bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary genetics of the mitochondrial genome: insights from Drosophila
Authors: Dowling Damian K , Wolff Jonci N 
Published: May 2023

Abstract
Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.
Strategies and techniques for quality control and semantic enrichment with multimodal data: a case study in colorectal cancer with eHDPrep
Authors: Toner Tom M , Pancholi Rashi , Miller Paul , Forster Thorsten , Coleman Helen G , Overton Ian M 
Published: May 2023

Abstract

Background
Integration of data from multiple domains can greatly enhance the quality and applicability of knowledge generated in analysis workflows. However, working with health data is challenging, requiring careful preparation in order to support meaningful interpretation and robust results. Ontologies encapsulate relationships between variables that can enrich the semantic content of health datasets to enhance interpretability and inform downstream analyses.

Findings
We developed an R package for electronic health data preparation, “eHDPrep,” demonstrated upon a multimodal colorectal cancer dataset (661 patients, 155 variables; Colo-661); a further demonstrator is taken from The Cancer Genome Atlas (459 patients, 94 variables; TCGA-COAD). eHDPrep offers user-friendly methods for quality control, including internal consistency checking and redundancy removal with information-theoretic variable merging. Semantic enrichment functionality is provided, enabling generation of new informative “meta-variables” according to ontological common ancestry between variables, demonstrated with SNOMED CT and the Gene Ontology in the current study. eHDPrep also facilitates numerical encoding, variable extraction from free text, completeness analysis, and user review of modifications to the dataset.

Conclusions
eHDPrep provides effective tools to assess and enhance data quality, laying the foundation for robust performance and interpretability in downstream analyses. Application to multimodal colorectal cancer datasets resulted in improved data quality, structuring, and robust encoding, as well as enhanced semantic information. We make eHDPrep available as an R package from CRAN (https://cran.r-project.org/package=eHDPrep) and GitHub (https://github.com/overton-group/eHDPrep).
Genome assembly of an Australian native grass species reveals a recent whole-genome duplication and biased gene retention of genes involved in stress response
Authors: De Silva Nissanka P , Lee Christopher , Battlay Paul , Fournier-Level A , Moore Joslin L , Hodgins Kathryn A 
Published: May 2023

Abstract

Background
The adaptive significance of polyploidy has been extensively debated, and chromosome-level genome assemblies of polyploids can provide insight into this. The Australian grass Bothriochloa decipiens belongs to the BCD clade, a group with a complex history of hybridization and polyploid. This is the first genome assembly and annotation of a species that belongs to this fascinating yet complex group.

Findings
Using Illumina short reads, 10X Genomics linked reads, and Hi-C sequencing data, we assembled a highly contiguous genome of B. decipiens, with a total length of 1,218.22 Mb and scaffold N50 of 42.637 Mb. Comparative analysis revealed that the species experienced a relatively recent whole-genome duplication. We clustered the 20 major scaffolds, representing the 20 chromosomes, into the 2 subgenomes of the parental species using unique repeat signatures. We found evidence of biased fractionation and differences in the activity of transposable elements between the subgenomes prior to hybridization. Duplicates were enriched for genes involved in transcription and response to external stimuli, supporting a biased retention of duplicated genes following whole-genome duplication.

Conclusions
Our results support the hypotheses of a biased retention of duplicated genes following polyploidy and point to differences in repeat activity associated with subgenome dominance. B. decipiens is a widespread species with the ability to establish across many soil types, making it a prime candidate for climate change– resilient ecological restoration of Australian grasslands. This reference genome is a valuable resource for future population genomic research on Australian grasses.
Spatiotemporal profiles of gene activity in stamen delineate nucleo-cytoplasmic interaction in a male-sterile somatic cybrid citrus
Authors: Jiang Nan , Feng Meng-Qi , Cheng Lai-Chao , Kuang Li-Hua , Li Chao-Chao , Yin Zhao-Ping , Wang Rong , Xie Kai-Dong , Guo Wen-Wu , Wu Xiao-Meng 
Published: May 2023

