bluuebunny/crossref_metadata_2025 huggingface dataset:
Hybrid heat pumps avoid extreme marginal abatement costs of electrifying peak heating loads in cold regions
Authors: Smillie Sean , Vaishnav Parth , Wade Cameron , Jordan Katherine , Venkatesh Aranya , Sinha Aditya , Apt Jay
Published: August 2024

Electrification with heat pumps is often cited as a preferred pathway to decarbonize US space heating in the transition to a net-zero energy system. However, fully electrifying building heat may significantly increase peak electric system loads during cold weather, thus challenging extensive adoption. A hybrid home heating system uses both heat pumps and conventional natural gas furnaces, where the gas appliance operates during peak heating periods. Here, we assess the marginal abatement costs of fully electrifying peak heating demands as opposed to allowing hybrid heating in current gas connected and ducted homes. We use a least-cost energy system optimization model that considers household, electric, and gas system costs, including electric distribution system expansion and gas system cost recovery. To ensure the cost of sufficient low-carbon dispatchable electric capacity is captured, the model includes historical days with peak heating demands and low wind and solar availability. We find hybrid heat pumps can achieve substantial decarbonization, with US natural gas residential heating consumption decreasing 70% to 95% from 2020 levels at marginal abatement costs below $200 per tonne CO2e. The cost of fully electrifying heating in cold regions is very high, with the marginal abatement cost of eliminating the last 1% of natural gas consumption exceeding $1000 per tonne CO2e even in scenarios designed to be favorable to electrification. The robust value of hybrid heat pumps in northern cold climates indicates the importance of flexible building heat decarbonization policies such as clean heat standards.
Sensitivity and vulnerability to summer heat extremes in major cities of the United States
Authors: Li Xiaojiang , Wang Guoqing , Zaitchik Benjamin , Hsu Angel , Chakraborty TC
Published: August 2024

Many cities are experiencing increases in extreme heat because of global temperature rise combined with the urban heat island effect. The heterogeneity of urban morphology also leads to fine-scale variability in potential for heat exposure. Yet, how this rise in temperature and local variability together impacts urban residents differently at exposure-relevant scales is still not clear. Here we map the Universal Thermal Climate Index, a more complete indicator of human heat stress at an unprecedentedly fine spatial resolution (1 m), for 14 major cities in the United States using urban microclimate modeling. We examined the different heat exposure levels across different socioeconomic and racial/ethnic groups in these cities, finding that income level is most consistently associated with heat stress. We further conducted scenario simulations for a hypothetical 1 °C increase of air temperature in all cities. Results show that a 1 °C increase would have a substantial impact on human heat stress, with impacts that differ across cities. The results of this study can help us better evaluate the impact of extreme heat on urban residents at decision-relevant scales.
Automated quantification of periodic discharges in human electroencephalogram
Authors: McGraw Christopher M , Rao Samvrit , Manjunath Shashank , Jing Jin , Brandon Westover M
Published: August 2024

Periodic discharges (PDs) are pathologic patterns of epileptiform discharges repeating at regular intervals, commonly detected in the human electroencephalogram (EEG) signals in patients who are critically ill. The frequency and spatial extent of PDs are associated with the tendency of PDs to cause brain injury, existing automated algorithms do not quantify the frequency and spatial extent of PDs. The present study presents an algorithm for quantifying frequency and spatial extent of PDs. The algorithm quantifies the evolution of these parameters within a short (10–14 second) window, with a focus on lateralized and generalized periodic discharges. We test our algorithm on 300 ‘easy’, 300 ‘medium’, and 240 ‘hard’ examples (840 total epochs) of periodic discharges as quantified by interrater consensus from human experts when analyzing the given EEG epochs. We observe 95.0% agreement with a 95% confidence interval (CI) of [94.9%, 95.1%] between algorithm outputs with reviewer clincal judgement for easy examples, 92.0% agreement (95% CI [91.9%, 92.2%]) for medium examples, and 90.4% agreement (95% CI [90.3%, 90.6%]) for hard examples. The algorithm is also computationally efficient and is able to run in 0.385 ± 0.038 seconds for a single epoch using our provided implementation of the algorithm. The results demonstrate the algorithm’s effectiveness in quantifying these discharges and provide a standardized and efficient approach for PD quantification as compared to existing manual approaches.
Impact of soil and water quality on the sustainable management of mangrove-compatible brackishwater aquaculture practices in Indonesia
Authors: Tarunamulia  , Ilman Muhammad , Sammut Jesmond , Paena Mudian , Basir  , Kamariah  , Taukhid Imam , Asaf Ruzkiah , Athirah Admi , Akmal  , Syaichudin Mohammad
Published: August 2024

