cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Prolutacea pulsator
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Prolutacea
Prolutacea pulsator

description: Prolutacea pulsator (Cicero, 1984)
USA; MEXICO: NA
= Lampyris pulsator Cicero, 1984
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
A phase I trial of caffeine to evaluate safety in infants with hypoxic-ischemic encephalopathy
Creators: name: Jackson, Wesley
name: Lee, Yueh Z.
name: Gonzalez, Daniel
name: Laughon, Matthew M.
name: Greenberg, Rachel G.
Publisher: name: Springer Nature
Year: 2023

description: OBJECTIVE: Caffeine provides neuroprotection following hypoxic-ischemic injury in animals. We characterized the safety of escalating doses of caffeine in infants with hypoxic-ischemic encephalopathy (HIE) receiving therapeutic hypothermia. STUDY DESIGN: Phase I trial of infants undergoing therapeutic hypothermia for HIE receiving IV caffeine 20 mg/kg followed by up to two daily doses of 5 mg/kg (n = 9) or 10 mg/kg (n = 8). Safety was evaluated based on adverse events and frequency of pre-specified outcomes compared to data from the Whole-Body Hypothermia for HIE trial (Shankaran, 2005). RESULTS: Twelve of 17 (71%) infants had ≥1 adverse event during the study period. The frequency of clinical outcomes related to HIE were not statistically different from outcomes in infants receiving hypothermia in the Whole-Body Hypothermia for HIE trial. CONCLUSION: Caffeine administration was well tolerated. A larger study is required to determine the optimal dose and evaluate drug safety and efficacy
Modeling the Mechanisms by Which Coexisting Biomolecular RNA-Protein Condensates Form
Creators: name: Newby, J. M.
name: Gladfelter, A. S.
name: Gasior, K.
name: Forest, M. G.
Publisher: name: Springer Nature
Year: 2020

description: Liquid–liquid phase separation is an emerging mechanism for intracellular organization. This work presents a mathematical model to examine molecular mechanisms that yield phase-separated droplets composed of different RNA–protein complexes. Using a Cahn–Hilliard diffuse interface model with a Flory–Huggins free energy scheme, we explore how multiple (here two, for simplicity) protein–RNA complexes (species) can establish a heterogeneous droplet field where droplets with single or multiple species phase separate and evolve during coarsening. We show that the complex–complex de-mixing energy tunes whether the complexes co-exist or form distinct droplets, while the transient binding kinetics dictate both the timescale of droplet formation and whether distinct species phase separate into droplets simultaneously or sequentially. For specific energetics and kinetics, a field of droplets driven by the formation of only one protein–RNA complex will emerge. Slowly, the other droplet species will accumulate inside the pre-formed droplets of the other species, allowing them to occupy the same droplet space. Alternatively, unfavorable species mixing creates a parasitic relationship: the slow-to-form protein–RNA complex will accumulate at the surface of a competing droplet species, siphoning off the free protein as it is released.Oncethis competing protein–RNA complex has sufficiently accumulated on the droplet surface, it can form a new droplet that is capable of sharing an interface with the first complex droplet but is not capable of mixing. These results give insights into a wide range of phase-separation scenarios and heterogeneous droplets that coexist but do not mix within the nucleus and the cytoplasm of cells.
Methods for estimating reliability of water treatment processes : an application to conventional and membrane technologies
Creators: name: Beauchamp, Nicolas
Publisher: name: University of British Columbia
Year: 2008

description: Water supply systems aim, among other objectives, to protect public health by reducing the concentration of, and potentially eliminating, microorganisms pathogenic to human beings. Yet, because water supply systems are engineered systems facing variable conditions, such as raw water quality or treatment process performance, the quality of the drinking water produced also exhibits variability. The reliability of a treatment system is defined in this context as the probability of producing drinking water that complies with existing microbial quality standards. This thesis examines the concept of reliability for two physicochemical treatment technologies, conventional rapid granular filtration and ultrafiltration, used to remove the protozoan pathogen Cryptosporidium parvum from drinking water. First, fault tree analysis is used as a method of identifying technical hazards related to the operation of these two technologies and to propose ways of minimizing the probability of failure of the systems. This method is used to compile operators’ knowledge into a single logical diagram and allows the identification of important processes which require efficient monitoring and maintenance practices. Second, an existing quantitative microbial risk assessment model is extended to be used in a reliability analysis. The extended model is used to quantify the reliability of the ultrafiltration system, for which performance is based on full-scale operational data, and to compare it with the reliability of rapid granular filtration systems, for which performance is based on previously published data. This method allows for a sound comparison of the reliability of the two technologies. Several issues remain to be addressed regarding the approaches used to quantify the different input variables of the model. The approaches proposed herein can be applied to other water treatment technologies, to aid in prioritizing interventions to improve system reliability at the operational level, and to determine the data needs for further refinements of the estimates of important variables.
Lucidota Laporte 1833
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Lucidota