Abstract
Cytoplasmic male sterility (CMS) has long been used to produce seedless fruits in perennial woody crops like citrus. A male-sterile somatic cybrid citrus (G1 + HBP) was generated by protoplast fusion between a CMS callus parent ‘Guoqing No. 1’ Satsuma mandarin (Citrus unshiu, G1) and a fertile mesophyll parent Hirado Buntan pummelo (Citrus grandis, HBP). To uncover the male-sterile mechanism of G1 + HBP, we compared the transcriptome profiles of stamen organ and cell types at five stages between G1 + HBP and HBP, including the initial stamen primordia, enlarged stamen primordia, pollen mother cells, tetrads, and microspores captured by laser microdissection. The stamen organ and cell types showed distinct gene expression profiles. A majority of genes involved in stamen development were differentially expressed, especially CgAP3.2, which was downregulated in enlarged stamen primordia and upregulated in tetrads of G1 + HBP compared with HBP. Jasmonic acid- and auxin-related biological processes were enriched among the differentially expressed genes of stamen primordia, and the content of jasmonic acid biosynthesis metabolites was higher in flower buds and anthers of G1 + HBP. In contrast, the content of auxin biosynthesis metabolites was lower in G1 + HBP. The mitochondrial tricarboxylic acid cycle and oxidative phosphorylation processes were enriched among the differentially expressed genes in stamen primordia, meiocytes, and microspores, indicating the dysfunction of mitochondria in stamen organ and cell types of G1 + HBP. Taken together, the results indicate that malfunction of mitochondria-nuclear interaction might cause disorder in stamen development, and thus lead to male sterility in the citrus cybrid.
From Peace Talks to Pandemics: The Continuum of Feminist Peace Activism
Authors: Anderson Miriam J , Eskandari Madeline F 
Published: May 2023

Abstract
Feminist scholarship has convincingly shown that violence is more accurately conceptualized as a continuum rather than a war/peace binary. While recent scholarship has elucidated women's peace activism during armed conflict, peace negotiations, and post-peace agreement transitions, we know little about the work of self-identified women peace activists beyond those highly visible moments. We examine the activities of a Burundian women's peace organization in exile, Mouvement Inamahoro, during COVID-19. Our data are derived from thirty-six semi-structured interviews with individual members of the organization and reviewing hundreds of primary-source documents. We find that from Inamahoro’s standpoint, the intersection of COVID-19 and exile constituted security threats, relevant to its mandate to build peace. Accordingly, it responded with humanitarian assistance, advocacy, and awareness-raising among its own members as well as with Burundians both inside and outside the country. Inamahoro also continued its regular activities to promote longer-term peace and security in Burundi through media programming, training women and girls for political leadership, and liaising with Burundian civil society and international non-governmental organizations (INGOs). Based on the continuum of violence concept and building inductively from the Inamahoro case, we propose a multidimensional continuum of activism that occurs before, during, and following conflict (dimension 1, time); is conducted in multiple arenas (dimension 2, space); deals with issues of insecurity at multiple levels (dimension 3, scale); and is concerned with threats that are structural, direct, and cultural/symbolic (dimension 4, type). In so doing, we offer a preliminary framework with which to examine the everyday activities of women peace activists, which constitute often overlooked interventions in global politics.
Validation of the AnticFast® Beta-Lactams Rapid Test Kit for Detection of Beta-Lactams (Penicillins and Cephalosporins) in Raw Cow’s Milk: AOAC Performance Tested MethodSM 032303
Authors: Broekaert Katrien , Ooghe Sigrid , Yang Meng , Tian Xiumei , Reybroeck Wim 
Published: May 2023

Abstract

Background
AnticFast® Beta-Lactams Rapid Test Kit is a qualitative two-step (2 min + 5 min) rapid lateral flow assay to detect β-lactam (penicillins and cephalosporins) antibiotic residues in raw commingled cow’s milk.