The widespread degradation of mangroves has been attributed to their conversion into other land uses and purposes, most notably their destruction to construct extensive brackishwater aquaculture ponds. This study investigated the relationship between environmental factors and management alternatives for an integrated mangrove-aquaculture system in Derawan Island District, Berau Regency, East Kalimantan Province, Indonesia. The study collected a total of 56 soil and water samples from around 50 ha to assess environmental limiting factors for integrated mangrove-brackishwater aquaculture management. The measured soil quality variables included field pH (pHF), pH of hydrogen peroxide extract (pHFOX), peroxide oxidizable sulfur (SPOS), pyrite (FeS2), organic matter (OM), nitrogen-total (N-TOT), iron (Fe), and aluminum (Al). Water quality variables included salinity, temperature, pH, dissolved oxygen (DO), different forms of nitrogen (NH3–ammonia, NO3–nitrate, and NO2–nitrite), phosphate (PO4), Fe, and total organic matter (TOM). The study employed a hydrological restoration approach to suggest a mangrove-friendly aquaculture pond design and layout. The study generally showed that Acid Sulfate Soils (ASS) significantly restricted the existing mixed-mangrove aquaculture pond management by negatively impacting water quality. This study highlights that, given the characteristics of ASS-affected aquaculture ponds, reducing pond size for shrimp culture (mangrove-to-pond ratio of 80% and 20%) will simplify managing ASS environmental limiting factors through cost-effective remediation techniques and a Balanced Fertilization Strategy (BFS). The reduced shrimp pond size will also provide direct opportunities for mangrove restoration and allow effective hydrological restoration. The economic benefit of the proposed pond design and management model focuses on diversifying production units which include shrimp aquaculture ponds, milkfish or tilapia culture in the peripheral canals of the mangrove compartment, juvenile shrimp production, and periodic harvest from the primary pond canal. The study findings are particularly applicable to ponds that have already been built in ASS to improve productivity in addition to supporting the mangrove rehabilitation program. Converting mangrove and ASS-affected land is not advisable for constructing new aquaculture ponds.
Effect of atmospheric response induced by preceding typhoon on movement of subsequent typhoon over Northwestern Pacific
Authors: Lee Su-Jung , Lee Joon-Ho , Kim Kuk Jin
Published: August 2024

This study investigates the atmospheric interactions between two closely located typhoons in 2019. Typhoons in the Western Pacific significantly impact Eastern and Southeastern Asian countries, leading to various damages. As global warming is expected to increase typhoon intensity, accurate track forecasting becomes crucial for coastal disaster management. Despite the existing knowledge about the influence of typhoon activities on the atmospheric background, limited research addresses the atmospheric response between two typhoons. The study focuses on the cases of LEKIMA and KROSA, occurring simultaneously in 2019, and utilizes the Weather Research and Forecasting (WRF) model for simulations. The experimental setup involves comparing two scenarios: one with both typhoons and one with LEKIMA removed. Results reveal LEKIMA-induced distinctive atmospheric responses, including the closure of the western North Pacific subtropical high (WNPSH) boundary and the formulation of a wave train, influencing KROSA’s stagnation. The absence of LEKIMA allows KROSA to move more freely along the steering flow. Furthermore, the study highlights the potential of atmospheric models for understanding typhoon effects at regional to mesoscale levels. A comprehensive analysis of similar cases could enhance typhoon predictions, contributing to better damage mitigation strategies.
Self-similarity of quantum transport in graphene using electrostatic gate and substrate
Authors: Miniya Mohammed , Gaggero-Sager Luis M , Mora-Ramos Miguel E , Pérez-Álvarez Rolando , Oubram Outmane
Published: August 2024

A particular design for multibarrier structure in graphene, yielding a self-similar transport response, is proposed. The potential profile is based on rectangular wells and barriers, generated according independent nth order scaling laws for their heights and widths. The barriers are constructed by means of two distinct approaches (electrostatic or substrate). Dirac equation and transfer matrix approach are used to calculate transmission properties which, in turn, allow to evaluate the conductance via Landauer–Büttiker formalism. It is found that self-similarity with determined scaling rules between nth and

(
n
+
1
)

th generations of transport properties appears when the order of generating laws is equal or greater than n = 7. Our proposal would be the first in which the self-similarity property is transferred from geometry to the spectrum, and consequently, to the transport properties of a quantum heterostructure. Possible ways of practical realization for the proposed structures are commented.
Productive use of electricity in agriculture in sub-Saharan Africa: a systematic review
Authors: Raji Tunmise , Allee Andrew , Williams Nathaniel J
Published: August 2024

Sub-Saharan African (SSA) countries often prioritize electrification as an important component of their infrastructure development, anticipating that electricity access will stimulate local economies. Agriculture, a significant contributor to employment and Gross Domestic Product in many of these countries, stands out as a crucial sector that could benefit from the expansion of electricity infrastructure. Thus, integrating electricity into agricultural practices presents a promising pathway for regional development. This review systematically analyzes the academic literature on the productive use of electricity in SSA’s agricultural sector, focusing on dominant trends, opportunities, and challenges at the electricity-agriculture nexus. Primary production activities, particularly irrigation, emerged as the most extensively studied application of electricity in the agricultural sector, and there was a limited number of studies focused on countries in Central Africa. Solar energy was the most assessed source of electricity, likely due to the abundance of solar resources in Africa. Less than half of the studies considered the economic or environmental impact of their proposed productive use activity, focusing more on the technical and operational feasibility of these initiatives. Also, we found that the productive use of electricity in agriculture is hindered by constraints such as a lack of technical expertise, unreliable power supply, limited market access, and inadequate financial services, and we quantitatively assessed the prevalence of each constraint in the selected studies. The review concludes by highlighting opportunities for future research and proposing strategic policy recommendations aimed at fostering the adoption of electrical technologies in agriculture across SSA, thereby enhancing the sector’s efficiency and productivity.
Protonic conduction on oxide surfaces—role and applications in electrochemical energy conversion
Authors: Norby Truls
Published: August 2024

