. Our panel data allows us to control for state and time fixed effects, state level economic conditions and beer consumption. We find higher ABV limits lead to a slight increase in alcohol consumption as well as a negative effect on alcohol-related fatality rate.
$F(R)$ Gravity with an Axion-like Particle: Dynamics, Gravity Waves, Late and Early-time Phenomenology
Creators: name: Nojiri, Shin'ichi
name: Odintsov, S. D.
name: Oikonomou, V. K.
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this work we investigate several theoretical and phenomenological implications of a scalar -$F(R)$ gravity containing a non-minimal coupling to the scalar curvature. This kind of model is a generalization of axion-$F(R)$ gravity models, so we shall examine several implications of the latter theory. Firstly we study in detail the Einstein frame picture of the model, and also we discuss the dynamics of the cosmological system. By appropriately using the equations of motion, we demonstrate that an arbitrary cosmological evolution can be realized. Also we study the gravitational waves of the theory, and we demonstrate that the speed of their propagation is the same as in $F(R)$ gravity, but there is the possibility of enhancement or dissipation of the gravitational waves, an effect quite similar to the propagation of gravity waves in a viscous fluid. Finally, we examine the energy momentum tensor and we investigate which quantities related to it are conserved. We also present the constraints imposed by the radiation domination era on the non-minimal coupling of the axion scalar field to the scalar curvature.
Consumer Preferences and Factors Affecting Consumer Purchases of Pomegranates
Creators: name: Kapllani, Armand
name: House, Lisa
name: Guan, Zhengfei
name: Kapllani, Armand
name: House, Lisa
name: Guan, Zhengfei
Publisher: name: Unknown
Year: 2015
Subjects: Consumer/Household Economics

description: Specialty crop production account for about 70% of Florida agriculture and is of great economic importance to the state. The farmers in Florida are facing competition from other US States and Mexico and this is pushing them to look for other specialty crops that can be grown in Florida and diversify their investment. Pomegranate is the specialty crop that farmers in Florida have expressed interest in the last years and currently farmers have started to experiment growing pomegranates in their farms. In this study we use a sample of data obtained from an online survey and the focus of our study is to analyze the consumers’ behavior and determine the factors that are significant in the consumption of the pomegranate. Besides preferences and tastes of consumers in the study we consider other factors such as health benefits due to the high nutritional value of pomegranates.
Variations of Core Luminosity and Solar Neutrino Fluxes
Creators: name: Grandpierre, Attila
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: In a Dynamic Solar Model (DSM) the temperature dependences of the pp cycle neutrinos will be different from the ones determined by solar model calculations with the luminosity constraint. Instead of the usual neutrino fluxes pp ~ T^{-1/2}, Be ~ T^8, B ~ T^{18}, we determined by the nuclear reaction rates formulas pp ~ T^{4.2}, Be ~ T^{-1/2}, B ~ T^{13.5}, for $τ< 10^2$ years. These latter relations have high significance at estimating the uncertainties of the solar central temperatures without assuming the luminosity constraint. Although the purely astrophysical solutions seem to be ruled out, this is not the case for a model in which astrophysical effects are included besides the neutrino oscillations. Therefore a combined, DSM+MSW model is suggested to calculate the observed solar neutrino fluxes. The combined SSM+MSW fits to the rates+spectra+D/N changes give a bad fit to the total rates, indicating the need to include the astrophysical factors besides the MSW effect. The DSM suggest that the core dynamics is induced by intermittent events of dissipation of rotational energy in the solar core, in relation to angular momentum dissipation arising from the relative motion of the Sun and the mass center of the Solar System, and it shifts the allowed ranges of the MSW parameters into a more acceptable region. The role of the astrophysical factors in the solar neutrino problem is behind the fact why the ``smoking guns'' of neutrino oscillations are not found yet.
description: 2 pages, extended abstract, LaTex
Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation
Creators: name: Garaizar, Adiran
name: Sanchez-Burgos, Ignacio
name: Collepardo-Guevara, Rosana
name: Espinosa, Jorge R.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: proteins
biological phase transitions
computer simulations

