bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations
Authors: Dunn Tamsen , Sethuraman Arun 
Published: November 2024

Abstract
Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history of angiosperms. Much work has been done to model the genomic consequences and evolutionary significance of WGD. While researchers have historically modeled polyploids as either allopolyploids or autopolyploids, the variety of natural polyploids span a continuum of differentiation across multiple parameters, such as the extent of polysomic versus disomic inheritance, and the degree of genetic differentiation between the ancestral lineages. Here we present a forward-time polyploid genome evolution simulator called SpecKS. SpecKS models polyploid speciation as originating from a 2D continuum, whose dimensions account for both the level of genetic differentiation between the ancestral parental genomes, as well the time lag between ancestral speciation and their subsequent reunion in the derived polyploid. Using extensive simulations, we demonstrate that changes in initial conditions along either dimension of the 2D continuum deterministically affect the shape of the Ks histogram. Our findings indicate that the error in the common method of estimating WGD time from the Ks histogram peak scales with the degree of allopolyploidy, and we present an alternative, accurate estimation method that is independent of the degree of allopolyploidy. Lastly, we use SpecKS to derive tests that infer both the lag time between parental divergence and WGD time, and the diversity of the ancestral species, from an input Ks histogram. We apply the latter test to transcriptomic data from over 200 species across the plant kingdom, the results of which are concordant with the prevailing theory that the majority of angiosperm lineages are derived from diverse parental genomes and may be of allopolyploid origin.
Intercellular mosaic methylation in fast-growing Mycobacterium tuberculosis clinical isolates
Authors: Ahmadi Jeshvaghane Maryam , Modlin Samuel J , Conkle-Gutierrez Derek , Espinoza Monica E , Valafar Faramarz 
Published: November 2024

Abstract
Orphan DNA adenine methyltransferases (MTases) of Mycobacterium tuberculosis (Mtb) exhibit diversity across clinical isolates, but the forces driving this variation are not entirely clear. Recently, we observed several isolates exhibiting anomalous hypomethylation by Type I MTase Mycobacterial Adenine Methyltransferase C (MamC) despite a wild-type mamC genotype (‘MamC-anomalous’ isolates). Investigating this hypomethylation through multiple analyses revealed three key findings. First, heterogeneity analysis revealed intercellular mosaic methylation (IMM) in MamC-anomalous isolates. While they often exhibit phase-variable heterogeneity, this is the first report of IMM by a prokaryotic Type I MTase. Second, MamC-anomalous isolates exhibited a large, stable difference in chromosome copy number along the replication axis (a proxy for bacterial growth rate), suggesting a distinct growth phase accompanied by MamC hypomethylation. Third, MamC methylation efficiency decreased progressively with distance from the origin of replication on both strands, with a marked exaggeration in MamC-anomalous isolates. In contrast, other Mtb MTases (MamA and MamB) exhibited lower methylation levels away from the origin only on the lagging strand, and without exaggeration in MamC-anomalous isolates. We conclude that, among Mtb MTases, MamC DNA methylation is uniquely linked to growth dynamics.
Machine learning prediction of brain metastasis invasion pattern on brain magnetic resonance imaging scans
Authors: Najafian Keyhan , Rehany Benjamin , Nowakowski Alexander , Ghazimoghadam Saba , Pierre Kevin , Zakarian Rita , Al-Saadi Tariq , Reinhold Caroline , Babajani-Feremi Abbas , Wong Joshua K , Guiot Marie-Christine , Lacasse Marie-Constance , Lam Stephanie , Siegel Peter M , Petrecca Kevin , Dankner Matthew , Forghani Reza 
Published: November 2024

Abstract

Background
Brain metastasis invasion pattern (BMIP) is an emerging biomarker associated with recurrence-free and overall survival in patients, and differential response to therapy in preclinical models. Currently, BMIP can only be determined from the histopathological examination of surgical specimens, precluding its use as a biomarker prior to therapy initiation. The aim of this study was to investigate the potential of machine learning (ML) approaches to develop a noninvasive magnetic resonance imaging (MRI)-based biomarker for BMIP determination.

