bluuebunny/crossref_metadata_2025 huggingface dataset:
Research and application of low-carbon economic dispatch of urban building integrated energy system
Authors: Tong Zhu , Songli Fan , Yulong Pan , Mingxuan Li , Yunhao Fan
Published: September 2024

Global warming is a serious threat common to all countries. The technological revolution and sustainable development of energy have become the international consensus. While ensuring economic benefits, promoting low carbon environmental protection of comprehensive energy system has become a top priority. Therefore, this paper designs a low-carbon economic scheduling system based on consistency theory. First, the importance of user demand response should be considered in the integrated energy system to ensure the economy of scheduling. Secondly, the improved step-step carbon trading mechanism is used in the algorithm to improve the low carbon performance of scheduling. Then, the distributed consistency algorithm is used to schedule the integrated energy system to realize the most energy output of each unit. In addition, a noise function is added to the algorithm for encryption and desensitization to prevent user privacy leakage. Finally, the effectiveness of the proposed economic scheduling method.
Fluctuation relations for a few observable currents at their own beat
Authors: Garilli Alberto , Harunari Pedro E , Polettini Matteo
Published: September 2024

Coarse-grained models are widely used to explain the effective behavior of partially observable physical systems with hidden degrees of freedom. Reduction procedures in state space typically disrupt Markovianity and a fluctuation relation cannot be formulated. A recently developed framework of transition-based coarse-graining gave rise to a fluctuation relation for a single current, while all others are hidden. Here, we extend the treatment to an arbitrary number of observable currents. Crucial for the derivation are the concepts of mixed currents and their conjugated effective affinities, that can be inferred from the time series of observable transitions. We also discuss the connection to generating functions, transient behavior, and how our result recovers the fluctuation relation for a complete set of currents.
Quantization of two- and three-player cooperative games based on QRA
Authors: Eryganov Ivan , Hrdina Jaroslav , Návrat Aleš
Published: September 2024

In this paper, a novel quantization scheme for cooperative games is proposed. The circuit is inspired by the Eisert–Wilkens–Lewenstein protocol, which was modified to represent cooperation between players and extended to 3–qubit states. The framework of Clifford algebra is used to perform necessary computations. In particular, we use a direct analogy between Dirac formalism and Quantum Register Algebra (QRA) to represent circuits. This analogy enables us to perform automated proofs of the circuit equivalence in a simple fashion. The expected value of the Shapley value concerning quantum probabilities is employed to distribute players’ payoffs after the measurement. We study how entanglement, representing the level of pre-agreement between players, affects the final utility distribution. The paper also demonstrates how the QRA and GAALOP software can automate all necessary calculations.
Qualitative analysis of rivers sand sources (Silica sand, Ravi river sand, Indus river sand, and Jhelum river sand) for metal casting: a comparative study
Authors: Channa Muhammad Yousaf , Anwar Jehanzaib , Kalsoom Razia , Abidi Syed Hussain Imam
Published: September 2024

Recent geological investigations revealed extensive use of Silica sand in Pakistan resulting in depletion of tectonic resources. Hence, it is important to explore cost-effective and alternative sources of sand for its applications. Also, Pakistan has a river network that provides river sand as a potential substitute for Silica sand. However, it is essential to systematically study and assess the potential applicability of river sand as an alternative to Silica sand. In this context, this study examined sand samples collected from various rivers in Pakistan to investigate their suitability for metal-casting molds. For that purpose, random samples were selected from major rivers in Pakistan for characterization by utilizing chemical composition analysis, microscopy, XRD, TGA-DSC (thermogravimetric analysis), clay content analysis, grain size distribution analysis, pH measurement, green and dry compression strength testing, shear strength testing, permeability analysis, shatter index analysis, compactibility testing, and Specific gravity measurement. The chemical composition analysis revealed that all types of sands contained over 90% SiO2 content. The mechanical tests demonstrated that river sand exhibited acceptable mechanical properties, with a moisture content ranging from 4.5%–5%. The pH value of all the sands exceeded 7, making them suitable for casting purposes. These investigations suggest that river sand can be effectively utilized in casting applications by implementing pre-processing techniques and incorporating additives.
Optimization of wear and friction behaviour of fish scale powder filled natural fibre/glass fibre hybrid epoxy composite in dry sliding condition
Authors: Sarkar Debrup , Teyi Nabam , Borah Pranjal , Chetia Pulakesh
Published: September 2024