Protonic conduction on surfaces of oxides has over the last two decades drawn attention for its possible utilisation in electrolytes for energy conversion at low temperatures and for its roles in enhancement of catalytic activity. This has led to deeper investigation and increased understanding of the phenomenon and development of quantifiable models. Along with this has emerged apparent demonstrations of use of such conduction in low-drain fuel cells as well as acknowledgement of the role of surface protonic conduction in electrodes for solid-state electrochemical and photoelectrochemical cells. Here is provided a brief review and elaboration of the fundamentals of the interaction of water and hydrogen with oxide surfaces, and models for the resulting protonic conduction in chemisorbed and physisorbed layers. We finally discuss aspects of surface protonic conduction in a range of applications, including sensors, catalysis, and electrochemical and photoelectrochemical energy conversion.
One dimensional multilayer structure for kerosene adulteration detection in petrol and diesel
Authors: Monika  , Prakash Suraj
Published: August 2024

We aim to design a multilayer periodic structure to detect the kerosene adulteration in the petrol and diesel fuels on a single processing setup. We built the structure by arranging TiO2 and SiO2 layers periodically in alternate manner with empty space at the middle. The optical response of the designed structure is then theoretically studied using transfer matrix method. Empty space of the design is filled with different kerosene adulterated petrol and diesel samples for inspecting structure response to incident electromagnetic waves. Theoretical calculations affirm that the proposed structure is capable to detect the fuel adulteration efficiently. Critical performance parameters like sensitivity, quality factor, figure of merit and limit of detection are calculated to check the effectiveness of the sensor. We also optimized the sensitivity of sensors design through modifying the defect thickness as well as angle of incidence of electromagnetic waves, and provides poly fit formula. It is observed that the sensitivity of sensor to detect kerosene adulteration in fuels highly depends on defect thickness and light incidence angle. An efficient sensor possessing high quality factor and figure of merit is realized from the designed structure that is capable of detecting

10

−
5

RIU.
Application of novel hybrid deep learning architectures combining Convolutional Neural Networks (CNN) and Recurrent Neural Networks (RNN): construction duration estimates prediction considering preconstruction uncertainties
Authors: Demiss Belachew A , Elsaigh Walied A
Published: August 2024

Construction duration estimation plays a pivotal role in project planning and management, yet it is often fraught with uncertainties that can lead to cost overruns and delays. To address these challenges, this review article proposes three advanced conceptual models leveraging hybrid deep learning architectures that combine Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) while considering construction delivery uncertainties. The first model introduces a Spatio-Temporal Attention CNN-RNN Hybrid Model with Probabilistic Uncertainty Modeling, which integrates attention mechanisms and probabilistic uncertainty modeling to provide accurate and probabilistic estimates of construction duration, offering insights into critical areas of uncertainty. The second model presents a Multi-Modal Graph CNN-RNN Hybrid Model with Bayesian Uncertainty Integration, which harnesses multi-modal data sources and graph representations to offer comprehensive estimates of construction duration while incorporating Bayesian uncertainty measures, facilitating informed decision-making and optimized resource allocation. Lastly, the third model introduces a Hierarchical Spatio-Temporal Transformer CNN-RNN Hybrid Model with Fuzzy Logic Uncertainty Handling, which addresses the inherent vagueness and imprecision in construction duration estimates by incorporating hierarchical spatio-temporal transformer architecture and fuzzy logic uncertainty handling, leading to more nuanced and adaptable project management practices. These advanced models represent significant advancements in addressing construction duration challenges, providing valuable insights and recommendations for future research and industry applications. Moreover, this review article critically examines the application of hybrid deep learning architectures, specifically the combination of CNNs RNNs, in predicting construction duration estimates at the preconstruction stage while considering uncertainties inherent in construction delivery systems.
The stabilization-free HDG method for fluid-structure interaction in a unified mixed formulation on Alfeld splits
Authors: Chung Eric , Zhao Lina
Published: August 2024

In this paper we propose and analyze a stabilization-free hybridizable discontinuous Galerkin (HDG) method in stress-velocity formulation for fluid-structure interaction based on Alfeld splits. A unified mixed formulation is employed for the Stokes equations and the elastodynamic equations. We use the standard polynomial space with strong symmetry to define the stress space, and use the broken

