bluuebunny/crossref_metadata_2025 huggingface dataset:
Global distribution and diversity of antimicrobial genes across subsurface bacterial and archaeal metagenome assembled genomes
Authors: Kiel Reese Brandi , Mullis Megan , Selwyn Jason
Published: October 2023

Microorganisms have the capability to produce antimicrobial compounds through secondary metabolism, which are not essential within their natural environments, but have been found to have many effects on the ecosystem. Antimicrobial production genes have been identified in a wide range of microorganisms; however, research into natural ecosystems has historically been limited to continental soil environments. Antimicrobial production research has been limited in the deep continental subsurface and marine environments, especially deeply buried marine sediments. We analyzed 466 high-quality metagenome assembled genomes (MAGs) collected from continental and marine subsurface environments through the Deep Carbon Observatory’s Census of Deep Life. A total of 383 MAGs contained biosynthetic gene clusters, namely Type I and Type III polyketide synthase genes, non-ribosomal peptide synthetase genes, and other unspecified ribosomally synthesized and post-translationally modified peptide products. All of these genes were found across continental mines, subglacial lakes, hotsprings, and serpentinizing environments. These environments have previously not been investigated via metagenomics for antimicrobial gene diversity, which may be produced for competition or communication purposes. All other biosynthetic genes identified in this study were less than 50% similar to reference biosynthesis genes indicating the novelty of secondary metabolism in subsurface microorganisms. The majority of predicted antimicrobial products were found to be produced exergonically, which could indicate microbial populations use energy-conserving mechanisms to produce compounds that could offer a competitive advantage.
Microbiological Treatment of Nitrate and Selenate from Coal Mine-Affected Water in a Subsurface,Semi-Passive, and in situ Water Treatment Facility
Authors: Spietz Rachel , Kirk Lisa
Published: October 2023

Metallurgical coal mining generates significant amounts of waste rock, which can release nitrate and selenate upon atmospheric exposure, with resulting changes in surface water and ground water quality. Microorganisms residing on waste rock in the local subsurface have the metabolic potential to denitrifyand reduce selenium to treat mine-affected waters and stabilize waste rock. To support these processes, waste rock facilities have been designed to inject nutrients (e.g., methanol and phosphoric acid) in semi-passive water treatment of mine-impacted waters. Microbial community data regularly collected fromsubsurface semi-passive reactors throughout the startup and operations phases showed that native heterotrophic denitrifying bacteria and selenium reducing bacteria were enriched as a result of nutrient amendment. The microbial community was stable while the source water and geochemical parameters remained unchanged; however, a significant shift in the microbial community coincided with changes in the source of water treated. Metagenomic sequencing of microbial communities within the active treatment zone revealed multiple biochemical pathways of nitrate reduction. Geochemical and water quality data indicate near complete selenate reduction, yet a low abundance of in known selenate reduction genes were recovered. This may suggest that biologically mediated selenium reduction may be more widespread, both functionally and taxonomically. Further research into these pathways and mechanisms for nitrate and selenium reduction will help to strengthen our understanding of selenium reduction mechanisms and their application in mine water waste management.
The Shoshone Canyon Conduit Cave: A Greater Yellowstone Ecosystem Sulfur Cave
Authors: Spear John , Robinson Sasha , Slayback Paul , Thieringer Patrick , Villarruel Carmen
Published: October 2023

Fve miles west of Cody, Wyoming and ~25 miles east of Yellowstone National Park lies the Shoshone Canyon Conduit Cave (Fig. 1, Suppl. material 1). Bisecting Cedar Mountain, an irrigation tunnel built by the Bureau of Reclamation (BoR), managed by the Heart Mountain Irrigation District, delivers water from the BoR Buffalo Bill Reservoir to more than 30,000 acres of irrigated lands in and around Cody. During the construction of that tunnel in the late 1940’s, a cave was discovered and the tunnel was made to travel though the cave with only light disturbance to the cave. The cave can only be accessed with permission in the non-irrigation time of year. The cave is rich in sulfides and sulfur deposits with unique speleothems.

To date, we have conducted a preliminary geobiological survey of the geochemistry, microbiology and mineralogy of this sulfur cave on its speleothems, mineral deposits and waters. Sampled waters, of which there is little, were all highly acidic (pH < 2). Microbiologically, an analysis of microbial communities present in approximately 25 sample locations (Fig. 1) to answer the question of—who is there?—was conducted via small subunit ribosomal 16S rRNA gene (for Bacteria and Archaea) and 18S rRNA (for Eukarya) analyses, prepared using a polymerase chain reaction (PCR) primer-pair that allows for the even amplification of all three domains of life. All samples were relatively low in biomass and resultant community analysis indicates a variety of Bacteria and Archaea phyla are represented with a dominance of known sulfur metabolizers. Mineralogically, petrography reveals a variety of crystal growth and habit in this sulfur-dominated, calcium carbonate-driven karstic ecosystem. X-ray diffraction analysis (XRD) was used to better determine the kinds and extant of mineral morphotypes and were surprisingly variable. The Shoshone Canyon Conduit Cave is a most intriguing sulfur cave to reveal what is known of the geobiology of sulfur caves in the Rocky Mountain Region. Findings from this work will likely apply to other cave systems such as Villa Luz (Mexico) and the Frasassi system (Italy). Finally, to learn about the Cedar Mountain Caves will inform on how either or both the National Park Service (NPS) and Bureau of Land Management (BLM) may better manage them as a meaningful component of the Greater Yellowstone Ecosystem.
A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide
Authors: Ruff S Emil , Hrabe de Angelis Isabella , Mullis Megan , Payet Jerome , Kiel Reese Brandi , Lloyd Karen , Steen Andrew , Morrison Hilary , Sogin Mitchell , Ladau Joshua , Colwell Frederick
Published: October 2023