description: Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid−liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, including conformational switching, where they transition between alternate conformational ensembles. Using Molecular Dynamics simulations of a minimal coarse-grained model for IDRs, we show that the role of protein conformation has a non-trivial effect in the liquid−liquid phase behaviour of IDRs. When an IDR transitions to a conformational ensemble enriched in disordered extended states, LLPS is enhanced. In contrast, IDRs that switch to ensembles that preferentially sample more compact and structured states show inhibited LLPS. This occurs because extended and disordered protein conformations facilitate LLPS-stabilising multivalent protein−protein interactions by reducing steric hindrance; thereby, such conformations maximize the molecular connectivity of the condensed liquid network. Extended protein configurations promote phase separation regardless of whether LLPS is driven by homotypic and/or heterotypic protein−protein interactions. This study sheds light on the link between the dynamic conformational plasticity of IDRs and their liquid−liquid phase behaviour.
Spillover Effect of Participation in Women, Infant and Children (WIC) Program on Consumer’s Purchasing Behavior of Private Label Goods
Creators: name: Zaffou, Madiha
name: Campbell, Benjamin
name: Rabinowitz, Adam
name: Zaffou, Madiha
name: Campbell, Benjamin
name: Rabinowitz, Adam
Publisher: name: Unknown
Year: 2016
Subjects: subject: Agribusiness
subject: Agricultural and Food Policy
subject: Consumer/Household Economics
subject: Demand and Price Analysis
subject: Food Consumption/Nutrition/Food Safety
subject: Food Security and Poverty
subject: Marketing
subject: FOS: Economics and business

description: The special supplemental nutrition program for women, infants, and children program (WIC) allows its participants to purchase food items from a WIC approved list at retail grocery stores. However, this program restricts not only the type and the quantity of food to be purchased but also the specific food brand. In fact, participants are often required to purchase private label brands –the least expensive brand- for some of the food products. Using Nileson home-scan data on daily food purchases across the county, this study aims to evaluate how these food brand restrictions may impact consumer brand preference even outside of the WIC program.
Why are patients dissatisfied following a total knee replacement? A systematic review
Creators: name: Nakano, Naoki
name: Shoman, Haitham
name: Olavarria, Fernando
name: Matsumoto, Tomoyuki
name: Kuroda, Ryosuke
name: Khanduja, Vikas
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Original Paper
Total knee replacement
Total knee arthroplasty
Satisfaction
Dissatisfaction
Systematic review

description: Funder: University of Cambridge
description: Abstract: Background: Although total knee replacement (TKR) is an effective intervention for end-stage arthritis of the knee, a significant number of patients remain dissatisfied following this procedure. Our aim was to identify and assess the factors affecting patient satisfaction following a TKR. Materials and methods: In accordance with the PRISMA guidelines, two reviewers searched the online databases for literature describing factors affecting patient satisfaction following a TKR. The research question and eligibility criteria were established a priori. Any clinical outcome study that described factors relating to overall satisfaction after primary TKR was included. Quality assessment for the included studies was performed by two accredited orthopaedic surgeons experienced in clinical research. Results: The systematic review identified 181 relevant articles in total. A history of mental health problems was the most frequently reported factor affecting patient satisfaction (13 reportings). When the results of the quality assessment were taken into consideration, a negative history of mental health problems, use of a mobile-bearing insert, patellar resurfacing, severe pre-operative radiological degenerative change, negative history of low back pain, no/less post-operative pain, good post-operative physical function and pre-operative expectations being met were considered to be important factors leading to better patient satisfaction following a TKR. Conclusion: Surgeons performing a TKR should take these factors into consideration prior to deciding whether a patient is suitable for a TKR. Secondarily, a detailed explanation of these factors should form part of the process of informed consent to achieve better patient satisfaction following TKR. There is a great need for a unified approach to assessing satisfaction following a TKR and also the time at which satisfaction is assessed.
Additional file 1 of Segmentor: a tool for manual refinement of 3D microscopy annotations
Creators: name: Borland, David
name: McCormick, Carolyn M.
name: Niyanta K. Patel
name: Krupa, Oleh
name: Mory, Jessica T.
name: Beltran, Alvaro A.
name: Farah, Tala M.
name: Escobar-Tomlienovich, Carla F.
name: Olson, Sydney S.
name: Minjeong Kim
name: Guorong Wu
name: Stein, Jason L.
Publisher: name: figshare
Year: 2021
Subjects: subject: Artificial Intelligence and Image Processing
subject: FOS: Computer and information sciences