H
(
d
i
v
;
Ω

H(div;\Omega

)-conforming space of the same degree to define the vector space in a careful way such that the resulting scheme is stable without resorting to any stabilization. In particular, the proposed scheme addresses the pressure-robustness, which is known to be important for incompressible flows. The transmission conditions can be incorporated naturally without resorting to additional variables or Nitsche-type stabilization owing to the bespoke construction of the discrete formulation. To show the optimal convergence, we establish a new projection operator for the stress space whose definition accounts for traces of the method. Furthermore, the pressure-independence and the robustness with respect to fluid viscosity and the Lamé constants are investigated. We also show the characterization of the hybridization and the size of the global system is greatly reduced, rendering the scheme computationally attractive. Several numerical experiments are presented to verify the proposed theories.
Wind Finslerian Structures: From Zermelo’s Navigation to the Causality of Spacetimes
Authors: Caponio Erasmo , Javaloyes Miguel , Sánchez Miguel
Published: August 2024

The notion of wind Finslerian structure

Σ
\Sigma

is developed; this is a generalization of Finsler metrics (and Kropina ones) where the indicatrices at the tangent spaces may not contain the zero vector. In the particular case that these indicatrices are ellipsoids, called here wind Riemannian structures, they admit a double interpretation which provides: (a) a model for classical Zermelo’s navigation problem even when the trajectories of the moving objects (planes, ships) are influenced by strong winds or streams, and (b) a natural description of the causal structure of relativistic spacetimes endowed with a non-vanishing Killing vector field

K
K

(SSTK splittings), in terms of Finslerian elements. These elements can be regarded as conformally invariant Killing initial data on a partial Cauchy hypersurface. The links between both interpretations as well as the possibility to improve the results on one of them using the other viewpoint are stressed.

The wind Finslerian structure

Σ
\Sigma

is described in terms of two (conic, pseudo) Finsler metrics,

F
F

and

F
l

F_l

, the former with a convex indicatrix and the latter with a concave one. Notions such as balls and geodesics are extended to

Σ
\Sigma

. Among the applications, we obtain the solution of Zermelo’s navigation with arbitrary time-independent wind, metric-type properties for

Σ
\Sigma

(distance-type arrival function, completeness, existence of minimizing, maximizing or closed geodesics), as well as description of spacetime elements (Cauchy developments, black hole horizons) in terms of Finslerian elements in Killing initial data. A general Fermat’s principle of independent interest for arbitrary spacetimes, as well as its applications to SSTK\xspace spacetimes and Zermelo’s navigation, are also provided.
Equivalent Definitions of Arthur Packets for Real Classical Groups
Authors: Adams J. , Arancibia Robert N. , Mezo P.
Published: August 2024

Arthur has conjectured the existence of what are now known as Arthur packets of representations of reductive algebraic groups over local and global fields. In the case of special orthogonal and symplectic groups, he subsequently gave a definition of these packets, using local and global methods. For general real groups, an alternative approach to the definition of Arthur packets has been given by Adams-Barbasch-Vogan. This construction is purely local and uses geometric methods. Our main result is that these two definitions agree in the case of real special orthogonal and symplectic groups.
Pullback operators on Bargmann spaces
Authors: Johnson Reid
Published: August 2024

We characterize boundedness and compactness of pullback operators under holomorphic maps between Bargmann spaces of entire holomorphic functions with quadratic strictly plurisubharmonic exponential weights, extending the result of Carswell, MacCluer, and Schuster [Acta Sci. Math. (Szeged) 69 (2003), pp. 871–887], obtained in the case of the radial quadratic weight. We also show that the pullback operator between Bargmann spaces is compact precisely when it is of trace class, with sub-exponentially decaying singular values.
A game for Baire’s grand theorem
Authors: Notaro Lorenzo
Published: August 2024

Generalizing a result of Kiss, we provide a game that characterizes Baire class

1
1

functions between arbitrary separable metrizable spaces. We show that the determinacy of our game is equivalent to a generalization of Baire’s grand theorem, and that both these statements hold under

A
D

\mathsf {AD}

and in Solovay’s model.
Quasi-tempered automorphic D-modules
Authors: Færgeman Joakim
Published: August 2024

In this paper, we introduce the category of quasi-tempered automorphic D-modules, which is a rather natural class of D-modules from the point of view of geometric Langlands. We provide a characterization of this category in terms of singular support, and as a consequence, we obtain certain microlocal categorical Künneth formulas.
Zinger, Clunker, Clanger, Flunker: On Two-Point Comparisons, and Why we Love Them
Authors: Landy Joshua
Published: August 2024

According to a now-standard theory, ‘Juliet is the sun’ is supposed to be a ‘pregnant’ metaphor, ready at any moment to beget a sprawling heap of adorable semantic puppies. Its two parts—‘Juliet’ and ‘the sun’—ostensibly meet at a virtually endless number of points, and it’s allegedly illuminating, enjoyable, or at least interesting to sit there all day spelling them out. But what if none of that is true? What if, instead, a successful creative comparison tends to offer exactly two points of contact, the first of which makes it adequate, while the second gives it power? To put it metaphorically (as is only appropriate): such an image is neither an iceberg (à la Cavell) nor a simple triangle (à la Aristotle) but a tetrahedron, a muscle, a covalent bond. And the telos of such images isn’t to transmit additional information but intensify, or disorient, or even—surprisingly—make us feel at home in this miserable world.
Continuity and Evolution in Vermeule on Legal Interpretation
Authors: Casey Conor
Published: August 2024