Marine and terrestrial subsurface sediments, rocks, and water may represent the largest habitat for microbial life on Earth. Despite the global importance of subsurface ecosystems for biogeochemical cycling and microbial diversity, essential questions remain unanswered. These concern the abundance of novel microbial clades in the subsurface, the difference between marine and terrestrial microbiomes, as well as between subsurface and surface microbiomes, and the adaptation of specific clades to environmental conditions of the subsurface. Here, we analyzed 523 archaeal and 1,211 bacterial 16S rRNA gene amplicon sequence datasets and 146 shotgun metagenomes from surface, interface, and subsurface ecosystems worldwide, including lakes, saltmarshes, hot springs, caves, mines, methane seeps, hydrothermal vents, and seafloor sediments. We found that archaeal and bacterial alpha diversity (per sample richness and evenness) and beta diversity (community differentiation) varied continuously between surface and subsurface biomes, but differed abruptly between marine and terrestrial subsurface ecosystems. Bacterial alpha diversity tended to be lower in subsurface than surface ecosystems. However, subsurface archaeal alpha diversity often exceeded that of surface ecosystems suggesting that the subsurface holds a considerable and largely underestimated fraction of Earth’s archaeal diversity. Overall, microbial communities of marine subsurface ecosystems exhibited greater alpha diversity, while gamma diversity (total richness and evenness) was higher in the terrestrial subsurface, potentially due to greater habitat diversity. We identify diagnostic clades, especially for the archaea, that are widespread in marine (e.g., Lokiarchaeia, Bathyarchaeia) and terrestrial (e.g., Hadarchaeia, Methanococci) subsurface ecosystems. The substantial community overlap along depth transects and between surface, interface and subsurface realms suggests a global gradient between the surface and subsurface rather than a discrete and defined subsurface biosphere. Finally, none of the included subsurface ecosystems seem to be exhaustively sampled, leaving much biodiversity and metabolic capability yet to be discovered.
Illegal Dumping of Oil and Gas Wastewaters Alters Semi-Arid Soil Microbial Communities
Authors: Akob Denise , Kashani Mitra , Engle Mark , Kent Douglas , Gregston Terry , Cozzarelli Isabelle , Mumford Adam , Varonka Matthew , Harris Cassandra
Published: October 2023

The Permian Basin, underlying New Mexico and Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries. The environmental health risks posed by these OG wastewaters are not well understood, particularly in the case of accidental or intentional releases. Starting in November 2017, 39 illegal dumps of OG wastewater were identified in southeastern New Mexico that released approximately 6.4x105 liters of fluid onto desert soils. To evaluate the impacts of these releases on soils, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected zones to corresponding unaffected zones with no known releases. We observed significant (p<0.01) changes in soil geochemistry for all dump-affected samples compared to controls, reflecting the residual salts and hydrocarbons left behind by the OG-wastewater release (e.g., enriched in sodium (Na), chloride (Cl), and bromide (Br)). Illumina 16S iTag sequencing revealed significant (p<0.01) differences in microbial community structure between dump and control zones. Furthermore, soils from dump areas had significantly (p<0.01) lower alpha diversity and exhibited differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, such as members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater exerted a selective pressure on microbial communities. Taxa related to known hydrocarbon-degrading organisms, e.g., Marinobacter, Salegentibacter, Chromohalobacter, and Alcanivorax, were also detected in the dump-affected soil-sample communities. The microbial communities in control soils were dominated by taxa ubiquitous in, and well adapted to, arid and nutrient-deprived soil environments including photosynthetic Cyanobacteria, hydrogen-oxidizing Actinobacteria and Acidobacteria, and nitrogen-fixing Alphaproteobacteria. This study demonstrated that OG-wastewater dumps can lead to shifts in microbial community composition and function towards salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that increase arid soil fertility, or promote plant health, could result in cascading affects to myriad ecosystem services such as loss of flora. Further studies are needed to explore the potential for using halophilic and hydrocarbon-degrading taxa to bioremediate OG-wastewater affected lands.
Prominence of Candidate Phyla Radiation (CPR) in Alberta Groundwater
Authors: Mosier Damon
Published: October 2023

