bluuebunny/crossref_metadata_2025 huggingface dataset:
High-throughput phenotyping of soybean (Glycine max) transpiration response curves to rising atmospheric drying in a mapping population
Authors: Monnens Daniel , López José R. , McCoy Erik , Tamang Bishal G. , Lorenz Aaron J. , Sadok Walid
Published: November 2024

In soybean (Glycine max), limiting whole-plant transpiration rate (TR) response to increasing vapor pressure deficit (VPD) has been associated with the ‘slow-wilting’ phenotype and with water-conservation enabling higher yields under terminal drought. Despite the promise of this trait, it is still unknown whether it has a genetic basis in soybean, a challenge limiting the prospects of breeding climate-resilient varieties. Here, we present the results of a first attempt at a high-throughput phenotyping of TR and stomatal conductance response curves to increasing VPD conducted on a soybean mapping population consisting of 140 recombinant inbred lines (RIL). This effort was conducted over two consecutive years, using a controlled-environment, gravimetric phenotyping platform that enabled characterizing 900 plants for these responses, yielding regression parameters (R2 from 0.92 to 0.99) that were used for genetic mapping. Several quantitative trait loci (QTL) were identified for these parameters on chromosomes (Ch) 4, 6, and 10, including a VPD-conditional QTL on Ch 4 and a ‘constitutive’ QTL controlling all parameters on Ch 6. This study demonstrated for the first time that canopy water use in response to rising VPD has a genetic basis in soybean, opening novel avenues for identifying alleles enabling water conservation under current and future climate scenarios.
Steady-states of the Gierer–Meinhardt system in exterior domains
Authors: Ghergu Marius , McNicholl Jack
Published: November 2024

We discuss the existence and nonexistence of solutions to the steady-state Gierer–Meinhardt system

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Analysis of the performance of the PPP-B2b satellite clock and its effects on time transfer
Authors: Qin Weijin , Zhang Zhe , Wei Pei , Su Hang , Yang Xuhai
Published: November 2024

BDS-3 is capable of providing precise point positioning (PPP) services via B2b signals for the Asia–Pacific region. The performance of the satellite clock plays a dominant role in the transmission interval of B2b clock correction and PPP time transfer. In this work, first, the coverage of B2b signals is analysed, and the performance of the satellite clock is evaluated (including orbit accuracy, clock stability, clock accuracy and prediction accuracy). Second, the results of time transfer based on BDS-3 PPP-B2b are investigated. The values show that the orbit error of BDS-3 recovered from PPP-B2b is better than that of the GPS recovered from PPP-B2b. The stability of BDS-3 recovered from the PPP-B2b clock is superior to that of the GPS PPP-B2b clock. The stability of the BDS-3 clock is approximately 1∼2 e-13, 5∼9 e-14, and 3∼5 e-14 at 100 s, 1000 s, and 10000 s, respectively. No obvious discrepancy exists in the BDS-3 clocks of different types. The mean prediction accuracy of BDS-3 is 0.03 ns when the prediction time is up to 120 s, and the prediction accuracy of the GPS is 0.28 ns when the prediction time is merely 30 s. This result shows that it is possible to decrease the transmission interval of BDS-3 B2b clock correction and save much space. The time transfer based on BDS-3 PPP-B2b can subsequently achieve a 0.50 ns level. The frequency stability of the time link is approximately 9.25E-14, 2.42E-14, and 9.34E-15 at 100 s, 1000 s, and 10000 s, respectively. We can conclude that the BDS-3 PPP-B2b solution is reliable for time transfer.
Proper time path integrals for gravitational waves: an improved wave optics framework
Authors: Braga Ginevra , Garoffolo Alice , Ricciardone Angelo , Bartolo Nicola , Matarrese Sabino
Published: November 2024

