cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Toward Automated Simulation Research Workflow through LLM Prompt Engineering Design
Creators: name: Liu, Zhihan
name: Chai, Yubo
name: Li, Jianfeng
Publisher: name: arXiv
Year: 2024
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Computation and Language (cs.CL)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: The advent of Large Language Models (LLMs) has created new opportunities for the automation of scientific research spanning both experimental processes and computational simulations. This study explores the feasibility of constructing an autonomous simulation agent (ASA) powered by LLMs through prompt engineering and automated program design to automate the entire simulation research process according to a human-provided research plan. This process includes experimental design, remote upload and simulation execution, data analysis, and report compilation. Using a well-studied simulation problem of polymer chain conformations as a test case, we assessed the long-task completion and reliability of ASAs powered by different LLMs, including GPT-4o, Claude-3.5, etc. Our findings revealed that ASA-GPT-4o achieved near-flawless execution on designated research missions, underscoring the potential of methods like ASA to achieve automation in simulation research processes to enhance research efficiency. The outlined automation can be iteratively performed for up to 20 cycles without human intervention, illustrating the potential of ASA for long-task workflow automation. Additionally, we discussed the intrinsic traits of ASA in managing extensive tasks, focusing on self-validation mechanisms, and the balance between local attention and global oversight.
description: The source code and example results of ASA can be found at https://github.com/zokaraa/autonomous_simulation_agent
R-matrices and Miura operators in 5d Chern-Simons theory
Creators: name: Ishtiaque, Nafiz
name: Jeong, Saebyeok
name: Zhou, Yehao
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We derive Miura operators for $W$- and $Y$-algebras from first principles as the expectation value of the intersection between a topological line defect and a holomorphic surface defect in 5-dimensional non-commutative $\mathfrak{gl}(1)$ Chern-Simons theory. The expectation value, viewed as the transition amplitude for states in the defect theories forming representations of the affine Yangian of $\mathfrak{gl}(1)$, satisfies the Yang-Baxter equation and is thus interpreted as an R-matrix. To achieve this, we identify the representations associated with the line and surface defects by calculating the operator product expansions (OPEs) of local operators on the defects, as conditions that anomalous Feynman diagrams cancel each other. We then evaluate the expectation value of the defect intersection using Feynman diagrams. When the line and surface defects are specified, we demonstrate that the expectation value precisely matches the Miura operators and their products.
description: 36+14 pages, 5 figures; v2. minor corrections, references added
title: Beach and Dune Conditions at South Padre Island, Texas - Assessment and Recommendations
Creators: name: Morton, Robert A.
Publisher: name: The University of Texas at Austin
Year: 1993
Subjects: subject: beaches
subject: dunes
subject: assessment
subject: South Padre Island
subject: Texas

description: An investigation of beach and dune conditions on South Padre Island was conducted for the Town of South Padre Island specifically to address two coastal issues: dune management and beach stability. The study results were organized and presented to assist City officials in their planning and management of beaches and dunes, which are vital to the economy and storm protection of the region. The study demonstrates that beach stability and dune development vary along the island and that management strategies need to be prepared for accreting, stable, and eroding beach segments. Furthermore, the study recognizes the need to begin planning for beach replenishment projects that will be required to maintain recreational beaches along eroding segments of South Padre Island in the future. Recommendations are made regarding the location and restoration of dunes, as well as options for beach replenishment. Additionally, it is recommended that the town initiate a beach-dune monitoring program that will provide a scientific basis for prudent management of the natural resources.
Dirofilaria
Creators: name: Muniz-Pereira, Luís C.
name: Vieira, Fabiano M.
name: Luque, José L.
Publisher: name: Zenodo
Year: 2009
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Secernentea
Spirurida
Onchocercidae
Dirofilaria

description: Dirofilaria sp.
Pteronura brasiliensis (Gmelin), under the skin, Mato Grosso do Sul, Rio de Janeiro (Vieira et al. 2008a) (CHIOC 15415, 22160).
description: Published as part of Muniz-Pereira, Luís C., Vieira, Fabiano M. & Luque, José L., 2009, Checklist of helminth parasites of threatened vertebrate species from Brazil, pp. 1-45 in Zootaxa 2123 on page 8, DOI: 10.5281/zenodo.188170
Globocassidulina subglobosa
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Globothalamea
Rotaliida
Cassidulinidae
Globocassidulina
Globocassidulina subglobosa

