bluuebunny/crossref_metadata_2025_split huggingface dataset:
MOIRE: a software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data
Authors: Murphy Maxwell , Greenhouse Bryan 
Published: October 2024

Abstract

Motivation
Malaria parasite genetic data can provide insight into parasite phenotypes, evolution, and transmission. However, estimating key parameters such as allele frequencies, multiplicity of infection (MOI), and within-host relatedness from genetic data is challenging, particularly in the presence of multiple related coinfecting strains. Existing methods often rely on single nucleotide polymorphism (SNP) data and do not account for within-host relatedness.

Results
We present Multiplicity Of Infection and allele frequency REcovery (MOIRE), a Bayesian approach to estimate allele frequencies, MOI, and within-host relatedness from genetic data subject to experimental error. MOIRE accommodates both polyallelic and SNP data, making it applicable to diverse genotyping panels. We also introduce a novel metric, the effective MOI (eMOI), which integrates MOI and within-host relatedness, providing a robust and interpretable measure of genetic diversity. Extensive simulations and real-world data from a malaria study in Namibia demonstrate the superior performance of MOIRE over naive estimation methods, accurately estimating MOI up to seven with moderate-sized panels of diverse loci (e.g. microhaplotypes). MOIRE also revealed substantial heterogeneity in population mean MOI and mean relatedness across health districts in Namibia, suggesting detectable differences in transmission dynamics. Notably, eMOI emerges as a portable metric of within-host diversity, facilitating meaningful comparisons across settings when allele frequencies or genotyping panels differ. Compared to existing software, MOIRE enables more comprehensive insights into within-host diversity and population structure.

Availability and implementation
MOIRE is available as an R package at https://eppicenter.github.io/moire/.
In vitro maturation of oocytes: what is already known?
Authors: Morato Ana Luiza Camargos , Verruma Carolina Gennari , Furtado Cristiana Libardi Miranda , dos Reis Rosana Maria 
Published: October 2024

Abstract
Assisted reproductive technologies (ARTs) involve the laboratory manipulation of gametes and embryos to help couples with fertility problems become pregnant. One of these procedures, controlled ovarian stimulation, uses pharmacological agents to induce ovarian and follicular maturation in vivo. Despite the effectiveness in achieving pregnancy and live births, some patients may have complications due to over-response to gonadotropins and develop ovarian hyperstimulation syndrome. In vitro maturation (IVM) of oocytes has emerged as a technique to reduce the risk of ovarian hyperstimulation syndrome, particularly in women with polycystic ovary syndrome, and for fertility preservation in women undergoing oncological treatment. Although there are some limitations, primarily due to oocyte quality, recent advances have improved pregnancy success rates and neonatal and infant outcomes. Different terms have been coined to describe variations of IVM, and the technique has evolved with the introduction of hormones to optimize results. In this review, we provide a comprehensive overview of IVM relating hormonal priming, culture system and media, and clinical indications for IVM with its reproductive outcomes during ARTs.
Contrasting patterns of differentiation among three taxa of the rapidly diversifying orchid genus Ophrys sect. Insectifera (Orchidaceae) where their ranges overlap
Authors: Salvado Pascaline , Gibert Anaïs , Schatz Bertrand , Vandenabeele Lucas , Buscail Roselyne , Vilasís David , Feldmann Philippe , Bertrand Joris A M 
Published: October 2024