description: Genus Lucidota Laporte, 1833
MTZ: SS, CS, TV; NTR: VE
= Rileya Olivier, 1911
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Molecular dynamics simulations to explore the structure and rheological properties of normal and hyperconcentrated airway mucus
Creators: name: Cao, Xue-Zheng
name: Boucher, Richard C.
name: Papanikolas, Micah J.
name: Freeman, Ronit
name: Ford, Andrew G.
name: Forest, Mark Gregory
name: Hill, David B.
name: Markovetz, Matthew R.
name: Kato, Takafumi
Publisher: name: Wiley
Year: 2021

description: We develop the first molecular dynamics model of airway mucus based on the detailed physical properties and chemical structure of the predominant gel-forming mucin MUC5B. Our airway mucus model leverages the LAMMPS open-source code [https://lammps.sandia.gov], based on the statistical physics of polymers, from single molecules to networks. On top of the LAMMPS platform, the chemical structure of MUC5B is used to superimpose proximity-based, non-covalent, transient interactions within and between the specific domains of MUC5B polymers. We explore feasible ranges of hydrophobic and electrostatic interaction strengths between MUC5B domains with 9 nanometer spatial and 1 nanosecond temporal resolution. Our goal here is to propose and test a mechanistic hypothesis for a striking clinical observation with respect to airway mucus: a 10-fold increase in non-swellable, dense structures called flakes during progression of cystic fibrosis disease. Among the myriad possible effects that might promote self-organization of MUC5B networks into flake structures, we hypothesize and confirm that the clinically confirmed increase in mucin concentration, from 1.5 to 5 mg/mL, alone is sufficient to drive the structure changes observed with scanning electron microscopy images from experimental samples. We post-process the LAMMPS simulated datasets at 1.5 and 5 mg/mL, both to image the structure transition and compare with scanning electron micrographs and to show that the 3.33-fold increase in concentration induces closer proximity of interacting electrostatic and hydrophobic domains, thereby amplifying the proximity-based strength of the interactions.
MOESM2 of Effect of Cichorium intybus L. on the expression of hepatic NF-κB and IKKβ and serum TNF-α in STZ− and STZ+ niacinamide-induced diabetes in rats
Creators: name: Lotfollah Rezagholizadeh
name: Pourfarjam, Yasin
name: Nowrouzi, Azin
name: Manuchehr Nakhjavani
name: Alipasha Meysamie
name: Ziamajidi, Nasrin
name: Nowrouzi, Peyman
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Marine Biology
subject: Science Policy
subject: 60506 Virology

description: Additional file 2. Western blot analysis on 4 members of each group.
title: PROTOTIPO DE UN SISTEMA DE VISUALIZACIÓN EN 3D BASADO EN REALIDAD AUMENTADA APLICADO A LA MATERIA DE PERFORACIÓN EN LA CARRERA DE INGENIERÍA PETROLERA DE LA ESCUELA MILITAR DE INGENIERA UNIDAD ACADÉMICA SANTA CRUZ
title: Prototype of a 3D Visualization System Based on Augmented Reality Applied to the Drilling Course in the Petroleum Engineering Program at the Military Engineering School, Santa Cruz Academic Unit
titleType: AlternativeTitle
Creators: name: ATAHUICHI PINTO, BRYAN JOSE
Publisher: name: Bryan Jose Atahuichi Pinto
Year: 2018

description: Desarrollo de aplicación de Realidad Aumentada, enficado al proceso de enseñanza apredizaje, en la materia de perforación 1
Additional file 1: of Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna
Creators: name: Poehlein, Anja
name: Freese, Heike
name: Daniel, Rolf
name: Simeonova, Diliana
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Composition of MDS3 medium and growth conditions in phosphite assimilation tests. (PDF 64.3Â kb)
Mucus and mucus flake composition and abundance reflect inflammatory and infection status in cystic fibrosis
Creators: name: Papanikolas, Micah J
name: Ghio, Andrew
name: Stick, Stephen M
name: Hill, David B
name: Garbarine, Ian C
name: Forest, M Gregory
name: Boucher, Richard C
name: Ceppe, Agathe
name: Muhlebach, Marianne S
name: Seim, Ian
name: Markovetz, Matthew R
name: Esther, Charles R
name: Kissner, William J
name: Morrison, Cameron B
name: Ehre, Camille
name: Alexis, Neil E
name: Freeman, Ronit
Publisher: name: Elsevier
Year: 2022

