bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents
Authors: Thomas Gregg W C , Hughes Jonathan J , Kumon Tomohiro , Berv Jacob S , Nordgren C Erik , Lampson Michael , Levine Mia , Searle Jeremy B , Good Jeffrey M 
Published: February 2025

Abstract
A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents—a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultraconserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.
Barberry Anthocyanins: Recent Advances in Extraction, Stability, Biological Activities and Utilization in Food Systems- A Review
Authors: Khezri Sima , Ghanbarzadeh Babak , Ehsani Ali 
Published: February 2025

Abstract
Barberry anthocyanins have attracted more attention in the food industry due to their natural red colourants and beneficial characteristics. These compounds exhibit a range of biological activities, such as antioxidant, antibacterial, anti-diabetic, anticancer and neuroprotective effects, which indicates their potential role in the development of functional foods and therapeutic formulations. To extract the optimal yield of these valuable pigments from barberry fruit, it is essential to use the most suitable extraction method. While traditional methods like solvent extraction are commonly used, novel techniques such as pulsed electric field processing, ultrasound-assisted extraction, and high-pressure carbon dioxide extraction offer advantages like reduced solvent demand, shorter processing time, higher yields and lower energy consumption. Despite the numerous beneficial features of anthocyanins, their application is restricted due to their low stability and bioavailability, which is affected by environmental factors such as pH, temperature, light, oxygen, enzymatic activity, and ascorbic acid. Strategies to enhance their structural stability, including copigmentation and encapsulation, are necessary to expand their further application in the food industry.
lPrediction of Vancomycin Area-under-the-curve using Trough Concentrations Only: Performance Evaluation of Pediatric Population Pharmacokinetic Models
Authors: Schouwenburg Stef , Preijers Tim , Flint Robert B , Wildschut Enno D , Koch Birgit C P , de Winter Brenda C M , Abdulla Alan 
Published: February 2025

Abstract

Objectives
In pediatric patients, vancomycin plays a pivotal role in combating infections, necessitating precise therapeutic drug monitoring to ensure efficacy and safety. The adoption of model-informed precision dosing (MIPD) has demonstrated potential in optimizing dosing strategies based on the area under the concentration-time curve (AUC24h). However, predictive performance of population pharmacokinetic models using only trough concentrations to estimate AUC24h has not been evaluated.

Methods
Predictive performance of 23 vancomycin population pharmacokinetic models was retrospectively evaluated in two cohorts; (A) 21 subjects with PNA&lt;50 days, (B) 124 subjects with PNA≥50 days. Multiple scenarios were investigated using; (a) peak and trough concentration, (b) using either peak or (c) trough concentration solely, (d) covariate information (a priori). The median AUC24h per subject across all models was used as ‘true’ AUC24h.

Results
For both cohorts, relative root mean square error (rRMSE) for the AUC24h precision using only trough concentrations was similar to the rRMSE using both a peak and trough sample. For cohort A, the model by Chen, Colin, and Mehrotra showed best trough-based performance with the lowest relative Bias (rBias) (-3.3% and -2.6%) and rRMSE (6.8% and 7.3%). For cohort B, the models from Alsultan and Lv illustrated the lowest rBias (1.75% and -5.4%) and rRMSE (16.6% and 15.1%).

Conclusions
This study illustrates that trough concentration-based AUC24h estimation is a feasible approach in vancomycin MIPD. These findings endorse the selected models for advanced MIPD vancomycin therapy in pediatrics, though further investigation into clinical outcomes is recommended.
A comprehensive analysis of antimicrobial resistance of clinical emm89 Streptococcus pyogenes in Japan
Authors: Gong Weichen , Ono Masayuki , Yamaguchi Masaya , Motooka Daisuke , Hirose Yujiro , Higashi Kotaro , Kobayashi Momoko , Ikeda Eri , Sumitomo Tomoko , Okuno Rumi , Yamaguchi Takahiro , Kawahara Ryuji , Otsuka Hitoshi , Nakanishi Noriko , Kazawa Yu , Nakagawa Chikara , Yamaguchi Ryo , Sakai Hiroo , Matsumoto Yuko , Ikebe Tadayoshi , Kawabata Shigetada 
Published: February 2025