Abstract
In rapidly diversifying groups, taxa defined on the basis of typological criteria can be difficult to support with genetic data. The diversity observed in the insect-mimicking orchid genus Ophrys perfectly illustrates this situation; among 400 described species only 9–10 lineages are detectable by genetic markers such as nrITS. The three taxa described in the Ophrys insectifera group, O. insectifera, O. subinsectifera, and O. aymoninii, can be clearly distinguished by their flowers, which have evolved different phenotypes as a result of adaptation to specific pollinator insect species from three different families. However, genetic differentiation between these three taxa has never been really supported by population genetic data and their taxonomic status is still debated. Using population genomic approaches, we found a clustering consistent with the existence of three genetic entities where the geographic distributions of the three taxa overlap. Two of these clusters correspond to France populations of the widespread O. insectifera and the micro-endemic O. aymoninii. However, the last cluster grouped together all the Iberian individuals, suggesting that individuals phenotypically identified as either O. insectifera or O. subinsectifera are genetically weakly differentiated there. Populations of the two pairs of taxa thus may have experienced different patterns of inter-specific gene flow.
REVEALS: an open-source multi-camera GUI for rodent behavior acquisition
Authors: Phadke Rhushikesh A , Wetzel Austin M , Fournier Luke A , Brack Alison , Sha Mingqi , Padró-Luna Nicole M , Williamson Ryan , Demas Jeff , Cruz-Martín Alberto 
Published: October 2024

Abstract
Deciphering the rich repertoire of mouse behavior is crucial for understanding the functions of both the healthy and diseased brain. However, the current landscape lacks effective, affordable, and accessible methods for acquiring such data, especially when employing multiple cameras simultaneously. We have developed REVEALS (Rodent Behavior Multi-Camera Laboratory Acquisition), a graphical user interface for acquiring rodent behavioral data via commonly used USB3 cameras. REVEALS allows for user-friendly control of recording from one or multiple cameras simultaneously while streamlining the data acquisition process, enabling researchers to collect and analyze large datasets efficiently. We release this software package as a stand-alone, open-source framework for researchers to use and modify according to their needs. We describe the details of the graphical user interface implementation, including the camera control software and the video recording functionality. We validate results demonstrating the graphical user interface’s stability, reliability, and accuracy for capturing rodent behavior using DeepLabCut in various behavioral tasks. REVEALS can be incorporated into existing DeepLabCut, MoSeq, or other custom pipelines to analyze complex behavior. In summary, REVEALS offers an interface for collecting behavioral data from single or multiple perspectives, which, when combined with deep learning algorithms, enables the scientific community to identify and characterize complex behavioral phenotypes.
Rearing fly larvae on various substrates: nutrient composition of larvae and frass
Authors: Klakankhai Warin , Nuntapong Nutt , Meesin Sawanya , Yongsue Tepyuda , Niyombandith Taweesak , Tainchum Krajana 
Published: October 2024

Abstract
Management solutions for waste in southern Thailand, such as fly larvae, are tested in a laboratory using different substrates and wastes from the Thai agricultural sector. The nutritional content of the immature stages of Musca domestica Linnaeus (Diptera: Muscidae) and Hermetia illucens (Linnaeus) (Diptera: Stratiomyidae) larvae, especially their protein and fat contents, makes them a potential animal feed. Laboratory strains of M. domestica and H. illucens were reared on selected substrates to examine how diet influenced their performance and nutritional composition. Waste from aquaculture, vegetables, and fruits in southern Thailand was examined for larval diet and showed promise as a rearing substrate for these insects. Musca domestica larvae reared on fishery waste achieved the highest larval weight and fat content, whereas H. illucens larvae reared on an aquaculture waste diet had the highest protein content. These findings imply aquaculture waste could be the best choice for large-scale fly larvae production, particularly as a protein feed additive.
Discovery of a glyphosate oxidase in nature
Authors: Ma Minghui , Ardalan Afshan , Van Dyk Adrian , Charles Trevor C , Horsman Geoff P 
Published: October 2024