description: Globocassidulina subglobosa (Brady, 1881)
Pl. 4, figs. 9–10
Cassidulina subglobosa Brady, 1881, p. 60; Brady, 1884, p. 430, pl. 54, fig. 17; Barker, 1960, pl. 54, fig. 17.
Globocassidulina subglobosa LeRoy & Levinson, 1974, p. 14, pl. 7, fig. 8; Tjalsma & Lohmann, 1983, p. 31, pl. 16, fig. 9; Lowry, 1987, p. 239, pl. 14, figs. 7a–c; Miller & Katz, 1987, p. 134, pl. 3, fig. 4; Hermelin, 1989, p. 74; Thomas, 1990, p. 590; Jones, 1994, p. 60, pl. 54, fig. 17; Robertson, 1998, p. 136, pl. 53, figs. 1–2; Kuhnt et al., 2002, p. 144, pl. 10, figs. 3–5; pl. 17, figs. 1–2; Kender et al., 2008, p. 512, pl. 17, fig. 1–2; Milker & Schmiedl, 2012, p. 85, figs. 20.13–20.14; Holbourn et al., 2013, p. 264.
Description: The test wall is calcareous and smooth. The test is small, subglobular and subcircular in cross-section. The chambers have a biserial arrangement, are inflated and globular in shape, separated by depressed sutures. The aperture is slit-like, situated interio-marginal and stretches along the margin of the terminal chamber.
Remarks: Specimens from this species comprise a trace component (<1%) in core 2658, a minor component (<5%) in core 2682 and major component (<40%) in core 2670. The tests from this study are smaller than those in LeRoy & Levinson (1974) (diameter of up to 0.75 mm), measuring 0.25 mm in diameter.
Life strategy: This species is epifaunal to shallow-infaunal (Kaiho, 1994; Vilela, 1995), generally unattached and prefers muddy sediments under oxic (Kaiho, 1994) to suboxic (De & Gupta, 2010) conditions. Schmiedl et al. (1997) recorded G. subglobosa in oligotrophic areas, under vigorous bottom currents and sandy substrates. Panieri & Gupta (2008) recorded this species in relatively high abundances in muddy substrates. The bathymetric range of G. subglobosa is broad, stretching from the middle shelf to abyssal depths (Murgese & de Deckker, 2005; Holbourn et al., 2013).
Global stratigraphic range: Globocassidulina subglobosa occurs from the Palaeocene to Recent (Holbourn et al., 2013).
Regional occurrence: This species is recorded in Miocene-aged strata from the Congo Basin (Kender et al., 2008) and the Namibian outer continental shelf, south of the Kunene River mouth (this study). Hay et al. (1984) and Wefer et al. (1998) reported the occurrence of Globocassidulina subglobosa in late Miocene to Pleistoceneaged sediments along the continental slope in relatively minor abundances (<10%) at most sites. Lowry (1987) recorded occurrences of G. subglobosa in surface sediments on the continental shelf, between Cape Town and Port Elizabeth.
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on page 22, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434
title: Sequence Stratigraphy and Composition of Late Quaternary Shelf-Margin Deltas, High Island Area, Offshore Texas
Creators: name: Morton, Robert A.
Publisher: name: The University of Texas at Austin
Year: 1993
Subjects: subject: stratigraphy
subject: depositional systems
subject: Quaternary
subject: deltas
subject: offshore Texas

description: High-resolution seismic profiles and foundation borings from the northwestern Gulf of Mexico reveal the physical attributes of several late Quaternary depositional sequences that were deposited by wave-modified, river-dominated shelf-margin deltas during successive periods of lowered sea level. Each progressively younger sequence is thinner, and overall they exhibit a systematic decrease in the abundance and concentration of sand, which is attributed to a shift in the axes of trunk streams and greater structural influence through time. Results of the study show that (1) contemporaneous structural deformation controlled the thickness of each sequence, the oblique directions of delta progradation at the shelf margin, and the axes of major fluvial channels; (2) a soil zone capping the oldest sequence is a regressive surface of subaerial exposure that was later preserved during marine transgression; (3) the downlap surfaces are not true surfaces but zones of parallel reflections that become progressively higher and younger in the direction of progradation; (4) the downlap zones are composed of marine muds that do not contain high concentrations of shell debris as would be expected in condensed sections; (5) evidence of submarine erosion and reworking of the delta surface during transgression (ravinement surface) is not widely observed probably because rapid subsidence coupled with rapid eustatic sea-level rise quickly submerged the delta plain below the depth of effective wave reworking; (6) no evidence exists that incised valleys or submarine canyons formed along the paleoshelf margin, even though moderately large rivers were present and sea-level curves indicate several periods of rapid sea level fall; and (7) boundaries of these high-frequency type 1 eustatic sequences are flooding surfaces that occupy the same stratigraphic position as boundaries separating parasequences.
[Un livre, une île – Édition 2015 – Cuba]
Creators: name: Comité De Lecture De L’association ''Un Livre, Une île''
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2024
Subjects: Littérature
Prix du Caillou
''Les trois frères Castro''

description: Sélection des titres choisis par l’Association ''Un livre, une île'' pour la remise du Prix du Caillou 2015. Parmi ceux-ci, l’ouvrage d’Eduardo Manet ''Les trois frères Castro'', publié aux Éditions Écriture. Biographie de l'auteur et présentation du livre par l'éditeur.
description: Selección de los títulos elegidos por la Asociación ''Un livre, une île'' (''Un libro, una isla'') para la entrega del Premio Caillou 2015. Entre ellos, la obra de Eduardo Manet ''Los tres hermanos Castro'', publicada en Ediciones Écriture. Biografía del autor y presentación del libro por el editor. .
description: Source: EM-C1-1-2015-00-00
description: Source: Localisation de la ressource : Centre de Recherches Latino-Américaines (CRLA–Archivos, ITEM UMR8132). MSHS - Bât. A5, 1er étage 5 rue Théodore Lefebvre - TSA21103. 86073 Poitiers cedex 9.
Dirofilaria spectans Freitas & Lent
Creators: name: Muniz-Pereira, Luís C.
name: Vieira, Fabiano M.
name: Luque, José L.
Publisher: name: Zenodo
Year: 2009
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Secernentea
Spirurida
Onchocercidae
Dirofilaria
Dirofilaria spectans