This article is a constructive interpretation of Adrian Vermeule’s thought on legal interpretation, putting his previous work on these issues in conversation with his explicit embrace of the classical legal tradition so prominently on display in Common Good Constitutionalism. What emerges is a picture of Vermeule’s contemporary thinking on interpretation that has an interesting core of continuity, one running concurrently with several significant conceptual and normative evolutions brought about by his more explicit embrace of a classical legal framework. Part I offers a synthesis of Vermeule’s treatment of core questions of legal interpretation pre-Common Good Constitutionalism. Part II begins by outlining Vermeule’s express turn to the classical legal tradition and how this tradition approaches important public law issues linked to interpretation. Part II then proceeds to pick out and elaborate on themes of continuity and evolution. I argue here that while Vermeule’s embrace of the classical legal tradition has involved several significant conceptual and normative shifts in his thinking, this has not involved repudiation of his prior work on legal interpretation. Rather, the thrust and insights of much of his previous public law thought on interpretation retain vibrancy within the explicitly classical framework he has now adopted. Overall, I suggest Common Good Constitutionalism, and the works accompanying and building upon it, can be profitably read as providing a form of retroactive coherence to Vermeule’s long-standing arguments concerning legal interpretation, offering them a unifying conceptual framework. From the perspective of a classical natural law jurist at least, Vermeule’s embrace of the classical tradition provides his extensive body of scholarship in this area a more explicit and robust conceptual and normative anchor.
Back to Basics in Measuring Lexical Diversity: Too Simple to Be True
Authors: Bestgen Yves
Published: August 2024

Measuring lexical diversity in texts that have different lengths is problematic because length has a significant effect on the number of types a text contains, thus hampering any comparison. Treffers-Daller et al. (2018) recommended a simple solution, namely counting the number of types in a section of a given length that was extracted from the middle of each of the texts to be analysed. By applying this approach to second language essays, the authors observed that using the number of types was slightly more effective for differentiating amongst the Common European Framework of Reference for Languages (CEFR) levels than were the Type-Token Ratio (TTR) and the Guiraud index and that these three indices were more effective than were mathematically more complex ones. However, their conclusions regarding these two points are incorrect, and a less basic approach should be used. The last section addresses two broader issues in applied linguistics that are highlighted by these problems.
A 360° Approach to Patient Care in Aesthetic Facial Rejuvenation
Authors: Humphrey Shannon , Bertucci Vince , Heydenrych Izolda , Ogilvie Patricia , Safa Marva , de la Guardia Carola
Published: August 2024

Background

Aesthetic medicine has traditionally focused on addressing perceived problem areas, with lack of long-term planning and engagement.

Objectives

This article describes a patient-centric model for nonsurgical aesthetic medical practice, termed the 360° approach to facial aesthetic rejuvenation.

Methods

The 360° approach was divided into 4 foundational pillars. Medical literature, the authors’ clinical experiences, and results from patient satisfaction surveys were used to support the approach.

Results

Pillar 1 describes the development of a complete understanding of the patient, based on the use of active listening principles, to characterize the patient's current aesthetic concerns, lifestyle, medical and treatment history, treatment goals, attitude toward aesthetic treatment, and financial resources. Pillar 2 involves conducting a comprehensive facial assessment in contrast to a feature-specific assessment, considering multiple facial tissues and structures and their interrelationships, thus helping to prevent the unanticipated consequences of narrowly focused treatment. Pillar 3 describes leveraging all available treatments and techniques in the development of an initial treatment plan arising from the facial assessment. Pillar 4 adds a time dimension to treatment planning, working toward the goal of a long-term modifiable treatment timeline, with full patient support and involvement; this is designed to facilitate a durable, sustained relationship between the patient and aesthetic healthcare professional (HCP).

Conclusions

Although implementation involves substantial commitment and time, the patient-oriented focus of the 360° approach can help achieve optimal patient outcomes and the development of enduring patient–HCP relationships.