When gravitational waves travel from their source to an observer, they interact with matter structures along their path, causing distinct deformations in their waveforms.
In this study we introduce a novel theoretical framework for wave optics effects in gravitational lensing, addressing the limitations of existing approaches. We achieve this by incorporating the proper time technique, typically used in field theory studies, into gravitational lensing.
This approach allows us to extend the standard formalism beyond the eikonal and paraxial approximations, which are traditionally assumed, and to account for polarization effects, which are typically neglected in the literature. We demonstrate that our method provides a robust generalization of conventional approaches, including them as special cases. Our findings enhance our understanding of gravitational wave propagation, which is crucial for accurately interpreting gravitational wave observations and extracting unbiased information about the lenses from the gravitational wave waveforms.
Gravitational waves from inflation in LISA: reconstruction pipeline and physics interpretation
Authors: Braglia Matteo , Calcagni Gianluca , Franciolini Gabriele , Fumagalli Jacopo , Nardini Germano , Peloso Marco , Pieroni Mauro , Renaux-Petel Sébastien , Ricciardone Angelo , Tasinato Gianmassimo , Vaskonen Ville ,   the LISA Cosmology Working Group
Published: November 2024

Various scenarios of cosmic inflation enhance the amplitude of the stochastic gravitational wave background (SGWB) at frequencies detectable by the LISA detector. We develop tools for a template-based analysis of the SGWB and introduce a template databank to describe well-motivated signals from inflation, prototype their template-based searches, and forecast their reconstruction with LISA. Specifically, we classify seven templates based on their signal frequency shape, and we identify
representative fundamental physics models leading to them. By running a template-based analysis, we forecast the accuracy with which LISA can reconstruct the template parameters of representative benchmark signals, with and without galactic and extragalactic foregrounds. We identify the parameter regions that can be probed by LISA within each template. Finally, we investigate how our signal reconstructions shed light on fundamental physics models of inflation: we discuss their impact for measurements of e.g.,  the couplings of inflationary axions to gauge fields; the graviton mass during inflation; the fluctuation seeds of primordial
black holes; the consequences of excited states during inflation, and the presence of small-scale spectral features.
CGGTTS-Version 2E: integration of BDS-3
Authors: Defraigne P , Tagliaferro G
Published: November 2024

The Common GNSS Generic Time Transfer Standard version 2E has been presented in Petit and Defraigne (2015 Metrologia
52 G1 10.1088/0026-1394/52/6/G1), covering clock solutions obtained with GPS, GLONASS, Galileo and BeiDou (also called BDS for BeiDou System). For this latter, only satellites from the second generation BDS-2 were however available at that time. Since then, the BeiDou constellation has been upgraded, with a new generation called BDS-3, containing more satellites and using new signals and frequencies. In particular, while BDS-2 was mainly dedicated to regional applications over Asia, BDS-3 proposes, as of 2024, about 25 satellites in Medium Earth Orbit, hence visible from all regions of the world.
Propagation of chaos in the random field Curie–Weiss model
Authors: Kabluchko Zakhar , Löwe Matthias
Published: November 2024

We prove quenched propagation of chaos in the Random field mean-field Ising model, also known ad the Random field Curie–Weiss model. We show that in the paramagnetic phase, i.e. in the regime where temperature and distribution of the external field admit a unique minimizer of the expected Helmholtz free energy, quenched propagation of chaos holds. By the latter we mean that the finite-dimensional marginals of the Gibbs measure converge towards a product measure with the correct expectation as the system size goes to infinity. This holds independently of whether the system is in a high-temperature phase or at a phase transition point and alsmost surely with respect to the random external field. If the Helmholtz free energy possesses several minima, there are several possible equilibrium measures. In this case, we show that the system picks one of them at random (depending on the realization of the random external field) and propagation of chaos with respect to a product measure with the same marginals as the one randomly picked holds true. We illustrate our findings in a simple example.
Spatio-temporal heterogeneity and scenario prediction of influencing factors of transportation carbon emissions in the Yangtze River Economic Belt, China
Authors: Liu Rong , Yuan Huimei , Chen Wanting , Hu Qingping , Zhou Mengxing , Bao Lingxin
Published: November 2024