description: Dirofilaria spectans Freitas & Lent
Pteronura brasiliensis (Gmelin), heart, pulmonary artery, Mato Grosso do Sul (Freitas & Lent 1949; Vicente et al. 1997; Vieira et al. 2008a) (CHIOC 13236 – paratype, 17704a̅b – holotype and allotype, 17705a–h – paratype).
description: Published as part of Muniz-Pereira, Luís C., Vieira, Fabiano M. & Luque, José L., 2009, Checklist of helminth parasites of threatened vertebrate species from Brazil, pp. 1-45 in Zootaxa 2123 on page 8, DOI: 10.5281/zenodo.188170
title: Physical and Environmental Assessment of Sand Resources - Texas Continental Shelf
Creators: name: Morton, Robert A.
name: Gibeaut, James
Publisher: name: The University of Texas at Austin
Year: 1993
Subjects: subject: sand resources
subject: assessment
subject: Texas continental shelf

description: A recent inventory of nonfuel minerals in the northwestern Gulf of Mexico demonstrated that potentially economic deposits of sand, gravel, and heavy minerals occur on the Texas continental shelf. Particularly promising for leasing and commercialization in the near term are deposits of sand that form shoals on the inner continental shelf. Preliminary analyses indicate that these sand deposits are suitable for beach replenishment because sediment textures of the shoals are generally compatible with those of native beach sand. Offshore sand extraction may become attractive economically if onshore sources of beach-quality sand are volumetrically limited. Offshore mining of sand could also reduce the degradation of wetlands caused by onshore mining activities. Demand for beach replenishment sand along the northwestern Gulf of Mexico is increasing as the combined effects of rising sea level and land subsidence are manifested as rapid beach erosion. In Texas, Sabine and Heald Banks are two offshore sand deposits that have the greatest economic potential for near-term exploitation because they are (1) suitable for beach replenishment, (2) the largest sand deposits located offshore of some of the most rapidly eroding developed shores, (3) relatively close to potential markets in both southeastern Texas and western Louisiana, and (4) relatively close to major ports that can support offshore mining activities.
Uvigerina peregrina Cushman 1923
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Globothalamea
Rotaliida
Uvigerinidae
Uvigerina
Uvigerina peregrina

description: Uvigerina peregrina Cushman, 1923a
Pl. 4, fig. 11
Uvigerina peregrina Cushman, 1923a, p. 166, pl. 42, figs. 7–10; Martin, 1981, p. 44, pl. 10, fig. 12–14; Milker & Schmiedl, 2012, p. 90, fig. 20.29.
Euuvigerina peregrina Barker, 1960, pl. 74, fig. 11–12.
Description: The test wall is calcareous and finely perforate. The test is broad, elongate, rounded in cross-section, triserial and covered in longitudinal costae. Later chambers become inflated with depressed sutures. The costae are separated by the sutures. The aperture is terminal, produced on a neck with a pronounced lip, bordering the edge of the aperture.
Remarks: The tests measure ~ 0.5 mm in cross section diameter and 0.8 mm in length. This species forms a major component (<50%) in all three cores.
Life strategy: Uvigerina peregrina is a shallow-infaunal species (Corliss and Chen, 1988), adapted to and most abundant under high organic carbon (Murray, 2006) and suboxic conditions (Kaiho, 1994).
Regional occurrence: This species is documented in middle Miocene sediments on the continental shelf of northern Namibia, south of the Kunene River mouth (this study). Schmiedl and Mackensen (1997) reported low to high abundances of U. peregrina in Pleistocene upper slope sediments of Namibia. This species is also abundant in Recent shelf to slope sediments along Namibia (Lowry, 1987; Schmiedl et al., 1997) and South Africa (Lowry, 1987).
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on page 23, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434
Virtual Fieldwork in Immersive Environments using Game Engines
Creators: name: Bernstetter, Armin
name: Kwasnitschka, Tom
name: Karstens, Jens
name: Schlüter, Markus
name: Peters, Isabella
Publisher: name: arXiv
Year: 2024
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Fieldwork still is the first and foremost source of insight in many disciplines of the geosciences. Virtual fieldwork is an approach meant to enable scientists trained in fieldwork to apply these skills to a virtual representation of outcrops that are inaccessible to humans e.g. due to being located on the seafloor. For this purpose we develop a virtual fieldwork software in the game engine and 3D creation tool Unreal Engine. This software is developed specifically for a large, spatially immersive environment as well as virtual reality using head-mounted displays. It contains multiple options for quantitative measurements of visualized 3D model data. We visualize three distinct real-world datasets gathered by different photogrammetric and bathymetric methods as use cases and gather initial feedback from domain experts.
description: Revised Manuscript Submitted to Computers & Geosciences, 15 pages, 9 figures
Pelecitus circularis Molin
Creators: name: Muniz-Pereira, Luís C.
name: Vieira, Fabiano M.
name: Luque, José L.
Publisher: name: Zenodo
Year: 2009
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Secernentea
Spirurida
Onchocercidae
Pelecitus
Pelecitus circularis