description: Additional file 1. Questionnaire provided to Segmentor users.
Bayesian Optimization of Composite Functions
Creators: name: Astudillo, Raul
name: Frazier, Peter I.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: Optimization and Control (math.OC)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We consider optimization of composite objective functions, i.e., of the form $f(x)=g(h(x))$, where $h$ is a black-box derivative-free expensive-to-evaluate function with vector-valued outputs, and $g$ is a cheap-to-evaluate real-valued function. While these problems can be solved with standard Bayesian optimization, we propose a novel approach that exploits the composite structure of the objective function to substantially improve sampling efficiency. Our approach models $h$ using a multi-output Gaussian process and chooses where to sample using the expected improvement evaluated on the implied non-Gaussian posterior on $f$, which we call expected improvement for composite functions (\ei). Although \ei\ cannot be computed in closed form, we provide a novel stochastic gradient estimator that allows its efficient maximization. We also show that our approach is asymptotically consistent, i.e., that it recovers a globally optimal solution as sampling effort grows to infinity, generalizing previous convergence results for classical expected improvement. Numerical experiments show that our approach dramatically outperforms standard Bayesian optimization benchmarks, reducing simple regret by several orders of magnitude.
description: In Proceedings of the 36th International Conference on Machine Learning, PMLR 97:354-363, 2019
A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans
Creators: name: Vieira, Paulo
name: Shao, Jonathan
name: Vijayapalani, Paramasivan
name: Maier, Thomas R.
name: Pellegrin, Clement
name: Eves-Van Den Akker, Sebastian
name: Baum, Thomas J.
name: Nemchinov, Lev G.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Research Article
Multicellular invertebrate genomics
Root lesion nematodes
Host-pathogen interaction
Secretome
Esophageal gland cells
Pioneer effectors

description: Abstract: Background: The root lesion nematode Pratylenchus penetrans is a migratory plant-parasitic nematode responsible for economically important losses in a wide number of crops. Despite the importance of P. penetrans, the molecular mechanisms employed by this nematode to promote virulence remain largely unknown. Results: Here we generated a new and comprehensive esophageal glands-specific transcriptome library for P. penetrans. In-depth analysis of this transcriptome enabled a robust identification of a catalogue of 30 new candidate effector genes, which were experimentally validated in the esophageal glands by in situ hybridization. We further validated the expression of a multifaceted network of candidate effectors during the interaction with different plants. To advance our understanding of the “effectorome” of P. penetrans, we adopted a phylogenetic approach and compared the expanded effector repertoire of P. penetrans to the genome/transcriptome of other nematode species with similar or contrasting parasitism strategies. Our data allowed us to infer plausible evolutionary histories that shaped the effector repertoire of P. penetrans, as well as other close and distant plant-parasitic nematodes. Two remarkable trends were apparent: 1) large scale effector birth in the Pratylenchidae in general and P. penetrans in particular, and 2) large scale effector death in sedentary (endo) plant-parasitic nematodes. Conclusions: Our study doubles the number of validated Pratylenchus penetrans effectors reported in the literature. The dramatic effector gene gain in P. penetrans could be related to the remarkable ability of this nematode to parasitize a large number of plants. Our data provide valuable insights into nematode parasitism and contribute towards basic understating of the adaptation of P. penetrans and other root lesion nematodes to specific host plants.
Enhanced glacial discharge from the eastern Antarctic Peninsula since the 1700s associated with a positive Southern Annular Mode
Creators: name: Dickens, W. A.
name: Kuhn, G.
name: Leng, M. J.
name: Graham, A. G. C.
name: Dowdeswell, J. A.
name: Meredith, M. P.
name: Hillenbrand, C.-D.
name: Hodgson, D. A.
name: Roberts, S. J.
name: Sloane, H.
name: Smith, J. A.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/704/106/125
/704/106/413
article