Reducing carbon emissions in the transportation sector is a crucial aspect of China achieving its carbon peak and carbon neutrality goals. This study investigates the spatiotemporal differentiation characteristics of carbon emissions from transportation in the Yangtze River Economic Belt. Using the Geographically and Temporally Weighted Regression(GTWR) model to reveal the spatio-temporal heterogeneity of factors influencing transportation carbon emissions. Additionally, the Support Vector Regression(SVR) is trained to predict the carbon emissions reduction potential of transportation under different scenarios. The results showed that: From 2000 to 2021, the transportation emissions of the Yangtze River economic belt showed an overall upward trend. The high carbon emission regions are Jiangsu Province, Shanghai, Zhejiang Province and Hubei Province, and the emission center is located in Hubei Province. The total population, urbanization rate, per capita GDP, carbon emission intensity, passenger turnover volume, and civilian vehicle ownership all have a positive effect on transportation carbon emissions, while energy structure has a negative impact. Moreover, the influence of each factor exhibits significant spatial heterogeneity. Under three scenarios: baseline, low-carbon scenario I, and low-carbon scenario II, transportation carbon emissions in the Yangtze River Economic Belt are projected to peak by 2030. With the application of clean energy and a reduction in population size, low carbon scenario II demonstrates greater potential for carbon emission reduction, with a projected value of 88.552 million tons by 2032.
Enhancing security and randomness in cryptography and non-cryptographic applications with ORNA algorithm
Authors: Goswami Yagyadatta , Mittal Avneesh , Das Kaushik , Kumar Smit , Gautam Kumar , Sai Manish Kumar
Published: November 2024

In this paper, we advocate for using PRNGs to generate long sequences of statistically random numbers, also known as pseudorandom numbers. It has several practical applications, including cryptography, weather-based stimulation, procedural environment noise generation in games and casinos, and scientific simulations of real-world problems, like city traffic systems that use it to stimulate cars. One distinctive feature of our approach is the PRNG algorithm we propose; this algorithm has successfully produced statistically sound long-term sequences. The properties of the PRNG are assessed using several statistical methods. Our work presents the Oscillating Random Number Algorithm (ORNA), a new kind of random number generator, and examines both the statistical tests proposed by NIST and the results that ORNA has generated. The following also describes the several preceding algorithms developed, including the Mersenne Twister Algorithm (MT19937) and the Permuted Congruential Algorithm (PCG128), and compares ORNA’s graphical efficiency to theirs. In this work, we compared ORNA to MT19937 and PCG128, and found that ORNA excels according to all 16 statistical tests. ORNA has three primary benefits, namely, superior statistical performance, quicker code execution, and simpler code implementation due to the algorithm’s reduced complexity.
Dominant negative mutations in yeast Hsp90 indicate triage decision mechanism targeting client proteins for degradation
Authors: Flynn Julia M. , Joyce Margot E. , Bolon Daniel N. A.
Published: November 2024

Dominant negative (DN) mutations provide valuable tools for investigating protein mechanisms but can be difficult to isolate because of their toxic effects. We used a mutational scanning approach to identify DN mutations in yeast Hsp90. In a previous mutational scan of the ATPase domain of Hsp90, we noticed that many mutations were at very low frequency after outgrowth in cells coexpressing wildtype Hsp90. Most of these depleted variants were located at the hinge of a lid that closes over ATP. To quantify toxic effects in the hinge regions, we performed mutational scanning using an inducible promoter and identified 113 variants with strong toxic effects. We analyzed individual DN mutations in detail and found that addition of the E33A mutation that prevents ATP hydrolysis by Hsp90 abrogated the DN phenotype. FRET assays performed on individual DN mutants indicate the linkage between ATPase activity and formation of the closed structure is disrupted. DN Hsp90 decreased the expression level of two model Hsp90 clients, glucocorticoid receptor (GR) and v-src kinase. Using MG132, we found that GR was rapidly destabilized in a proteasome-dependent manner. Biochemical analyses indicate that ATP hydrolysis by Hsp90 from open conformations can lead to ubiquitin-dependent client degradation.
Introduction
Authors: Janssen K P S
Published: November 2024

The introduction discusses the key objectives of the book, and provides information on the applied methodology and terminology, as well as the scope of the study. The book’s primary goal is to place investigate the way in which members of marginalized religious groups were embedded within, and interacted with, the wider legal and administrative framework of the Roman Empire, and thereby to provide a broader perspective on the legal treatment of marginalized religion in the Roman world. It seeks to do so by presenting an introductory chapter on Roman law and administration before delving into the treatment of divination, Judaism, and Christianity. The study is furthermore focused not just on legal measures in the strict sense of the word, but it also takes into account the entirety of the legal process, including the origins and implementation of such measures. In doing so, the goal is to firmly root our understanding of legal interactions between the Roman authorities and marginalized religious groups within their wider societal and historical context.
Roman Law and Administration
Authors: Janssen K P S
Published: November 2024