The purpose of this research is to look at the wear and friction properties of a unique composite material made up of fish scale powder, natural fibres, and glass fibres embedded in an epoxy matrix. The growing demand in many industries for eco-friendly and sustainable materials has resulted in the development of hybrid composites that combine natural and synthetic reinforcements. The goal of this study is to improve the wear resistance and frictional qualities of composite material under dry sliding conditions. The wear and friction behaviour of the composite is optimized using the Response Surface and Taguchi approach, which entails constructing a set of trials based on a statistical model. The significant components, which include fish scale powder content, natural fibre type and content, and sliding parameters, are carefully varied to determine the best combination that results in the least amount of wear and friction. The accuracy of the regression models exceeded expectations. According to Taguchi’s findings, F and V have the largest impact on wear loss and friction, respectively. Fish scale powder has shown great promise as a filler for enhancing the wear resistance of composites, as seen by the study’s findings. The optimized composite has exceptional wear resistance and low friction, making it a suitable alternative for dry sliding applications.
Loss of intermicrovillar adhesion factor CDHR2 impairs basolateral junctional complexes in transporting epithelia
Authors: Cencer Caroline S. , Robinson Kianna L. , Tyska Matthew J.
Published: September 2024

Transporting epithelial cells in the gut and kidney rely on protocadherin-based apical adhesion complexes to organize microvilli that extend into luminal space. In these systems, CDHR2 and CDHR5 localize to the distal ends of microvilli, where they form an intermicrovillar adhesion complex (IMAC) that links the tips of these structures, promotes the formation of a well-ordered array of protrusions, and thus maximizes apical membrane surface area. Recently, we discovered that IMACs can also form between microvilli that extend from neighboring cells, across cell-cell junctions. As an additional point of physical contact between cells, transjunctional IMACs are well positioned to impact the integrity of canonical tight and adherens junctions that form more basolaterally. To begin to test this idea, we examined cell culture and mouse models that lacked CDHR2 expression and were unable to form IMACs. CDHR2 knockout perturbed cell and junction morphology, reduced key components from tight and adherens junctions, impaired barrier function, and increased the motility of single cells within established monolayers. These results support the hypothesis that, in addition to organizing apical microvilli, IMACs provide a layer of cell-cell contact that functions in parallel with canonical tight and adherens junctions to promote epithelial functions.
Discretionary Punishment (Ta’zir) in Islamic Jurisprudence and the Islamic Penal Code
Authors: Khodadadi Bahman
Published: September 2024

Chapter 3 takes up the first type of punishment incorporated into the Islamic Penal Code of 2013 under the rubric of ‘ta’zir’. The definition, sphere, and limits of the discretionary punishment (ta’zir), as it occurs in Shiite Islamic jurisprudence, are discussed to elucidate a theoretical justification according to which Iranian legislators have criminalized a wide range of behaviours. The chapter focuses on the critical evaluation of how the religious coercive rule of ta’zir is supported by the Constitution in practice and how it can be applied by criminal court judges as an instrument for punishing a sinner whose sin has not necessarily been codified as a crime in the Islamic Penal Code (i.e. at a judicial level). Accordingly, the argument points to the fact that we are facing a so-called umbrella sentencing theory that not only addresses deliberate rule violations stipulated in the Islamic Penal Code but also an unwritten catalogue of sins.
Animal Biographies
Authors: Sugiyama Nawa
Published: September 2024

This chapter builds on zooarchaeological and isotopic data from previous chapters to narrate osteobiographies of key participants of the ritual spectacle. These biographies center the experiential narratives of the complex and sometimes tenuous relationships during direct human–predator contact, including the perils and hardships of management in captivity. These encounters are part of the ritualization process, including specific decision nodes to “set apart” or consecrate the wild carnivore into a ritualized body. The Aztec Toxcatl festival, featuring the transformation of a war captive into the deity Tezcatlipoca, demonstrates how inter-corporeal relations produced the ritualized body. Likewise, the decision nodes in the ritualization process of acquisition, management, postmortem manipulation, and sacrifice and/or deposition for corporeal animal forms coordinated intimate interpersonal ties, transforming these apex predators into master guardian animals and mediators of Teotihuacan’s sovereignty formations.
Forest (landscape) restoration governance
Authors: Kleinschmit Daniela , Blum Mareike , Brockhaus Maria , Karambiri Mawa , Kröger Markus , Ramcilovic-Suominen Sabaheta , Reinecke Sabine , Ongolo Symphorien
Published: September 2024

Taking a critical social-constructivist perspective and highlighting the power of ideas in forest landscape restoration (FLR) governance, this historically informed contribution seeks to unpack the different rationales at play in global FLR governance. Drawing on three interlinked analytical dimensions—institutions, interests, and ideas (3Is)—the chapter elaborates on three (de)legitimizing narratives of FLR (win-win, implementation, critique) and on the underlying institutions and interests in which their discursive power rests. Based on the 3Is, we identify and critically discuss three key distinct logics that drive FLR policy and practice: (i) the global sustainability logic, (ii) the community logic, and (iii) the production logic. We conclude that if the inherent historical power structures in FLR design and implementation are not recognized and addressed, then the currently dominant FLR logics are likely to produce many “win-lose” or “lose-lose” projects.
Forest restoration, biodiversity, and ecosystem services
Authors: Brouwer Rens , Bongers Frans , Peña-Claros Marielos , Zuidema Pieter A , Brancalion Pedro , Lohbeck Madelon , Hernández Guzmán Alejandra , Heinze Alan , Guillemot Joannès , Kramer Koen , Sheil Douglas
Published: September 2024