Abstract
Glyphosate is the most used herbicide on Earth. After a half-century of use we know only two biodegradative pathways, each of which appears to degrade glyphosate incidentally. One pathway begins with oxidation of glyphosate catalysed by glycine oxidase (GO). To date, no naturally occurring GO enzymes preferentially oxidize glyphosate but nonetheless are sufficiently active to initiate its degradation. However, GO enzymes that preferentially oxidize glyphosate over glycine—i.e. glyphosate oxidases (GOXs)—may have evolved in environments facing prolonged glyphosate exposure. To test this hypothesis, we screened a metagenomic library from glyphosate-exposed agricultural soil and identified a GOX from clone 11AW19 (GO19) that prefers glyphosate over glycine by four orders of magnitude. This is the first GO isolated from a natural source exhibiting a glyphosate preference. Not only have we discovered the first GOX in nature, but we have also demonstrated the utility of functional metagenomics to find a GOX with greater catalytic efficiency and specificity than those engineered using directed evolution.
Gut Microbial Signatures in Pediatric Crohn’s Disease Vary According to Disease Activity Measures and Are Influenced by Proxies of Gastrointestinal Transit Time: An ImageKids Study
Authors: Nichols Ben , Russell Richard K , Short Bryn , Papadopoulou Rodanthi , Focht Gili , Ijaz Umer Z , Walters Thomas D , Sladek Malgorzata , Hansen Richard , Mack David R , Wine Eytan , Griffiths Anne M , Turner Dan , Gerasimidis Konstantinos 
Published: October 2024

Abstract

Introduction
We investigated relationships between disease activity measures and the gut microbiome in children with Crohn’s disease (CD) and how these were confounded by gastrointestinal transit time.

Methods
Microbiome was profiled (16S rRNA sequencing) in feces from 196 children with CD. Sixty participants also provided samples after 18 months. Mural inflammation (Pediatric Inflammatory Crohn’s Magnetic Resonance Enterography Index, PICMI), the simple endoscopic score for CD, and the weighted pediatric Crohn’s disease activity index (wPCDAI) were assessed. Fecal calprotectin, plasma C-reactive protein (CRP), and fecal water content (FWC), a proxy of gastrointestinal transit time, were measured too.

Results
Microbiome α diversity, clustering, and differential taxa were related to disease status, but varied remarkably by disease activity measure used. The strongest relationships between microbiome and disease activity status were observed using wPCDAI; fewer or no relationships were seen using more objective measures like PICMI. Taxa predictive of disease activity status were dependent on the disease activity measure used with negligible overlap. Active disease was associated with more pathobionts (eg, Viellonella, Enterobacterales) and fewer fiber-fermenting organisms. The effect FWC had on microbiome superseded the effect of active disease for all disease activity measures, particularly with wPCDAI. Accounting for FWC, the differences in microbial signatures explained by disease activity status were attenuated or lost.

Conclusions
In CD, microbiome signatures fluctuate depending on the measure used to assess disease severity; several of these signals might be secondary disease effects linked with changes in gut motility in active disease. PICMI appears to be less influenced when studying relationships between microbiome and mural inflammation in CD.
A new perspective on denoising based on optimal transport
Authors: García Trillos Nicolás , Sen Bodhisattva 
Published: October 2024

Abstract
In the standard formulation of the classical denoising problem, one is given a probabilistic model relating a latent variable $\varTheta \in \varOmega \subset{\mathbb{R}}^{m} \; (m\ge 1)$ and an observation $Z \in{\mathbb{R}}^{d}$ according to $Z \mid \varTheta \sim p(\cdot \mid \varTheta )$ and $\varTheta \sim G^{*}$, and the goal is to construct a map to recover the latent variable from the observation. The posterior mean, a natural candidate for estimating $\varTheta $ from $Z$, attains the minimum Bayes risk (under the squared error loss) but at the expense of over-shrinking the $Z$, and in general may fail to capture the geometric features of the prior distribution $G^{*}$ (e.g. low dimensionality, discreteness, sparsity). To rectify these drawbacks, in this paper we take a new perspective on this denoising problem that is inspired by optimal transport (OT) theory and use it to study a different, OT-based, denoiser at the population level setting. We rigorously prove that, under general assumptions on the model, this OT-based denoiser is mathematically well-defined and unique, and is closely connected to the solution to a Monge OT problem. We then prove that, under appropriate identifiability assumptions on the model, the OT-based denoiser can be recovered solely from information of the marginal distribution of $Z$ and the posterior mean of the model, after solving a linear relaxation problem over a suitable space of couplings that is reminiscent of standard multimarginal OT problems. In particular, due to Tweedie’s formula, when the likelihood model $\{ p(\cdot \mid \theta ) \}_{\theta \in \varOmega }$ is an exponential family of distributions, the OT-based denoiser can be recovered solely from the marginal distribution of $Z$. In general, our family of OT-like relaxations is of interest in its own right and for the denoising problem suggests alternative numerical methods inspired by the rich literature on computational OT.
Open and closed structures of L-arginine oxidase by cryo-electron microscopy and X-ray crystallography
Authors: Yamaguchi Hiroki , Takahashi Kazutoshi , Numoto Nobutaka , Suzuki Hiroshi , Tatsumi Moemi , Kamegawa Akiko , Nishikawa Kouki , Asano Yasuhisa , Mizukoshi Toshimi , Miyano Hiroshi , Fujiyoshi Yoshinori , Sugiki Masayuki 
Published: October 2024