Methods
From an initial cohort of 329 patients, a subset of 132 patients met the inclusion criteria for this retrospective study. We evaluated the ability of an expert neuroradiologist to reliably predict BMIP. Thereafter, the dataset was randomly divided into training/validation (80% of cases) and test subsets (20% of cases). The ground truth for BMIP was the histopathologic evaluation of resected specimens. Following MRI sequence co-registration, advanced feature extraction techniques deriving hand-crafted radiomic features with traditional ML classifiers and convolution-based deep learning (CDL) models were trained and evaluated. Different ML approaches were used individually or using ensembling techniques to determine the model with the best performance for BMIP prediction.

Results
Expert evaluation of brain MRI scans could not reliably predict BMIP, with an accuracy of 44%–59% depending on the semantic feature used. Among the different ML and CDL models evaluated, the best-performing model achieved an accuracy of 85% and an F1 score of 90%.

Conclusions
ML approaches can effectively predict BMIP, representing a noninvasive MRI-based approach to guide the management of patients with brain metastases.
A tactile perception method with flexible grating structural color
Authors: Qiu Yuze , Yan Chunfei , Zhang Yan , Yang Shengxuan , Yao Xiang , Ai Fawen , Zheng Jinjin , Zhang Shiwu , Yu Xinge , Dong Erbao 
Published: November 2024

ABSTRACT
Affordable high-resolution cameras and state-of-the-art computer vision techniques have led to the emergence of various vision-based tactile sensors. However, current vision-based tactile sensors mainly depend on geometric optics or marker tracking for tactile assessments, resulting in limited performance. To solve this dilemma, we introduce optical interference patterns as the visual representation of tactile information for flexible tactile sensors. We propose a novel tactile perception method and its corresponding sensor, combining structural colors from flexible blazed gratings with deep learning. The richer structural colors and finer data processing foster the tactile estimation performance. The proposed sensor has an overall normal force magnitude accuracy of 6 mN, a planar resolution of 79 μm and a contact-depth resolution of 25 μm. This work presents a promising tactile method that combines wave optics, soft materials and machine learning. It performs well in tactile measurement, and can be expanded into multiple sensing fields.
Influence of global warming and human activity on mercury accumulation patterns in wetlands across the Qinghai–Tibet Plateau
Authors: Feng Xinbin , Wang Xun , Jia Longyu , Yuan Wei , Lu Meng , Liu Nantao , Wu Fei , Cai Xinyuan , Wang Feiyue , Lin Che-Jen 
Published: November 2024

ABSTRACT
Wetlands in the Qinghai–Tibet Plateau are a unique and fragile ecosystem undergoing rapid changes. We show two unique patterns of mercury (Hg) accumulation in wetland sediments. One is the ‘surface peak’ in monsoon-controlled regions and the other is the ‘subsurface peak’ in westerly-controlled regions. The former is attributed to the combined effects of increasing anthropogenic emissions and climate-induced changes in the cryosphere and wetland hydrology in the last 100−150 years. The climate changes in westerly-controlled regions in the last 50−70 years led to a fluctuation in hydrology and Hg peak in the sediment subsurface. The increase in legacy Hg input from soil erosion has largely enhanced the Hg accumulation rate in wetlands since the 1950s, especially in the proglacial wetlands. We highlight that accelerated glacier melting and permafrost thawing caused by global warming have altered geomorphology and hydrology, and affected Hg transport and accumulation in wetlands.
Etiology, Risk Factors, and Outcomes of Bacteremia in Patients With Hematologic Malignancies and Febrile Neutropenia in Uganda
Authors: Lubwama Margaret , Holte Sarah E , Zhang Yuzheng , Mubiru Kelvin R , Katende George , Orem Jackson , Kateete David P , Bwanga Freddie , Phipps Warren 
Published: November 2024

Abstract

Background
We determined the etiology, risk factors, and outcomes associated with bacteremia in patients with hematologic malignancies and febrile neutropenia (FN) at the Uganda Cancer Institute (UCI).

Methods
UCI adult and pediatric inpatients with hematologic malignancies and FN were prospectively enrolled and followed up to determine 30-day mortality. Blood drawn from participants with FN was cultured in the BACTEC 9120 blood culture system. Antimicrobial susceptibility testing was performed with the disk diffusion method on identified bacteria. Logistic regression and Cox proportional hazards regression were applied to estimate associations between participant characteristics and FN, bacteremia, and mortality.