This chapter uses the CICES framework to review results from studies on forest restoration’s effects on ecosystem services (ES), focusing on biodiversity, nutrient cycling, water cycling, and provisioning and cultural services. We discuss trade-offs between ES for different restoration methods and their specific applications, examine disservices resulting from forest restoration, and detail variation in outcomes across time and space. Our review shows most studies focus on just a few regulating and maintenance services. Provisioning and cultural services remain underrepresented. Very little research is devoted to disservices. It is poorly understood how these (unintentional) restoration results balance with services and how they differ between stakeholders. We find that context matters in forest restoration projects, as it defines appropriate methods, outcomes, and implications. A broad, multifunctional focus in restoration is needed to identify trade-offs between ES in different forms of restoration, to weigh services and disservices, and to evaluate total restoration success.
Financial, ecological, political, and social feasibility of forest restoration targets
Authors: Keenan Rodney J , Louman Bas , Brand David , Ojha Hemant , Xi Luo
Published: September 2024

This chapter reviews the feasibility, constraints, and opportunities of global restoration goals, including the extent of suitable land, technical issues, financial investment, and social factors. Sufficient suitable and degraded agriculture or forest land exists to meet global area targets for restoration; but availability of this land is questionable, given it is currently used by local people. Sufficient capital is also potentially available, but it is mostly in private or institutional funds that seek a financial return along with social or environmental outcomes. Achieving global forest restoration goals will need to encompass multiple restoration approaches and enjoy social and political support. Approaches will need to include productive forest uses and integrating trees with agriculture, involve local people in goalsetting and implementation, and clarify their ownership of restored trees and forests. Improving institutional arrangements and coordination across government agencies and private stakeholders can support integrated investment at the required scale.
The Suicidal State
Authors: Kishi Madoka
Published: September 2024

The Suicidal State theorizes a biopolitics of suicide by mapping the entwinement between the Progressive Era discourse of “race suicide” and period representations of literary suicide. Like the present-day white nationalist discourse of “replacement theory,” race suicide frames white Americans’ low birth rate as a sign of their imminent extinction caused by over-fertile immigrants. Casting willful nonreproduction as racial self-killing, race suicide played a fundamental role in the transformation of racial and sexual taxonomies, consolidating the US biopolitical state. While race suicide thus endowed the populational subject—the “race”—with suicidal subjectivity, Progressive Era literature gave birth to a microgenre of literary suicides, including works by Henry James, Kate Chopin, Jack London, Gertrude Stein, and a series of Madame Butterfly texts. The Suicidal State reads these suicides as literalizing the fear of race suicide as they articulate queer deathways that betray the nation’s reproductive imperative. In examining suicide’s aspiration to sidestep the biopolitical imperative to live and reproduce, The Suicidal State examines the ways in which the suicidal undoing of the self reconfigures agency, subjectivity, and intimacies with its attempt to elude biopower’s discipline of the individual and its management of the population. Through tracking queer potentialities of suicide, The Suicidal State offers a new account of sex and race, of the relation between the individual and the collective, and of the formation of a biopolitical state that Foucault calls a “racist State, a murderous State, and a suicidal State.”
Gertrude Stein’s Melting Pot
Authors: Kishi Madoka
Published: September 2024

Charting the gradual assimilation of eastern and southern European immigrants into the US social body, this chapter argues that a range of alimentary metaphors for the huge influx of immigrants—“racial indigestion,” “alien indigestion,” and the “melting pot”—were deployed to imagine their digestive assimilation into the US social body. In The Making of Americans (1925), Gertrude Stein takes up an alimentary metaphor from the other end of the gastrointestinal tract: excretion. Reading Stein’s text across several drafts, this chapter argues that Stein dismantles the earlier versions’ Jewish familialism to reimagine the production of Americans as the social body’s excremental process. In so doing, Stein replaces the cluster of associations between Judaism, racial reproduction, and heterosexuality with linkages between queerness, anal pregnancy, and literary production. David Hersland’s suicidal self-starvation, in this reading, erases his own Jewishness, transforming himself and other descendants of immigrants into unmarked Americans.
Introduction
Authors: MacDonald Scott
Published: September 2024

Scott MacDonald explains the background and structure of the final part of his “avant-doc” trilogy, in which he explores the work of filmmakers, many of them underappreciated, who create films that combine documentary and “avant-garde” approaches in inventive and revealing ways. Comprehending Cinema combines in-depth interviews with accomplished filmmakers interspersed with panoramic essays that explore particular bodies of cinema, including the modern “cinematic nocturne” and widely varied archival responses to the anniversary of World War 1.
Su Friedrich, part 2
Authors: MacDonald Scott
Published: September 2024