description: Pelecitus circularis (Molin)
Anodorhynchus hyacinthinus (Latham), tendon of the foot, Mato Grosso do Sul (Travassos 1930; Pinto et al. 1993; Vicente et al. 1995).
Thamnophilus caerulescens cearensis (Cory), foot joint, Mato Grosso (Oniki et al. 2002).
description: Published as part of Muniz-Pereira, Luís C., Vieira, Fabiano M. & Luque, José L., 2009, Checklist of helminth parasites of threatened vertebrate species from Brazil, pp. 1-45 in Zootaxa 2123 on page 8, DOI: 10.5281/zenodo.188170
title: East Texas and Western Louisiana Coastal Erosion Study, Year 2
Creators: name: Morton, Robert A.
name: Gibeaut, James
name: White, William Allen, 1939-
Publisher: name: The University of Texas at Austin
Year: 1993
Subjects: subject: erosion
subject: East Texas
subject: Louisiana

description: The following report summarizes the major accomplishments achieved by the Bureau of Economic Geology during the second year of study of coastal erosion and wetlands loss along the southeastern Texas coast. The report covers activities between July 1, 1992, and June 30, 1993, and includes the activities for the eighth quarter of the project. Major accomplishments are reported for each work element and task identified in the cooperative agreement. Documents summarizing the major accomplishments and containing the important scientific conclusions are included as Addendums 1-8.
Uvigerina pygmaea d'Orbigny 1826
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Globothalamea
Rotaliida
Uvigerinidae
Uvigerina
Uvigerina pygmaea

description: Uvigerina pygmaea d’Orbigny, 1826
Pl. 4, fig. 12
Uvigerina pigmea d’Orbigny, 1826, p. 269, pl. 12, figs. 8–9; Cushman, 1921, p. 269, pl. 55, fig. 1.
Uvigerina pygmaea Brady, 1884, p. 575; pl. 74, figs. 11–14; Bermúdez, 1949, p. 209, pl. 13, fig. 44; Holbourn et al., 2013, p. 600.
Description: The test wall is calcareous and the test is strongly ribbed, short elongate, fusiform, rounded in crosssection, triserial and covered in longitudinal costae with short spines at the end of each chamber. The costae are irregular in length and separated by sutures. Later chambers become inflated with distinct depressed sutures. The aperture is terminal, produced on a long neck, with a pronounced lip.
Remarks: Very few tests of this species were documented, forming a trace component (<1%) in core 2670. Specimens of this species are moderate in size, measuring 0.5 mm in cross section and 0.8 mm in length.
Synonymised forms show variations between tests, with some figured specimens not entirely enclosed by the thick costae, while others are (e.g., Brady, 1884; Holbourn et al., 2013). Some forms, which have also been identified as U. pygmaea, may also be slightly elongated (figs. 13–14 in Brady, 1884).
Life strategy: This species has an upper slope distribution (Holbourn et al., 2013) under suboxic conditions (Kaiho, 1994).
Global stratigraphic range: Holbourn et al. (2013) confine the chronostratigraphy of U. pygmaea from the late Eocene to the early Pliocene.
Regional occurrence: This study records U. pygmaea to occur in middle Miocene sediments on the Namibian outer continental shelf, south of the Kunene River mouth.
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on page 23, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434
Pelecitus helicinus Molin
Creators: name: Muniz-Pereira, Luís C.
name: Vieira, Fabiano M.
name: Luque, José L.
Publisher: name: Zenodo
Year: 2009
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Secernentea
Spirurida
Onchocercidae
Pelecitus
Pelecitus helicinus

description: Pelecitus helicinus (Molin)
Anodorhynchus hyacinthinus (Latham), tendon of the foot, Mato Grosso do Sul (Vicente et al. 1995).
description: Published as part of Muniz-Pereira, Luís C., Vieira, Fabiano M. & Luque, José L., 2009, Checklist of helminth parasites of threatened vertebrate species from Brazil, pp. 1-45 in Zootaxa 2123 on page 9, DOI: 10.5281/zenodo.188170
Uvigerina spinulosa Hadley 1934
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Globothalamea
Rotaliida
Uvigerinidae
Uvigerina
Uvigerina spinulosa

description: Uvigerina spinulosa Hadley, 1934
Pl. 5, fig. 1
Uvigerina spinulosa Hadley, 1934, pl. 18, fig. 5; Boersma, 1984, p. 163, pl. 1, figs 1–6; Van Morkhoven et al., 1986, p. 218, pl. 74, figs 1–3; Kender et al., 2018, p. 515, pl. 18, fig. 5.
Description: The test wall is calcareous and perforate. The test is triserial, elongate, rounded in cross-section and covered in longitudinal costae which end in spines at the base of the chambers. Later chambers are inflated with depressed sutures. The aperture is terminal on a neck, with a pronounced lip.
Remarks: The tests of this species in this study measure ~ 0.2 mm in cross section diameter and ~ 0.5 mm in length. This species is less abundant in the samples than U. peregrina.
This species was originally identified as Uvigerina caneriensis d’Orbigny var. spinulosa by Hadley (1934). Coryell and Embich (1937) identified another hispid uvigerinid species as U. spinulosa. The accepted name for Uvigerina caneriensis d’Orbigny var. spinulosa Hadley (1934) has become Uvigerina spinulosa, but there are clear differences in the figures and original descriptions of the two specimens. The entire test of the figured specimen in Coryell and Embich (1937) is covered in fine, short hispid structures, but the figured and described specimen in Hadley (1934) has longitudinal costae covering the test. It may be that the specimen described by Coryell and Embich (1937) might be related to Uvigerina hispida. In fact, Coryell and Embich (1937) describe U. spinulosa as closely resembling U. hispida, but differs only in shape and the neck. These two species bearing the same name should therefore not be synonymised.
Life strategy: The species of the genus Uvigerina are generally shallow-infaunal and most abundant under high organic carbon (Murray, 2006), adapted to suboxic conditions (Kaiho, 1994).
Regional occurrence: U. spinulosa Hadley, 1934 is recorded to occur in middle Miocene strata on the continental shelf of northern Namibia, south of the Kunene River mouth (this study) and in the Congo Basin (Kender et al., 2018).
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on page 24, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434
Pelecitus
Creators: name: Muniz-Pereira, Luís C.
name: Vieira, Fabiano M.
name: Luque, José L.
Publisher: name: Zenodo
Year: 2009
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Secernentea
Spirurida
Onchocercidae
Pelecitus