description: BACKGROUND: Mucus hyperconcentration in cystic fibrosis (CF) lung disease is marked by increases in both mucin and DNA concentration. Additionally, it has been shown that half of the mucins present in bronchial alveolar lavage fluid (BALF) from preschool-aged CF patients are present in as non-swellable mucus flakes. This motivates us to examine the utility of mucus flakes, as well as mucin and DNA concentrations in BALF as markers of infection and inflammation in CF airway disease. METHODS: In this study, we examined the mucin and DNA concentration, as well as mucus flake abundance, composition, and biophysical properties in BALF from three groups; healthy adult controls, and two CF cohorts, one preschool aged and the other school aged. BALFs were characterized via refractometry, PicoGreen, immunofluorescence microscopy, particle tracking microrheology, and fluorescence image tiling. RESULTS: Mucin and DNA BALF concentrations increased progressively from healthy young adult controls to preschool-aged people and school-aged people with CF. Notably, mucin concentrations were increased in bronchoalveolar lavage fluid (BALF) from preschool-aged patients with CF prior to decreased pulmonary function. Infrequent small mucus flakes were identified in normal subjects. A progressive increase in the abundance of mucus flakes in preschool and school-aged CF patients was observed. Compositionally, MUC5B dominated flakes from normal subjects, whereas an increase in MUC5AC was observed in people with CF, reflected in a reduced flaked MUC5B/MUC5AC mucin ratio. CONCLUSION: These findings suggest mucus composition and flake properties are useful markers of inflammatory and infection-based changes in CF airways.
Lucidota bella Gorham 1880
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Lucidota
Lucidota bella

description: Lucidota bella Gorham, 1880
MEXICO: CM, CS, EM, OA, TB, VE; Guatemala; Honduras; Nicaragua
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Observation of transition cascades in sheared liquid crystalline polymers
Creators: name: Picken, Stephen J
name: Forest, M Gregory
name: Dingemans, Theo J
name: Fox, Ryan J
Publisher: name: Royal Society of Chemistry (RSC)
Year: 2020

description: We report on the shear rheology of liquid crystalline solutions composed of charged, rodlike polymers that form supramolecular assemblies dispersed in water. Under steady shear, we observe shear thickening behavior, followed by a hesitation in the viscosity accompanied by an extremely narrow range of negative first normal stress difference. The Peclet number (Pe, shear rate normalized by rod rotational diffusivity) for the onset of shear thickening is in agreement with previous, high-resolution numerical simulations of the Doi-Edwards-Hess kinetic theory. We interrogate these dynamic responses through shear step-down experiments, revealing a complex evolution of transient responses. Detailed analysis of the stress transients provides compelling evidence that the principal axis of the rod orientational distribution, the nematic director, undergoes a cascade of transitions and coexistence of periodic states known as kayaking, tumbling, and wagging, before transitioning to steady flow alignment above a critical shear rate.
Additional file 17: of Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments
Creators: name: Kargarfard, Fatemeh
name: Ashkan Sami
name: Mohammadi-Dehcheshmeh, Manijeh
name: Esmaeil Ebrahimie
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Gives details of the developed approach in this study in increasing the support and accuracy of prediction and generation of more informative rules through making secondary datasets. The components of secondary datasets are discovered spots at the first run of rule discovery instead of sequence features. We extracted combinational association rules from several tables to gain rules with higher support and confidence. (DOCX 37 kb)
Additional file 4: of Diagnostic accuracy of methacholine challenge tests assessing airway hyperreactivity in asthmatic patients - a multifunctional approach
Creators: name: Kraemer, Richard
name: Hans-JĂźrgen Smith
name: Sigrist, Thomas
name: Giger, Gabi
name: Keller, Roland
name: Frey, Martin
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Statistical approach. (DOCX 128Â kb)
Nanoparticle Loading of Unentangled Polymers Induces Entanglement-Like Relaxation Modes and a Broad Sol-Gel Transition
Creators: name: Forest, M. Gregory
name: Merlitz, Holger
name: Cao, Xue-Zheng
Publisher: name: American Chemical Society (ACS)
Year: 2019

