bluuebunny/crossref_metadata_2025 huggingface dataset:
A Method to Redesign and Simplify Schedules of Assessment and Quantify the Impacts. Applications to Merck Protocols
Authors: Cummings Steven R. , Chetham Scott , Lee Andy
Published: May 2024

The growing complexity of biopharmaceutical sponsored trials has adverse impacts on increased burdens on participants, clinical sites, and sponsors, including greater difficulty recruiting and retaining participants, difficulty engaging sites to participate in trials, excessive cost of trials, and increased cycle times. The schedule of assessments (SoAs) is the origin of and blueprint for complexity that is often generated by copying and pasting from previous SoAs. We developed an approach, termed Lean Design, for redesigning the assessments in SoAs that generate data, the ‘Data SoA.’ It starts with a simple “ground zero” SoA. Any addition is challenged using several principles of trial design. We employed a system, the Faro Trial Designer Tool, to quantify the impacts of changes in an SoA to provide real-time feedback to the team and sponsor. We applied the approach in workshops with teams for six clinical trials in various stages of design and implementation. The approach resulted in recommendation for substantial potential savings in participant and site staff time, costs, and complexity of the trials. Application of this approach to very early stages of protocol design has the potential to reduce the complexity of biopharmaceutical sponsored trials and its consequences.
Cultural Burning
Authors: David Bruno , Fletcher Michael-Shawn , Connor Simon , Pullin Virginia Ruth , Birkett-Rees Jessie , Delannoy Jean-Jacques , Mariani Michela , Romano Anthony , Maezumi S. Yoshi
Published: May 2024

This Element addresses a burning question – how can archaeologists best identify and interpret cultural burning, the controlled use of fire by people to shape and curate their physical and social landscapes? This Element describes what cultural burning is and presents current methods by which it can be identified in historical and archaeological records, applying internationally relevant methods to Australian landscapes. It clarifies how the transdisciplinary study of cultural burning by Quaternary scientists, historians, archaeologists and Indigenous community members is informing interpretations of cultural practices, ecological change, land use and the making of place. This title is also available as Open Access on Cambridge Core.
African Migration and the Novel
Authors: Taylor Jack
Published: May 2024

Examines how current novels dealing with African migration address social issues, immigrant subjectivity, and the politics of migration.
The Musical Relationship between Claude Debussy and Igor Stravinsky
Authors: McFarland Mark
Published: May 2024

Stravinsky's influence on Debussy in 1910-13 is demonstrated here in the many modernistic features of such works as the Preludes Book II, 'Khamma', 'Jeux'.
Semantic agent framework for automated flood assessment using dynamic knowledge graphs
Authors: Hofmeister Markus , Bai Jiaru , Brownbridge George , Mosbach Sebastian , Lee Kok F. , Farazi Feroz , Hillman Michael , Agarwal Mehal , Ganguly Srishti , Akroyd Jethro , Kraft Markus
Published: May 2024

This article proposes a framework of linked software agents that continuously interact with an underlying knowledge graph to automatically assess the impacts of potential flooding events. It builds on the idea of connected digital twins based on the World Avatar dynamic knowledge graph to create a semantically rich asset of data, knowledge, and computational capabilities accessible to humans, applications, and artificial intelligence. We develop three new ontologies to describe and link environmental measurements and their respective reporting stations, flood events, and their potential impact on population and built infrastructure as well as the built environment of a city itself. These coupled ontologies are deployed to dynamically instantiate near real-time data from multiple fragmented sources into the World Avatar. Sequences of autonomous agents connected via the derived information framework automatically assess consequences of newly instantiated data, such as newly raised flood warnings, and cascade respective updates through the graph to ensure up-to-date insights into the number of people and building stock value at risk. Although we showcase the strength of this technology in the context of flooding, our findings suggest that this system-of-systems approach is a promising solution to build holistic digital twins for various other contexts and use cases to support truly interoperable and smart cities.
Distribution and palaeoecology of scleractinian corals during the Maastrichtian (Late Cretaceous)
Authors: Baron-Szabo Rosemarie C. , Leloux Jacob
Published: May 2024

Maastrichtian scleractinian corals from 94 localities in 26 Maastrichtian regions world-wide with strata of that age are taxonomically and palaeobiogeographically evaluated. A total of 205 taxa, belonging to 116 genera and 37 families, are included in the present study. Most coral taxa have been recorded from non-reefal environments. A significant majority of these taxa (genera = 70.7%; species = 75.6%) appear to have been endemic during the Maastrichtian. The Maastrichtian coral fauna is dominated by solitary and cerioid-plocoid forms (both accounting for 41 genera = 70%), having mainly medium- and large-sized corallites. The most diverse coral assemblages are those that have been recorded from arid (Jamaica: 63 species, Mexico: 29 species), warm-temperate (the Netherlands-Belgium: 32 species) and tropical regions (Iran: 27 species). The occurrence of Cunnolites polymorphus (Goldfuss) is newly recorded for the Netherlands (southern Limburg). Compared to the microstructural composition of the coral fauna of the lowermost Cretaceous (Berriasian; 91% of the species and 83% of the genera belonged to previously established microstructural groups), in the Maastrichtian, corals belonging to previously established microstructural groups were of minor importance (genera = 26%; species = 29.3%). The majority of Maastrichtian scleractinian taxa (both solitary and colonial) from the type area of the Maastrichtian Stage in the southeast Netherlands and northeast Belgium are illustrated.
The Fezouata Shale Formation biota is typical for the high latitudes of the Early Ordovician—a quantitative approach
Authors: Richards Jared C. , Nanglu Karma , Ortega-Hernández Javier
Published: May 2024