Results
Of 495 participants, the majority (n = 306 [62%]) were male. Median age was 23 years (interquartile range, 11–42 years). Of the 132 participants who experienced FN, 43 (33%) had bacteremia. Participants with younger age (odds ratio [OR], 0.98; P = .05), severe neutropenia (OR, 2.9; P = .01), hypotension (OR, 2.46; P = .04), mucositis (OR, 2.77; P = .01), and receipt of chemotherapy (OR, 2.25; P = .03) were more likely to have bacteremia. Fifty (78%) bacteria isolated were gram negative. Escherichia coli (n = 25 [50%]) was predominant. Thirty-seven of 43 (86%) episodes were caused by multidrug-resistant (MDR) bacteria. Thirty-day overall survival for participants with bacteremia was significantly lower than that for participants with no bacteremia (P = .05). MDR bacteremia (hazard ratio, 1.84; P = .05) was associated with increased risk of death.

Conclusions
Bacteremia was frequent in patients with hematologic cancer and FN and was associated with poor survival. MDR bacteria were the main cause of bacteremia and mortality. There is a need for robust infection control and antimicrobial stewardship programs in cancer centers in sub-Saharan Africa.
Prosper’s Law: putting the lex back into orandi and credendi
Authors: Wright O T I 
Published: November 2024

Abstract
This article demonstrates the centrality of ‘law’ to the famous dictum of Prosper of Aquitaine, lex orandi lex credendi. In its various appearances since the fifth century AD, the relationship in Prosper’s dictum between worship and belief has been, at best, assumed. I propose that the nature of that relationship is actually explicit in the dictum itself. That is, Prosper’s invocation of law—‘lex’. In particular, I demonstrate the importance of that term from a modern and an ancient perspective: the modern notion of speech-act theory; and the historical context of the Codex Theodosius, newly promulgated at the time of Prosper’s writing. From those perspectives, Prosper’s dictum is newly perceived as words which do things. It is both an example of heresiology and also seeks to establish the law. On the one hand, there appears to be a normativity newly prescribed for doctrine (credendi) following the lead of worship (orandi). On the other hand, I argue that Prosper’s prescription is for something more lively than ‘mere’ ritual normativity, namely established custom. This, as I will show, emerges from the contribution of the familiar Roman pair ius and lex.
Global Comparative Law?
Authors: Pirie Fernanda 
Published: November 2024

Abstract
The Cambridge Handbook of Comparative Law, edited by Matthias Siems and Po Jen Yap, continues recent calls to expand the field of comparative law. By including authors drawn from all parts of the world, it presents ‘new perspectives’ on the field. This wide geographic remit proves successful as a way of moving beyond traditional ‘families’ and doctrinal topics. The contributors raise new themes for comparison, many related to public law and processes of change. But this, in turn, raises questions about the purposes of expanding the field. The volume largely concerns the laws and legal issues of modern states, and the authors do not venture far into history. Nor do they consider the alternatives offered by religious and traditional legal systems or forms of non-state ordering. I suggest that these subjects could productively expand the field even further, raising more theoretical questions about what law is and does.
Maternally expressed FERTILIZATION-INDEPENDENT ENDOSPERM1 regulates seed dormancy and aleurone development in rice
Authors: Cheng Xiaojun , Zhang Su , E Zhiguo , Yang Zongju , Cao Sijia , Zhang Rui , Niu Baixiao , Li Qian-Feng , Zhou Yong , Huang Xin-Yuan , Liu Qiao-Quan , Chen Chen 
Published: November 2024

Abstract
Seed dormancy, an essential trait for plant adaptation, is determined by the embryo itself and the surrounding tissues. Here, we found that rice (Oryza sativa) FERTILIZATION-INDEPENDENT ENDOSPERM1 (OsFIE1) regulates endosperm-imposed dormancy and the dorsal aleurone thickness in a manner dependent on the parent of origin. Maternally expressed OsFIE1 suppresses gibberellin (GA) biosynthesis in the endosperm by depositing trimethylation of lysine 27 on histone H3 (H3K27me3) marks on GA biosynthesis-related genes, thus inhibiting germination and aleurone differentiation. Knockout of rice GA 20-oxidase1 (OsGA20ox1) alleviated the phenotypic defects in osfie1. The aleurone-positive determinant Crinkly 4 (OsCR4) is another target of the OsFIE1-containing Polycomb repressive complex 2 (PRC2). We found that OsFIE1 plays an important role in genomic imprinting in the endosperm of germinating seeds, particularly for paternally expressed genes associated with H3K27me3. The increased aleurone thickness of osfie1 substantially improved grain nutritional quality, indicating that the osfie1 gene may be utilized for breeding nutrient-enriched rice. The findings provide insights into the essential roles of PRC2-mediated H3K27me3 methylation in the acquisition of seed dormancy and endosperm cell differentiation in rice.
How far have we advanced in simulation-based training for policing and law enforcement? A literature review 2014–24
Authors: See Pei Jun , Davies Amanda 
Published: November 2024