description: We combine molecular dynamics simulations, imaging and data analysis, and the Green−Kubo summation formula for the relaxation modulus G(t) to elicit the structure and rheology of unentangled polymer−nanoparticle composites distinguished by small NPs and strong NP−monomer attraction, εNPM ≫ kBT. A reptation-like plateau emerges in G(t) beyond a terminal relaxation time scale as the volume fraction, cNP, of NPs increases, coincident with a structure transition. A condensed phase of NP-aggregates forms, tightly interlaced with thin sheets of polymer chains, the remaining phase consisting of free chains void of NPs. Rouse mode analyses are applied to the two individual phases, revealing that long-wavelength Rouse modes in the aggregate phase are the source of reptation-like relaxation. Imaging reveals chain motion confined within the thin sheets between NPs and exhibits a 2D analogue of classical reptation. In the NP-free phase, Rouse modes relax indistinguishable from a neat polymer melt. The Fourier transform of G(t) reveals a sol−gel transition across a broad frequency spectrum, tuned by cNP and εNPM above critical thresholds, below which all structure and rheological transitions vanish.
Additional file 2: of Diagnostic accuracy of methacholine challenge tests assessing airway hyperreactivity in asthmatic patients - a multifunctional approach
Creators: name: Kraemer, Richard
name: Hans-JĂźrgen Smith
name: Sigrist, Thomas
name: Giger, Gabi
name: Keller, Roland
name: Frey, Martin
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: The Aerosol Provocation System (APS). (DOCX 545Â kb)
Lucidota bicellonycha McDermott 1958
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Lucidota
Lucidota bicellonycha

description: Lucidota bicellonycha McDermott, 1958
MEXICO: OA Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
MOESM1 of Effect of Cichorium intybus L. on the expression of hepatic NF-κB and IKKβ and serum TNF-α in STZ− and STZ+ niacinamide-induced diabetes in rats
Creators: name: Lotfollah Rezagholizadeh
name: Pourfarjam, Yasin
name: Nowrouzi, Azin
name: Manuchehr Nakhjavani
name: Alipasha Meysamie
name: Ziamajidi, Nasrin
name: Nowrouzi, Peyman
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Marine Biology
subject: Cancer

description: Additional file 1. Body weights and fasting blood sugar (FBS) levels upon ET2D and LT2D induction and during 21-day treatment with CSE, metformin and aspirin; same data as Table 1.
Additional file 9: Table S7. of Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments
Creators: name: Kargarfard, Fatemeh
name: Ashkan Sami
name: Mohammadi-Dehcheshmeh, Manijeh
name: Esmaeil Ebrahimie
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Listing the rules extracted from NS2 protein of influenza A in identification of host ranges. (DOCX 20 kb)
Additional file 1: of Characterizing the vulnerability of frequent emergency department users by applying a conceptual framework: a controlled, cross-sectional study
Creators: name: Bodenmann, Patrick
name: StĂŠphanie Baggio
name: Iglesias, Katia
name: Althaus, Fabrice
name: Venetia-Sofia Velonaki
name: Stucki, Stephanie
name: Ansermet, Corine
name: Paroz, Sophie
name: Trueb, Lionel
name: Hugli, Olivier
name: Griffin, Judith
name: Jean-Bernard Daeppen
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology

description: Questionnaire on sexual risk behaviors (self-administered). (DOC 22Â kb)
Temperature-dependent vibrational spectroscopy to study order-disorder transitions in charge transfer complexes
Creators: name: Goetz, Katelyn P.
name: McNeil, L. E.
name: Jurchescu, Oana D.
name: Isaac, Rohan
name: Roberts, Drew
Publisher: name: AIP Publishing
Year: 2018

description: Charge-transfer (CT) complexes are a promising class of materials for the semiconductor industry because of their versatile properties. This class of compounds shows a variety of phase transitions, which are of interest because of their potential impact on the electronic characteristics. Here temperature-dependent vibrational spectroscopy is used to study structural phase transitions in a set of organic CT complexes. Splitting and broadening of infrared-active phonons in the complex formed between pyrene and pyromellitic dianhydride (PMDA) confirm the structural transition is of the order-disorder type and complement previous x-ray diffraction (XRD) results. We show that this technique is a powerful tool to characterize transitions, and apply it to a range of binary CT complexes composed of polyaromatic hyrdocarbons (anthracene, perylene, phenanthrene, pyrene, and stilbene) and PMDA. We extend the understanding of transitions in perylene-PMDA and pyrene-PMDA, and show that there are no order-disorder transitions present in anthracene-PMDA, stilbene-PMDA and phenanthrene-PMDA in the temperature range investigated here.
Lucidota binotatens McDermott 1966
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Lucidota
Lucidota binotatens