The Fezouata Shale Formation has dramatically impacted our understanding of Early Ordovician marine ecosystems before the great Ordovician biodiversification event (GOBE), thanks to the abundance and quality of exceptionally preserved animals within it. Systematic work has noted that the shelly fossil subassemblages of the Fezouata Shale biota are typical of open-marine deposits from the Lower Ordovician, but no studies have tested the quantitative validity of this statement. We extracted 491 occurrences of recalcitrant fossil genera from the Paleobiology Database to reconstruct 31 subassemblages to explore the paleoecology of the Fezouata Shale and other contemporary, high-latitude (66°S–90°S) deposits from the Lower Ordovician (485.4–470 Ma) and test the interpretation that the Fezouata Shale biota is typical for an Ordovician open-marine environment. Sørensen's dissimilarity metrics and Wilcoxon tests indicate that the subassemblages of the Tremadocian-aged lower Fezouata Shale are approximately 20% more heterogenous than the Floian-aged upper Fezouata Shale. Dissimilarity metrics and visualization suggest that while the lower Fezouata and upper Fezouata share faunal components, the two sections have distinct faunas. We find that the faunal composition of the lower Fezouata Shale is comparable with other Tremadocian-aged subassemblages from high latitudes, suggesting that it is typical for an Early Ordovician open-marine environment. We also find differences in faunal composition between Tremadocian- and Floian-aged deposits. Our results corroborate previous field-based and qualitative systematic studies that concluded that the shelly assemblages of the Fezouata Shale are comparable with those of other Lower Ordovician deposits from high latitudes. This establishes the first quantitative baseline for examining the composition and variability within the assemblages of the Fezouata Shale and will be key to future studies attempting to discern the degree to which it can inform our understanding of marine ecosystems just before the start of the GOBE.
Catenaries and minimal surfaces of revolution in hyperbolic space
Authors: da Silva Luiz C. B. , López Rafael
Published: May 2024

We introduce the concept of extrinsic catenary in the hyperbolic plane. Working in the hyperboloid model, we define an extrinsic catenary as the shape of a curve hanging under its weight as seen from the ambient space. In other words, an extrinsic catenary is a critical point of the potential functional, where we calculate the potential with the extrinsic distance to a fixed reference plane in the ambient Lorentzian space. We then characterize extrinsic catenaries in terms of their curvature and as a solution to a prescribed curvature problem involving certain vector fields. In addition, we prove that the generating curve of any minimal surface of revolution in the hyperbolic space is an extrinsic catenary with respect to an appropriate reference plane. Finally, we prove that one of the families of extrinsic catenaries admits an intrinsic characterization if we replace the extrinsic distance with the intrinsic length of horocycles orthogonal to a reference geodesic.
Health technology assessment and healthcare environmental sustainability: Prioritizing effort and maximizing impact
Authors: Hensher Martin
Published: May 2024

The growing global focus on and sense of urgency toward improving healthcare environmental sustainability and moving to low-carbon and resilient healthcare systems is increasingly mirrored in discussions of the role of health technology assessment (HTA). This Perspective considers how HTA can most effectively contribute to these goals and where other policy tools may be more effective in driving sustainability, especially given the highly limited pool of resources available to conduct environmental assessments within HTA. It suggests that HTA might most productively focus on assessing those technologies that have intrinsic characteristics which may cause specific environmental harms or vulnerabilities, while the generic environmental impacts of most other products may be better addressed through other policy and regulatory mechanisms.
Disability and costs of IHD attributable to the consumption of trans-fatty acids in Brazil
Authors: Parajára Magda do Carmo , Fogal Vegi Aline Siqueira , Machado Ísis Eloah , Menezes Mariana Carvalho de , Verly-Jr Eliseu , Meireles Adriana Lúcia
Published: May 2024

Objective:

To estimate the disability and costs of the Brazilian Unified Health System for IHD attributable to trans-fatty acid (TFA) consumption in 2019.

Design:

This ecological study used secondary data from the Global Burden of Disease (GBD) Study 2019 to estimate the years lived with disability from IHD attributable to TFA in Brazil in 2019. Data on direct costs (purchasing power parity: 1 Int$ = R$ 2·280) were obtained from the Hospital and Ambulatory Information Systems of the Brazilian Unified Health System. Moreover, the total costs in each state were divided by the resident population in 2019 and multiplied by 10 000 inhabitants. The relationship between the socio-demographic index, disease and economic burden was investigated.

Setting:

Brazil and its twenty-seven states.

Participants:

Adults aged ≥ 25 years of both sexes.

Results:

IHD attributable to TFA consumption resulted in 11 165 years lived with disability (95 % uncertainty interval 932–18 462) in 2019 in Brazil. A total of Int$ 54 546 227 (95 % uncertainty interval 4 505 792–85 561 810) was spent in the Brazilian Unified Health System in 2019 due to IHD attributable to TFA, with the highest costs of hospitalisations, for males and individuals aged ≥ 50 years or over. The highest costs were observed in Sergipe (Int$ 6508/10 000; 95 % uncertainty interval 576–10 265), followed by the two states from the South. Overall, as the socio-demographic index increases, expenditures increase.