This chapter provides an overview of the workings of Roman law and administration in order to establish the institutional framework in which legal interactions between marginalized religious groups and the Roman authorities took place. It first discusses the sources of law that were available in the Roman world and establishes that regulations could be created in a variety of ways, an important number of which were both flexible and reactive in nature. Subsequently, the workings of different trial procedures are discussed, alongside alternative ways of maintaining public order. Finally, the chapter delves into the workings of Roman provincial administration, discussing the interplay between the emperor, governor, and the local population in particular. It argues that these levels of government were often highly dependent on each other, and that frequent negotiation and re-negotiation was therefore necessary. Roman administration, then, was characterized by a significant degree of flexibility, as well as a reliance on precedent and local custom that led to notable legal diversity within the empire.
The Onomastics of the Batavian civitas in the Context of the Latinization of Gallia Belgica and Germania Inferior
Authors: Raepsaet-Charlier Marie-Thérèse
Published: November 2024

The chapter has two parts. The first part describes the linguistic characteristics of the onomastics of the civitas of the Batavians (area of the Rhine and the Waal around Nijmegen, The Netherlands, in Germania Inferior) and attempts to define the status of the population (Roman citizens and peregrini) differentiating between civilians and military. The Latinization of anthroponyms can be seen alongside names in Celtic or Germanic languages. The second part provides comparisons with the onomastics of neighbouring communities (Tungri, Nervii, Frisiavones, Cananefates, Menapii) as well as the Treviri, in order to reach a differentiated picture of the Latinization of northern Gaul: the civitates with a Germanic ethnic element are more Latinized than those with a Celtic population, where the indigenous language remains strongly anchored in naming practices.
The Lady and the Beast
Authors: Whitehouse Deja
Published: November 2024

This book presents a critical analysis of the life and works of Frieda, Lady Harris (1877–1962), wife of Sir Percy Harris (1876–1952), Liberal MP and party Chief Whip. Although Lady Harris is acknowledged as the artist of Aleister Crowley’s Book of Thoth, this monograph is the first academic consideration of Harris’s full contribution to Western esotericism. To date, studies have focused on Harris’s role as Crowley’s artist executant, and almost exclusively from Crowley’s perspective. As argued in this study, Harris’s involvement extended far beyond the artwork itself: The Book of Thoth was a collaboration in which each partner fulfilled a variety of roles, building on Crowley’s magical theories and practices and Harris’s artistic skills and social awareness that enabled her to promote and exhibit their work as it evolved. Harris’s life before, during, and after her collaboration with Crowley is presented. The book assesses the influences that drew her to Crowley, and the impact their partnership had on her before and after his death. Using a variety of contemporary and historical written sources, including diaries and personal correspondence, this monograph seeks to establish how such an ostensibly conventional Victorian middle-class woman, married to a prominent Liberal politician, became involved with someone of Crowley’s notoriety. The study is presented within the context of British social, cultural and art history, illustrating the actual and perceived changes in women’s status during the period 1877–1962, thereby contributing to gender studies as well as esotericism in general and Crowley scholarship in particular.
Conclusion
Authors: Whitehouse Deja
Published: November 2024

This chapter consolidates the study, presenting an assessment of Harris’s formative years, her adult life prior to her meeting with Crowley, and her subsequent development spiritually and artistically as a result of their partnership. Her position as a middle-class woman involved in esoteric circles is considered and comparisons drawn with her female contemporaries, such as Annie Besant and Dion Fortune. Specific consideration is given to Harris’s position in society and how she was prepared to jeopardise her marriage and social standing in order to fulfil her commitment to Crowley and his Great Work. Conclusions are drawn on her contribution to Western esotericism and the mutual proximal significance from which both Harris and Crowley benefitted.
Equality of opportunity for timely dementia diagnosis (EQUATED): a qualitative study of how people from minoritised ethnic groups experience the early symptoms of dementia and seek help
Authors: Carter Christine , Roche Moïse , Whitfield Elenyd , Budgett Jessica , Morgan-Trimmer Sarah , Zabihi Sedigheh , Birks Yvonne , Walter Fiona , Wilberforce Mark , Jiang Jessica , Ahmed Refah , Dowridge Wesley , Marshall Charles R , Cooper Claudia
Published: November 2024

Introduction

People from minoritised ethnic groups are diagnosed with dementia later in the disease. We explored pathways that may determine the timing of diagnoses in a UK ethnically diverse, urban area.