Groundwater is an essential part of everyday life, serving as agricultural irrigation, supporting numerous industrial processes, and providing drinking water for many. It is also home to a diverse range of unexplored microbial communities. This is especially true in Alberta, Canada, due to the rich geological history of the region and the close proximity of aquifer locations to areas ranging from oil sand-rich to agricultural to populous cities. Through collaborations with the Environment and Protected Areas division of the Alberta government we have access to more than 250 wells throughout the province, 25 of which were selected for metagenomics analysis. More than 750 metagenome-assembled genomes were recovered and coupled with historic geochemical, isotopic, and dissolved gas data, allowing us to interpret the lifestyles of microbial communities inhabiting Alberta groundwater. Results show a strong presence of organisms involved in C1-cycling, indicative of a productive subsurface environment, as well as members belonging to the Candidate Phyla Radiation (CPR). We explore likely roles of CPR, including their potential for ecological interactions via secondary metabolites. This research shows that Alberta groundwater is home to diverse, productive microbial communities that have the capacity to further our knowledge in microbial ecology.
Mollusca collected by Agassiz trawl from the 2016 SO-AntEco (JR15005) expedition to the South Orkney Islands, Antarctica - data
Authors: Steger Jan , Linse Katrin , Gan Yi-Ming , Griffiths Huw
Published: October 2023

This dataset contributes to the knowledge of macro- and megafaunal Mollusca associated with a range of benthic habitat types in the South Orkney Islands, Antarctica, an exceptionally diverse region of the Southern Ocean. The information presented is derived from Agassiz trawl samples collected on the archipelago’s shelf plateau and slope, within and outside of the South Orkney Islands Southern Shelf Marine Protected Area (SOISS MPA). Sampling was conducted in the framework of the British Antarctic Survey/SCAR “South Orkneys - State of the Antarctic Ecosystem” (SO-AntEco) project aboard RRS James Clark Ross during expedition JR15005 in Austral summer 2016. This dataset is published by the British Antarctic Survey under the licence CC-BY 4.0. We would appreciate it if you could follow the guidelines from the SCAR Data Policy (SCAR 2023) when using the data. If you have any questions regarding this dataset, do not hesitate to contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with the dataset can be reported at https://github.com/biodiversity-aq/data-publication/. This dataset is part of the Biodiversity, Evolution and Adaptation Project of the Environmental Change and Evolution Program of the British Antarctic Survey. The cruise report of the expedition is available at https://www.bodc.ac.uk/resources/inventories/cruise_inventory/reports/jr15005.pdf.

We report occurrences of Mollusca from individual samples taken with a 2 m-wide Agassiz trawl (AGT) in the framework of the February – March 2016 research expedition JR15005 of RRS James Clark Ross to the SOISS MPA and adjacent shelf and slope areas. Of 78 successful AGT deployments, 44 trawls at depths ranging from 235-2194 m yielded living Mollusca, totalling 2276 individuals, 67 morphospecies and 163 distributional records. One hundred and fifteen empty shells were also collected and recorded in the dataset. Three morphospecies (one Bivalvia and two Gastropoda) were sampled exclusively as empty shells, yielding a total of 70 morphospecies and 2391 specimens represented in the dataset. All specimens were preserved in 96% undenatured ethanol and are stored as vouchers in the collections of the British Antarctic Survey (BAS), Cambridge, United Kingdom. The publication of this dataset aims at increasing the knowledge on the biodiversity, abundance and geographical and bathymetric distribution of larger-sized epi- and shallow infaunal Mollusca of the South Orkney Islands.
The behaviour of recently-hatched caddis larvae from temporary water bodies in the British Isles
Authors: Wallace Ian
Published: October 2023

Caddisflies use four basic methods to ensure that newly-hatched larvae become aquatic insects.

One is to lay the eggs underwater so larvae can start a free life immediately after hatching.

Another method is to lay the eggs above water and the hatched larvae fall or wriggle into the water.

Caddisflies from waters that dry out in summer often have a female diapause gradually becoming sexually mature and often do not lay their clutches until late summer or autumn, when rising water levels flood the eggs. The hatched larvae develop into pupae by March-May, from which adult caddisflies hatch again emergence beginning in spring.

Some caddisflies from waters that dry out lay in summer and those eggs hatch soon after laying so it is as a larva that they survive the dry period.
Analysis of the effects of habitat characteristics, human disturbance and prey on felids presence using long-term community monitoring information
Authors: Sosa-López J. Roberto , Díaz Bernal Nydia Nicté , Padilla Eugenio , Briones-Salas Miguel
Published: October 2023