Conclusions:

TFA consumption results in a high disease and economic IHD burden in Brazil, reinforcing the need for more effective health policies, such as industrial TFA elimination, following the international agenda.
Beyond retribution: Individual reparations for IHL violations as peace facilitators
Authors: van de Put Steven , Pacholska Magdalena
Published: May 2024

Three decades after the United Nations Security Council invoked its Chapter VII powers to create the ad hoc criminal tribunals, there can be little doubt that the prosecution of individuals responsible for serious violations of international humanitarian law (IHL) contributes to restoring and maintaining peace. While there is little doubt that the reparatory function of justice is just as crucial as retribution, under international law today, reparations for IHL violations remain harrowingly insufficient or borderline non-existent. In scholarship and strategic litigation, various attempts have been made to distil an individual right to reparations from black-letter IHL. This article argues that such approaches are doomed to fail, as procedural aspects of international obligations rarely, if ever, emerge through the evolution of an existing customary international obligation, let alone via the crystallization of a new customary international norm. They are usually triggered by a political shift that makes States adopt novel regulations setting forth the jurisdictional ramifications of enforcing a pre-existing right or obligation. This article thus advances a two-fold argument. First, it asserts that States’ increased compliance with the obligation to provide compensation for violations of IHL attributable to them would contribute to “the restoration and maintenance of peace” just as much as the prosecution of persons responsible for serious violations thereof. Second, it argues that the individual right to claim reparations for IHL violations can only be established through a political decision of States, and that the establishment of an international mechanism for Ukraine might be an important precedent for the evolution of the current international system.
Long-term outcomes of visual motor integration and motor development children with retinopathy of prematurity
Authors: Kutlutürk Yıkılmaz Seval , Celik Gokhan , Gunay Murat , Kizilay Osman , Algun Zeliha Candan
Published: May 2024

Premature infants have a risk of neurodevelopmental deficits. Little is known, however, about how retinopathy of prematurity (ROP) affects visual motor integration (VMI), which is necessary for both fine motor skills and further school abilities. Due to the systemic escape of bevacizumab in the treatment of ROP, concerns regarding the long-term neurodevelopmental effect of the drug have arisen. The aim is to evaluate VMI and motor development long-term outcomes after intravitreal bevacizumab (IVB) injection and laser treatment for ROP. Two groups of premature children were included: Bevacizumab group – 16 premature children who received IVB treatment and laser group – 23 premature children who underwent laser photocoagulation treatment in this single center cross-sectional study. At 2–6 years of age, VMI (Beery–Buktenica Developmental Test), motor development (Peabody Developmental Motor Scales-2), visual acuity, and refractive status were assessed. The incidence of abnormal visual function was significantly higher in bevacizumab group than in laser group (p = 0.022). The incidence of abnormal VMI skill was significantly higher in bevacizumab group than in laser group (p = 0.024). Incidences of abnormal gross, fine, and total motor skills were significantly higher in bevacizumab group compared to laser group (p < 0.05). Premature children who received bevacizumab for ROP demonstrated significantly lower VMI and motor development features than those with laser treatment at preschool age. Although our results suggest the relevance of bevacizumab injection in impaired VMI and motor development outcomes, general level of sickness rather than treatment might be the cause of delayed motor development.
Impact of Dynamic Phytoplankton Stoichiometry on Global Scale Patterns of Nutrient Limitation, Nitrogen Fixation, and Carbon Export
Authors: Hagstrom George I. , Stock Charles A. , Luo Jessica Y. , Levin Simon A.
Published: May 2024

Phytoplankton stoichiometry modulates the interaction between carbon, nitrogen and phosphorus cycles. Environmentally driven variations in phytoplankton C:N:P can alter biogeochemical cycling compared to expectations under fixed ratios. In fact, the assumption of fixed C:N:P has been linked to Earth System Model (ESM) biases and potential misrepresentation of responses to future change. Here we integrate key elements of the Adaptive Trait Optimization Model (ATOM) for phytoplankton stoichiometry with the Carbon, Ocean Biogeochemistry and Lower Trophics (COBALT) ocean biogeochemical model. Within a series of global ocean‐ice‐ecosystem retrospective simulations, ATOM‐COBALT reproduced observations of phytoplankton N:P, and compared to static ratios, exhibited reduced phytoplankton P‐limitation, enhanced N‐fixation, and increased low‐latitude export, improving consistency with observations and highlighting the biogeochemical implications of dynamic N:P. We applied ATOM‐COBALT to explore the impacts of different physiological mechanisms hypothesized to underlie N:P variation, finding that two mechanisms together drove the observed patterns: proportionality of P‐rich ribosomes in phytoplankton cells to growth rates and reductions in P‐storage during scarcity. A third mechanism which linked temperature with phytoplankton biomass allocations to non‐ribosomal proteins, led only to relatively modest impacts because this mechanism decreased the temperature dependence of phytoplankton growth rates, compensating for changes in N:P. We find that there are quantitative response differences that associate distinctive biogeochemical footprints with each mechanism, which are most apparent in highly productive low‐latitude regions. These results suggest that variable phytoplankton N:P makes phytoplankton productivity and export resilient to environmental changes, and support further research on the physiological and environmental drivers of phytoplankton stoichiometry and biogeochemical role.
Numerical Simulation of Electromagnetic Responses to an Earthquake Source Due To the Piezoelectric Effect of ‘∞m’ Symmetry
Authors: Zhao Jie , Gao Yongxin , Cheng Qianli , Zhou Guanqun , Chen Chieh‐Hung , Zhang Xuemin , Sun Yang‐yi
Published: May 2024