Level of Evidence: 5
Microbial production of aromatic compounds and synthesis of high-performance bioplastics
Authors: Masuo Shunsuke
Published: August 2024

Microbial fermentation has provided fermented foods and important chemicals such as antibiotics, amino acids, and vitamins. Metabolic engineering of synthetic microbes has expanded the range of compounds produced by fermentation. Petroleum-derived aromatic compounds are widely used in industry as raw materials for pharmaceuticals, dyes, and polymers and are in great demand. This review highlights the current efforts in the microbial production of various aromatic chemicals such as aromatic amines, cinnamic acid derivatives, and flavoring aromatics, including their biosynthesis pathways. In addition, the unique biosynthetic mechanism of pyrazine, a heterocyclic compound, from amino acids is described to expand the use of biomass-derived aromatic compounds. I also discuss our efforts to develop high-performance bioplastics superior to petroleum plastics from the aromatic compounds produced by microbial fermentation.
Galaxy Helm chart: a standardized method for deploying production Galaxy servers
Authors: Goonasekera Nuwan , Mahmoud Alexandru , Suderman Keith , Afgan Enis
Published: August 2024

Motivation

The Galaxy application is a popular open-source framework for data intensive sciences, counting thousands of monthly users across more than 100 public servers. To support a growing number of users and a greater variety of use cases, the complexity of a production-grade Galaxy installation has also grown, requiring more administration effort. There is a need for a rapid and reproducible Galaxy deployment method that can be maintained at high-availability with minimal maintenance.

Results

We describe the Galaxy Helm chart that codifies all elements of a production-grade Galaxy installation into a single package. Deployable on Kubernetes clusters, the chart encapsulates supporting software services and implements the best-practices model for running Galaxy. It is also the most rapid method available for deploying a scalable, production-grade Galaxy instance on one’s own infrastructure. The chart is highly configurable, allowing systems administrators to swap dependent services if desired. Notable uses of the chart include on-demand, fully-automated deployments on AnVIL, providing training infrastructure for the Bioconductor project, and as the AWS-recommended solution for running Galaxy on the Amazon cloud.

Availability and implementation

The source code for Galaxy Helm is available at https://github.com/galaxyproject/galaxy-helm, the corresponding Helm package at https://github.com/CloudVE/helm-charts, and the required Galaxy container image https://github.com/galaxyproject/galaxy-docker-k8s.
R2Dtool: integration and visualization of isoform-resolved RNA features
Authors: Sethi Aditya J , Acera Mateos Pablo , Hayashi Rippei , Shirokikh Nikolay E , Eyras Eduardo
Published: August 2024

Motivation

Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions.

Results

We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool’s capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms.

Availability and implementation

R2Dtool is freely available under the MIT license at github.com/comprna/R2Dtool.
GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console
Authors: Nath Anindita , Mwesigwa Savannah , Dai Yulin , Jiang Xiaoqian , Zhao Zhongming
Published: August 2024

The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data generation and biomedical knowledge discovery. Leveraging generative AI, notably ChatGPT, it serves as a biologist’s “copilot.” It automates the analysis, retrieval, and visualization of customized domain-specific genetic information, and integrates functionalities to generate protein interaction networks, enrich gene sets, and search scientific literature from PubMed, Google Scholar, and arXiv, making it a comprehensive tool for biomedical research. In its pilot phase, GENEVIC is assessed using a curated database that ranks genetic variants associated with Alzheimer’s disease, schizophrenia, and cognition, based on their effect weights from the Polygenic Score (PGS) Catalog, thus enabling researchers to prioritize genetic variants in complex diseases. GENEVIC’s operation is user-friendly, accessible without any specialized training, secured by Azure OpenAI’s HIPAA-compliant infrastructure, and evaluated for its efficacy through real-time query testing. As a prototype, GENEVIC is set to advance genetic research, enabling informed biomedical decisions.

Availability and implementation

GENEVIC is publicly accessible at https://genevicanath2024.streamlit.app. The underlying code is open-source and available via GitHub at https://github.com/bsml320/GENEVIC.git (also at https://github.com/anath2110/GENEVIC.git).
Critical appraisal of the adequacy of surgical indications for non-functioning pancreatic neuroendocrine tumours
Authors: Partelli Stefano , Battistella Anna , Andreasi Valentina , Muffatti Francesca , Tamburrino Domenico , Pecorelli Nicolò , Crippa Stefano , Balzano Gianpaolo , Falconi Massimo
Published: August 2024

Background

The lack of preoperative prognostic factors to accurately predict tumour aggressiveness in non-functioning pancreatic neuroendocrine tumours may result in inappropriate management decisions. This study aimed to critically evaluate the adequacy of surgical treatment in patients with resectable non-functioning pancreatic neuroendocrine tumours and investigate preoperative features of surgical appropriateness.

Methods

A retrospective study was conducted on patients who underwent curative surgery for non-functioning pancreatic neuroendocrine tumours at San Raffaele Hospital (2002–2022). The appropriateness of surgical treatment was categorized as appropriate, potential overtreatment and potential undertreatment based on histologic features of aggressiveness and disease relapse within 1 year from surgery (early relapse).