description: Abstract: The Antarctic Peninsula Ice Sheet is currently experiencing sustained and accelerating loss of ice. Determining when these changes were initiated and identifying the main drivers is hampered by the short instrumental record (1992 to present). Here we present a 6,250 year record of glacial discharge based on the oxygen isotope composition of diatoms (δ18Odiatom) from a marine core located at the north-eastern tip of the Antarctic Peninsula. We find that glacial discharge - sourced primarily from ice shelf and iceberg melting along the eastern Antarctic Peninsula – remained largely stable between ~6,250 to 1,620 cal. yr BP, with a slight increase in variability until ~720 cal. yr. BP. An increasing trend in glacial discharge occurs after 550 cal. yr BP (A.D. 1400), reaching levels unprecedented during the past 6,250 years after 244 cal. yr BP (A.D. 1706). A marked acceleration in the rate of glacial discharge is also observed in the early part of twentieth century (after A.D. 1912). Enhanced glacial discharge, particularly after the 1700s is linked to a positive Southern Annular Mode (SAM). We argue that a positive SAM drove stronger westerly winds, atmospheric warming and surface ablation on the eastern Antarctic Peninsula whilst simultaneously entraining more warm water into the Weddell Gyre, potentially increasing melting on the undersides of ice shelves. A possible implication of our data is that ice shelves in this region have been thinning for at least ~300 years, potentially predisposing them to collapse under intensified anthropogenic warming.
The Angel shipwreck: A 19th-century brig named Jane discovered in Chinchorro Bank, México.
Creators: name: Río, Octavio Del
Publisher: name: figshare
Year: 2020
Subjects: subject: 210110 Maritime Archaeology
subject: FOS: History and archaeology

description: Two decades after its discovery, and 200 years after it was shipwrecked in the shallow coral banks of Banco Chinchorro in the Mexican Caribbean, the identity of the wreck “El Ángel” finally emerges from the depths. It has been identified as a merchant vessel which sailed in the area during a time of heavy commercial traffic, and due to the characteristics of the materials used in its construction, its naval architecture, and the cargo transported, places it as an English merchant ship from the mid-19th century identify as Jane.
Additional file 3 of Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks
Creators: name: Cherchame, Emeline
name: Guillier, Laurent
name: Lailler, Renaud
name: Vignaud, Marie-Leone
name: Jourdan-Da Silva, Nathalie
name: Le Hello, Simon
name: Weill, François-Xavier
name: Cadel-Six, Sabrina
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Figure S3. Decision tree to select the reference genome for SNP analyses when complete genome is not available for serovar of interest. Enterobase Salmonella database (at https://enterobase.warwick.ac.uk/species/index/senterica ) log in is required before starting. Light blue and purple blocks describe the actions to carry up to reference genome selection with specific instruction in italic indicated by a cog icon. At the right, red boxes display selection following SISTR and SeqSero2 results. The focus points are indicated by an eye icon in blue boxes.
Listroderes bimaculatus Boheman 1842
Creators: name: Morrone, Juan J.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Curculionidae
Listroderes
Listroderes bimaculatus