Abstract
L-arginine oxidase (AROD, EC 1.4.3.25) is an oxidoreductase that catalyses the deamination of L-arginine, with flavin adenine dinucleotide (FAD) as a cofactor. Recently identified AROD from Pseudomonas sp. TPU 7192 (PT-AROD) demonstrates high selectivity for L-arginine. This enzyme is useful for accurate assays of L-arginine in biological samples. The structural characteristics of the FAD-dependent AROD, however, remain unknown. Here, we report the structure of PT-AROD at a resolution of 2.3 Å by cryo-electron microscopy. PT-AROD adopts an octameric structure with D4 symmetry, which is consistent with its molecular weight in solution, estimated by mass photometry. Comparative analysis of this structure with that determined using X-ray crystallography reveals open and closed forms of the lid-like loop at the entrance to the substrate pocket. Furthermore, mutation of Glu493, located at the substrate binding site, diminishes substrate selectivity, suggesting that this residue contributes significantly to the high selectivity of PT-AROD.
Don’t touch me! Mating not always preceded by courtship behavior in predatory coccinellids
Authors: Zeni Valeria , Ricciardi Renato , Valicenti Marta , Nieri Rachele , Mazzoni Valerio , Canale Angelo , Desneux Nicolas , Lucchi Andrea , Benelli Giovanni 
Published: October 2024

Abstract
Knowledge of the ecology and behavior of biological control agents is essential for their effective use in biocontrol and Integrated Pest Management (IPM) programs. There is a lack of information regarding the courtship and mating traits that are crucial for successful mating in biocontrol population of coccinellids. To expand our current understanding in this area, 2 coccinellid species commonly used for the biocontrol of soft-bodied insects, Cryptolaemus montrouzieri (Mulsant) and Propylea quatuordecimpunctata (Linnaeus) (Coleoptera: Coccinellidae), were studied. A quantitative analysis was performed to compare their courtship and mating displays. Key behavioral traits of the precopulatory, copulatory, and postcopulatory phases were investigated. The courtship and mating sequences of C. montrouzieri and P. quatuordecimpunctata were similar to each other. During the mating phase, the key displays were the opening of the elytrae and wings followed by body shaking in C. montrouzieri and leg tapping followed by body shaking in P. quatuordecimpunctata. The mating success of both species was not correlated with any courtship display, such as antennal tapping. Only in C. montrouzieri mounting attempt showed a higher frequency from the backside without affecting male mating success. This research adds baseline knowledge about the courtship and mating behavior of the biocontrol population of coccinellids, contributing to the identification of potentially useful benchmarks (e.g., body shaking, leg tapping) for monitoring prolonged mass-rearing processes, thus reducing mating failures.
Publicity of proceedings before the Unified Patent Court
Authors: Schröder Vilhelm 
Published: October 2024