Abstract
The twenty-first century demands on police and law enforcement similarly demand effective, efficient and relevant officer training endeavours. Guided by the PRISMA literature review model this study identified and analysed a total of 35 peer-reviewed studies (2014–24) centred on simulation scenario-based training offering insight into (1) what are the different types and platforms used in scenario-based simulation training and (2) what skills are being trained in simulation-based exercises. The findings revealed a preference for high-fidelity technological tools for short training scenarios centred on tactical and procedural knowledge. Conversely, incidents that require conversations and negotiations remain restricted to platforms with limited technological integration or live role-players. The review identified (1) skills for daily operations, decision making, de-escalation training, major incident management were those most commonly attributed to simulation-based training and (2) the extent to which virtual environments can replicate major incidents that are sufficiently immersive for training continues to be a work in progress.
Reconceptualizing Administrative Burden Around Onerous Experiences
Authors: Daigneault Pierre-Marc 
Published: November 2024

ABSTRACT
Despite ongoing discussions on the need to improve the conceptualization and measurement of administrative burden, several conceptual problems remain. This study offers the first systematic analysis and evaluation of this increasingly central public management concept. Using an ontological-semantic approach, I show that the current conceptualization fails to fully and directly account for individuals’ onerous experiences. I address five interrelated issues, including the overlap of cost categories and the conflation of state actions with onerous experiences. While psychological costs should be retained, I argue for abandoning the other cost categories. Building on previous reconceptualization efforts, I propose a new framework focused on time, money, effort, and psychological costs. Additionally, I explore the structure of the concept and propose specific indicators for each dimension. I then discuss the independence of these dimensions, their capacity to reflect the distributive nature of burdens, and avenues for empirical validation.
Long-term effects of the Targeting the Ultra Poor program—A reproducibility and replicability assessment of Banerjee et al. (2021)
Authors: Rose Julian , Neubauer Florian , Ankel-Peters Jörg 
Published: November 2024

Abstract
Banerjee, Duflo, and Sharma (BDS, 2021, American Economic Review: Insights, 3, 471–86) conduct a 10-year follow-up of a randomized transfer program in West Bengal. BDS find large effects on consumption, food security, income, and health. We conduct a replicability assessment. First, we successfully reproduce the results, thanks to a perfectly documented reproduction package. Results are robust across alternative specifications. We furthermore assess the paper's pre-specification diligence and the reporting in terms of external and construct validity. While the paper refers to a pre-registration, it lacks a pre-analysis plan. Assessing the validity of findings for other contexts is difficult absent necessary details about the exact treatment delivery.
Anti- Inflammatory Activities Of The Methanol Leaf Extract And Fractions Of Elaesis Guineensis In In-Vivo Animals
Authors: Uwamusi Marvellous 
Published: November 2024

Abstract

Objective
Objective of this paper is to investigate the preliminary anti-inflammatory property of the leaves and its fractions of Elaesis guineensis using egg induced albumin and formaldehyde induced arthritis models in rats.

Method
Egg albumin induced inflammation was induced by sub-plantar injection of 0.1 ml of fresh undiluted egg albumin. The volume of distilled water displaced by the treated paw was measured at 0.5,1, 2, 3, 4, 5, and 6 hours after induction of inflammation. Formaldehyde-induced arthritis was induced after 30 min by sub-plantar injection of 0.1 ml of 2.5% formaldehyde solution and was repeated on day 3. Arthritis was assessed by measuring the volume of distilled water displaced by the paw before induction of arthritis and once every day for ten days, starting from day one, after induction of arthritis.