It is reported that earthquakes are accompanied by electromagnetic (EM) anomalies. These anomalies are thought to be caused by earthquakes but their generation mechanism is still unclear. The piezoelectric effect has been proposed as a possible mechanism, particularly in quartz‐rich rocks. However, the EM responses to earthquakes due to such an effect have not been well understood. In this article, we study the EM signals generated by an earthquake source due to the piezoelectric effect. We develop a semi‐analytical method to simulate the EM responses to earthquake sources in a 3‐D layered model and conduct numerical simulations to investigate the characteristics of the EM fields. The results show that the piezoelectric effect in quartz‐rich rocks could be the responsible mechanism for the EM signals recorded during the earthquake. Two kinds of EM signals can be generated by the earthquake, namely, the early EM wave arriving before the seismic waves and the coseismic EM field accompanying the seismic waves. For an Mw 6.1 earthquake, the coseismic electric field is ∼0.1 μV/m and the magnetic field can only reach ∼10−5 nT. We also study the sensitivity of the coseismic EM fields to the rock conductivity. The results indicate that the coseismic EM fields are mainly affected by the conductivity of the shallow layer where the receiver is located, and if the top layer is thin, they are also affected by the conductivity of the deeper layer due to the contribution of the evanescent EM wave created at the interface.
Using Shelf‐Edge Transport Composition and Sensitivity Experiments to Understand Processes Driving Sea Level on the Northwest European Shelf
Authors: Wise A. , Calafat F. M. , Hughes C. W. , Jevrejeva S. , Katsman C. A. , Oelsmann J. , Piecuch C. , Polton J. , Richter K.
Published: May 2024

Variability in ocean currents, temperature and salinity drive dynamic sea level (DSL) variability on the Northwest European Shelf (NWES). It is dominated by mass variations, with steric signals relatively small. A mechanistic explanation of how ocean dynamics relates to the mass component of NWES sea level variability is required. We use regional ocean model experiments to isolate sources of variability and then investigate the effect on monthly to‐interannual DSL variability together with the simulated momentum budgets along the shelfbreak. Regional (local) wind and non‐regional (remote) forcing are important on the NWES. For the local wind forcing, the net mass flux onto the shelf, which drives a shelf‐mean mode of DSL variability, results from a combination of surface Ekman, bottom Ekman and geostrophic flows and explains 73% of the variance in transport across the shelf‐edge. The geostrophic flow is closely related to wind stress with a flow about half that of surface Ekman transport but in the opposite direction. For the remotely forced mass‐flux across the shelf‐edge, the geostrophic component explains 62% of the variance and bottom friction plays an important indirect role. The remotely forced variability, while relatively spatially uniform, is more important for explaining DSL variance over the western NWES. This mode of variability is sensitive to signals propagating northward via a thin strip of the southern boundary near the Portuguese coast, consistent with coastal trapped wave signals. It also appears to drive steric height in the Bay of Biscay, which is related to DSL on the shelf.
Thank You to Our 2023 Peer Reviewers
Authors: Wysession Michael , Grimm Nancy , Hofmann Eileen , Illangasekare Tissa , Peterson Bill , Zhang Renyi
Published: May 2024

We are very grateful for the reviews done in 2023 to support the published articles of Perspectives of Earth and Space Sciences. Last year we had 56 reviews and this year it was 49. As a relatively young journal, Perspectives is still defining its role withing AGU. This year Perspectives added several new article formats in order to help support intra‐AGU communication. These new formats included Commentaries, Opinions, News Items, and Memorials, which means additional challenges for reviewers, as the review criteria for these new formats vary from each other. This year also saw an increase in the diversity of styles and authorships of Perspectives Articles, which are the primary format of the journal, but the bulk of these Articles still took a large‐scale big‐picture view of a particular scientific perspective, across the full range of Earth and space sciences. Once again this year, we are very grateful for the wisdom and flexibility shown by our reviewers, and the entire editorial board of Perspectives would like to express our deep appreciation for all the work they have done. Thank you!
Magnesium Isotopes of Carbonate Reveal Seasonal Climate Variation in the Central East Asia During the Middle Eocene
Authors: Zhu Huaxi , Hu Rong , Li Weiqiang , Long Yinshuang , Lai Wen , Zhang Yang , Zhang Xia , Guo Yangrui , Ji Junfeng , Lu Huayu
Published: May 2024

It is debated whether there was strong climate seasonality during the Eocene, which provides a close geological analogy for near‐future scenarios of greenhouse gas emissions. Lithological data suggest the existence of a broad arid zone centered around 30°N paleo‐latitude, while a humid climate was supported by palaeobotanic assemblages in East Asia. Here, we report the occurrence of massive primary lacustrine dolomite and magnesite in the central East Asia during the middle Eocene. We provide a novel perspective from magnesium isotopes to link the formation of Mg‐carbonates to seasonal dry‐wet cycles. Rapid magnesium input during the rainy season and intense evaporation in the dry season likely caused the formation of magnesium carbonates in an enclosed lake. These findings provide insights into hydroclimatic seasonality during the Eocene, contributing to our understanding of the hydrological cycle response to a greenhouse climate.
Attention towards chemistry agnostic and explainable battery lifetime prediction
Authors: Rahmanian Fuzhan , Lee Robert M. , Linzner Dominik , Michel Kathrin , Merker Leon , Berkes Balazs B. , Nuss Leah , Stein Helge Sören
Published: May 2024