description: Listroderes bimaculatus Boheman, 1842
 Listroderes bimaculatus Boheman, 1842: 187 (type locality: Chile; type material: H: NHRS).
 Listroderes acutesquamosus Germain, 1895: 90 (type locality: Chile; type material: H: MHNS); Kuschel, 1986: 113 (= L. bimaculatus).
 Listroderes costulatus Germain, 1895: 86 (type locality: Chile: Cerro de “Lo Águila”, near Santiago; type material: lost [Elgueta & Morrone, 1993]); Kuschel, 1986: 113 (= L. bimaculatus).
 Listroderes chilensis Germain, 1895: 88 (type locality: Chile: Cordillera Choapa; type material: L: MHNS and PL: 11 MHNS); Kuschel, 1986: 113 (= L. bimaculatus).
 Listroderes sticticus Germain, 1895: 93 (type locality: Chile: Valparaíso; type material: L: MHNS and PL: 35 MHNS); Kuschel, 1946: 140 (= L. bimaculatus).
 Listroderes reticulatus Germain, 1895: 96 (type locality: Chile: Valparaíso; type material: H: MHNS); Kuschel, 1986: 113 (= L. bimaculatus).
 Listroderes subaeneus Germain, 1895: 97 (type locality: Chile: Lota; type material: L: MHNS and PL: 1 MHNS); Kuschel, 1986: 113 (= L. bimaculatus).
 Host plants. Baccharis linearis (Ruiz and Pav.) Pers. (Asteraceae) and Puya chilensis Molina (Bromeliaceae) (Morrone, 1993d).
 Distribution. Southern Argentina and central and southern Chile (Morrone, 1993d).
description: Published as part of Morrone, Juan J., 2011, Annotated checklist of the tribe Listroderini (Coleoptera: Curculionidae: Cyclominae) 3119, pp. 1-68 in Zootaxa 3119 (1) on page 28, DOI: 10.11646/zootaxa.3119.1.1, http://zenodo.org/record/5246257
Additional file 2 of Segmentor: a tool for manual refinement of 3D microscopy annotations
Creators: name: Borland, David
name: McCormick, Carolyn M.
name: Niyanta K. Patel
name: Krupa, Oleh
name: Mory, Jessica T.
name: Beltran, Alvaro A.
name: Farah, Tala M.
name: Escobar-Tomlienovich, Carla F.
name: Olson, Sydney S.
name: Minjeong Kim
name: Guorong Wu
name: Stein, Jason L.
Publisher: name: figshare
Year: 2021
Subjects: subject: Artificial Intelligence and Image Processing
subject: FOS: Computer and information sciences

description: Additional file 2: Table 1. Table with results of case study.
The Practice of Naturalness: A Historical-Philosophical Perspective
Creators: name: Borrelli, Arianna
name: Castellani, Elena
Publisher: name: arXiv
Year: 2019
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: The fact that no evidence of new physics was found so far by LHC experiments has led some to call for the abandonment of the naturalness criterion. Others, on the contrary, have felt the need to break a lance in its defense by claiming that it should not be dismissed too quickly, but rather only reshaped to fit new needs. In this paper we argue that present pro or contra naturalness debates often miss an important historical point: that naturalness is essentially a hazily defined notion which, in the course of more than four decades, has been steadily, and often not coherently, shaped by its interplay with different branches of model-building in high-energy physics and cosmology on the one side, and new experimental results on the other side. The paper endeavours to clear up some of the physical and philosophical haze by taking a closer look back at the origin of naturalness in the 1970s and 1980s, with particular attention to the early work of Kenneth Wilson.
description: Based on a talk delivered at the 2018 Aachen Workshop on "Naturalness, Hierarchy, and Fine Tuning". Forthcoming in Foundations of Physics
Evolving generalists via dynamic sculpting of rugged landscapes
Creators: name: Wang, Shenshen
name: Dai, Lei
Publisher: name: arXiv
Year: 2019
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to genotypes that remain fit across diverse selective pressures; cross-reactive antibodies are much wanted but rare, while multi-drug resistant microbes are undesired yet prevalent. However, little is known about under what conditions such solutions with a high capacity to adapt would be efficiently discovered by evolution, as environmental changes alter the relative fitness and accessibility of neighboring genotypes. In addition, can epistasis --- the source of landscape ruggedness and path constraints --- play a different role, if the environments are correlated in time? We present a generative model to estimate the propensity of evolving generalists in rugged landscapes that are tunably related and cycling relatively slowly. We find that environment cycling can substantially facilitate the search for fit generalists by dynamically enlarging their effective basins of attraction. Importantly, these high performers are most likely to emerge at an intermediate level of both ruggedness and environmental relatedness, trading diversity for fitness and accessibility. Our work provides a conceptual framework to study evolution in correlated varying complex environments, and offers statistical understanding that suggests general strategies for speeding up the generation of broadly neutralizing antibodies or preventing microbes from evolving multi-drug resistance.
description: 9 pages, 4 figures
Listroderes brevirostris Germain 1895
Creators: name: Morrone, Juan J.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Curculionidae
Listroderes
Listroderes brevirostris