Results

A total of 384 patients were included. Among them, 230 (60%) received appropriate surgical treatment, whereas the remaining 154 (40%) underwent potentially inadequate treatment: 129 (34%) experienced potential overtreatment and 25 (6%) received potential undertreatment. The appropriateness of surgical treatment was significantly associated with radiological tumour size (P < 0.001), tumour site (P = 0.012), surgical technique (P < 0.001) and year of surgical resection (P < 0.001). Surgery performed before 2015 (OR 2.580, 95% c.i. 1.570 to 4.242; P < 0.001), radiological tumour diameter < 25.5 mm (OR 6.566, 95% c.i. 4.010 to 10.751; P < 0.001) and pancreatic body/tail localization (OR 1.908, 95% c.i. 1.119 to 3.253; P = 0.018) were identified as independent predictors of potential overtreatment. Radiological tumour size was the only independent determinant of potential undertreatment (OR 0.291, 95% c.i. 0.107 to 0.791; P = 0.016). Patients subjected to potential undertreatment exhibited significantly poorer disease-free survival (P < 0.001), overall survival (P < 0.001) and disease-specific survival (P < 0.001).

Conclusions

Potential overtreatment occurs in nearly one-third of patients undergoing surgery for non-functioning pancreatic neuroendocrine tumours. Tumour diameter emerges as the sole variable capable of predicting the risk of both potential surgical overtreatment and undertreatment.
Nuclear factor of activated T-cells 5 is indispensable for a balanced adaptive transcriptional response of lung endothelial cells to hypoxia
Authors: Laban Hebatullah , Siegmund Sophia , Schlereth Katharina , Trogisch Felix A , Ablieh Alia , Brandenburg Lennart , Weigert Andreas , De La Torre Carolina , Mogler Carolin , Hecker Markus , Kuebler Wolfgang M , Korff Thomas
Published: August 2024

Aims

Chronic hypoxia causes detrimental structural alterations in the lung, which may cause pulmonary hypertension and are partially mediated by the endothelium. While its relevance for the development of hypoxia-associated lung diseases is well known, determinants controlling the initial adaptation of the lung endothelium to hypoxia remain largely unexplored.

Methods and results

We revealed that hypoxia activates the transcription factor nuclear factor of activated T-cells 5 (NFAT5) and studied its regulatory function in murine lung endothelial cells (MLECs). EC-specific knockout of Nfat5 (Nfat5(EC)−/−) in mice exposed to normobaric hypoxia (10% O2) for 21 days promoted vascular fibrosis and aggravated the increase in pulmonary right ventricular systolic pressure as well as right ventricular dysfunction as compared with control mice. Microarray- and single-cell RNA-sequencing-based analyses revealed an impaired growth factor-, energy-, and protein–metabolism-associated gene expression in Nfat5-deficient MLEC after exposure to hypoxia for 7 days. Specifically, loss of NFAT5 boosted the expression and release of platelet-derived growth factor B (Pdgfb)—a hypoxia-inducible factor 1 alpha (HIF1α)-regulated driver of vascular smooth muscle cell (VSMC) growth—in capillary MLEC of hypoxia-exposed Nfat5(EC)−/− mice, which was accompanied by intensified VSMC coverage of distal pulmonary arteries.

Conclusion

Collectively, our study shows that early and transient subpopulation-specific responses of MLEC to hypoxia may determine the degree of organ dysfunction in later stages. In this context, NFAT5 acts as a protective transcription factor required to rapidly adjust the endothelial transcriptome to cope with hypoxia. Specifically, NFAT5 restricts HIF1α-mediated Pdgfb expression and consequently limits muscularization and resistance of the pulmonary vasculature.
Sudden cardiac death after early-onset myocardial infarction: a multicentre longitudinal cohort study with a 20-year follow-up
Authors: Bricoli Serena , Magnani Giulia , Ardissino Maddalena , Maglietta Giuseppe , Celli Patrizia , Ferrario Maurizio , Canosi Umberto , Cernetti Carlo , Negri Francesco , Merlini Piera Angelica , Tubaro Marco , Berzuini Carlo , Manzalini Chiara , Moschini Luigi , Ponte Elisabetta , Pozzi Roberto , Buratti Silvia , Botti Andrea , Barocelli Federico , Biagi Andrea , Bonura Rosario , Bearzot Luca , Moccetti Tiziano , Crocamo Antonio , Notarangelo Maria Francesca , Moscarella Elisabetta , Calabrò Paolo , Niccoli Giampaolo , Ardissino Diego
Published: August 2024

Aims

Sudden cardiac death (SCD) is a serious consequence of a myocardial infarction (MI), but identifying patients at risk of developing SCD remains a major clinical challenge, especially in the case of juvenile MI. The aim of this study is to identify predictors of SCD after early-onset MI using long-term follow-up data relating to a large nationwide patient cohort.

Methods and results

The Italian Genetic Study on Early-onset MI enrolled 2000 patients experiencing a first MI before the age of 45 years, who were followed up for a median of 19.9 years. Fine–Gray proportional hazard models were used to assess the associations between their clinical, demographic, and index event data and the occurrence of SCD. Sudden cardiac death occurred in 195 patients, who were more frequently males, were hypertensive and/or diabetic, had a history of previous thrombo-embolic events with a greater atherosclerotic burden, and had a lower left ventricular ejection fraction (LVEF) after the index event. A multivariable analysis showed that the independent predictors of SCD were diabetes, hypertension, previous thrombo-embolic events, a higher SYNTAX score, and a lower LVEF. There was no clear evidence of the clustering of SCD events during the follow-up. Sudden cardiac death was the first post-MI clinical event in 101 patients; the remaining 94 experienced SCD after a non-fatal MI or hospitalization for coronary revascularization.