Predicting and monitoring battery life early and across chemistries is a significant challenge due to the plethora of degradation paths, form factors, and electrochemical testing protocols. Existing models typically translate poorly across different electrode, electrolyte, and additive materials, mostly require a fixed number of cycles, and are limited to a single discharge protocol. Here, an attention-based recurrent algorithm for neural analysis (ARCANA) architecture is developed and trained on an ultra-large, proprietary dataset from BASF and a large Li-ion dataset gathered from literature across the globe. ARCANA generalizes well across this diverse set of chemistries, electrolyte formulations, battery designs, and cycling protocols and thus allows for an extraction of data-driven knowledge of the degradation mechanisms. The model’s adaptability is further demonstrated through fine-tuning on Na-ion batteries. ARCANA advances the frontier of large-scale time series models in analytical chemistry beyond textual data and holds the potential to significantly accelerate discovery-oriented battery research endeavors.
Growing strings in a chemical reaction space for searching retrosynthesis pathways
Authors: Zipoli Federico , Baldassari Carlo , Manica Matteo , Born Jannis , Laino Teodoro
Published: May 2024

Machine learning algorithms have shown great accuracy in predicting chemical reaction outcomes and retrosyntheses. However, designing synthesis pathways remains challenging for existing machine learning models which are trained for single-step prediction. In this manuscript, we propose to recast the retrosynthesis problem as a string optimization problem in a data-driven fingerprint space, leveraging the similarity between chemical reactions and embedding vectors. Based on this premise, multi-step complex synthesis can be conceptualized as sequences that link multidimensional vectors (fingerprints) representing individual chemical reaction steps. We extracted an extensive corpus of chemical synthesis from patents and converted them into multidimensional strings. While optimizing the retrosynthetic path, we use the Euclidean metric to minimize the distance between the expanded trajectory of the growing retrosynthesis string and the corpus of extracted strings. By doing so, we promote the assembly of synthetic pathways that, in the chemical reaction space, will be more similar to existing retrosyntheses, thereby inheriting the strategic guidelines designed by human experts. We integrated this approach into the RXN platform (https://rxn.res.ibm.com/) and present the method’s application to complex synthesis as well as its ability to produce better synthetic strategies than current methodologies.
A maturity model for catalogues of semantic artefacts
Authors: Corcho Oscar , Ekaputra Fajar J. , Heibi Ivan , Jonquet Clement , Micsik Andras , Peroni Silvio , Storti Emanuele
Published: May 2024

This work presents a maturity model for assessing catalogues of semantic artefacts, one of the keystones that permit semantic interoperability of systems. We defined the dimensions and related features to include in the maturity model by analysing the current literature and existing catalogues of semantic artefacts provided by experts. In addition, we assessed 26 different catalogues to demonstrate the effectiveness of the maturity model, which includes 12 different dimensions (Metadata, Openness, Quality, Availability, Statistics, PID, Governance, Community, Sustainability, Technology, Transparency, and Assessment) and 43 related features (or sub-criteria) associated with these dimensions. Such a maturity model is one of the first attempts to provide recommendations for governance and processes for preserving and maintaining semantic artefacts and helps assess/address interoperability challenges.
A tree-based corpus annotated with Cyber-Syndrome, symptoms, and acupoints
Authors: Wang Wenxi , Zhao Zhan , Ning Huansheng
Published: May 2024

Prolonged and over-excessive interaction with cyberspace poses a threat to people’s health and leads to the occurrence of Cyber-Syndrome, which covers not only physiological but also psychological disorders. This paper aims to create a tree-shaped gold-standard corpus that annotates the Cyber-Syndrome, clinical manifestations, and acupoints that can alleviate their symptoms or signs, designating this corpus as CS-A. In the CS-A corpus, this paper defines six entities and relations subject to annotation. There are 448 texts to annotate in total manually. After three rounds of updating the annotation guidelines, the inter-annotator agreement (IAA) improved significantly, resulting in a higher IAA score of 86.05%. The purpose of constructing CS-A corpus is to increase the popularity of Cyber-Syndrome and draw attention to its subtle impact on people’s health. Meanwhile, annotated corpus promotes the development of natural language processing technology. Some model experiments can be implemented based on this corpus, such as optimizing and improving models for discontinuous entity recognition, nested entity recognition, etc. The CS-A corpus has been uploaded to figshare.
Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities
Authors: Tshisekedi Kalonji A. , De Maayer Pieter , Botes Angela
Published: May 2024

Barley (Hordeum vulgare) is essential to global food systems and the brewing industry. Its physiological traits and microbial communities determine malt quality. Although microbes influence barley from seed health to fermentation, there is a gap in metagenomic insights during seed storage. Crucially, elucidating the changes in microbial composition associated with barley seeds is imperative for understanding how these fluctuations can impact seed health and ultimately, influence both agricultural yield and quality of barley-derived products. Whole metagenomes were sequenced from eight barley seed samples obtained at different storage time points from harvest to nine months. After binning, 82 metagenome-assembled genomes (MAGs) belonging to 26 distinct bacterial genera were assembled, with a substantial proportion of potential novel species. Most of our MAG dataset (61%) showed over 90% genome completeness. This pioneering barley seed microbial genome retrieval provides insights into species diversity and structure, laying the groundwork for understanding barley seed microbiome interactions at the genome level.
SAROS: A dataset for whole-body region and organ segmentation in CT imaging
Authors: Koitka Sven , Baldini Giulia , Kroll Lennard , van Landeghem Natalie , Pollok Olivia B. , Haubold Johannes , Pelka Obioma , Kim Moon , Kleesiek Jens , Nensa Felix , Hosch René
Published: May 2024