Abstract

Objectives
Streptococcus pyogenes is involved in a wide range of diseases, including pharyngitis and life-threatening invasive infections. Increasing prevalence of antimicrobial resistance (AMR) has been reported worldwide in various bacteria, limiting the use of antibiotics in infection cases. The present study investigated the AMR of most prevalent S. pyogenes emm types, including emm89 strains in Japan.

Methods
A total of 368 previously identified S. pyogenes isolates (311 emm89 strains and 57 of other emm types), which were previously isolated from patients with invasive and non-invasive infections throughout Japan, were used in the analyses. The minimum inhibitory concentrations of seven antibiotics, including penicillin-G, azithromycin (AZM) and clindamycin, were determined, and whole-genome sequences of AMR-associated genes were screened.

Results
We identified 47 resistant strains, of which 91.49% (43/47) were resistant to AZM and/or clindamycin. A strong correlation was observed between non-invasive phenotypes and AMR. Whole-genome analysis indicated the wide distribution of three AMR-related genes, ermT, folP and lmrP, among the emm89 strains. Additionally, tetO was detected in tetracycline-resistance and soxS and mel was detected in chloramphenicol-resistance only in emm4 strains.

Conclusions
The high prevalence of S. pyogenes resistance to AZM and/or clindamycin poses a threat to public health in Japan; thus, the development of next-generation antimicrobial therapies is imperative.
Grapevine leafroll-associated virus 3: A global threat to the grape and wine industries but a gold mine for scientific discovery
Authors: Fust Catherine , Lameront Patrick , Shabanian Mehdi , Song Yashu , Abou Kubaa Raied , Bester Rachelle , Maree Hans J , Al Rwahnih Maher , Meng Baozhong 
Published: February 2025

Abstract
Grapevine leafroll disease is the most damaging viral disease afflicting global grape and wine production. Of the five viruses likely associated with the disease, grapevine leafroll-associated virus 3 (GLRaV3) is believed to be the predominant agent, albeit its role as the causal agent has remained uncertain. GLRaV3 (species Ampelovirus trivitis, genus Ampelovirus, family Closteroviridae) has the third largest single-stranded, positive-sense RNA genome among plant viruses at ~18.5 kb, only surpassed by two other members of the family Closteroviridae, citrus tristeza virus, and GLRaV1. GLRaV3 is unique among plant viruses in several ways including the size of its genome, the long non-coding regions, and its association with the outer mitochondrial membrane for viral replication. Unfortunately, our understanding of the molecular mechanisms governing GLRaV3 genome replication, gene expression and virus-host interactions is poor due to many factors, including the unavailability of infectious cDNA clones and effective experimental system to initiate grapevine infection with viral clones until recently. In this review, we capture some recent advances in GLRaV3 research towards the establishment of infectious clones, grapevine inoculation systems, as well as approaches towards elucidating the function of GLRaV3-encoded proteins. We also present a working model to explain GLRaV3 pathogenesis.
Preliminary Effectiveness of a Companion Dog Whole Health Intervention for Improving Balance and Gait Quality in Veterans
Authors: Rekant Julie , Giffuni Jamie , Addison Odessa , Ortmeyer Heidi 
Published: February 2025

ABSTRACT

Introduction
The benefits of exercise for older adults are well known; however, most older adults do not meet recommendations for regular physical activity. Alternative methods of improving physical activity are important and can be effective at improving mobility. This analysis evaluated if participation in a Whole Health companion dog adoption program supported changes in balance and gait performance for veterans. The role of time veteran and dog spent being physically active together (i.e., walking) on observed balance and gait changes was also explored.