description: Lucidota binotatens McDermott, 1966
MEXICO Endemic
= Lucidota binotata Pic, 1930
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
The smooth forcing extension method: A high-order technique for solving elliptic equations on complex domains
Creators: name: Qadeer, Saad
name: Griffith, Boyce E.
Publisher: name: Elsevier
Year: 2021

description: High-order numerical methods for solving elliptic equations over arbitrary domains typically require specialized machinery, such as high-quality conforming grids for finite elements method, and quadrature rules for boundary integral methods. These tools make it difficult to apply these techniques to higher dimensions. In contrast, fixed Cartesian grid methods, such as the immersed boundary (IB) method, are easy to apply and generalize, but typically are low-order accurate. In this study, we introduce the Smooth Forcing Extension (SFE) method, a fixed Cartesian grid technique that builds on the insights of the IB method, and allows one to obtain arbitrary orders of accuracy. Our approach relies on a novel Fourier continuation method to compute extensions of the inhomogeneous terms to any desired regularity. This is combined with the highly accurate Non-Uniform Fast Fourier Transform for interpolation operations to yield a fast and robust method. Numerical tests confirm that the technique performs precisely as expected on one-dimensional test problems. In higher dimensions, the performance is even better, in some cases yielding sub-geometric convergence. We also demonstrate how this technique can be applied to solving parabolic problems and for computing the eigenvalues of elliptic operators on general domains, in the process illustrating its stability and amenability to generalization.
MOESM1 of Elucidation of the glycosylation steps during biosynthesis of antitumor macrolides PM100117 and PM100118 and engineering for novel derivatives
Creators: name: Salcedo, Raúl
name: Olano, Carlos
name: Fernández, Rogelio
name: Braña, Alfredo
name: Méndez, Carmen
name: Calle, Fernando
name: Salas, José
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Additional file 1. In silico analysis of sugar biosynthesis and glycosyltransferase genes.
The speeding up of marine ecosystems
Creators: name: Bruno, John F.
name: Clark, Graeme F.
name: Johnston, Emma L.
Publisher: name: Elsevier
Year: 2022

description: Four drivers of global change are acting in concert to speed up the ecology of our coastal and open ocean ecosystems. Ocean warming, nutrient pollution, disturbance, and species additions increase biological and ecological rates, favoring weedy communities and causing pervasive human impacts. Ocean warming via greenhouse gas emissions is accelerating metabolic processes, with effects scaling up to populations and ecosystems. Likewise, supercharging primary production via increased resources (e.g., nutrients and light) is leading to faster, weedier communities in estuarine and coastal ecosystems. Disturbances like ocean heat waves are becoming more frequent, resetting succession, and creating permanently young assemblages, while species additions are transporting the quick-growing and the fecund. The speeding up of marine ecosystems will necessitate changes in the ways we do science, attempt conservation, and use ecosystem services.
MOESM3 of Effect of Cichorium intybus L. on the expression of hepatic NF-κB and IKKβ and serum TNF-α in STZ− and STZ+ niacinamide-induced diabetes in rats
Creators: name: Lotfollah Rezagholizadeh
name: Pourfarjam, Yasin
name: Nowrouzi, Azin
name: Manuchehr Nakhjavani
name: Alipasha Meysamie
name: Ziamajidi, Nasrin
name: Nowrouzi, Peyman
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Physiology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified

description: Additional file 3. Evaluation of metformin. The HPLC system consisted of PLATIN Blue (KNAUER, Germany) with a PDA detector. The wavelength was set at 233 nm. The column was Nucleosil-100, C-18 (250 4.6 mm, 5 nm). The software was EZChrom Elite. The mobile phase comprised 0.01 M potassium dihydrogen orthophosphate (adjusted to pH 4.5 with glacial acetic acid) and acetonitrile (60:40, v/v). Analyses were run at a flow-rate of 1.0 ml/min and the samples were quantified using peak area. Initial weight of each 500 mg pill: Merck, 516.63 mg; and Chemidaru, 582.50 mg. 2.5, 5, 10, 50, and 100 mg of the powdered pills were dissolved in 1 ml of deionized H2O. Merck metformin dissolved completely in water, whereas metformin from Chemidaru consisted of insoluble part. Injection volumes were 5 µl; each sample was injected only once. The corresponding peaks for 10 mg/ml sample and the resulting standard curves for two metformin brands are compared in graphs.
Transition in swimming direction in a model self-propelled inertial swimmer
Creators: name: Dombrowski, Thomas
name: Bhalla, Amneet Pal Singh
name: Griffith, Boyce E.
name: Katsikis, Georgios
name: Jones, Shannon K.
name: Klotsa, Daphne
Publisher: name: American Physical Society (APS)
Year: 2019