Su Friedrich talks about her films since Sink or Swim (1990), about working through a break-up with her partner, about making her first feature for independent television (about the struggles of young girls recognizing their same-sex preference), about confronting her many medical procedures, about where her cheap cup of morning coffee comes from, about switching from analog shooting and editing to digital, about losing a loft to the gentrification of her longtime Brooklyn neighborhood, about struggling with moving her independent mother to an assisted-living facility—then about producing a major website about the history of women film editors, and about working with Louise Archambault Greaves to create a new website for canonical filmmaker William Greaves, and most recently to document her day-to-day life today.
Lunar Phases
Authors: MacDonald Scott
Published: September 2024

Irish filmmaker Tadhg O’Sullivan’s cine-rumination, To the Moon (2021), evokes the moon as it has been represented through history and across geography in cinema and literature. O’Sullivan created a network of filmmakers from many countries to shoot moonlight scenes, and asked archivists from various national archives to find representations of the moon that moved them. He combined clips from a century of cinema with his own images and the images offered by other contemporary filmmakers, organizing all of this into complex representations of the various phases of the moon. O’Sullivan’s commitment to analog shooting allows film imagery shot a century ago and ten years ago to evoke the continuity of cinema over its first century, as a metaphor for the moon’s continuing presence throughout every human generation.
Dean Fleischer Camp, from Marcel the Shell with Shoes On to Fraud, and Back Again
Authors: MacDonald Scott
Published: September 2024

After Dean Fleischer Camp and Jenny Slate’s YouTube video Marcel the Shell with Shoes On (2010) went viral, they worked for years to find a way to make a feature-length stop-motion/normal action hybrid with Marcel as the main character. In the meantime, Fleischer Camp directed Fraud (2016), transforming family YouTube postings into a suspense narrative (would the audience suspect what he was doing?)—a modern day David Holzman’s Diary (1967). Finally, Fleischer Camp and Slade were able to find support from Cinereach, A24, Isabella Rossellini, and Leslie Stahl, and the feature Marcel the Shell premiered in 2022 and was nominated for an Oscar.
Bill Morrison
Authors: MacDonald Scott
Published: September 2024

Bill Morrison’s recent films are revelatory in very different ways. In The Village Detective (2021) reels of film dredged up from the ocean floor led to an exploration of popular cinema produced in the USSR and a popular film star, Mikhail Zharov—a world of cinema the inverse of both the Soviet montage explorations of the 1920s and modern, “slow cinema” reactions to it. Morrison provides a sense of what Russian movie lovers were seeing as the Communist project evolved during Stalin’s reign. Buried News revives attention to early twentieth-century racial incidents, revealing similarities and differences to the current moment; and Incident (2023) reveals the unprovoked killing of an African American barber and its immediate aftermath, using only imagery and sound from police body cameras, dashboard cameras, PODs (Police Observational Devices), and security cameras.
Climate Change and Baltic Sea Genetic Diversity
Authors: Johannesson Kerstin
Published: September 2024

Up until the beginning of the previous millennium, threats to the environment were mostly local and hence less difficult to combat. In the early 21st century, a large human population and high and increasing demands of energy, food, and other resources have led to a global climate crisis affecting nearly all life on Earth, biodiversity, and human societies alike. How will such a dramatic environmental shift affect the ecosystems? The Baltic Sea ecosystem is an interesting example in this respect, as it includes a dramatic environmental shift, starting from a freshwater lake but 8,000 years ago turning into a marine (brackish) sea with initially somewhat higher salinity than in the early 21st century. Marine populations of species that colonized the brackish water basin had to tolerate or adapt to one third their original salinity, lower density of the water, no regular tides, winter ice, and generally colder waters. Overall, these were dramatic environmental changes of magnitudes and rates of change similar to what is predicted from contemporary global environmental changes, including climate change. Indeed, the Baltic Sea is a “Darwinian laboratory” that can be explored to understand the role of plasticity, genetic variation, genetic structure and architecture, and demography using the sharp footprints of both phenotypic and genetic changes of organisms that survived this rapid environmental shift. What is observed is firstly that many marine species outside did not make it into the Baltic Sea, but among those that were successful, almost all (among the >30 studied macrospecies) show large genetic changes due to genetic drift and directional selection. The latter show that adaptation to a strong environmental shift is possible over a relatively short period of time for some species. Among successful survivors were species with very large population sizes and thus large standing genetic variation. In some species, hybridization contributed to increased levels of genetic variation. Only very few macroscopic species show evidence of recent adaptation following new mutations, while this was common among microbes. Reduced rates of recombination among genes through chromosomal inversions enable local adaptation, and it certainly supported the establishment of at least a handful of Baltic populations of species. Cloning, is also overrepresented among Baltic populations, and there may be several reasons for this. Cloning conserves suitable genotypes in marginal environments, and it also supports efficient range expansion in species that under sexual reproduction would require two individuals (one female and one male) to arrive close together after migration into a new spot. Being in an enclosed sea, the Baltic populations of largely cold water–adapted species are now facing the next large challenge—a much more rapid warming than elsewhere in the oceans.
Islamic Bioethics: Religion, Science, and Technology
Authors: Bakar Osman
Published: September 2024