Objective
The method performance was evaluated according to Commission Decision 2002/657/EC, Commission Implementing Regulation 2021/808, and Community Reference Laboratories Residues Guidelines for the Validation of Screening Methods for Residues of Veterinary Medicines.

Methods
The AnticFast Beta-Lactams Rapid Test Kit was evaluated for detection capability, selectivity, false-positive results, repeatability, robustness, suitability for various milk types and milk compositions, milks from various species, and test kit consistency and stability. Samples included milks spiked at concentrations bracketing the EU maximum residue limits (MRLs) for β-lactams as well as bulk farm and tanker milks.

Results
The AnticFast Beta-Lactams Rapid Test Kit is specific for the detection of β-lactams in milk and does not detect compounds from other antibiotic families. Interference was seen with clavulanic acid, a β-lactamase inhibitor, which was expected. The test can detect all residues of β-lactams (penicillins and cephalosporins) present on the EU-MRL list for milk at their respective MRL except for desfuroylceftiofur and cephalexin, which were above the MRL. No false positives were detected in the 602 (300 blank farm and 302 tanker load) samples tested. Robustness testing indicated that the detection in heat-treated milk types may be slightly hampered. For substances with a detection capability well below the MRL, this interference does not cause problems since detection at MRL remains guaranteed, but care should be taken for substances with a CCβ at or near their MRL. Diminished sample flow was seen with reconstituted milk powder and blank ewes’ milk, so sample flow should always be verified for these milk types.

Conclusions
Results of this validation show that the AnticFast Beta-Lactams Rapid Test Kit is a reliable test for rapid screening of raw cows’ milk for residues of β-lactam antibiotics.

Highlights
AnticFast Beta-Lactams Rapid Test Kit is an easy, realiable, robust and highly specific test for screening of raw cows' milk for residues of penicillins and cephalosporins.
Sensitive Instrumental Method for Quantitative Determination of High-Brominated Flame Retardants in Human Serum Samples
Authors: Grande Cristina , Castaño Argelia , Ramos Juan José 
Published: May 2023

Abstract

Background
High-brominated flame retardants (BFRs) can be released into the environment from consumer products, such as electric and electronic equipment, and enter the human body by different pathways. Because of their toxicity and the regulations, it is very relevant to know their levels and trends in human samples. However, chromatographic serum analysis of some of these compounds represents nowadays a challenge in the general population.

Objective
To optimize and validate an instrumental method based on gas chromatography coupled to mass spectrometry, which, together with a simple sample preparation procedure, allows the analysis of decabromodiphenyl ether (BDE-209), decabromodiphenyl ethane (DBDPE), and tetrabromobisphenol A-bis(2,3-dibromopropyl ether) (TBBPA-DBPE) in human serum samples from the general population.

Method
To minimize the high degradation during instrumental analysis, GC parameters such as injection volumes, carrier flow rates, and column lengths were assessed and optimized. This instrumental approach in combination with solid-phase extraction (SPE) followed by multilayer silica gel column purification allowed satisfactory analysis using only 1 mL of serum.

Results
The performance of the complete method was evaluated at three spiking levels, 0.01, 0.05, and 0.2 ng/mL. Recoveries in the range 87–108% were obtained whereas the relative standard deviation in interday measurements, were, in general, lower than 19%. Limits of detection were in the range of 0.0045–0.0070 ng/mL. The optimized procedure was successfully applied to the determination of the investigated pollutants in real human samples of general population.

Conclusions
The proposed method could contribute to the inclusion of these environmental pollutants in human biomonitoring (HBM) studies, increasing the knowledge of levels and trends in the general population.