Predator species are essential for ecosystems as they maintain the ecological integrity of the habitat. Particularly, felids populations have declined globally due to their sensitivity to habitat disturbances. Nevertheless, in Mexico, there are areas protected by indigenous communities to preserve a portion of their territory, benefiting multiple species, including felids. Although the National Commission of Natural Protected Areas of Mexico sponsors a long-term national-wide communal monitoring programme using camera traps, there is not a systematic analysis of the information generated by the programme. We assessed the occurrence of three felids species known to occur in a Zapotec indigenous community conservation area in Oaxaca, Mexico. Specifically, we evaluated how habitat characteristics, human disturbance and prey influence felids’ occurrence across the protected area. None of the variables explained better than the null model the proportion of sites used by Pumas (Puma concolor). Bobcats and Margays favour areas with medium-sized prey. Our study shows the importance of community-based monitoring and information systems (CBMIS) for identifying communal reserve characteristics that contribute to the occupation of carnivores. Further, our results also suggest that management should consider the habitat requirements of felids´ prey. By understanding wildlife habitat use, communal authorities could improve sustainable forest management within the reserves.
The first record of a stygobiotic form of Garra rufa (Heckel, 1843), sympatric with Garra tashanensis Mousavi-Sabet, Vatandoust, Fatemi & Eagderi, 2016 (Teleostei, Cyprinidae), in Iranian subterranean waters
Authors: Malek-Hosseini Mohammad Javad , Flot Jean-François , Fatemi Yaser , Babolimoakher Hamid , Kuntner Matjaž , Diripasko Oleg A. , Jelić Dušan , Bogutskaya Nina G.
Published: October 2023

We report the first finding of the stygobiotic form of the cyprinid fish Garra rufa (Heckel, 1843), discovered in a single locality in southwestern Iran, while the epigean form of the species is widely distributed in western Asia (Iran, Jordan, Lebanon, Turkey, and Syria). We also report a new locality for its hypogean congener, Garra tashanensis, about 5 km east of its type locality. The two species occur in syntopy in outflows of the Tang-e-Ban, a seasonal karstic spring that only has flowing water during winter and spring, when fish individuals are washed from the cave to the surface. Identification of the investigated samples was confirmed by morphological analyses, COI distances, and a phylogenetic tree. These findings suggest the existence of a large karst aquifer in the Tashan area that harbours several cave species of fish, crustaceans, and gastropods and may have considerable conservation implications.
Accès aux actes et consultations de second recours en région Centre-Val de Loire
Authors: de Fontgalland Charlotte , Lecourieux Sébastien , Ménoret Frédérique , Bidaut Pierre , Rouzaud-Cornabas Mylène , Rogez Raphaël
Published: October 2023

Introduction : En région Centre-Val de Loire, l’offre de soins de second recours se caractérise par une démographie déficitaire et par de fortes inégalités territoriales, entraînant d’importantes difficultés d’accès aux soins. L’étude a été menée à l’échelle des communautés professionnelles territoriales de santé (CPTS) maillant la région, cadre idéal pour concrétiser des actions de santé publique. But de l’étude : Le but de cette étude était d’objectiver ces difficultés et leur géographie, sur la base du calcul de l’indice comparatif de consommation (ICC), afin de mesurer les écarts entre la consommation attendue et la consommation observée, et de quantifier le nombre de médecins nécessaires pour répondre aux besoins de la population, et qui sont donc actuellement « manquants ». Résultats : On observe un sous-recours aux soins de spécialité, notamment une inadéquation entre les besoins et l’offre de soins sur les lieux de vie, ainsi que de fortes inégalités territoriales, avec des différences marquées entre le recours libéral et le recours aux actes et consultations externes en secteur hospitalier. La région connaîtrait un déficit de 25 % de médecins spécia- listes libéraux pour répondre aux besoins de sa population. Conclusions : L’accessibilité aux soins ne se résume pas à la proximité des soignants ni à leur densité, la proximité de zones d’activité étant un facteur associé à un meilleur recours aux soins. Cette étude permet d’identifier des zones d’action prioritaire par spécialité, pour renforcer l’accès au second recours et construire une plus juste répartition de l’offre, notamment par le déploiement de stages d’internes et l’organisation coordonnée et territoriale des médecins spécialistes hors médecine générale.
Pertinence d’une plateforme technologique de participation citoyenne pour consolider les systèmes de santé subsahariens
Authors: Ouedraogo Wendkouni Adelphe , Biau Sandrine , Bonnet Emmanuel , Ridde Valéry
Published: October 2023

Introduction : Une intervention de participation citoyenne par téléphone, via un numéro vert combiné à un serveur vocal interactif pour recueillir les opinions des citoyens sur leurs systèmes de santé a été déployée au Burkina Faso, au Bénin et en République démocratique du Congo entre 2020 et 2021. But de l’étude : Cet article évalue l’efficacité, la viabilité et la transférabilité de cette intervention participative pour consolider les systèmes de santé. Résultats : L’analyse montre une pertinence du téléphone pour impliquer les citoyens dans la gouvernance des systèmes de santé subsahariens. Conclusion : Les technologies de l’information et de la communication sont un soutien important dans la quête d’une meilleure démocratie sanitaire en Afrique subsaharienne.
Cartographie et analyse du financement de la santé dans la province du Sud-Kivu (RDC)
Authors: Tapsoba Yann , Ndokabilya Eustache , Wema Jean-Claude , Engels Thomas , Paul Élisabeth
Published: October 2023