Methods

We conducted 61 semi-structured interviews: 10 community-dwelling older people from minoritised ethnic backgrounds with diagnosed and undiagnosed dementia (mean age = 72 years; males = 5/10), 30 family members (51; 10/30), 16 health or social care professionals (42; 3/15), 3 paid carers and 2 interpreters for people with dementia. We used reflexive thematic analysis and the Model of Pathways to Treatment to consider diagnostic delay.

Findings

We identified three themes: (1) Cultural identity and practices shape responses: gendered expectations that families relieve elders of household roles reduce awareness or concern when functioning declines; expectations that religious practices are maintained mean problems doing so triggers help-seeking. Second-generation family members often held insider and outsider identities, balancing traditional and Western perspectives. (2) Becoming like a tourist: daily experiences became unfamiliar for people developing dementia in an adopted country, sometimes engendering a need to reconnect with a home country. For professionals and interpreters, translating meanings faithfully, and balancing relatives’ and clients’ voices, were challenging. (3) Naming and conceptualising dementia: the term dementia was stigmatised, with cultural nuances in how it was understood; initial presentations often included physical symptoms with cognitive concerns.

Conclusion

Greater understanding of dilemmas faced by minoritised ethnic communities, closer collaboration with interpreters and workforce diversity could reduce time from symptom appraisal to diagnosis, and support culturally competent diagnostic assessments.
Menopause age and type and dementia risk: a pooled analysis of 233 802 women
Authors: Dobson Annette J , XU Zhiwei , Wilson Louise F , Chung Hsin-Fang , Sandin Sven , Van der Schouw Yvonne T , Demakakos Panayotes , Weiderpass Elisabete , Mishra Gita D
Published: November 2024

Objectives

It is not clear whether the association between younger age at menopause and increased risk of dementia is modified by type of menopause. We examined the association of age at menopause or hysterectomy with dementia risk in three groups of women: those with natural menopause, premenopausal bilateral oophorectomy (surgical menopause) or premenopausal hysterectomy (without bilateral oophorectomy).

Study design

Individual-level data from 233 802 women in five prospective cohort studies (from four countries) were harmonized and pooled. Cox proportional hazards models were used to assess the associations of age at natural menopause, surgical menopause or premenopausal hysterectomy, with age at dementia, death (where available) or end of follow-up, whichever came first.

Results

The study followed women to the median age of 72 years (quartiles 67, 76 years). The median follow-up time was 13 years, with 3262 dementia cases during this period. Compared with women with menopause at 50–52 years, women with menopause <40 years had a higher risk of dementia (adjusted hazard ratio (aHR): 1.47, 95% confidence interval (CI): 1.39, 1.56). This level of risk was comparable to that of current smoking and stroke, which are well-established risk factors for dementia. Increased risk of dementia associated with surgical menopause or premenopausal hysterectomy (compared to natural menopause) was not apparent after adjustment for age at menopause (aHR 0.99, 95% CI: 0.93, 1.04 and aHR 0.97, 95% CI: 0.95, 1.00, respectively).

Conclusion

Women who experience menopause before the age of 40 years have a higher risk of dementia irrespective of type of menopause.
Do MMPI-3 Validity Scale Findings Generalize to Concurrently Administered Measures? Validation with a Forensic Disability Sample
Authors: Holmes Kaci F , Whitman Megan R , Gervais Roger O , Ben-Porath Yossef S
Published: November 2024

Objective

Research has demonstrated that over-reporting and under-reporting, when detected by the MMPI-2/-RF Validity Scales, generalize to responses to other self-report measures. The purpose of this study was to investigate whether the same is true for the Minnesota Multiphasic Personality Inventory–3 (MMPI-3) Validity Scales. We examined the generalizability of over-reporting and under-reporting detected by MMPI-3 Validity Scales to extra-test self-report, performance-based, and performance validity measures.

Method

The sample included 665 majority White, male disability claimants who, in addition to the MMPI-3, were administered several self-report measures, some with embedded symptom validity tests (SVTs), performance-based measures, and performance validity tests (PVTs). Three groups were identified based on MMPI-3 Validity Scale scores as over-reporting (n = 276), under-reporting (n = 100), or scoring within normal limits (WNL; n = 289).