Abstract
On 1 June 2023, the Unified Patent Court (UPC) opened its doors. One of the most discussed and debated topics during the first year of operation of the UPC has been the publicity of the proceedings. This article discusses (i) access requests by the public, and (ii) restricting access within the proceedings. The court has now handed down several decisions on access requests by the public. Different approaches were adopted by the Munich section of the central division and the Nordic-Baltic regional division. The order by the latter division was appealed and we now have guidelines from the Court of Appeal on how the rules should be interpreted. The UPC has also given several orders related to the protection of trade secrets and confidential information within the proceedings. The questions the court has had to deal with are far from easy. They require careful balancing of several interests, such as publicity and confidentiality as well as the right to a fair trial. The Hague local division held that access to certain documents could be restricted only to legal representatives (‘attorneys’ eyes only’), where the relevant party had waived its right to review the documents. Generally, however, the UPC has in its orders allowed at least one natural person from each party to review all documents, which follows the wording of the Rules of Procedure. The Court of Appeal is yet to rule on these questions.
The peripheral neuroimmune system
Authors: Song Keaton , Kim Brian S 
Published: October 2024

Abstract
Historically, the nervous and immune systems were studied as separate entities. The nervous system relays signals between the body and the brain by processing sensory inputs and executing motor outputs, whereas the immune system provides protection against injury and infection through inflammation. However, recent developments have demonstrated that these systems mount tightly integrated responses. In particular, the peripheral nervous system acts in concert with the immune system to control reflexes that maintain and restore homeostasis. Notwithstanding their homeostatic mechanisms, dysregulation of these neuroimmune interactions may underlie various pathological conditions. Understanding how these two distinct systems communicate is an emerging field of peripheral neuroimmunology that promises to reveal new insights into tissue physiology and identify novel targets to treat disease.
Influence of artificial intelligence on modern book design
Authors: Liu Qi , Wu Zijing 
Published: October 2024

Abstract
The study addresses the necessity to investigate the influence of artificial intelligence (AI) on book design in a variety of socio-cultural contexts. The objective is to conduct a cross-cultural analysis of contemporary AI applications in book design in the USA, Finland, and China. The research employs a cross-cultural, systemic, and structural approach, utilizing theoretical methods such as analysis, synthesis, and comparison. The study identifies the current design trends, which include space aestheticization, communication, and AI integration. The study examines the relationship between AI and book design, with a particular focus on the role of the creator’s subjectivity and the potential for enhanced creative output. The necessity of a comparative approach to the analysis of AI-driven book design is underscored. The particulars of AI utilization in American book design are examined, emphasizing the infusion of cultural value, communication of environmental concerns, and the creation of heritage-based works. In contrast, the Finnish design approach prioritizes human resources and pragmatic solutions in book product design. In contrast, the Chinese approach addresses key socio-cultural issues through AI in book design. The study’s practical value lies in applying these local design characteristics to interpret cultural codes through AI.
scTML: a pan-cancer single-cell landscape of multiple mutation types
Authors: Li Haochen , Ma Tianxing , Zhao Zetong , Chen Yixin , Xi Xi , Zhao Xiaofei , Zhou Xiaoxiang , Gao Yibo , Wei Lei , Zhang Xuegong 
Published: October 2024

Abstract
Investigating mutations, including single nucleotide variations (SNVs), gene fusions, alternative splicing and copy number variations (CNVs), is fundamental to cancer study. Recent computational methods and biological research have demonstrated the reliability and biological significance of detecting mutations from single-cell transcriptomic data. However, there is a lack of a single-cell-level database containing comprehensive mutation information in all types of cancer. Establishing a single-cell mutation landscape from the huge emerging single-cell transcriptomic data can provide a critical resource for elucidating the mechanisms of tumorigenesis and evolution. Here, we developed scTML (http://sctml.xglab.tech/), the first database offering a pan-cancer single-cell landscape of multiple mutation types. It includes SNVs, insertions/deletions, gene fusions, alternative splicing and CNVs, along with gene expression, cell states and other phenotype information. The data are from 74 datasets with 2 582 633 cells, including 35 full-length (Smart-seq2) transcriptomic single-cell datasets (all publicly available data with raw sequencing files), 23 datasets from 10X technology and 16 spatial transcriptomic datasets. scTML enables users to interactively explore multiple mutation landscapes across tumors or cell types, analyze single-cell-level mutation-phenotype associations and detect cell subclusters of interest. scTML is an important resource that will significantly advance deciphering intra-tumor and inter-tumor heterogeneity, and how mutations shape cell phenotypes.