Introduction : Au Sud-Kivu, en République démocratique du Congo, le système de santé est sous-financé dû à de nombreuses contraintes. Plusieurs initiatives ont été testées mais restent insuffisantes pour augmenter et pérenniser le financement de la santé. But de l’étude : Analyser le système de financement de la santé au Sud-Kivu, par une cartographie et une analyse quantitative et qualitative des mécanismes de financement. Résultats : Le système de financement de la santé de la province est fragmenté, avec des mécanismes et interventions peu coordonnés, suscitant des duplications d’activités d’appui au système de santé, en plus de la quasi-absence de mécanisme de mise en commun des appuis extérieurs. Le recouvrement des coûts et les financements extérieurs sont les mécanismes les plus utilisés alors que l’État contribue très faiblement au financement du système provincial de santé. Les mutuelles de santé sont censées améliorer l’accès aux soins, mais leur taux de couverture reste extrêmement faible. Le financement basé sur les résultats et la gratuité des soins, intégralement compensés par les donateurs extérieurs, sont irréguliers et insuffisamment pérennes. Conclusions : Il serait essentiel d’adopter au Sud-Kivu un modèle d’achat stratégique, ancré dans les institutions locales, approprié par l’ensemble des parties prenantes, qui intègre l’ensemble des mécanismes de financement existants et qui soit appuyé par un fonds commun d’appui au système provincial de santé. L’initiative du Contrat unique développée pour harmoniser, mettre en commun et pérenniser les programmes extérieurs peut servir de base pour élaborer un tel modèle. Ceci impliquerait de renforcer le dialogue politique, d’élaborer un dossier d’investissement pour soutenir la mobilisation des ressources et de créer une plateforme conjointe de suivi et d’évaluation des décaissements, pilotée par les autorités provinciales de santé.
Concurrent Foveoschisis and Atrophy in a Patient With X-Linked Retinoschisis and Type 1 Diabetes Mellitus
Authors: Hoyek Sandra , da Cruz Natasha F. S. , Sengillo Jesse , Patel Nimesh A. , Eliott Dean , Berrocal Audina M.
Published: October 2023

We report the case of a 28-year-old man with X-linked retinoschisis (XLRS) and type I diabetes mellitus. The patient had bilateral foveoschisis with a tractional retinal fold in the right eye. Optical coherence tomography (OCT) revealed hyperreflective material within the inner nuclear and outer plexiform layers, photoreceptor atrophy, and retinal pigment epithelium irregularities in both eyes. Fluorescein angiography showed hyperfluorescent foveal spots corresponding to the hyperreflective material observed on OCT. This is a unique presentation of XLRS, with concurrent foveoschisis and photoreceptor atrophy in both eyes. The hyperreflective material on OCT serves as a distinctive feature of XLRS.

[
Ophthalmic Surg Lasers Imaging Retina
2023;54:603–606.]
Analog interface based on capacitance multiplier for capacitive sensors and application to evaluate the quality of oils
Authors: Delimaras Vasileios , Tsiakmakis Kyriakos , Hatzopoulos Argyrios T.
Published: October 2023

Currently, interdigital capacitive (IDC) sensors are widely used in science, industry and technology. To measure the changes in capacitance in these sensors, many methods such as differentiation, phase delay between two signals, capacitor charging/discharging, oscillators and switching circuits have been proposed. These techniques often use high frequencies and high complexity to measure small capacitance changes of fF or aF with high sensitivity. An analog interface based on a capacitance multiplier for capacitive sensors is presented. This study includes analysis of the interface error factors, such as the error due to the components of the capacitance multiplier, parasitic capacitances, transient effects and non-ideal parameters of OpAmp. A design approach based on an IDC sensor to measure the quality of edible oils is presented and implemented. The quality relates to the total polar compounds (TPC) and consequently to relative electrical permittivity \begin{document}$ {\varepsilon }_{r} $\end{document} of the oils. A measurement system has been implemented to measure the capacitance of the IDC sensor, which depended on \begin{document}$ {\varepsilon }_{r} $\end{document}. The simulation and experimental results showed that, for a capacitance multiplication factor equal to 1000, changes of 3.3 µs/100 fF can be achieved with an acceptable level of noise, which can be easily measured by a microcontroller.
$ n $-quasi-$ A $-$ (m, q) $-isometry on a Banach space
Authors: Gherairi Khadija , Hajjej Zayd , Li Haiyan , Regeiba Hedi
Published: October 2023

In this paper, we introduce the class of $ n $-quasi-$ A $-$ (m, q) $-isometry operators on a Banach space $ X $, which represents a generalization of the $ n $-quasi-$ (m, q) $-isometry on a Banach space and the $ n $-quasi-$ (A, m) $-isometry on a Hilbert space. After giving some basic properties of this class of operators, we study the product and the power of such operators in this class.
TransUFold: Unlocking the structural complexity of short and long RNA with pseudoknots
Authors: Wang Yunxiang , Zhang Hong , Xu Zhenchao , Zhang Shouhua , Guo Rui
Published: October 2023