description: Pelecitus sp.
Gubernatrix cristata Vieillot, unspecified site of infection, unspecified locality (Pinto & Noronha 2003).
description: Published as part of Muniz-Pereira, Luís C., Vieira, Fabiano M. & Luque, José L., 2009, Checklist of helminth parasites of threatened vertebrate species from Brazil, pp. 1-45 in Zootaxa 2123 on page 9, DOI: 10.5281/zenodo.188170
title: Seismic Reflection, Refraction, and Surface Wave Studies at the Proposed Low-Level Radioactive Waste Repository, Hudspeth County, Texas
Creators: name: Paine, Jeffrey G.
Publisher: name: The University of Texas at Austin
Year: 1993
Subjects: subject: seismic methods
subject: radioactive waste
subject: waste disposal
subject: site investigation
subject: Hudspeth County
subject: Texas

description: Seismic reflection, refraction, and surface wave methods were employed to characterize the shallow subsurface at the proposed low-level radioactive waste repository site located on Faskin Ranch about 5 miles (8 km) southeast of Sierra Blanca, Texas. Reversed seismic refraction data were used to (1) determine near-surface compressional velocities for elevation datum corrections, (2) obtain preliminary velocity profiles for processing seismic reflection data, and (3) obtain depth-to-bedrock estimates. Seismic reflection data were used to determine basin geometry beneath the site, depth to bedrock, and internal basin-fill stratigraphy. Surface waves were analyzed to generate shear-wave-velocity models of the shallow subsurface. Seismic reflection, refraction, and surface wave data were acquired in May and June of 1992 using a 500-lb (230-kg) accelerated weight drop seismic source, a 48-channel seismograph, and an acquisition crew supplied by the Bureau of Economic Geology (BEG) and The University of Texas at El Paso (UTEP). Refraction data were collected at six sites on Faskin Ranch and were processed and analyzed at BEG. Nearly 3.9 miles (6.2 km) of seismic reflection data were collected along one line oriented northwest-southeast across the site and three crossing lines oriented northeast-southwest. These data were processed and analyzed at both BEG and UTEP. Surface wave data were collected near the center of the proposed repository and were processed and analyzed at UTEP.
Orthomorphina jedlitschkai
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Nodosariata
Nodosariida
Glandulonodosariidae
Orthomorphina
Orthomorphina jedlitschkai