description: Listroderes brevirostris Germain, 1895
 Listroderes brevirostris Germain, 1895: 496 (type locality: Chile: Maule; type material: L: MHNS).
 Distribution. Central Chile (Morrone, 1993e).
description: Published as part of Morrone, Juan J., 2011, Annotated checklist of the tribe Listroderini (Coleoptera: Curculionidae: Cyclominae) 3119, pp. 1-68 in Zootaxa 3119 (1) on page 29, DOI: 10.11646/zootaxa.3119.1.1, http://zenodo.org/record/5246257
A new weak-field magnetic DA white dwarf in the local 20 pc volume. The frequency of magnetic fields in DA stars
Creators: name: Landstreet, John D.
name: Bagnulo, Stefano
Publisher: name: arXiv
Year: 2019
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We report the discovery of a new magnetic DA white dwarf (WD), WD0011-721, which is located within the very important 20pc volume-limited sample of the closest WDs to the Sun. This star has a mean field modulus of 343 kG, and from the polarisation signal we deduce a line-of-sight field component of 75 kG. The magnetic field is sufficiently weak to have escaped detection in classification spectra. We then present a preliminary exploration of the data concerning the frequency of such fields among WDs with hydrogen-rich atmospheres (DA stars). We find that 20 +- 5% of the DA WDs in this volume have magnetic fields, mostly weaker than 1 MG. Unlike the slow field decay found among the magnetic Bp stars of the upper main sequence, the WDs in this sample show no evidence of magnetic field or flux changes over several Gyr.
Additional file 5 of Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks
Creators: name: Cherchame, Emeline
name: Guillier, Laurent
name: Lailler, Renaud
name: Vignaud, Marie-Leone
name: Jourdan-Da Silva, Nathalie
name: Le Hello, Simon
name: Weill, François-Xavier
name: Cadel-Six, Sabrina
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5: Figure S5. Representation of recombination events for each branch and node of the phylogenetic inference of the S. Welikade genomes. Recombination corrected maximum likelihood tree are shown on the left. The yellow dotted lines indicate the nodes with a high number of recombination events. To the right of the tree, dark blue horizontal bars show recombination events along the concatenated genome segments. Invariant sites are shown in light blue (i.e., the background). White bars indicate non-homoplastic nucleotide substitutions. The increasing level of redness indicates the increasing degree of probable homoplastic nucleotide substitutions (Didelot & Wilson, [25]).
Additional file 2 of Cost-effectiveness of strategies to control the spread of carbapenemase-producing Enterobacterales in hospitals: a modelling study
Creators: name: Kardaś-Słoma, Lidia
name: Fournier, Sandra
name: Dupont, Jean-Claude
name: Rochaix, Lise
name: Birgand, Gabriel
name: Zahar, Jean-Ralph
name: Lescure, François-Xavier
name: Kernéis, Solen
name: Durand-Zaleski, Isabelle
name: Lucet, Jean-Christophe
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 2. The summary and details of results from the deterministic sensitivity analysis.
Open Pharma position statement on open access
Creators: name: Sabir, Sarah
name: Winchester, Chris
name: Skobe, Catherine
name: Rains, Chris
name: Newman, Julie
name: Baltzer, Lise
name: Philippon, Valerie
Publisher: name: Open Pharma
Year: 2025
Subjects: classificationCode: 321403
subject: Clinical pharmacy and pharmacy practice
classificationCode: 350505
subject: Occupational and workplace health and safety
classificationCode: 420306
subject: Health care administration
classificationCode: 429999
subject: Other health sciences not elsewhere classified
classificationCode: 390113
subject: Science, technology and engineering curriculum and pedagogy