The Sparsely Annotated Region and Organ Segmentation (SAROS) dataset was created using data from The Cancer Imaging Archive (TCIA) to provide a large open-access CT dataset with high-quality annotations of body landmarks. In-house segmentation models were employed to generate annotation proposals on randomly selected cases from TCIA. The dataset includes 13 semantic body region labels (abdominal/thoracic cavity, bones, brain, breast implant, mediastinum, muscle, parotid/submandibular/thyroid glands, pericardium, spinal cord, subcutaneous tissue) and six body part labels (left/right arm/leg, head, torso). Case selection was based on the DICOM series description, gender, and imaging protocol, resulting in 882 patients (438 female) for a total of 900 CTs. Manual review and correction of proposals were conducted in a continuous quality control cycle. Only every fifth axial slice was annotated, yielding 20150 annotated slices from 28 data collections. For the reproducibility on downstream tasks, five cross-validation folds and a test set were pre-defined. The SAROS dataset serves as an open-access resource for training and evaluating novel segmentation models, covering various scanner vendors and diseases.
Peripheral blood transcriptomic profiling of molecular mechanisms commonly regulated by binge drinking and placebo effects
Authors: Shetty Amol Carl , Sivinski John , Cornell Jessica , McCracken Carrie , Sadzewicz Lisa , Mahurkar Anup , Wang Xing-Qun , Colloca Luana , Lin Weihong , Pilli Nageswara , Kane Maureen A. , Seneviratne Chamindi
Published: May 2024

Molecular responses to alcohol consumption are dynamic, context-dependent, and arise from a complex interplay of biological and external factors. While many have studied genetic risk associated with drinking patterns, comprehensive studies identifying dynamic responses to pharmacologic and psychological/placebo effects underlying binge drinking are lacking. We investigated transcriptome-wide response to binge, medium, and placebo alcohol consumption by 17 healthy heavy social drinkers enrolled in a controlled, in-house, longitudinal study of up to 12 days. Using RNA-seq, we identified 251 and 13 differentially expressed genes (DEGs) in response to binge drinking and placebo, respectively. Eleven protein-coding DEGs had very large effect sizes in response to binge drinking (Cohen’s d > 1). Furthermore, binge dose significantly impacted the Cytokine-cytokine receptor interaction pathway (KEGG: hsa04060) across all experimental sequences. Placebo also impacted hsa04060, but only when administered following regular alcohol drinking sessions. Similarly, medium-dose and placebo commonly impacted KEGG pathways of Systemic lupus erythematosus, Neutrophil extracellular trap formation, and Alcoholism based on the sequence of drinking sessions. These findings together indicate the “dose-extending effects” of placebo at a molecular level. Furthermore, besides supporting alcohol dose-specific molecular changes, results suggest that the placebo effects may induce molecular responses within the same pathways regulated by alcohol.
Low-density lipoprotein particle profiles compared with standard lipids measurements in the association with asymptomatic intracranial artery stenosis
Authors: Vu Thien , Yano Yuichiro , Pham Huy Kien Tai , Mondal Rajib , Ohashi Mizuki , Kitaoka Kaori , Moniruzzaman Mohammad , Torii Sayuki , Shiino Akihiko , Tsuji Atsushi , Hisamatsu Takashi , Okamura Tomonori , Kondo Keiko , Kadota Aya , Watanabe Yoshiyuki , Nozaki Kazuhiko , Ueshima Hirotsugu , Miura Katsuyuki
Published: May 2024

The Shiga Epidemiological Study of Subclinical Atherosclerosis was conducted in Kusatsu City, Shiga, Japan, from 2006 to 2008. Participants were measured for LDL-p through nuclear magnetic resonance technology. 740 men participated in follow-up and underwent 1.5 T brain magnetic resonance angiography from 2012 to 2015. Participants were categorized as no-ICAS, and ICAS consisted of mild-ICAS (1 to < 50%) and severe-ICAS (≥ 50%) in any of the arteries examined. After exclusion criteria, 711 men left for analysis, we used multiple logistic regression to examine the association between lipid profiles and ICAS prevalence. Among the study participants, 205 individuals (28.8%) had ICAS, while 144 individuals (20.3%) demonstrated discordance between LDL-c and LDL-p levels. The discordance “low LDL-c–high LDL-p” group had the highest ICAS risk with an adjusted OR (95% CI) of 2.78 (1.55–5.00) in the reference of the concordance “low LDL-c–low LDL-p” group. This was followed by the concordance “high LDL-c–high LDL-p” group of 2.56 (1.69–3.85) and the discordance “high LDL-c–low LDL-p” group of 2.40 (1.29–4.46). These findings suggest that evaluating LDL-p levels alongside LDL-c may aid in identifying adults at a higher risk for ICAS.
Molecular characteristics and phylogenetic analysis of pigeon paramyxovirus type 1 isolates from pigeon meat farms in Shanghai (2009–2012)
Authors: Sheng Wenwei , Wang Kexuan , Gui Yaping , Qi Xinyong , Shen Liping , Zhang Yujie , Tang Congsheng , Li Xin , Tao Jun , Cao Chuangui , Qian Weidong , Liu Jian
Published: May 2024