Unlike views prevailing in certain cultures that insist on the separation of science and technology from religion, Islamic tradition argues for their interrelatedness, unity, and harmony. Islamic bioethics is both an old and a new field of academic inquiry. It is old in the sense that the practical concern with what are now considered bioethical issues has been present in Islam since its early history. But it is also new in the sense that its domain of inquiry now covers a much wider range of modern ethical issues that do not originate from the Muslim world. Rather, they largely originate from the modern West. It is also new with respect to the kind of philosophical challenges it has to grapple with in response to the competing theories of ethics that seek to best explain the meaning and significance of contemporary bioethics, as well as its relations—especially with its neighboring academic disciplines.
A Survey of Morpho-Phonology in Chinese Languages
Authors: Wang Xiaopei , Li Bing
Published: September 2024

The majority of morphemes are assigned a tone in Chinese languages. Tone fulfills the equivalent function as consonant and vowel phonemes. In Chinese, tonology interacts with morphology in two ways. First, in concatenative morphology, wherein morphemes or words are combined to form new words, tones in adjacent positions may affect each other and tone sandhi occurs. Tone sandhi rules display a high degree of sensitivity to morpho-syntax in many Chinese languages. Different types of tone sandhi take place in different construction types in one single language. A common tendency observed is that tone sandhi rules generally fall into two types, depending on the structural relation held between two subcomponents of a disyllabic structure (either a word or a phrase). One type demonstrates the lexical syndrome in that it applies merely in words of cohesion, including suffixed words, disyllabic compounds of the coordinate or modifier-head structure. In contrast, the other type applies in less cohesive constructions, such as words and phrases of the verb-object or subject-predicate structure. The sensitivity of tone sandhi to morpho-syntax across Chinese is of theoretical significance for understanding the overall organization of the grammar in general and the interaction between phonology and morpho-syntax in particular.

On the other hand, the special property of tone being superimposed on syllables enables it to act as a floating entity to convey grammatical or semantic meanings. In order to be phonologically licensed, the floating morphemic tone usually anchors on the stem. A rich body of morphemic tones are reported across Chinese languages, and their theoretical significance awaits further exploration.
The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring
Authors: Pain Oliver , Al-Chalabi Ammar , Lewis Cathryn M
Published: September 2024

Motivation

Polygenic scoring is an approach for estimating an individual’s likelihood of a given outcome. Polygenic scores are typically calculated from genome-wide association study (GWAS) summary statistics and individual-level genotype data for the target sample. Going from genotype to interpretable polygenic scores involves many steps and there are many methods available, limiting the accessibility of polygenic scores for research and clinical application. Additional challenges exist for studies in ancestrally diverse populations. We have implemented the leading polygenic scoring methodologies within an easy-to-use pipeline called GenoPred.

Results

Here, we present the GenoPred pipeline, an easy-to-use, high-performance, reference-standardized, and reproducible workflow for polygenic scoring. It requires minimal inputs and offers various configuration options to cater to a range of use cases. GenoPred implements a comprehensive set of analyses, including genotype and GWAS quality control, target sample ancestry inference, polygenic score file generation using a range of leading methods, and target sample scoring. GenoPred standardizes the polygenic scoring process using reference genetic data, providing interpretable polygenic scores. The pipeline is applicable to GWAS and targets data from any population within the reference, facilitating studies of diverse ancestry. GenoPred is a Snakemake pipeline with associated Conda software environments, ensuring reproducibility. We apply the pipeline to UK Biobank data demonstrating the pipeline’s simplicity, efficiency, and performance. The GenoPred pipeline provides a novel resource for polygenic scoring, integrating a range of complex processes within an easy-to-use framework. GenoPred widens access to the leading polygenic scoring methodology and their application to studies of diverse ancestry.

Availability and implementation

Freely available on the web at https://github.com/opain/GenoPred.
AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors
Authors: Fernández-Díaz Raúl , Cossio-Pérez Rodrigo , Agoni Clement , Lam Hoang Thanh , Lopez Vanessa , Shields Denis C
Published: September 2024

Motivation

Automated machine learning (AutoML) solutions can bridge the gap between new computational advances and their real-world applications by enabling experimental scientists to build their own custom models. We examine different steps in the development life-cycle of peptide bioactivity binary predictors and identify key steps where automation cannot only result in a more accessible method, but also more robust and interpretable evaluation leading to more trustworthy models.

Results

We present a new automated method for drawing negative peptides that achieves better balance between specificity and generalization than current alternatives. We study the effect of homology-based partitioning for generating the training and testing data subsets and demonstrate that model performance is overestimated when no such homology correction is used, which indicates that prior studies may have overestimated their performance when applied to new peptide sequences. We also conduct a systematic analysis of different protein language models as peptide representation methods and find that they can serve as better descriptors than a naive alternative, but that there is no significant difference across models with different sizes or algorithms. Finally, we demonstrate that an ensemble of optimized traditional machine learning algorithms can compete with more complex neural network models, while being more computationally efficient. We integrate these findings into AutoPeptideML, an easy-to-use AutoML tool to allow researchers without a computational background to build new predictive models for peptide bioactivity in a matter of minutes.