The RNA secondary structure is like a blueprint that holds the key to unlocking the mysteries of RNA function and 3D structure. It serves as a crucial foundation for investigating the complex world of RNA, making it an indispensable component of research in this exciting field. However, pseudoknots cannot be accurately predicted by conventional prediction methods based on free energy minimization, which results in a performance bottleneck. To this end, we propose a deep learning-based method called TransUFold to train directly on RNA data annotated with structure information. It employs an encoder-decoder network architecture, named Vision Transformer, to extract long-range interactions in RNA sequences and utilizes convolutions with lateral connections to supplement short-range interactions. Then, a post-processing program is designed to constrain the model's output to produce realistic and effective RNA secondary structures, including pseudoknots. After training TransUFold on benchmark datasets, we outperform other methods in test data on the same family. Additionally, we achieve better results on longer sequences up to 1600 nt, demonstrating the outstanding performance of Vision Transformer in extracting long-range interactions in RNA sequences. Finally, our analysis indicates that TransUFold produces effective pseudoknot structures in long sequences. As more high-quality RNA structures become available, deep learning-based prediction methods like Vision Transformer can exhibit better performance.
Value Assessment of Online Educational Resources in the Context of Blended Learning
Authors: Sun Chen
Published: October 2023

In the context of promoting informatization education and reforming blended learning, how to accurately assess the value of online educational resources has become an important research topic. However, most existing assessment methods rely on direct data statistics and experience-based judgment, lacking scientific prediction models and comprehensive consideration of learning cycles. To solve this problem, this study constructed a hit prediction model of online educational resources based on the fusion of extreme learning machine and grey Verhulst model, and a hit-based value assessment model of the resources considering the learning cycles of students. The research results showed that the proposed model not only predicted and assessed the value of online educational resources more accurately, but also provided theoretical support and decision-making reference for the implementation of blended learning reform, thereby promoting the effective utilization of online educational resources.
De chair et de sons : Kate Bush et la théâtralité sonore intime
Authors: Brachet Marion
Published: October 2023

Cet article vise à mettre en lumière la construction de l’une des marques de fabrique du son de Kate Bush, à savoir sa facette intime, grâce à une analyse phononarratologique de la chanson « The Infant Kiss » (1980), c’est-à-dire une analyse portant sur la manière dont les spécificités de la musique en tant qu’objet enregistré soutiennent ou créent du récit, ici en renforçant la caractérisation de la protagoniste et de ses réactions émotionnelles aux événements. Le personnage féminin mis en scène dans « The Infant Kiss », comme souvent chez Kate Bush, est non seulement incarné sur un mode intimiste grâce à une vocalité nuancée, mais aussi à travers une instrumentation et un environnement sonore qui cultivent une impression d’intimité. Il s’agira ici de détailler comment s’articule cette mise en scène typique de Kate Bush, mais aussi de démontrer que cette théâtralité intime reste centrale dans l’héritage de l’artiste, à travers d’autres chanteuses telles que Björk ou Émilie Simon.
« The Sensual world » de Kate Bush : une réécriture poético-musicale au/du féminin
Authors: Plana Muriel
Published: October 2023

« The Sensual world » de Kate Bush, premier titre de l’album éponyme de 1989, est un hymne à l’érotisme féminin, inspiré de la fin du célèbre monologue de Molly Bloom, extrait du roman Ulysses de Joyce (1922). La chanson est assez caractéristique des hybridations pop-savantes dont l’artiste est coutumière. En la comparant avec sa source joycienne et avec « The Flower of the Mountain », reprise plus fidèle (et moins subversive) du même passage, produite en 2011, nous montrerons en quoi le travail de réécriture poétique et musicale accompli dans « The Sensual world » est novateur en termes d’hybridation inter-artistique et, d’un point de vue féministe, par sa mise en scène d’un autre sujet féminin du désir que le sujet lyrique joycien.
Conducting Literature Reviews in Resource-poor Settings: Perks of Collaboration and Technology to Overcome Challenges
Authors: Dissanayake D. M. A. P. , Warnakulasuriya S. S. P. , Baduge M. S. D. S. Pincha , Dharmasena K. P.
Published: October 2023

No abstract available
Automatic Well Test Validation Empowered By Machine Learning and Natural Language Processing
Authors: Gao Chao , Vo Nghia Tri , Zam Fathin Shalihah Hasnol Zam , Salleh Nurul Fadhilah Bt , Sidek Sulaiman B
Published: October 2023

The standard operating procedure (SOP) requires a well test monthly for every active producer to assess performance behavior. With over 100 new well tests daily, a busy operation schedule can lead to delayed validation, causing high accumulated amounts throughout the month and spill over to the next month. If the well-test quality does not meet the expectation, it should be rejected and required to retest immediately to comply with SOP. The significant effort and delayed well-test validation will cause inaccuracy in production performance analysis, diagnostics, and potential issue detection.

This solution aims to significantly reduce processing time from gathering enough historical information to validating with engineering models and limits human error by checking all available well tests and preparing detailed analysis for engineers to make the final decision. By having more updated accepted well tests to update well engineering models, the solution helps to improve accuracy and more confident outputs in other engineering workflows like production back allocation, well rate estimation, well and network model calibrations, and production optimization.