description: Open Pharma position statement on open access
Additional file 1 of Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome
Creators: name: Papanicolas, Lito E.
name: Sims, Sarah K.
name: Taylor, Steven L.
name: Miller, Sophie J.
name: Karapetis, Christos S.
name: Wesselingh, Steve L.
name: Gordon, David L.
name: Rogers, Geraint B.
Publisher: name: figshare
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1: Supplementary Figure 1. Non-metric multi-dimensional scaling (nMDS) plot showing between group comparisons of faecal microbiome distribution and dispersal. nMDS plots depicted from Bray-Curtis resemblance of square root transformed, genus-level, relative abundance data. Shaded ovals represent 80% confidence interval. There is no difference between the pre-chemotherapy and post-chemotherapy (post-1) faecal microbiome distribution (PERMANOVA; p=0.99) or dispersion (PERMDISP; p=0.90). Supplementary Figure 2. Taxa bar plot showing the 11 phyla detected. Grouped by time point with Pre=pre-chemotherapy, Post1=7-12 days following chemotherapy, and Post2= at the end of a chemotherapy cycle (median 21 days post-chemotherapy). Showing predominance of Bacteroidetes and Firmicutes. Supplementary Figure 3. Taxa bar plot showing the 95 genera detected in ≥20% of samples. Grouped by time point with Pre = pre-chemotherapy, Post1 = 7–12 days following chemotherapy, and Post2 = at the end of a chemotherapy cycle (median 21 days post-chemotherapy).
Multilevel Sequential Importance Sampling for Rare Event Estimation
Creators: name: Wagner, Fabian
name: Latz, Jonas
name: Papaioannou, Iason
name: Ullmann, Elisabeth
Publisher: name: arXiv
Year: 2019
Subjects: subject: Numerical Analysis (math.NA)
subject: Computation (stat.CO)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 35R60, 65C40, 65C60, 65N30

description: The estimation of the probability of rare events is an important task in reliability and risk assessment. We consider failure events that are expressed in terms of a limit state function, which depends on the solution of a partial differential equation (PDE). Since numerical evaluations of PDEs are computationally expensive, estimating such probabilities of failure by Monte Carlo sampling is intractable. More efficient sampling methods from reliability analysis, such as Subset Simulation, are popular, but can still be impracticable if the PDE evaluations are very costly. In this article, we develop a novel, highly efficient estimator for probabilities of rare events. Our method is based on a Sequential Importance sampler using discretizations of PDE-based limit state functions with different accuracies. A twofold adaptive algorithm ensures that we obtain an estimate based on the desired discretization accuracy. In contrast to the Multilevel Subset Simulation estimator of [Ullmann, Papaioannou 2015; SIAM/ASA J. Uncertain. Quantif. 3(1):922-953], our estimator overcomes the nestedness problem. Of particular importance in Sequential Importance sampling algorithms is the correct choice of the MCMC kernel. Instead of the popular adaptive conditional sampling method, we propose a new algorithm that uses independent proposals from an adaptively constructed von Mises-Fischer-Nakagami distribution. The proposed algorithm is applied to test problems in 1D and 2D space, respectively, and is compared to the Multilevel Subset Simulation estimator and to single-level versions of Sequential Importance Sampling and Subset Simulation.