Availability and implementation

Source code, documentation, and data are available at https://github.com/IBM/AutoPeptideML and a dedicated web-server at http://peptide.ucd.ie/AutoPeptideML. A static version of the software to ensure the reproduction of the results is available at https://zenodo.org/records/13363975.
Dynamic category-sensitive hypergraph inferring and homo-heterogeneous neighbor feature learning for drug-related microbe prediction
Authors: Xuan Ping , Xu Zelong , Cui Hui , Gu Jing , Liu Cheng , Zhang Tiangang , Wu Peiliang
Published: September 2024

Motivation

The microbes in human body play a crucial role in influencing the functions of drugs, as they can regulate the activities and toxicities of drugs. Most recent methods for predicting drug–microbe associations are based on graph learning. However, the relationships among multiple drugs and microbes are complex, diverse, and heterogeneous. Existing methods often fail to fully model the relationships. In addition, the attributes of drug–microbe pairs exhibit long-distance spatial correlations, which previous methods have not integrated effectively.

Results

We propose a new prediction method named DHDMP which is designed to encode the relationships among multiple drugs and microbes and integrate the attributes of various neighbor nodes along with the pairwise long-distance correlations. First, we construct a hypergraph with dynamic topology, where each hyperedge represents a specific relationship among multiple drug nodes and microbe nodes. Considering the heterogeneity of node attributes across different categories, we developed a node category-sensitive hypergraph convolution network to encode these diverse relationships. Second, we construct homogeneous graphs for drugs and microbes respectively, as well as drug–microbe heterogeneous graph, facilitating the integration of features from both homogeneous and heterogeneous neighbors of each target node. Third, we introduce a graph convolutional network with cross-graph feature propagation ability to transfer node features from homogeneous to heterogeneous graphs for enhanced neighbor feature representation learning. The propagation strategy aids in the deep fusion of features from both types of neighbors. Finally, we design spatial cross-attention to encode the attributes of drug–microbe pairs, revealing long-distance correlations among multiple pairwise attribute patches. The comprehensive comparison experiments showed our method outperformed state-of-the-art methods for drug–microbe association prediction. The ablation studies demonstrated the effectiveness of node category-sensitive hypergraph convolution network, graph convolutional network with cross-graph feature propagation, and spatial cross-attention. Case studies on three drugs further showed DHDMP’s potential application in discovering the reliable candidate microbes for the interested drugs.

Availability and implementation

Source codes and supplementary materials are available at https://github.com/pingxuan-hlju/DHDMP.
Structure-inclusive similarity based directed GNN: a method that can control information flow to predict drug–target binding affinity
Authors: Huang Jipeng , Sun Chang , Li Minglei , Tang Rong , Xie Bin , Wang Shuqin , Wei Jin-Mao
Published: September 2024

Motivation

Exploring the association between drugs and targets is essential for drug discovery and repurposing. Comparing with the traditional methods that regard the exploration as a binary classification task, predicting the drug–target binding affinity can provide more specific information. Many studies work based on the assumption that similar drugs may interact with the same target. These methods constructed a symmetric graph according to the undirected drug similarity or target similarity. Although these similarities can measure the difference between two molecules, it is unable to analyze the inclusion relationship of their substructure. For example, if drug A contains all the substructures of drug B, then in the message-passing mechanism of the graph neural network, drug A should acquire all the properties of drug B, while drug B should only obtain some of the properties of A.

Results

To this end, we proposed a structure-inclusive similarity (SIS) which measures the similarity of two drugs by considering the inclusion relationship of their substructures. Based on SIS, we constructed a drug graph and a target graph, respectively, and predicted the binding affinities between drugs and targets by a graph convolutional network-based model. Experimental results show that considering the inclusion relationship of the substructure of two molecules can effectively improve the accuracy of the prediction model. The performance of our SIS-based prediction method outperforms several state-of-the-art methods for drug–target binding affinity prediction. The case studies demonstrate that our model is a practical tool to predict the binding affinity between drugs and targets.

Availability and implementation

Source codes and data are available at https://github.com/HuangStomach/SISDTA.
Are cows pickier than goats? Linnaeus’s innovative large-scale feeding experiment
Authors: Carlsson Bengt Å , Björkman Camilla , Rydin Håkan
Published: September 2024