Results

Over-reporting on the MMPI-3 generalized to symptom over-reporting on concurrently administered self-report measures of psychopathology and was associated with evidence of over-reporting from other embedded SVTs. It was also associated with poorer performance on concurrently administered measures of cognitive functioning and PVTs. Under-reporting on the MMPI-3 generalized to symptom minimization on collateral measures of psychopathology. On measures of cognitive functioning, we found no differences between the under-reporting and WNL groups, except for the Wisconsin Card Sorting Test–64 Card Version and Wide Range Achievement Test–Fifth Edition (each with negligible effect sizes).

Conclusions

MMPI-3 Validity Scales can identify possible over- and under-reporting on concurrently administered measures. This can be of particular value when such measures lack validity indicators.
Retainer Bias: Ethical and Practical Considerations for the Forensic Neuropsychologist
Authors: Goldstein Diana S , Morgan Joel E
Published: November 2024

How is it that practicing forensic neuropsychologists occasionally see substandard work from other colleagues, or more fundamentally, have such disparate opinions on the same case? One answer might be that in every profession, competence varies. Another possibility has little to do with competence, but professional conduct. In this paper we discuss the process by which retainer bias may occur. Retainer bias is a form of confirmatory bias, i.e., in assessment, the tendency to seek, favor, and interpret data and make judgments and decisions that support a predetermined expectation or hypothesis, ignoring or dismissing data that challenge that hypothesis ( Nickerson, 1998). The tendency to interpret data in support of the retaining attorney’s position of advocacy may be intentional – that is, within conscious awareness and explicit, or it may be unintentional, outside of one’s awareness, representing implicit bias. While some practitioners accept referrals from both sides in litigation, numerous uncontrollable factors converge in such a manner that one's practice may nevertheless become associated with one side. Such imbalance is not a reliable index of bias. With brief hypothetical scenarios, in this paper we discuss contextual factors that increase risk for retainer bias and problematic practice approaches that may be used to support one side in litigation, violating ethical principles, codes of conduct and guidelines for engaging in forensic work. We also discuss debiasing techniques recommended within the empirical literature and call on the subspecialty field of forensic neuropsychology to conduct research into retainer bias and other sources of opinion variability.
Biological effects of Maillard reaction products: Use of Caenorhabditis elegans as an in vivo model
Authors: Yokoyama Issei
Published: November 2024

Maillard reaction products (MRPs), including melanoidins and volatile odor compounds, are associated with distinct flavors and colors during food processing and cooking. Although MRPs have health benefits, such as antioxidant activity, they are also associated with pathophysiological effects. Several in vivo models, especially rodents, are used to demonstrate physiological effects. Caenorhabditis elegans (C. elegans), an easy-to-rear free-living nematode with a short lifespan, has been used as a promising in vivo organism for the evaluation of functional properties in food components, including antiaging, antioxidant, and antiobesity properties. Furthermore, the high olfactory discrimination of this organism allows for the basic elucidation of behavior and regulation of aging. In this minireview, I discuss the various attributes of C. elegans that make it a promising in vivo model for studying the biological effects of MRPs.
Animal personalities influence male mating behavior and reproductive fitness
Authors: Li Ruonan , Yang Chen , Lou Yingqiang , Lü Jianhua , Lyu Nan
Published: November 2024

The relationship between individual personality and sexual selection has the potential to provide insights into how variation in personality traits is maintained. However, whether and how individuals with different personality traits have different mating behaviors and the fitness consequences has remained largely unexplored. We tested the hypothesis that male individuals have different mating behavior depending on their personality traits, and that there are fitness effects of personality traits. To do so, we conducted trials to quantify personality traits and observed mating behavior under standardized conditions in the red flour beetle (Tribolium castaneum). We also collected the number of offspring produced by their female mates to assess the association between male personality and their reproductive fitness. We found that male beetles showed consistent inter-individual differences in walking distance, emergence time from shelter, and death-feigning time, which likely corresponding to 2 personality traits of activity and boldness. Although larger males had higher mating success and produced more offspring, some personality traits were also strongly related to mating behavior and reproductive fitness. Males with longer walking distances tended to seek female mates more promptly. Other than the morphological trait of body size, the emergence time from shelter (boldness) also showed a positive relationship with the number of matings and offspring reproduced. Furthermore, we found that the interaction between death-feigning time and walking distance in males influenced the number of matings they obtain, with either shy but active or bold but inactive males achieving more matings. We therefore highlight that alongside morphological traits, certain personality traits can also play a role in affecting mating behaviors and even reproductive fitness in males.
Nonreproductive division of labor in staghorn ferns
Authors: Cronin Kahurangi , Hutton Ian , Burns K C
Published: November 2024