The majority of pigeon paramyxovirus type 1 (PPMV-1) strains are generally non-pathogenic to chickens; however, they can induce severe illness and high mortality rates in pigeons, leading to substantial economic repercussions. The genomes of 11 PPMV-1 isolates from deceased pigeons on meat pigeon farms during passive monitoring from 2009 to 2012 were sequenced and analyzed using polymerase chain reaction and phylogenetic analysis. The complete genome lengths of 11 isolates were approximately 15,192 nucleotides, displaying a consistent gene order of 3′-NP-P-M-F-HN-L-5′. ALL isolates exhibited the characteristic motif of 112RRQKRF117 at the fusion protein cleavage site, which is characteristic of velogenic Newcastle disease virus. Moreover, multiple mutations have been identified within the functional domains of the F and HN proteins, encompassing the fusion peptide, heptad repeat region, transmembrane domains, and neutralizing epitopes. Phylogenetic analysis based on sequences of the F gene unveiled that all isolates clustered within genotype VI in class II. Further classification identified at least two distinct sub-genotypes, with seven isolates classified as sub-genotype VI.2.1.1.2.2, whereas the others were classified as sub-genotype VI.2.1.1.2.1. This study suggests that both sub-genotypes were implicated in severe disease manifestation among meat pigeons, with sub-genotype VI.2.1.1.2.2 displaying an increasing prevalence among Shanghai’s meat pigeon population since 2011. These results emphasize the value of developing pigeon-specific vaccines and molecular diagnostic tools for monitoring and proactively managing potential PPMV-1 outbreaks.
Enhancing Ethiopian power distribution with novel hybrid renewable energy systems for sustainable reliability and cost efficiency
Authors: Agajie Takele Ferede , Fopah-Lele Armand , Amoussou Isaac , Khan Baseem , Bajaj Mohit , Zaitsev Ievgen , Tanyi Emmanuel
Published: May 2024

Economic development relies on access to electrical energy, which is crucial for society’s growth. However, power shortages are challenging due to non-renewable energy depletion, unregulated use, and a lack of new energy sources. Ethiopia’s Debre Markos distribution network experiences over 800 h of power outages annually, causing financial losses and resource waste on diesel generators (DGs) for backup use. To tackle these concerns, the present study suggests a hybrid power generation system, which combines solar and biogas resources, and integrates Superconducting Magnetic Energy Storage (SMES) and Pumped Hydro Energy Storage (PHES) technologies into the system. The study also thoroughly analyzes the current and anticipated demand connected to the distribution network using a backward/forward sweep load flow analysis method. The results indicate that the total power loss has reached its absolute maximum, and the voltage profiles of the networks have dropped below the minimal numerical values recommended by the Institute of Electrical and Electronics Engineers (IEEE) standards (i.e., 0.95–1.025 p.u.). After reviewing the current distribution network’s operation, additional steps were taken to improve its effectiveness, using metaheuristic optimization techniques to account for various objective functions and constraints. In the results section, it is demonstrated that the whale optimization algorithm (WOA) outperforms other metaheuristic optimization techniques across three important objective functions: financial, reliability, and greenhouse gas (GHG) emissions. This comparison is based on the capability of the natural selection whale optimization algorithm (NSWOA) to achieve the best possible values for four significant metrics: Cost of Energy (COE), Net Present Cost (NPC), Loss of Power Supply Probability (LPSP), and GHG Emissions. The NSWOA achieved optimal values for these metrics, namely 0.0812 €/kWh, 3.0017 × 106 €, 0.00875, and 7.3679 × 106 kg reduced, respectively. This is attributable to their thorough economic, reliability, and environmental evaluation. Finally, the forward/backward sweep load flow analysis employed during the proposed system’s integration significantly reduced the impact of new energy resources on the distribution network. This was evident in the reduction of total power losses from 470.78 to 18.54 kW and voltage deviation from 6.95 to 0.35 p.u., as well as the voltage profile of the distribution system being swung between 1 and 1.0234 p.u., which now comply with the standards set by the IEEE. Besides, a comparison of the cost and GHG emission efficiency of the proposed hybrid system with existing (grid + DGs) and alternative (only DGs) scenarios was done. The findings showed that, among the scenarios examined, the proposed system is the most economical and produces the least amount of GHG emissions.
Integrated multi-omic approach reveals the effect of a Graminaceae-derived biostimulant and its lighter fraction on salt-stressed lettuce plants
Authors: Monterisi Sonia , Zhang Leilei , Garcia-Perez Pascual , Alzate Zuluaga Monica Yorlady , Ciriello Michele , El-Nakhel Christophe , Buffagni Valentina , Cardarelli Mariateresa , Colla Giuseppe , Rouphael Youssef , Cesco Stefano , Lucini Luigi , Pii Youry
Published: May 2024