In 1749, Linnaeus published Pan Svecicus, a thesis that was defended by his student Nils Hesselgren. The thesis describes food preference trials in cows, goats, sheep, horses, and pigs, and includes 2325 tests with 643 plant species. The data had surprisingly little bearing on the text in the thesis, and even though the experiments quickly became internationally known, the data were merely repeated, rather than discussed. We have digitized the data and linked the species names to modern nomenclature and present the first analysis and discussion of the results. Pigs were most selective (eating 32% of the 204 plant species that were tested on all animals), followed by horses (59%), cows (66%), sheep (82%), and goats (85%). The ruminants (especially goats and sheep) had high overlap in food choice, and the pigs deviated most (despite the fact that pigs are more closely related to the ruminants than are horses). Among plant orders, Fabales and Poales were generally preferred, while Lamiales and Ranunculales were avoided, especially by cows and horses. Cows and horses were also more keen to avoid toxic plant species. All animals showed a preference for species that are today considered nutritious. We now make the data available, for further analyses in ecology, history of science, and other disciplines.
Apolipoprotein B-48 and late graft failure in kidney transplant recipients
Authors: Szili-Torok Tamas , de Borst Martin H , Soteriou Alexandra , Post Laura , Bakker Stephan J L , Tietge Uwe J F
Published: September 2024

Introduction

Transplant vasculopathy resembles atherosclerotic plaque formation and is a major contributor to late graft failure in kidney transplant recipients (KTR). Remnant lipoproteins and associated triglycerides are causal risk factors for atherosclerotic plaques and have been implicated in late kidney graft failure. However, whether remnants derived from liver (containing apolipoprotein [apo] B100) or intestine (containing apoB48) are clinically more important is unclear. The current study investigated the association between baseline fasting apoB48 levels and late kidney graft failure.

Methods

481 KTR with a functioning graft for at least 1 year were included in this retrospective, observational longitudinal single center cohort study. The primary endpoint was death-censored late graft failure, defined as need for initiation of dialysis or re-transplantation. ApoB48 was measured by enzyme-linked immunosorbent assay.

Results

During a median follow-up of 9.5 years, 61 KTR developed graft failure (12.7%). At baseline, KTR with higher apoB48 levels had lower eGFR (P < .001), lower high-density lipoprotein (HDL) cholesterol (P < .001), increased triglycerides (P < .001) and used cyclosporine more frequently (P = .003). Cox regression showed that higher baseline apoB48 was associated with higher risk of late graft failure [hazard ratio (95% confidence interval), 1.59 (1.22, 2.07), P < .001], independent of stepwise adjustment for potential confounders, including age and sex, immunosuppression type and proteinuria, triglycerides, and waist circumference (fully adjusted HR, 1.78 (1.29, 2.47), P < .001].

Conclusion

ApoB48 is strongly associated with late graft failure, independent of potential confounders. Since apoB48-containing lipoproteins originate from the intestine, this study provides a rationale for considering pharmacological interventions targeting lipid absorption to improve graft outcome.
Cardiac anatomic digital twins: findings from a single national centre
Authors: Lippert Matthias , Dumont Karl-Andreas , Birkeland Sigurd , Nainamalai Varatharajan , Solvin Håvard , Suther Kathrine Rydén , Bendz Bjørn , Elle Ole Jakob , Brun Henrik
Published: September 2024

Aims

New three-dimensional cardiac visualization technologies are increasingly employed for anatomic digital twins in pre-operative planning. However, the role and influence of extended reality (virtual, augmented, or mixed) within heart team settings remain unclear. We aimed to assess the impact of mixed reality visualization of the intracardiac anatomy on surgical decision-making in patients with complex heart defects.

Methods and results

Between September 2020 and December 2022, we recruited 50 patients and generated anatomic digital twins and visualized them in mixed reality. These anatomic digital twins were presented to the heart team after initial decisions were made using standard visualization methods. Changes in the surgical strategy were recorded. Additionally, heart team members rated their mixed reality experience through a questionnaire, and post-operative outcomes were registered. Anatomic digital twins changed the initially decided upon surgical strategies for 68% of cases. While artificial intelligence facilitated the rapid creation of digital anatomic twins, manual corrections were always necessary.

Conclusion

In conclusion, mixed reality anatomic digital twins added information to standard visualization methods and significantly influenced surgical planning, with evidence that these strategies can be implemented safely without additional risk.
A new perspective on tumor progression
Authors: Thomas Frédéric , DeGregori James , Marusyk Andriy , Dujon Antoine M , Ujvari Beata , Capp Jean-Pascal , Gatenby Robert , Nedelcu Aurora M
Published: September 2024

Tumorigenesis is commonly attributed to Darwinian processes involving natural selection among cells and groups of cells. However, progressing tumors are those that also achieve an appropriate group phenotypic composition (GPC). Yet, the selective processes acting on tumor GPCs are distinct from that associated with classical Darwinian evolution (i.e. natural selection based on differential reproductive success) as tumors are not genuine evolutionary individuals and do not exhibit heritable variation in fitness. This complex evolutionary scenario is analogous to the recently proposed concept of ‘selection for function’ invoked for the evolution of both living and non-living systems. Therefore, we argue that it is inaccurate to assert that Darwinian processes alone account for all the aspects characterizing tumorigenesis and cancer progression; rather, by producing the genetic and phenotypic diversity required for creating novel GPCs, these processes fuel the evolutionary success of tumors that is dependent on selection for function at the tumor level.
Adaptive small-scale fisheries in the eastern Cantabrian coast through reliance on essential species
Authors: Bachiller Eneko , Mugerza Estanis , Murillas-Maza Arantza , Mateo Maria , Korta Maria , Zarauz Lucia
Published: September 2024