In complex animal societies, group members often subdivide labor by focusing on different tasks such as reproduction and defense. While division of labor is well documented in animals, little is known about whether colonial plants exhibit similar patterns in task differentiation. To help bridge this gap in our understanding of sociality, we investigated nonreproductive division of labor in the staghorn fern (Platycerium bifurcatum, Polypodiaceae), an epiphyte that forms colonies of many individual plants, which coalesce into a communal water and nutrient store. We conducted a series of field observations and glasshouse experiments to answer 3 questions: (1) Are individuals in the upper regions of colonies shaped in ways that facilitate the capture of airborne particulate matter (e.g. leaf litter)? (2) Do individuals at the apex of colonies decay in ways that inhibit the invasion of colonies by other plant species? (3) Does the anatomy of fronds at the bottom of colonies facilitate water storage? Results show that individuals at the top of colonies were larger and more lobed, which fostered the retention of leaf litter within communal nests. Plants located at the top of colonies also repetitively collapsed over the upper surface of nests as they decayed, inhibiting the germination and growth of foreign plant species. Lastly, individuals at the bottom of colonies produced thicker fronds with larger intracellular spaces, which facilitated the storage of rainwater captured above. Overall results demonstrate clear patterns in nonreproductive division of labor within staghorn fern colonies that are similar to highly social animals.
KTED: a comprehensive web-based database for transposable elements in the Korean genome
Authors: Lee Jin-Ok , Lee Sejoon , Lee Dongyoon , Hwang Taeyeon , Joe Soobok , Yang Jin Ok , Jeong Jibin , Ohn Jung Hun , Kim Jee Hyun
Published: November 2024

Transposable elements (TEs), commonly referred to as “mobile elements,” constitute DNA segments capable of relocating within a genome. Initially disregarded as “junk DNA” devoid of specific functionality, it has become evident that TEs have diverse influences on an organism’s biology and health. The impact of these elements varies according to their location, classification, and their effects on specific genes or regulatory components. Despite their significant roles, a paucity of resources concerning TEs in population-scale genome sequencing remains. Herein, we analyze whole-genome sequencing data sourced from the Korean Genome and Epidemiology Study, encompassing 2500 Korean individuals. To facilitate convenient data access and observation, we developed a web-based database, KTED. Additionally, we scrutinized the differential distributions of TEs across five distinct common disease groups: dyslipidemia, hypertension, diabetes, thyroid disease, and cancer.

Availability and implementation

https://snubh.shinyapps.io/KTED.
Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of Plasmodium falciparum genes
Authors: Lee Chiyun , Ünlü Eyyüb S , White Nina F D , Almagro-Garcia Jacob , Ariani Cristina V , Pearson Richard D
Published: November 2024

Motivation

Monitoring the genomic evolution of Plasmodium falciparum—the most widespread and deadliest of the human-infecting malaria species—is critical for making decisions in response to changes in drug resistance, diagnostic test failures, and vaccine effectiveness. The MalariaGEN data resources are the world’s largest whole genome sequencing databases for Plasmodium parasites. The size and complexity of such data is a barrier to many potential end users in both public health and academic research. A user-friendly method for accessing and exploring data on the genetic variation of P. falciparum would greatly enable efforts in studying and controlling malaria.

Results

We developed Pf-HaploAtlas, a web application enabling exploratory data analysis of genomic variation without requiring advanced technical expertise. The app provides analysis-ready data catalogues and visualizations of amino acid haplotypes for all 5102 core P. falciparum genes. Pf-HaploAtlas facilitates comprehensive spatial and temporal exploration of genes and variants of interest by using data from 16 203 samples, from 33 countries, and spread between the years 1984 and 2018. The scope of Pf-HaploAtlas will expand with each new MalariaGEN Plasmodium data release.