Materials and Methods
Veterans were paired with companion dogs and physical function, self-reported physical activity, and gait quality with an instrumented 6-minute walk test were assessed at baseline and after 1 year of participation. Physical activity was captured by accelerometers worn by both the veteran and dog. Paired samples t-tests were used to evaluate change in gait and physical performance measures from baseline to follow-up. Simple linear regressions were used to explore the role of time the veteran and companion dog spent being active together on observed changes in gait and physical function. Participants completed informed consent before participation in the IRB-approved study procedures (HP-97664; 1651218).

Results
Fourteen veterans (71.4% male, 62.3 ± 12.0 years) participated in the program. Improvements were seen in balance (Four Square Step Test change 95% CI: −3.94 to -1.36 s), lower body strength (30-second Chair Stand change 95% CI: 1.89–6.40 reps), and endurance (6-Minute Walk Test change 95% CI: 27.03–80.55 m). Gait quality improved (stance time 95% CI: −0.11 to -0.03 s, stride time 95% CI: −0.09 to -0.02 s). Of participants, 42% reported increased physical activity at follow-up. The percentage of the day veterans and their dogs spent being active together explained 31%-33% of the changes in functional performance.

Conclusions
A Whole Health companion dog adoption intervention can improve gait, balance, physical functioning, and physical activity.
ACACIAS I: element abundance labels for 192 stars in the dwarf galaxy NGC 6822
Authors: Ness Melissa K , Mendel J Trevor , Buder Sven , Wheeler Adam , Ji Alexander P , Mijnarends Luka , Venn Kim , Starkenburg Else , Leaman Ryan , Grasha Kathryn , Aquilina Sarah 
Published: February 2025

ABSTRACT
The element abundances of local group galaxies connect enrichment mechanisms to galactic properties and serve to contextualize the Milky Way’s abundance distributions. Individual stellar spectra in nearby galaxies can be extracted from integral field unit (IFU) data, and provide a means to take an abundance census of the local group. We introduce a programme that leverages $R=1800$, $\mathrm{SNR}=15$, IFU resolved spectra from the multi unit spectroscopic explorer . We deploy the data-driven modelling approach for labelling stellar spectra with stellar parameters and abundances, of The Cannon, on resolved stars in NGC 6822. We construct our model for The Cannon using $\approx$19 000 Milky Way lamost spectra with apogee labels. We report six inferred abundance labels (denoted $\ell _\mathrm{X}$), for 192 NGC 6822 disc stars, precise to $\approx$0.15 dex. We validate our generated spectral models provide a good fit to the data, including at individual atomic line features. We infer mean abundances of $\ell _\mathrm{[Fe/H]} = -0.90 \pm 0.03$, $\ell _\mathrm{[Mg/Fe]} = -0.01 \pm 0.01$, $\ell _\mathrm{[Mn/Fe]} = -0.22 \pm 0.02$, $\ell _\mathrm{[Al/Fe]} = -0.33 \pm 0.03$, $\ell _\mathrm{[C/Fe]} =-0.43 \pm 0.03$, $\ell _\mathrm{[N/Fe]} =0.18 \pm 0.03$. These abundance labels are similar to those of dwarf galaxies observed by apogee, and the lower enhancements for NGC 6822 compared to the Milky Way are consistent with expectations. This approach supports a new era in extragalactic archaeology of characterizing the local group enrichment diversity using low-resolution, low signal to noise ratio IFU resolved spectra. Furthermore, we conclude that it is feasible to build a model based on spectra observed with one instrument and apply it to spectra obtained with another.
PSR J1631−4722: the discovery of a young and energetic pulsar in the supernova remnant G336.7+0.5
Authors: Ahmad A , Dai S , Lazarević S , Filipović M D , Johnston S , Kerr M , Li D , Maitra C , Manchester R N 
Published: February 2025