description: Orthomorphina jedlitschkai (Thalmann, 1937)
Pl. 5, fig. 2
Nodogenerina jedlitschkai Thalmann, 1937, p. 341.
Orthomorphina jedlitschkai Barker, 1960, pl. 62, fig. 1–2; Jones, 1994, pl. 62, fig. 1–2, suppl. pl. 1, fig. 16, suppl. pl. 2, fig. 6–7; Hayward et al., 2012, p. 136, pl. 8, fig. 24–27.
Description: The test wall is calcareous and generally smooth. The test is elongate, uniserial, with globular chambers and circular in cross-section. The chambers are of different diameters and separated from each other by deep incised sutures. The penultimate chamber is larger than the terminal chamber. The aperture is surrounded by a round thick rim.
Remarks: Few tests of this species were recorded in this study, forming a trace component (<1%) in core 2670. The tests are moderate in size. The broadest chamber measures 0.3 mm in cross section and the test measures up to 0.8 mm in length.
Jones (1994) illustrated the similarity in test morphology between O. jedlitschkai and Glandulonodosaria spp. Based on the shape of the aperture (slightly protruding and rounded) and resemblance to the test morphology displayed in Jones (1994), this specimen has been assigned to Orthomorphina jedlitschkai.
Life strategy: Species of the genus Orthomorphina are recorded to be infaunal under suboxic conditions (Pezelj et al., 2013 and references therein).
Global stratigraphic range: Orthomorphina jedlitschkai is an extinct species, occurring from the Cretaceous to Pleistocene (Hayward et al., 2012).
Regional occurrence: This is the first documentation of this species to occur in the region and in middle Miocene sediments on the Namibian outer continental shelf, south of the Kunene River mouth (this study).
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on page 24, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434
A neural network emulator of the Advanced LIGO and Advanced Virgo selection function
Creators: name: Callister, Thomas A.
name: Essick, Reed
name: Holz, Daniel E.
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Characterization of search selection effects comprises a core element of gravitational-wave data analysis. Knowledge of selection effects is needed to predict observational prospects for future surveys and is essential in the statistical inference of astrophysical source populations from observed catalogs of compact binary mergers. Although gravitational-wave selection functions can be directly measured via injection campaigns -- the insertion and attempted recovery of simulated signals added to real instrumental data -- such efforts are computationally expensive. Moreover, the inability to interpolate between discrete injections limits the ability to which we can study narrow or discontinuous features in the compact binary population. For this reason, there is a growing need for alternative representations of gravitational-wave selection functions that are computationally cheap to evaluate and can be computed across a continuous range of compact binary parameters. In this paper, we describe one such representation. Using pipeline injections performed during Advanced LIGO & Advanced Virgo's third observing run (O3), we train a neural network emulator for $P(\mathrm{det}|θ)$, the probability that given a compact binary with parameters is successfully detected, averaged over the course of O3. The emulator captures the dependence of $P(\mathrm{det}|θ)$ on binary masses, spins, distance, sky position, and orbital orientation, and it is valid for compact binaries with components masses between $1$--$100\,M_\odot$. We test the emulator's ability to produce accurate distributions of detectable events, and demonstrate its use in hierarchical inference of the binary black hole population.
description: Minor update to match published version. 26 pages, 16 figures. Code is available at https://github.com/tcallister/learning-p-det/ and data at https://doi.org/10.5281/zenodo.13362691 . Neural network emulator is released at https://github.com/tcallister/pdet/
title: Shallow Seismic Studies of an Ephemeral Lake (Playa A) Basin on the Southern High Plains, Texas Panhandle
Creators: name: Paine, Jeffrey G.
Publisher: name: The University of Texas at Austin
Year: 1993
Subjects: subject: seismic methods
subject: playas
subject: basins
subject: Texas Panhandle

description: Shallow seismic data collected at Sevenmile Basin, a large ephemeral lake (playa) basin in the Texas Panhandle, reveal that subsidence has been an important agent in the formation of the basin. Several hypotheses have been considered for the origin of thousands of playa basins on the Southern High Plains of Texas and New Mexico, including eolian deflation, evaporite or carbonate dissolution and subsidence, piping, and animal activity. Seismic methods, adapted to investigations in the shallow subsurface (200 m or less), provide data that indicate subsidence caused by evaporite dissolution is the most important of these mechanisms at Sevenmile Basin. Sevenmile Basin is 5.5 by 3.6 km across and 14 m deep and is inset into the Quaternary Blackwater Draw Formation. The Blackwater Draw overlies the upper Tertiary Ogallala Formation, which hosts the economically important Ogallala aquifer. Shallow seismic refraction and reflection data were collected from this unconsolidated and variably saturated elastic sequence to understand the physical properties, geological history, and hydrogeological framework of playa basins, which are the principal recharge areas for the Ogallala aquifer.
Supporting open science and data through an R package ecosystem
Creators: name: Hufkens, Koen
name: Kearsley, Elizabeth
Publisher: name: Zenodo
Year: 2024

description: Biodiversity research relies on the easy accessibility of large amounts of data for hypothesis testing, modelling efforts and informing policy. Access to these data, as well as documenting these workflows and supporting code are key in biodiversity research and open science in general.

 

In this context, we present a comprehensive ecosystem of R packages designed to provide researchers with a transparent, end-to-end framework for reproducible and open scientific practices. These tools span the entire research pipeline from knowledge acquisition through documentation and course material over automating data acquisition, analysis/modelling and reporting for a variety of ecological applications (https://github.com/bluegreen-labs).

 

Here, we highlight a subset of our 11 packages listed on the The Comprehensive R Archive Network (CRAN) that enable access, modelling and processing of environmental variables at both point and grid scales, which can be used in “rapid prototyping” hypothesis testing and model development. For example, the {ecmwfr} package streamlines access to data within the European Center for Medium-Range Weather Forecasts Climate Data Store (CDS), including the widely used ERA5 re-analysis dataset. Similarly, the {appeears} package provides access to a diverse range of remote sensing products, such as Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices, in support of ecological research.

 

We believe that our open-source R software and workflows offer significant value to biodiversity research and hope to solicit feedback from the community on our R package ecosystem.
title: Regional Geologic Setting of the Eagle Flat Study Area, Hudspeth County, Texas
Creators: name: Raney, J. A.
name: Collins, Edward W.
Publisher: name: The University of Texas at Austin
Year: 1993
Subjects: subject: regional geology
subject: Eagle Flat
subject: Hudspeth County
subject: Texas