In recent decades, small-scale fisheries (SSF) activity along the Basque coast (eastern Cantabrian) has declined, which has led remaining vessels to undergo notable shifts in their targeted species and therefore the fishing gears used, aimed at enhancing efficiency. Within that context, this study combines logbooks and sales notes spanning from 1995 to 2022 to assess inter-annual and seasonal variations in fishing activity and the main target species across different fishing gears, namely ‘fleet segments’. Results reveal that the spring Atlantic mackerel (Scomber scombrus) and summer albacore (Thunnus alalunga) seasons, with an intensified harvesting under favourable conditions during the past decade, affected the activity of all other segments throughout the year. In the face of climate change affecting harvested species, a scenario where mackerel and/or albacore seasons are disturbed would lead the SSF to predominantly depend on European hake, mainly caught by declining longlines and set nets, as well as on complementary species. Assessing essential species targeted by each SSF segment relies on is crucial for stakeholders as it helps manage interactions between fleets targeting the same species (e.g. SSF vs. industrial and recreational fisheries), and understand gear shifts by vessels targeting specific species in certain seasons.
HiMAL: Multimodal

Hi

erarchical

M

ulti-task

A

uxiliary

L

earning framework for predicting Alzheimer’s disease progression
Authors: Kumar Sayantan , Yu Sean C , Michelson Andrew , Kannampallil Thomas , Payne Philip R O
Published: September 2024

Objective

We aimed to develop and validate a novel multimodal framework Hierarchical Multi-task Auxiliary Learning (HiMAL) framework, for predicting cognitive composite functions as auxiliary tasks that estimate the longitudinal risk of transition from Mild Cognitive Impairment (MCI) to Alzheimer’s Disease (AD).

Materials and Methods

HiMAL utilized multimodal longitudinal visit data including imaging features, cognitive assessment scores, and clinical variables from MCI patients in the Alzheimer’s Disease Neuroimaging Initiative dataset, to predict at each visit if an MCI patient will progress to AD within the next 6 months. Performance of HiMAL was compared with state-of-the-art single-task and multitask baselines using area under the receiver operator curve (AUROC) and precision recall curve (AUPRC) metrics. An ablation study was performed to assess the impact of each input modality on model performance. Additionally, longitudinal explanations regarding risk of disease progression were provided to interpret the predicted cognitive decline.

Results

Out of 634 MCI patients (mean [IQR] age: 72.8 [67-78], 60% male), 209 (32%) progressed to AD. HiMAL showed better prediction performance compared to all state-of-the-art longitudinal single-modality singe-task baselines (AUROC = 0.923 [0.915-0.937]; AUPRC = 0.623 [0.605-0.644]; all P < .05). Ablation analysis highlighted that imaging and cognition scores with maximum contribution towards prediction of disease progression.

Discussion

Clinically informative model explanations anticipate cognitive decline 6 months in advance, aiding clinicians in future disease progression assessment. HiMAL relies on routinely collected electronic health records (EHR) variables for proximal (6 months) prediction of AD onset, indicating its translational potential for point-of-care monitoring and managing of high-risk patients.
Management of Acute Hand Burns: A Survey of American Burn Association-Verified Burn Centers
Authors: Liu Hilary Y , Alessandri-Bonetti Mario , Shockey Siddhi , Corcos Alain C , Ziembicki Jenny A , Stofman Guy M , Egro Francesco M
Published: September 2024

Hand burns have a significant impact on the long-term function of burn patients. Recently, new protocols and technologies, such as dermal substitutes, have been introduced for the treatment of hand burns. This cross-sectional study investigates the preferred current management of acute hand burns and the role of dermal substitutes in treatment. A 10-question survey related to acute hand burns management was sent to 64 directors of American Burn Association (ABA)-verified burn centers. A total of 51.6% (n = 33) directors of ABA-verified burn centers responded to the survey. For the treatment of superficial partial-thickness hand burns, 90.9% preferred a nonoperative approach. Conversely, most respondents chose a single-stage excision and skin graft for deep partial-thickness hand burns (75.8%) and full-thickness hand burns (51.5%). However, for full-thickness hand burns, some surgeons prefer a 2-stage reconstruction involving excision and placement of a skin substitute (27.3%) or allograft (9.1%), followed by a skin graft. Only 6.1% would utilize a 3-stage reconstruction involving excision and allograft, excision and skin substitute, followed by skin grafting. Among surgeons who used skin substitutes (n = 26), Integra (42.3%) and Novosorb-Biodegradable Temporizing Matrix (23.1%) were preferred. The top reasons for choosing 1 specific dermal substitute were surgeon’s preference (n = 20; 76.9%) and cost (n = 9; 34.6%). While a conservative nonoperative approach is preferred for superficial partial-thickness hand burns, excision and skin grafting as a 1-stage procedure remains the most common strategy for deep partial-thickness and full-thickness hand burns.