The proposed solution leverages artificial intelligence (AI) capability learns from historical well test data with accepted and rejected flag to build a rule-based deterministic machine learning (ML) model to automatically validate and detect the possible rejected or accepted well test. The solution also considers well test comments or remarks provided by well-testing engineers which are processed via Natural Language Processing (NLP) engine. ML model can propose to accept a well test with confidence score to automate the validation and support engineer's decision. On the other hand, if the model detects a possible rejected well test, it suggests engineer to review the new well test information versus historical performance and takes actions, where early rejection triggers retesting requirement to the offshore team to prioritize the well to the test plan. Periodically, the ML model may require updates based on the most recent well test data in order to maintain its accuracy.

The solution significantly reduces well test validation time from weeks to hours, improving the accuracy of other production performance analysis and optimizations. The data-driven approach can easily be adapted to different fields’ needs, offering a more flexible and efficient alternative to hard-coded rule-based well test validation.
Lower FPSO Carbon Footprint Through Hydrocarbon Blanketing
Authors: Bárcia G. S. , Bronneberg J. , Cerqueira H.
Published: October 2023

FPSO crude oil storage tanks require a blanketing on top of the stored crude and FPSO Cargo Tank operations are characterized (for the purpose of current paper) by the displacement of the tank vapor during the loading cycle by produced oil and, reversibly by the vapor re-filling of the tank volume during the offloading operations.

In cargo oil tanks during offloading operations the tank is "topped-up" with blanketing gas to replace the displaced liquid volume and, during loading cycles the vapor is displaced so that the liquid can occupy the volume. Traditionally, the vapor ullage in the tank is composed of inert gas and, during the loading cycle until the start of the offloading, the gas is in equilibrium with the crude oil, so its composition changes through time due to the vaporization of hydrocarbons. Consequently, its calorific power is not constant so it cannot be reused in the process stream. For this reason, at every loading cycle the vapor phase of the cargo oil tank is vented, contributing to greenhouse gases emissions.

There are several possible methods to decarbonize offshore operations of FPSOs, as shown in Figure 1. Hydrocarbon Blanketing is one of these several alternatives and it allows for the recovery of volatile components otherwise released to atmosphere. As will be demonstrated in the paper, it has a considerable positive environmental impact, reduction in corrosion and safety benefits and is relatively simple to implement ("low hanging fruit").
Assessment Methodology for Transition of Offshore Brownfield Platforms to Remote Operations
Authors: Aisamuddin Pi Remli M. , Fatimah Samsu M. , Halim Firdaus A. , Kuanji Jennyfer Joseph
Published: October 2023

Remote Operations (RO) for offshore brownfield platforms in PETRONAS (to be referred as Company) refers to the use of digital technologies and remote monitoring systems to operate and manage existing oil and gas facilities. It involves the implementation of digital solutions and advanced technologies such as the Industrial Internet of Things (IIoT), Artificial Intelligence (AI), and Time to Failure (TTF) Machine Learning (ML) to optimize the performance of existing assets and ensure safe and efficient operations.

The detailed assessment to evaluate and frame RO gaps and requirements are divided into three main processes consisting of Operability Assessment, Reliability, Availability and Maintainability (RAM) Assessment and Value Trade-Off Assessment to ensure the delivery of value driven design and concept for RO.

The details of the three processes are as follows:

Operability Assessment – To identify manual intervention activities that are required in managing normal and abnormal operations by evaluating as is gaps for each level of RO. RAM & Scenario – To simulate the platform availability number for each scenario according to RO modes. Value Trade Off Assessment – To evaluate each RO scenarios against CAPEX investment and OPEX reduction where the optimum scenario should be selected.

Through Detailed Assessment, each platform in Malaysia Assets was evaluated on the potential of RO end state level to be implemented.​ Implementation of RO is targeted to minimize or eliminate human intervention at site as well on console by improving control and automation. The implementation shall give significant value with unmanned philosophy since it will require less support in logistic and eliminate other associated cost for manned operation.

Subscribing to this new operating condition through detailed assessment evaluation while embracing digital and technology transformation for current oil and gas platform in operation is novel in COMPANY operation. Rethinking of the current Asset Operation & Maintenance (O&M) towards Remote & Integrated Operations results in value driven operations, improved operational efficiency, enhanced safety, increased asset reliability and reduced costs. In addition, it opens the door to be agile in addressing current pain points and provide solutions to sustain asset life in view of declining production.
Challenging the 30 m Annulus Cement Requirement
Authors: Arild Øystein , Lohne Hans Petter
Published: October 2023

The permanent plugging and abandonment of a well requires the establishment of at least two barriers according to the NORSOK D-010 standard. In common practice, a barrier is either a cement plug from formation to formation, which is all cement, or a combination of existing cement behind the annulus, the casing steel itself and a cement plug inside the casing, see Figure 1. The latter case is a cheaper and preferred solution as milling can be avoided and thus reducing cost, environmental footprint and a number of potential operational hazards. The cement between the casing and the formation is called the cement sheath and has typically been in place since the well was constructed. The evaluation of the status of this barrier element after years of production – called verification in many standards – is conducted using different types of logs. Leakage through the cement sheath can happen in three ways; along the interface between the cement sheath and the casing, leakage through the bulk cement itself as the cement has a certain permeability, leakage in cracks or channels present in the cement sheath and finally leakage between the cement sheath and the formation. Significant leakage through the cement sheath prior to permanent P&A typically causes an increased annulus pressure, which is monitored and dealt with if it happens prior to permanent P&A.