description: The Eagle Flat study area lies near the eastern limit of the Basin and Range geologic province in Trans-Pecos Texas. The geologic features of the region record a long history of geologic events. By describing the regional geologic setting, we can place the Eagle Flat study area within a larger context, and the significance of the site-specific investigations can be more properly understood. In general, the discussions are arranged chronologically, from oldest to youngest; each characterizes the regional geologic framework and describes how the proposed site at Faskin Ranch fits within that geologic setting. The oldest rocks in the region are metamorphosed Precambrian sedimentary and igneous rocks. Precambrian rocks crop out about 6 miles (9 km) east of the proposed repository site and are extensively exposed in the hills in the northeast part of the study area and in the Carrizo Mountains east of the Eagle Flat study area. Precambrian rocks are also present in isolated occurrences on the northeast flank of the Eagle Mountains, southeast of the site, on the Diablo Plateau, and in the Franklin Mountains, and in New Mexico. In northeastern Chihuahua, Precambrian rocks are present in limited outcrops but are known primarily from deep exploratory drilling. The Precambrian rocks show evidence of sedimentation, magmatism, metamorphism, and deformation before deposition of overlying Paleozoic and younger strata. The greater depth of burial of Precambrian rocks in Chihuahua is interpreted to be partly a manifestation of Precambrian faulting and subsidence associated with a wide northwest-trending zone that parallels the Rio Grande. This zone, the Texas Lineament, broadly trends through the study area and locally coincides with younger geologic structures.
Siphonina pulchra Cushman 1919
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Globothalamea
Rotaliida
Siphoninidae
Siphonina
Siphonina pulchra

description: Siphonina pulchra Cushman, 1919
Pl. 5, figs. 4–6
Siphonina pulchra Cushman, 1919, p. 42, pl. 14, fig. 7a–c; Cushman, 1922a, p. 49, pl. 7, fig. 11–12; Cushman, 1927b, p. 8, pl. 2, fig. 5; Cushman, 1931, p. 69, pl. 14, fig. 2–3; Palmer, 1945, p. 61.
Description: The test wall is calcareous and perforate. The test is circular in outline, rounded, compressed and biconvex in side view. There are five chambers in the last whorl, gradually increasing toward the apertural end of the test. Sutures are coarsely perforate, distinct and oblique, radiating from the broad macroperforate centre of the test. The periphery of the test is unevenly carinate around the margin. The chambers are separated by flush oblique sutures. The elliptical-shaped aperture is produced on a broad tubular neck with a thick bordering lip.
Remarks: The relative abundances recorded for S. pulchra are trace (<1%) in all three cores. Several specimens were found to be partially broken or with the aperture missing. The diameter of the tests in Cushman (1931) was reported to be 0.65 mm. Tests in this study are slightly smaller, measuring 0.5 mm in diameter.
Life strategy: The genus Siphonina is epifaunal and prefers oxic bottom water conditions (Kaiho, 1994), with a bathymetric distribution from shelf to slope depths (Phleger & Parker, 1951).
Regional occurrence: This species is reported in middle Miocene sediments on the Namibian outer continental shelf, south of the Kunene River mouth (this study).
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on pages 25-26, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434
Additional file 1: Figure S1. of Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
Creators: name: Rurika Oka
name: Zicola, Johan
name: Weber, Blaise
name: Anderson, Sarah
name: Hodgman, Charlie
name: Gent, Jonathan
name: Jan-Jaap Wesselink
name: Springer, Nathan
name: Hoefsloot, Huub
name: Turck, Franziska
name: Stam, Maike
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: The tissues used in this study. Figure S2. Reproducibility of RNA-seq data. Figure S3. Randomised distributions of features over genomic regions within the uniquely mappable part of the genome. Figure S4. (A) The size distributions of the different features in base pairs and (B) the distributions of the gene expression levels in the two tissues. Figure S5. Characteristics of enhancer-overlapping TEs. Figure S6. Examples of (A, B) enhancers that contain TEs and (C, D) TEs that contain an enhancer. Figure S7. Example of data on tb1 enhancer. Figure S8. Asymmetric H3K9ac enrichment at candidate DHSs. Figure S9. Average profiles of the enhancer candidates in V2-IST and husk for each category. Figure S10. Heatmaps of chromatin, DNA and transcript features at TSSs. Figure S11. Average profiles of randomly selected TSSs in V2-IST and husk for each category. Figure S12. Comparison of expression levels between genes and enhancer candidates in V2-IST and husk. Figure S13. Heatmaps and average profiles of H3K9ac and H3K4me3 at (A, B, D) candidates and (A, C, E) TSSs. Figure S14. ChIP-qPCR data on H3K9ac and H3K4me1 enrichment at enhancer candidate regions. Figure S15. DNase I experiments resulting in the libraries sequenced and analysed in this study. Table S1. Sequencing datasets generated in this study. Table S2. Number of DHSs that overlap between replicates. Table S3. Number of H3K9ac peaks that overlap between replicates. Table S4. Number of TEs (for RLG family with and without candidates) and enhancers that carried the GGCCCA motif. Supplemental Methods. (PDF 2730 kb)
Cibicidoides crebbsi
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Globothalamea
Rotaliida
Cibicididae
Cibicidoides
Cibicidoides crebbsi