ABSTRACT
Detecting a pulsar associated with a supernova remnant (SNR) and/or pulsar wind nebula (PWN) is crucial for unraveling its formation history and pulsar wind dynamics, yet the association with a radio pulsar is observed only in a small fraction of known SNRs and PWNe. In this paper, we report the discovery of a young pulsar J1631−4722, associated with the Galactic SNR G336.7$+$0.5 using Murriyang, Commonwealth Scientific and Industrial Research Organisation (CSIRO)’s Parkes radio telescope. It is also potentially associated with a PWN revealed by the Rapid ASKAP (Australian Square Kilometre Array Pathfinder) Continuum Survey (RACS). This 118 ms pulsar has a high dispersion measure of $\sim$873 pc cm$^{-3}$ and a rotation measure of –1004 rad m$^{-2}$. Because of such a high DM, at frequencies below 2 GHz, the pulse profile is significantly scattered, making it effectively undetectable in previous pulsar surveys at $\sim$1.4 GHz. Follow-up observations yield a period derivative of $\dot {P} = 5.5\times 10^{-14}$, implying a characteristic age, $\tau _{\mathrm{ c}} = 33.9$ kyr, and spin-down luminosity, $\dot {E} = 1.3\times 10^{36}$ erg s$^{-1}$. PSR J1631−4722, with its high spin-down luminosity and potential link to a PWN, stands out as a promising source of the high-energy $\gamma$-ray emission observed in the region.
Courtship behavior of a secretive forest tinamou, Tinamus major (Great Tinamou)
Authors: Guo Yinger , Falk Jay J , Medina-Madrid Jorge L , Wang Silu 
Published: February 2025

Abstract
The mating systems of many rainforest birds remain poorly understood, especially those that elude observation in dense forest understories. Here we documented mating behaviors in a pair of Tinamus major (Great Tinamou), a secretive species with a wide distribution across the lowland Central and South American tropics. Despite anecdotal preconceptions that males court females, we observed predominant courtship displays from the putative female tinamou. In this mating ritual recorded in the birds’ natural habitat, only the putative female vocalized in the form of clucking and soft-rolling songs, and courted the putative male with a suite of courtship displays, such as neck-elongation, tail-raising, crouching, and feather-fluffing. In contrast, the putative male watched while standing still, approached, tail-raised, walked away, and mounted the putative female a few times. The clucking song of the putative female had not been described previously but we repeatedly observed this song type immediately before the soft-rolling songs during the courtship interaction. Clucking was of lower frequency and around 10 times shorter than the soft-rolling songs. The clucking and soft-rolling songs sung by the putative female were of lower frequency than the common morning territorial songs recorded in the vicinity. This behavioral auditory analysis of the secretive mating ritual of a rainforest tinamou reveals a previously underappreciated female role in their courtship displays.
Classifiers
Authors: Aikhenvald Alexandra Y 
Published: February 2025

Abstract
Almost all languages have some grammatical means for the linguistic categorization of nouns. Well-known systems such as the lexical numeral classifiers of South-East Asia, on the one hand, and the highly grammaticalized gender agreement classes of Indo-European languages, on the other, are the extremes of a contiuum. They can have a similar semantic basis, and one can develop from the other. Classifiers come in different morphological forms; they can be free nouns, clitics, or affixes. Some languages combine several varieties of classifiers. Different types of classifiers show varying correlations with other grammatical categories. In addition, they differ in their semantics, in the way they develop, and in the way they become obsolescent and disappear. These parameters are the basis for the typology of classifiers presented here. This book is almost certainly the most substantial cross-linguistic account of classifiers ever published. Its range of exemplification includes major and minor languages from every continent (several from the author's own fieldwork). The work combines original research with innovative analysis and will interest typologists, those working in the field of morphosyntactic variation and lexical semantics, and exponents of formal theories who wish to explain the range of linguistic diversity found in natural language.
Noun Classifiers
Authors: Aikhenvald Alexandra Y 
Published: February 2025