Plant biostimulants are widely applied in agriculture for their ability to improve plant fitness. In the present work, the impact of Graminaceae-derived protein hydrolysate (P) and its lighter molecular fraction F3 (< 1 kDa) on lettuce plants, subjected to either no salt or high salt conditions, was investigated through the combination of metabolomics and transcriptomics. The results showed that both treatments significantly modulated the transcriptome and metabolome of plants under salinity stress, highlighting an induction of the hormonal response. Nevertheless, P and F3 also displayed several peculiarities. F3 specifically modulated the response to ethylene and MAPK signaling pathway, whereas P treatment induced a down-accumulation of secondary metabolites, albeit genes controlling the biosynthesis of osmoprotectants and antioxidants were up-regulated. Moreover, according with the auxin response modulation, P promoted cell wall biogenesis and plasticity in salt-stressed plants. Notably, our data also outlined an epigenetic control of gene expression induced by P treatment. Contrarily, experimental data are just partially in agreement when not stressed plants, treated with P or F3, were considered. Indeed, the reduced accumulation of secondary metabolites and the analyses of hormone pathways modulation would suggest a preferential allocation of resources towards growth, that is not coherent with the down-regulation of the photosynthetic machinery, the CO2 assimilation rate and leaves biomass. In conclusion, our data demonstrate that, although they might activate different mechanisms, both the P and F3 can result in similar benefits, as far as the accumulation of protective osmolytes and the enhanced tolerance to oxidative stress are concerned. Notably, the F3 fraction exhibits slightly greater growth promotion effects under high salt conditions. Most importantly, this research further corroborates that biostimulants’ mode of action is dependent on plants’ physiological status and their composition, underscoring the importance of investigating the bioactivity of the different molecular components to design tailored applications for the agricultural practice.
Metabolic network analysis of pre-ASD newborns and 5-year-old children with autism spectrum disorder
Authors: Lingampelly Sai Sachin , Naviaux Jane C. , Heuer Luke S. , Monk Jonathan M. , Li Kefeng , Wang Lin , Haapanen Lori , Kelland Chelsea A. , Van de Water Judy , Naviaux Robert K.
Published: May 2024

Classical metabolomic and new metabolic network methods were used to study the developmental features of autism spectrum disorder (ASD) in newborns (n = 205) and 5-year-old children (n = 53). Eighty percent of the metabolic impact in ASD was caused by 14 shared biochemical pathways that led to decreased anti-inflammatory and antioxidant defenses, and to increased physiologic stress molecules like lactate, glycerol, cholesterol, and ceramides. CIRCOS plots and a new metabolic network parameter, $$\dot{{{\boldsymbol{V}}}}\!$$

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net, revealed differences in both the kind and degree of network connectivity. Of 50 biochemical pathways and 450 polar and lipid metabolites examined, the developmental regulation of the purine network was most changed. Purine network hub analysis revealed a 17-fold reversal in typically developing children. This purine network reversal did not occur in ASD. These results revealed previously unknown metabolic phenotypes, identified new developmental states of the metabolic correlation network, and underscored the role of mitochondrial functional changes, purine metabolism, and purinergic signaling in autism spectrum disorder.
Fluorescence imaging sheds light on the immune evasion mechanisms of hepatic stellate cells mediated by superoxide anion
Authors: Mao Yuantao , Wu Chuanchen , Wang Xin , Zhang Fanghui , Qi Xinru , Li Xia , Li Ping , Tang Bo
Published: May 2024

Whether and how the reactive oxygen species generated by hepatic stellate cells (HSCs) promote immune evasion of hepatocellular carcinoma (HCC) remains mysterious. Therefore, investigating the function of superoxide anion (O2•−), the firstly generated reactive oxygen species, during the immune evasion become necessary. In this work, we establish a novel in situ imaging method for visualization of O2•− changes in HSCs based on a new two-photon fluorescence probe TPH. TPH comprises recognition group for O2•− and HSCs targeting peptides. We observe that O2•− in HSCs gradually rose, impairing the infiltration of CD8+ T cells in HCC mice. Further studies reveal that the cyclin-dependent kinase 4 is deactivated by O2•−, and then cause the up-regulation of PD-L1. Our work provides molecular insights into HSC-mediated immune evasion of HCC, which may represent potential targets for HCC immunotherapy.
Tunable magnetism in titanium-based kagome metals by rare-earth engineering and high pressure
Authors: Chen Long , Zhou Ying , Zhang He , Ji Xuecong , Liao Ke , Ji Yu , Li Ying , Guo Zhongnan , Shen Xi , Yu Richeng , Yu Xiaohui , Weng Hongming , Wang Gang
Published: May 2024

Rare-earth engineering is an effective way to introduce and tune magnetism in topological kagome materials, which have been acting as a fertile platform to investigate the quantum interactions between geometry, topology, spin, and correlation. Here, we report the synthesis, structure, and physical properties of titanium-based kagome metals RETi3Bi4 (RE = Yb, Pr, and Nd) with various magnetic states. They all crystallize in the orthogonal space group Fmmm (No. 69), featuring distorted titanium kagome lattices and rare-earth zig-zag chains. By changing the rare earth atoms in the zig-zag chains, the magnetism can be tuned from nonmagnetic YbTi3Bi4 to short-range ordered PrTi3Bi4 (Tanomaly ~ 8.2 K), and finally to ferromagnetic NdTi3Bi4 (Tc ~ 8.5 K). In-situ resistance measurements of NdTi3Bi4 under high pressure further reveal a tunable ferromagnetic ordering temperature. These results highlight RETi3Bi4 as a promising family of kagome metals to explore nontrivial band topology and exotic phases.