description: We propose a reciprocal, self-propelled model swimmer at intermediate Reynolds numbers (Re). Our swimmer consists of two unequal spheres that oscillate in antiphase, generating nonlinear steady streaming (SS) flows. We show computationally that the SS flows enable the swimmer to propel itself, and also switch direction as Re increases. We quantify the transition in the swimming direction by collapsing our data on a critical Re and show that the transition in swimming directions corresponds to the reversal of the SS flows. Based on our findings, we propose that SS can be an important physical mechanism for motility at intermediate Re.
Lucidota diaphanura Gorham 1881
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Lucidota
Lucidota diaphanura

description: Lucidota diaphanura Gorham, 1881
MEXICO: VE Endemic
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 1: of Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments
Creators: name: Kargarfard, Fatemeh
name: Ashkan Sami
name: Mohammadi-Dehcheshmeh, Manijeh
name: Esmaeil Ebrahimie
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Includes whole accession numbers of sequences used in the current study. (DOCX 37 kb)
Hydrodynamic controls on the movement of invertebrate larvae and organic matter in small streams
Creators: name: Hoover, Trent
Publisher: name: University of British Columbia
Year: 2008

description: The movement of organisms and resources within ecosystems are essential elements in the productivity, stability, and distribution of communities. This thesis examines how water velocity, a defining factor of lotic systems, influences the dispersion of benthic organisms and particulate organic matter in small stream ecosystems. Variation in movement-related behaviours in two rheophilous (‘flow-loving’) mayflies (Epeorus and Baetis) and two rheophobic (‘flow-avoiding’) mayflies (Ameletus and Paraleptophlebia) were compared to determine how benthic organisms disperse between and within habitat patches in hydrodynamically complex landscapes. The degree to which water velocity and particle shape influence the retention of organic matter (including deciduous leaves, conifer needles, red-cedar fronds, and branch fragments) was examined to determine how physical factors determine detrital resource availability in streams. Although water velocity did not influence the crawling rates of Baetis and Ameletus in daylight conditions, both mayflies dispersed rapidly upstream in low-velocity flows in dark conditions. Drift rates of both mayflies were lower in daylight than dark conditions, and were generally inversely related to their habitat preferences. Escape responses in grazing Epeorus, Baetis, and Ameletus larvae in a range of flow conditions showed that retreat distance was more sensitive than flight initiation distance to variation in water velocity, suggesting that hydrodynamics mediate the risks of predation and the costs of flight in stream systems. Comparisons of the transport distances of live larvae, dead larvae, and passive tracer particles in low and high water velocities showed that drift distance varied substantially among taxa, and that behavioural control over drift distance generally declined as water velocity increased. While organic matter particles generally travelled further in high-velocity reaches, leaves were retained in riffles when they impacted on protruding clasts, while ‘stiff’ particles were retained when they settled into streambed interstices. Leaves placed in high-velocity microhabitats were broken down more slowly than leaves in low-flow areas, likely due to the exclusion of large-bodied detritivores. In conclusion, this thesis supports the view that hydrodynamic forces control trophic interactions and local population dynamics in stream ecosystems by directly altering the physical – and sometimes behavioural – processes of particle entrainment, transport, and deposition.
MOESM3 of Elucidation of the glycosylation steps during biosynthesis of antitumor macrolides PM100117 and PM100118 and engineering for novel derivatives
Creators: name: Salcedo, Raúl
name: Olano, Carlos
name: Fernández, Rogelio
name: Braña, Alfredo
name: Méndez, Carmen
name: Calle, Fernando
name: Salas, José
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences

description: Additional file 3. Fig. S2. Effect of gonR2 over-expression on PM100117/18 biosynthesis. Fig. S3. Effects of gonG4 over-expression on S. caniferus GUA-06-05-006A and ΔgonG2. Methods: Feeding experiment. Fig. S4. Heterologous expression of gonG4 in Streptomyces albus J1074 and feeding with PM100118.
MOESM1 of Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199
Creators: name: López-Mondéjar, Rubén
name: Zühlke, Daniela
name: Tomáš Větrovský
name: Becher, Dörte
name: Riedel, Katharina
name: Baldrian, Petr
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biotechnology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: Additional file 1: Figure S1. Cellulolytic ability of Paenibacillus O199. A) Growth in minimal medium containing filter paper as the sole carbon source. The deconstruction of the paper by bacterial enzymes was complete after 7 days (on the right), in comparison with the control (on the left). B) Activity of enzymes involved in the degradation of polysaccharides in the culture. “–“: no activity detected.
Lucidota discolor Gorham 1881
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Lucidota
Lucidota discolor