Highlights
GC-MS parameters optimization to minimize instrumental analytes degradation. Successful application to human serum samples from the general population. Tetrabromobisphenol A bis(2,3-dibromopropyl ether) human serum levels are reported for the first time.
Application of Rapid Identification and Determination of Moisture Content of Coptidis Rhizoma From Different Species Based on Data Fusion
Authors: Tian Mengyin , Ma Xiaobo , Liang Mengying , Zang Hengchang 
Published: May 2023

Abstract

Background
For thousands of years, traditional Chinese medicine (TCM) has been clinically proven, and doctors have highly valued the differences in utility between different species.

Objective
This study aims to replace the complex methods traditionally used for empirical identification by compensating for the information loss of a single sensor through data fusion. The research object of the study is Coptidis rhizoma (CR).

Method
Using spectral optimization and data fusion technology, near infrared (NIR) and mid-infrared (MIR) spectra were collected for CR. PLS-DA (n = 134) and PLSR (n = 63) models were established to identify the medicinal materials and to determine the moisture content in the medicinal materials.

Results
For the identification of the three species of CR, the mid-level fusion model performed better than the single-spectrum model. The sensitivity and specificity of the prediction set coefficients for NIR, MIR, and data fusion qualitative models were all higher than 0.95, with an AUC value of 1. The NIR data model was superior to the MIR data model. The results of low-level fusion were similar to those of the NIR optimization model. The RPD of the test set of NIR and low-level fusion model was 3.6420 and 3.4216, respectively, indicating good prediction ability of the model.

Conclusions
Data fusion technology using NIR and MIR can be applied to identify CR species and to determine the moisture content of CR. It provides technical support for the rapid determination of moisture content, with a fast analysis speed and without the need for complex pretreatment methods.

Highlights
This study is the first to introduce spectral data fusion technology to identify CR species. Data fusion technology is feasible for multivariable calibration model performance and reduces the cost of manual identification. The moisture content of CR can be quickly evaluated, reducing the difficulty of traditional methods.
Virtual reality-based assembly-level design for additive manufacturing decision framework involving human aspects of design
Authors: Auyeskhan Ulanbek , Steed Clint Alex , Park Soohyung , Kim Dong-Hyun , Jung Im Doo , Kim Namhun 
Published: May 2023

Abstract
There is a combinatorial explosion of alternative variants of an assembly design owing to the design freedom provided by additive manufacturing (AM). In this regard, a novel virtual reality-based decision-support framework is presented herein for extracting the superior assembly design to be fabricated by AM route. It specifically addresses the intersection between human assembly and AM hence combining design for assembly, and design for additive manufacturing using axiomatic design theory. Several virtual reality experiments were carried out to achieve this with human subjects assembling parts. At first, a two-dimensional table is assembled, and the data are used to confirm the independence of non-functional requirements such as assembly time and assembly displacement error according to independence axiom. Then this approach is demonstrated on an industrial lifeboat hook with three assembly design variations. The data from these experiments are utilized to evaluate the possible combinations of the assembly in terms of probability density based on the information axiom. The technique effectively identifies the assembly design most likely to fulfill the non-functional requirements. To the authors’ best knowledge, this is the first study that numerically extracts the human aspect of design at an early design stage in the decision process and considers the selection of the superior assembly design in a detailed design stage. Finally, this process is automated using a graphical user interface, which embraces the practicality of the currently integrated framework and enables manufacturers to choose the best assembly design.
The Non-Triliteral Theory of Verbal Morphology of the Karaite Joseph IBN Nūḥ
Authors: Dachman Joshua 
Published: May 2023

Abstract
This study examines the morphological theory of Joseph (Yūsuf) Ibn Nūḥ, a tenth-century Hebraist with a non-triliteral theory of Hebrew. Ibn Nūḥ’s approach is first outlined using the previously-developed framework for non-triliteral Hebrew verbal morphology. Ibn Nūḥ’s morphological model is then explored and it is determined that Ibn Nūḥ has an Item-and-Process model of morphology. With that insight it is suggested that Ibn Nūḥ recognizes roots only ‘abstractively’, with word-forms being constructed from ‘bases’ rather than ‘roots’. Example passages are presented to demonstrate the contrast between Ibn Nūḥ’s and Dunash Ibn Labraṭ’s respective models of morphology.
Estimation of Covid-19 Prevalence Dynamics from Pooled Data
Authors: Scherting Braden , Peel Alison J , Plowright Raina , Hoegh Andrew 
Published: May 2023