Results
The acute toxicity test revealed that the plant extract was safe even at 5000 mg/kg dose level. The methanol extract (ME) showed a dose-dependent inhibition of egg albumin-induced acute inflammation that peaked at the dose of 200 mg/kg, while the fractions of the extract showed that the hexane and ethyl acetate fractions had the highest activity during the experiment. Similarly, the crude extract of the formaldehyde induced arthritis showed a dose-dependent inhibition making the 200 mg/kg the most active dose level. Additionally, it was observed that among the fractions of the extract the hexane fraction (HF) showed the most significant inhibitory activity when compared to other fractions

Conclusion
this study establishes that the methanol leaf extract and fractions ofElaesis guineensis possess significant anti-inflammatory activity
Defenders of the status quo: energy protests and policy (in)action in Sweden
Authors: Uba Katrin , Engeman Cassandra 
Published: November 2024

Abstract
Are the positions that protesters take—in favor or against change—consequential for their ability to affect policy? While previous research suggests that protests can inform legislative priorities and facilitate policy introduction, this paper emphasizes policy inaction and stasis as goals of some protest actions. Analysis uses novel and detailed data on energy-related protest and policy actions in Sweden covering a forty-year period and considers protest frequency and size in relation to proposal introduction. The research design uniquely distinguishes between protests in favor or against a specific energy source and proposal activity in line with those demands and also controls for public opinion on each energy source. Findings suggest that pro-renewable energy protests do not yield pro-renewable policies but prevent undesired policies that support non-renewable energy sources. In contrast to pro-renewable protests, protests against renewable energy sources are somewhat more influential. They likewise prevent the introduction of their undesired proposals and also influence the introduction of proposals supporting non-renewable energy sources. Overall, the paper examines policy inaction as a desired protest outcome and argues protest—as a tactic—may be more effective when pushing against rather than for policy change.
Development of slow oscillation–spindle coupling from infancy to toddlerhood
Authors: Kurz Eva-Maria , Bastian Lisa , Mölle Matthias , Born Jan , Friedrich Manuela 
Published: November 2024

Abstract
Sleep has been demonstrated to support memory formation from early life on. The precise temporal coupling of slow oscillations (SOs) with spindles has been suggested as a mechanism facilitating this consolidation process in thalamocortical networks. Here, we investigated the development of sleep spindles and SOs and their coordinate interplay by comparing frontal, central, and parietal electroencephalogram recordings during a nap between infants aged 2–3 months (n = 31) and toddlers aged 14–17 months (n = 49). Spindles and SOs showed quite different maturational patterns between age groups, as to topography, amplitude, and density. Notably, spindle–SO co-occurrence in the infants did not exceed chance levels and was increased to significant levels only in the toddlers. In the infants, the slow SO upstate over frontocortical regions was even associated with a significant decrease in spindles, contrasting with the adult-like increase in spindles seen in toddlers. These results point to an immature processing in thalamocortical networks during sleep in early infancy, possibly diminishing the efficacy of sleep-dependent memory formation at this age.
Microglia in the spinal cord stem cell niche regulate neural precursor cell proliferation via soluble CD40 in response to myelin basic protein
Authors: Lakshman Nishanth , Stojic Filip , Morshead Cindi M 
Published: November 2024

Abstract
Neural stem cells (NSCs) are found along the neuraxis of the developing and mature central nervous system. They are found in defined niches that have been shown to regulate NSC behavior in a regionally distinct manner. Specifically, previous research has shown that myelin basic protein (MBP), when presented in the spinal cord niche, inhibits NSC proliferation and oligodendrogenesis. Herein, we investigate the cell-based mechanism(s) underlying this spinal-cord niche-derived MBP-mediated inhibition. We used reporter mice to sort for subpopulations of cells and found that spinal cord niche-derived microglia release a soluble factor in response to MBP that is responsible for NSC inhibition. Microglia, but not other niche cells, release soluble CD40/TNFRSF5 (sCD40) in the presence of MBP which may indirectly reduce activation of transmembrane CD40/TNFRSF5 receptor on both spinal cord and brain NSCs. This is consistent with sCD40 binding to CD40 ligand (CD40L) thereby preventing CD40 receptor binding on NSCs and inhibiting NSC proliferation. The identification of the cell-based mechanism that regulates NSC behavior in response to MBP, which is dysregulated in injury/disease, provides insight into a potential target for strategies to enhance neural repair through endogenous stem cell activation.