description: Cibicidoides crebbsi (Hedberg, 1937)
Pl. 5, figs. 7a–c
Eponides crebbsi Hedberg, 1937, p. 679, pl. 92, fig. 1; Bolli et al. 1994, p. 240, pl. 55, figs 16–17, p. 298, pl. 79, fig. 8.
Truncatulina floridana Nuttall, 1928, p. 98, pl. 7, figs. 14, 16.
Cibicidoides crebbsi van Morkhoven et al., 1986, p. 139, pl. 45; Katz & Miller, 1993a, pl. 2, fig. 5; Kender et al., 2008, p. 516, pl. 20, figs. 4–5; Holbourn et al., 2013, p. 168 –169.
Description:The test wall is calcareous and macroperforate.The test is slightly inflated, trochospiral and planoconvex to unequally biconvex in side view and in cross-section. Approximately ten chambers are visible in the final whorl. The chambers gradually increase in size toward the terminal apertural end. The chambers are separated by flush, less perforate sutures. The sutures on the spiral side are oblique, whereas sutures on the umbilical side are more radial and irregular. The aperture is an interio-marginal basal slit.
Remarks: The relative abundances for Cibicidoides crebbsi decrease toward deeper depths, forming minor (<10%) components in the samples of all three cores. Tests are relatively moderate to large in size, measuring up to 1 mm in diameter.
Life strategy: Species of the genus Cibicidoides are generally unattached, epifaunal to shallow infaunal under oxic conditions (Pezelj et al., 2013 and references therein), preferring muddy substrates (Murray, 1991). The species C. crebbsi has a slope distribution (Holbourn et al., 2013).
Global stratigraphic range: This species occurs from the early Oligocene to early Pliocene (Holbourn et al., 2013).
Regional occurrence: Cibicidoides crebbsi is documented to occur in middle Miocene strata on the outer continental shelf of Namibia, south of the Kunene River mouth (this study) and in the Congo Basin (Kender et al., 2008).
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on page 26, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434
Additional file 1: of Collaborative care for depression in general practice: study protocol for a randomised controlled trial
Creators: name: Brinck-Claussen, Ursula
name: Curth, Nadja
name: Davidsen, Annette
name: Mikkelsen, John
name: Lau, Marianne
name: Lundsteen, Merete
name: Csillag, Claudio
name: Christensen, Kaj
name: HjorthĂ¸J, Carsten
name: Nordentoft, Merete
name: Eplov, Lene
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: SPIRIT 2013 checklist: recommended items to address in a clinical trial protocol and related documents*. (DOC 124 kb)
Cibicidoides pseudoungerianus
Creators: name: Bergh, Eugene W.
name: Compton, John S.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Chromista
Foraminifera
Globothalamea
Rotaliida
Cibicididae
Cibicidoides
Cibicidoides pseudoungerianus

description: Cibicidoides pseudoungerianus (Cushman, 1922b)
Pl. 5, figs. 8–10
Truncatulina ungeriana Brady, 1884, p. 664, pl. 94, fig. 9.
Truncatulina pseudoungeriana Cushman, 1922b, p. 96, pl. 10, fig. 9.
Cibicides pseudoungeriana Cushman, 1931, p. 123, pl. 22, figs. 3–7.
Cibicidoides pseudoungerianus Cimerman & Langer, 1991, p. 69, pl.74, fig. 2–3; Milker & Schmiedl, 2012, p. 103, fig.24.5– 24.9.
Cibicides pseudoungerianus Barker, 1960, pl. 94, fig. 9; Lowry, 1987, p. 322, pl. 21, figs. 3a–c; Milker et al., 2009, p. 218, pl. 3, fig.11.
Description: The test wall is calcareous and perforate. The test is trochospiral, subcircular in outline and unequally biconvex in side view and in cross-section. The spiral side is coarsely perforate and the umbilical side is smoother. The umbilical side is more convex than the spiral side. The approximately ten chambers in the final whorl gradually increase in size toward the apertural end. The earlier chambers are not visible on the spiral side, as the test wall is thickened in the central part of the test. The chambers are separated by flush, thick sutures. The sutures on the spiral side are oblique, whereas sutures on the umbilical side radiate from a thick central umbo. The aperture is interiomarginal, bordered by a thin lip.
Remarks: The relative abundances of C. pseudoungerianus decrease toward the deeper cores, forming major (<20%) to minor (<5%) components in the samples of all three cores. Tests of this species in this study are moderate in size, measuring up to 0.6 mm in diameter.
This species differs from C. ungerianus by its smoother test surface and the hidden earlier chambers on the spiral side. Cushman (1922b) re-identified the figured specimen of Truncatulina ungeriana as Truncatulina pseudoungeriana (= Cibicidoides pseudoungerianus), based on the similarities with those illustrated in Cushman (1922b). The specimens from this study resemble those in Brady (1884) and Cushman (1922b), in its thickened central portion and finer, smoother test wall, compared to C. ungerianus.
Life strategy: Cibididoides pseudoungerianus is an epifaunal to shallow-infaunal species, adapted to oxic bottom water conditions (Murgese & de Deckker, 2005; Murray, 2006). This species is documented to have shelf to slope distributions, but more typical of upper slope environments (Murgese & de Deckker, 2005).
Global stratigraphic range: Cibididoides pseudoungerianus occurs in Oligocene to Recent strata (Jones, 1994).
Regional occurrence: This species is recorded in middle Miocene sediments on the Namibian outer continental shelf, south of the Kunene River mouth (this study).
description: Published as part of Bergh, Eugene W. & Compton, John S., 2022, Taxonomy of Middle Miocene foraminifera from the northern Namibian continental shelf, pp. 1-55 in Zootaxa 5091 (1) on pages 26-27, DOI: 10.11646/zootaxa.5091.1.1, http://zenodo.org/record/5840434