Conclusion

Sudden cardiac death frequently occurs during the 20 years after early-onset MI. The nature of the identified predictors and the absence of clustering suggest that the pathophysiological basis of SCD may be related to progressive coronary atherosclerosis.
Steep right anterior oblique view of self-expandable transcatheter aortic valve to timely detect stent under-expansion or non-uniform expansion before final release: a case series
Authors: Kaneko Umihiko , Hachinohe Daisuke , Kobayashi Ken , Shitan Hidemasa , Horita Ryo , Ootake Ryo , Fujita Tsutomu
Published: August 2024

Background

Severely calcified aortic valves are a major limitation of transcatheter aortic valve replacement, because eccentric and heavy calcification of the aortic valve occasionally inhibits self-expansion of the valve frame, resulting in stent under-expansion, including non-uniform expansion or infolding. Nevertheless, the two-dimensional nature of fluoroscopic projection imaging can limit detection of stent under-expansion prior to the final release.

Case summary

We present two cases demonstrating the importance of the steep right anterior oblique (RAO) view (>50°) in detecting significant stent under-expansion of a self-expanding valve prior to the final release. In Case 1, despite enough pre-dilatation, the partially deployed transcatheter heart valve (THV) appeared to be a substantial under-expansion, which was detected only in steep RAO view. Immediately after the final release, the THV was spontaneously embolized into the ascending aorta (the so-called ‘pop-up’ phenomenon). Emergent implantation of balloon-expandable valve proved to be successful as a bailout. In Case 2, significant stent distortion and infolding, especially on the non-coronary cusp side, was successfully diagnosed only in a steep RAO view prior to the final release. This finding allowed THV recapture and replacement with a new THV.

Discussion

Notably, the steep RAO view can visualize the THV from its short axis while eliminating parallax, allowing for accurate diagnosis of THV under-expansion particularly in patients with severe calcification in the non- or right-coronary cusp. Therefore, the steep RAO view allows timely detection of THV under-expansion before the final release, enabling THV recapture and the adoption of several management strategies.
Hypothyroidism due to biallelic variants in IYD: description of 4 families and a novel variant
Authors: Boros Emese , Vilain Catheline , Driessens Natacha , Heinrichs Claudine , Van Vliet Guy , Brachet Cécile
Published: August 2024

Biallelic loss-of-function variants in the IYD gene cause hypothyroidism resulting from iodine wasting. We describe 8 patients (from 4 families in which the parents are first cousins) who are homozygous for a variant in IYD (including a novel missense deleterious variant, c.791C>T [P264L], in 1 family). Seven patients presented between 5 and 16 years of age with a large goiter, overt hypothyroidism, and a high serum thyroglobulin. The goiter subsided with levothyroxine therapy in most. Upon stopping levothyroxine in 5 patients, goiter and hypothyroidism reappeared in 3. In these 3 patients, a rising serum thyroglobulin concentration preceded hypothyroidism and goiter and urinary iodine excretion was low. In patients who remained euthyroid, urinary iodine was normal. In conclusion, these patients bearing biallelic pathogenic variants in IYD developed a large goiter, a high serum thyroglobulin, and overt hypothyroidism when their iodine intake was low.
The simple macroeconomics of AI
Authors: Acemoglu Daron
Published: August 2024

This paper evaluates claims about the large macroeconomic implications of new advances in Artificial intelligence (AI). It starts from a task-based model of AI’s effects, working through automation and task complementarities. So long as AI’s microeconomic effects are driven by cost savings/productivity improvements at the task level, its macroeconomic consequences will be given by a version of Hulten’s theorem: Gross Domestic Product (GDP) and aggregate productivity gains can be estimated by what fraction of tasks are impacted and average task-level cost savings. Using existing estimates on exposure to AI and productivity improvements at the task level, these macroeconomic effects appear non-trivial but modest – no more than a 0.66% increase in total factor productivity (TFP) over 10 years. The paper then argues that even these estimates could be exaggerated, because early evidence is from easy-to-learn tasks, whereas some of the future effects will come from hard-to-learn tasks, where there are many context-dependent factors affecting decision-making and no objective outcome measures from which to learn successful performance. Consequently, predicted TFP gains over the next 10 years are even more modest and are predicted to be less than 0.53%. I also explore AI’s wage and inequality effects. I show theoretically that even when AI improves the productivity of low-skill workers in certain tasks (without creating new tasks for them), this may increase rather than reduce inequality. Empirically, I find that AI advances are unlikely to increase inequality as much as previous automation technologies because their impact is more equally distributed across demographic groups, but there is also no evidence that AI will reduce labour income inequality. Instead, AI is predicted to widen the gap between capital and labour income. Finally, some of the new tasks created by AI may have negative social value (such as the design of algorithms for online manipulation), and I discuss how to incorporate the macroeconomic effects of new tasks that may have negative social value.