In order to qualify the cement sheath when using the NORSOK D-010, 30 m of good bonding is required, i.e. the interface between casing surface and the cement is good in terms of that it most likely will not represent a leakage path along the interface, so called micro annuli. Logs are best at detecting interface phenomena and good logs means that we have strong indications that there are no micro annuli, but logs may also indicate weaknesses in the bulk cement between the casing and the formation.
Shallow Water Mapping: Remote Solution for Global Satellite-Derived Sea-Floor Mapping
Authors: van de Poll Robert , Smith Jason , Chatten John
Published: October 2023

Qualitative site reconnaissance from satellite imagery offers critical insights about shallow-water areas, including coastal zones, river deltas, estuaries, lakes, ponds, etc. This information is critical when considering proposed sites for new infrastructure. Whether a ports and harbor project, fiber-optic cable landing site, offshore pipeline or power cable landing for a new offshore wind development, identifying potential hazards or constraints saves time and money. Using 2D raw global coverage satellite imagery, it is possible to create 3D seabed geomorphologic deliverables for preliminary shallow water hazard and site assessment. This approach has been used in 145 Countries on 2,200 projects over the past 07 years. Because underlying data deliverables are sourced from 2D optical satellite imagery, assessments are limited to 10-20 m water depth, dependent on the atmospheric and water quality conditions. Archived images can deliver a 10-year historical analysis, offering valuable insights to seabed changes over time. Deliverables of this technique comprise a series of satellite images, referred to as 4D seabed surface morphology (4DSSM) image technology. Deliverables are offered at two precision levels. Level 1 involves 6300-plus TB of global coverage imagery available in archives, where 10 m ground resolution 3D image deliverables enable shallow-water seabed assessments. Level 2 involves 10-plus PB of global coverage imagery available in archives, where 30-70 cm ground resolution 3D image deliverables enable shallow-water seabed assessments (needing higher resolution localized analysis), depending on site specific requirements. While true depths are not determinable from optical imagery, qualitative information on hazards and changes in sedimentation distribution patterns, uncharted seabed hazards, existing seabed infrastructure and other constraints are easily identified, providing a valuable tool for nearshore vessel activity and infrastructure development needs. Satellite imagery is an effective tool for qualitative site reconnaissance in the shallow water coastal zones. As offshore development becomes more prevalent, accurate seabed mapping is crucial. While nautical charts were once the primary source of information about the seabed, these data are often outdated and inadequate to inform early planning of new offshore developments. Advanced satellite-based mapping techniques can provide up-to-date seabed morphology data for advanced planning and decision-making on offshore projects.
A Comparative Approach to Gas/Liquid Separation Technologies for Subsea Applications
Authors: Shaiek S. , Giolo R. , Moraes C. A Capela , Bacati F.
Published: October 2023

Objectives/Scope

Subsea separation refers to separating the production flow into its different phases (gas/liquid or liquid/liquid), mainly based on density differences between components, at the seabed.

The implementation of a subsea separation system allows for reduced back pressure on the subsea wellheads resulting to the increase of oil recovery and to the extension of production field lifetime while optimizing surface or onshore facilities.

Subsea Gas/Liquid separation allows to develop deepwater oil and gas fields with improved Flow Assurance philosophy while optimizing the overall production operability and fluid processing on topside.

As the industry needs to tackle challenges of deeper and higher-pressure fields, the subsea Gas/Liquid separation systems need to fulfil many requirements to allow for effective developments.

The paper focuses on Gas/Liquid separation providing a comparison of different separation technologies that could be applied subsea. A systematic approach is proposed to cover process performances, operational robustness, flexibility, and maintenance requirements.

Process

An initial description of available technologies is presented. Gravity based separation vessels cyclones, including Gas Liquid Cylindrical Cyclone technology (GLCC) and inline cyclonic devices, and the subsea Vertical MultiPipe (VMP) are discussed.

The main parameters evaluated for each technology with respect to their potential subsea use is listed.

Also, to guide the assessment of separation technologies, a notional reference case, featuring typical specifications for a deepwater development, is proposed.

Results, Observations, Conclusions

Based on the relevant parameters, especially identified for subsea applications, and reference case data, a ranking of technologies is presented. Moreover, a sensitivity allows to extend the considerations beyond the studied case showing where the various technologies are advantageous. Additionally, maturity and technology gaps for subsea applications is discussed.

Finally, the results show that, compared with the other technologies, the VMP provides a simpler and reliable design while providing a maintenance free solution.

Novel/Additive Information

The paper presents a thorough analysis of Gas/Liquid separation technologies applicable to subsea deepwater field development based on qualitative and quantitative results.

It gives an overview of advantages and limitations of each solution to support proper selection to any specific field.