Abstract
Estimating the prevalence of a disease, such as COVID-19, is necessary for evaluating and mitigating risks of its transmission. Estimates that consider how prevalence changes with time provide more information about these risks but are difficult to obtain due to the necessary survey intensity and commensurate testing costs. Motivated by a dataset on COVID-19, from the University of Notre Dame, we propose pooling and jointly testing multiple samples to reduce testing costs. A nonparametric, hierarchical Bayesian model is used to infer population prevalence from the pooled test results without needing to retest individuals from pools that test positive. This approach is shown to reduce uncertainty compared to individual testing at the same budget and to produce similar estimates compared to individual testing at a much higher budget through simulation studies and an analysis of COVID-19 infections at Notre Dame.
The extended predicative Mahlo universe in Martin-Löf type theory
Authors: Dybjer Peter , Setzer Anton 
Published: May 2023

Abstract
This paper addresses the long-standing question of the predicativity of the Mahlo universe. A solution, called the extended predicative Mahlo universe, has been proposed by Kahle and Setzer in the context of explicit mathematics. It makes use of the collection of untyped terms (denoting partial functions) which are directly available in explicit mathematics but not in Martin-Löf type theory. In this paper, we overcome the obstacle of not having direct access to untyped terms in Martin-Löf type theory by formalizing explicit mathematics with an extended predicative Mahlo universe in Martin-Löf type theory with certain indexed inductive-recursive definitions. In this way, we can relate the predicativity question to the fundamental semantics of Martin-Löf type theory in terms of computation to canonical form. As a result, we get the first extended predicative definition of a Mahlo universe in Martin-Löf type theory. To this end, we first define an external variant of Kahle and Setzer’s internal extended predicative universe in explicit mathematics. This is then formalized in Martin-Löf type theory, where it becomes an internal extended predicative Mahlo universe. Although we make use of indexed inductive-recursive definitions that go beyond the type theory $\mathbf {IIRD}$ of indexed inductive-recursive definitions defined in previous work by the authors, we argue that they are constructive and predicative in Martin-Löf’s sense. The model construction has been type-checked in the proof assistant Agda.
Melanoma-related costs by disease stage and phase of management in Ireland
Authors: Crealey Grainne E , Hackett Caitriona , Harkin Katharine , Heckmann Patricia , Kelleher Fergal , Lyng Áine , McCarthy Triona , McEnery Maria , Meaney Clare , Roche Darren , Tobin Anne-Marie 
Published: May 2023

Abstract

Background
Management options for the treatment of melanoma have expanded in recent years. In an era of promising, but expensive novel pharmacological treatments, robust stage-specific melanoma-related cost estimates are necessary to support budgetary planning, evaluation of cost-effectiveness and to contribute to the investment case for prevention.

Methods
A detailed decision model, describing the melanoma care pathway (by disease stage) from diagnosis, through treatment and follow-up was developed over a 5-year time frame from the perspective of the Irish healthcare system. The model was populated with real-world data from the National Cancer Registry Ireland. Uncertainty was explored using one-way and probabilistic sensitivity analysis.

Results
The cost of managing a case of melanoma diagnosed at Stage IV (€122 985) was more than 25 times more expensive than managing a case diagnosed at Stage IA (€4269). Total costs were sensitive to the choice of immunotherapeutic and targeted drug, duration of treatment and proportion of patients receiving immunotherapy agents.

Conclusions
The rising incidence of melanoma and high cost of new novel therapies presents an immediate challenge to cancer control and public health globally. This study highlights the cost differential between early and late detection and the potential return on investment for prevention versus high-cost treatment.