description: Lucidota discolor Gorham, 1881
MEXICO: VE; Belize; Guatemala; Honduras; Nicaragua; Panama
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Assesment of drinking water quality using disinfection by-products in a distribution system following a treatment technology upgrade
Creators: name: Bush, Kelly Lynn
Publisher: name: University of British Columbia
Year: 2008

description: Chlorine is the most widely used disinfectant for drinking water treatment. Chlorine canreact with natural organic matter (NOM) in water sources resulting in the formation of potentially carcinogenic disinfection by-products (DBPs). The most common DBPs measured in chlorinated drinking water distribution systems are trihalomethanes (THMs) and haloacetic acids (HAAs). In 2005, the City of Kamloops, British Columbia upgraded the drinking water treatment system to ultrafiltration membrane treatment. The objective of this study was to determine the extent to which upgrades to a drinking water treatment system, specifically, implementation of an ultrafiltration treatment process, impacted DBP formation within a distribution system. This study used a two-phase research approach. Phase I of the study was a distribution system monitoring program that collected water samples and physical and chemical information using data loggers at five sampling sites within the distribution system. Phase II of the study used bench-scale simulations that modeled DBP formation using a flow-through reactor system, the material-specific simulated distribution system (MS-SDS), constructed of pipe material resurrected from the City of Kamloops distribution system. Phase I results suggested that implementation of the ultrafiltration treatment process and accompanying treatment system upgrade was not effective at reducing the concentration of DBPs delivered to consumers. Concentrations of THMs remained relatively constant at sampling sites, while concentrations of HAAs increased following implementation of the ultrafiltration treatment process. The increase in HAA formation was likely due to an increase in retention time of the water within the distribution system following implementation of the ultrafiltration treatment process, rather than due to the treatment process itself. The results of this study are consistent with previous work on South Thompson River water DBP precursors, which suggested that THM and HAA precursors of this source water are small and hydrophilic, and therefore cannot be removed by ultrafiltration processes. Phase II results showed that the MS-SDS was more representative of distribution system c onditions than traditional glass bottles to estimate DBP formation. It is recommended that the MS-SDS be used in parallel with a simultaneous distribution system monitoring program to estimate distribution system retention times from THM and HAA concentrations.
MOESM1 of Mycofier: a new machine learning-based classifier for fungal ITS sequences
Creators: name: Delgado-Serrano, Luisa
name: Restrepo, Silvia
name: Bustos, Jose
name: Zambrano, Maria
name: Anzola, Juan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Plant Biology

description: Additional file 1: Table S1. Comparisons of the accuracy percentage obtained by the two models (1 and 2) for each genus.
Taking advantage of existing research data -  University of Bergen Library Presentation 13/12/2024
Creators: name: Ostrop, Jenny
Publisher: name: Zenodo
Year: 2024
Subjects: subject: FAIR
subject: Open Data
subject: FAIR Data
subject: Data reuse
subject: Research Data Life Cycle
subject: Data Management
subject: Research Data
subject: Academic Library
subject: Library Services
subject: Library Science/methods

description: Presentation slides for webinar "Taking advantage of existing research data" by the University of Bergen Library, 13.12.2024.This webinar gives introduction to finding and reusing existing datasets as a resource in research.Aspects covered:

FAIR principles as prerequisites for data reuse

Data citation

Strategies to efficiently discover data from public sector, data in digital archives, and scientific dataset

 

Contact: research-data[at]uib.no
title: Engaging Crimea and Beyond: Perspectives on Conflict, Cooperation and Civil Society Development
Creators: name: Carment, David
name: Nikolko, Milana
Publisher: name: GCR21- Käte Hamburger Kolleg/Center for Global Cooperation Research
Year: 2016
Subjects: subject: 10505 International Relations, International Politics, Foreign Affairs, Development Policy
subject: 10507 Peace and Conflict Research, International Conflicts, Security Policy
subject: 10506 European Politics
subject: KAT12 International Institutions, Relations, Conditions