Abstract
Noun classifiers characterize the noun and cooccur with it in a noun phrase. They have been recognized in Australian (Dixon 1977; 1982; Wilkins 1989; Sands 1995: 269-70) and in Mesoamerican languages (Craig 1986b; 1986c). Their properties have been discussed by Craig (1992; forth coming; §3.2.3 below). In the Australianist tradition, they are called ‘generic classifiers’, or ‘generics’ (Sands 1995: 269-70; Harvey and Reid 1997: 9-10).The definitional property of noun classifiers is that their presence in a noun phrase is independent of other constituents inside or outside it. Their ‘scope’ is a noun phrase. They are a type of non-agreeing noun categorization device, their choice being determined by lexical selection, and not by matching any inflectional properties of nouns with any other constituents of a noun phrase.
Multiple Classifier Languages
Authors: Aikhenvald Alexandra Y 
Published: February 2025

Abstract
The same, or almost the same, set of morphemes can be used in more than one classifier environment. These morphemes may have different grammatical properties, or be more or less obligatory depending on what classifier environment they are in. We label them ‘multiple classifier’ systems. Noun categorization in multiple classifier languages is discussed in §9.1. In §9.2 the multiple classifier systems are compared with noun class agreement on different targets. In §9.3 we discuss some borderline cases.
Semantics of Noun Categorization Devices
Authors: Aikhenvald Alexandra Y 
Published: February 2025

Abstract
All noun categorization devices have some semantic basis. Different classifier types tend to correlate with different semantic parameters. Many systems allow variable choice of classifiers; then classifiers may specify the meaning of a polysemous noun. The semantic parameters employed in noun categorization are discussed in §11.1. The semantics of each type of classifier is considered in §11.2. The semantic organization of classifier systems and their functions are considered in the next chapter.
Semantic Organization and Functions of Noun Categorization
Authors: Aikhenvald Alexandra Y 
Published: February 2025

Abstract
This chapter considers various aspects of the semantics of noun categorization devices and their implications for the study of human cognition and culture. Semantic features encoded in noun categorization reflect principles of human cognition and world perception. This is why it has often been argued that classifiers offer ‘a unique window’ into studying how humans construct representations of the world and encode them into their languages (Lakoff 1986; Craig forthcoming). The semantics of classifiers is often conditioned by the socio-cultural and physical environment in which a language is spoken and is often affected by social changes, language planning, and cultural obsolescence.
Origin and Development of Noun Categorization Devices
Authors: Aikhenvald Alexandra Y 
Published: February 2025

Abstract
This chapter deals with the origin, evolution, and decay of classifiers of different kinds which may have different language-internal-lexical or grammatical-sources and may involve different grammaticalization paths. I also discuss the paths of evolution and restructuring of noun categorization devices, and the development and loss of agreement on different targets. Language-internal and language-external motivation for the emergence, restructuring and decay of classifiers are considered next. Further on, I analyse the semantic changes within classifier systems which take place in the course of grammaticalization-from a lexical source to a classifier--as well as within an already established classifier system. Appendix 2 provides further examples of semantic changes in classifiers. Different kinds of classifiers tend to have different language-internal sources-some have lexical sources (see §13.1), while others come from closed grammatical classes; for instance, a demonstrative can become a gender agreement affix, or an adposition can become a locative classifier (see §13.2).
Conclusions
Authors: Aikhenvald Alexandra Y 
Published: February 2025

Abstract
This concluding chapter recapitulates and summarizes the general themes which have emerged from a cross-linguistic study of noun categorization devices. An overview of established classifier types used in different morphosyntactic environments and of their synchronic and diachronic properties-which cover their morphological realization and role in agreement, principles of assignment, interaction with other grammatical categories, semantics, and functions, as well as their origin and role in language acquisition and dissolution-are summarized in §15.currence of different classifiers in one language, multiple classifier languages, and the problem of prototypes and continua in noun categorization are discussed in §15.2. The last section, §15.3, considers further prospects for the study of noun categorization devices. Properties of classifier types In this section I present an overview of the established types of classifiers.