description: This issue of Global Dialogues draws on a two-day event organized by the Centre for
        Global Cooperation Research in the spring of 2015. Bringing together academics and
        policymakers from Crimea, Russia, Ukraine, Canada, and Germany, the meeting explored the
        current situation in Crimea, day-today life in the region, relations – present and future –
        between Ukraine and Russia, and the role of the West in finding a cooperative solution to
        the conflict.
description: 6 Introduction, Milana Nikolko and David Carment
Part I: Engaging Crimea: Prospects for Conflict and Cooperation
11 The Future of Crimea: the Crimean Tatar Perspective, Elmira Muratova
14 Crimea: Russia‘s Other Chechnya? Ivan Preobrazhenskiy
16 Crimea in Retrospect: Missed Opportunities? David Carment
21 Three Myths for Crimea: Does Ukraine’s Version Have a Chance? Pavel Kazarin
25 The Quest for a Political Mythology: Ukraine and the Crimean Tatar Story, Serhii Kostynskyi
Part II: Constructing ‘the Ukrainian Nation’: the Role of Civil Society in the Nation Building Process After the Crimean Referendum
29 Symbols, Meanings, and Conflicts: How the Interpretation of History Influences
Contemporary Events in Ukraine, Oksana Danylenko
34 Anti-corruption Reform in Ukraine: Prospects and Challenges, Oksana Huss
38 History and Gender in the Euromaidan Protests, Olena Petrenko
43 Phantom Pain Syndrome: The Ukrainian Nation One Year after the Annexation of Crimea, Milana Nikolko
47 Information about the Authors and Editors
Appendices of the Conference Paper Titiled "An Empirical Study Evaluating ChatGPT’s Performance in Generating Search Strategies for Systematic Reviews"
Creators: name: Fei Yu
name: Heather Kincaide
name: Rebecca Beth Carlson
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2024

description: Appendices A through D are supplementary materials for the conference paper titled “An Empirical Study Evaluating ChatGPT’s Performance in Generating Search Strategies for Systematic Reviews”. This paper has been accepted for presentation at the 87th Annual Meeting of the Association for Information Science & Technology, which will be held from October 25 to 29, 2024, in Calgary, AB, Canada
Quantifying Task Priority for Multi-Task Optimization
Creators: name: Jeong, Wooseong
name: Yoon, Kuk-Jin
Publisher: name: arXiv
Year: 2024
Subjects: subject: Machine Learning (cs.LG)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: The goal of multi-task learning is to learn diverse tasks within a single unified network. As each task has its own unique objective function, conflicts emerge during training, resulting in negative transfer among them. Earlier research identified these conflicting gradients in shared parameters between tasks and attempted to realign them in the same direction. However, we prove that such optimization strategies lead to sub-optimal Pareto solutions due to their inability to accurately determine the individual contributions of each parameter across various tasks. In this paper, we propose the concept of task priority to evaluate parameter contributions across different tasks. To learn task priority, we identify the type of connections related to links between parameters influenced by task-specific losses during backpropagation. The strength of connections is gauged by the magnitude of parameters to determine task priority. Based on these, we present a new method named connection strength-based optimization for multi-task learning which consists of two phases. The first phase learns the task priority within the network, while the second phase modifies the gradients while upholding this priority. This ultimately leads to finding new Pareto optimal solutions for multiple tasks. Through extensive experiments, we show that our approach greatly enhances multi-task performance in comparison to earlier gradient manipulation methods.
Lucidota purulana
Creators: name: Pérez-Hernández, Cisteil X.
name: Zaragoza-Caballero, Santiago
name: Romo-Galicia, Alberto
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Lampyridae
Lucidota
Lucidota purulana

description: Lucidota purulana (Gorham, 1884)
MEXICO; Guatemala
= Photinus purulanus Gorham, 1884
description: Published as part of Pérez-Hernández, Cisteil X., Zaragoza-Caballero, Santiago & Romo-Galicia, Alberto, 2022, Updated checklist of the fireflies (Coleoptera: Lampyridae) of Mexico, pp. 291-317 in Zootaxa 5092 (3) on page 300, DOI: 10.11646/zootaxa.5092.3.3, http://zenodo.org/record/5881269
Additional file 1: Table S1. of Patientsâ   perspectives can be integrated in health technology assessments: an exploratory analysis of CADTH Common Drug Review
Creators: name: Berglas, Sarah
name: Jutai, Lauren
name: MacKean, Gail
name: Weeks, Laura
Publisher: name: Figshare
Year: 2016
Subjects: Biochemistry
Medicine
Developmental Biology

description: Inclusion of patient insights in 30 CADTH CDR assessments. (DOCX 15Â kb)