Availability and implementation

Pf-HaploAtlas is available online for public use at https://apps.malariagen.net/pf-haploatlas, which allows users to download the underlying amino acid haplotype data for further analyses, and its source code is freely available on GitHub under the MIT licence at https://github.com/malariagen/pf-haploatlas.
MMOSurv: meta-learning for few-shot survival analysis with multi-omics data
Authors: Wen Gang , Li Limin
Published: November 2024

Motivation

High-throughput techniques have produced a large amount of high-dimensional multi-omics data, which makes it promising to predict patient survival outcomes more accurately. Recent work has showed the superiority of multi-omics data in survival analysis. However, it remains challenging to integrate multi-omics data to solve few-shot survival prediction problem, with only a few available training samples, especially for rare cancers.

Results

In this work, we propose a meta-learning framework for multi-omics few-shot survival analysis, namely MMOSurv, which enables to learn an effective multi-omics survival prediction model from a very few training samples of a specific cancer type, with the meta-knowledge across tasks from relevant cancer types. By assuming a deep Cox survival model with multiple omics, MMOSurv first learns an adaptable parameter initialization for the multi-omics survival model from abundant data of relevant cancers, and then adapts the parameters quickly and efficiently for the target cancer task with a very few training samples. Our experiments on eleven cancer types in The Cancer Genome Atlas datasets show that, compared to single-omics meta-learning methods, MMOSurv can better utilize the meta-information of similarities and relationships between different omics data from relevant cancer datasets to improve survival prediction of the target cancer with a very few multi-omics training samples. Furthermore, MMOSurv achieves better prediction performance than other state-of-the-art strategies such as multitask learning and pretraining.

Availability and implementation

MMOSurv is freely available at https://github.com/LiminLi-xjtu/MMOSurv
Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies
Authors: Zou Jian , Li Zheqi , Carleton Neil , Oesterreich Steffi , Lee Adrian V , Tseng George C
Published: November 2024

Motivation

Biomarker detection plays a pivotal role in biomedical research. Integrating omics studies from multiple cohorts can enhance statistical power, accuracy, and robustness of the detection results. However, existing methods for horizontally combining omics studies are mostly designed for two-class scenarios (e.g. cases versus controls) and are not directly applicable for studies with multi-class design (e.g. samples from multiple disease subtypes, treatments, tissues, or cell types).

Results

We propose a statistical framework, namely Mutual Information Concordance Analysis (MICA), to detect biomarkers with concordant multi-class expression pattern across multiple omics studies from an information theoretic perspective. Our approach first detects biomarkers with concordant multi-class patterns across partial or all of the omics studies using a global test by mutual information. A post hoc analysis is then performed for each detected biomarkers and identify studies with concordant pattern. Extensive simulations demonstrate improved accuracy and successful false discovery rate control of MICA compared to an existing multi-class correlation method. The method is then applied to two practical scenarios: four tissues of mouse metabolism-related transcriptomic studies, and three sources of estrogen treatment expression profiles. Detected biomarkers by MICA show intriguing biological insights and functional annotations. Additionally, we implemented MICA for single-cell RNA-Seq data for tumor progression biomarkers, highlighting critical roles of ribosomal function in the tumor microenvironment of triple-negative breast cancer and underscoring the potential of MICA for detecting novel therapeutic targets.

Availability and implementation

The source code is available on Figshare at https://doi.org/10.6084/m9.figshare.27635436. Additionally, the R package can be installed directly from GitHub at https://github.com/jianzou75/MICA.
Tailored bioengineering and nanomedicine strategies for sex-specific healing of chronic wounds
Authors: Mahmoudi Negar , Sharifi Shahriar , Leshchiner Dmitry , Horibata Sachi , Lin Zijin , Ghazali Noor , Shahbazi Mohammad-Ali , Priyam Ayushi , Williams Richard J , Pastar Irena , Gould Lisa , Matoori Simon , Nisbet David R , Mahmoudi Morteza
Published: November 2024

Chronic wounds, defined by their prolonged healing process, significantly impair patients’ quality of life and impose a hefty financial burden on healthcare systems worldwide. Sex- and gender-specific mechanisms regulate inflammation and infection, angiogenesis, matrix synthesis and cell recruitment. All of these processes contribute to cutaneous wound healing but remain largely understudied. This review aims to spotlight the innovative realm of bioengineering and nanomedicine, which is at the helm of revolutionizing complex chronic wound care. It underscores the significance of integrating patient sex into the development and (pre)clinical testing of these avant-garde treatment modalities, in order to enhance healing prospects for all patients regardless of sex. Moreover, we explore the representation of male and female patients in clinical trials of bioengineered and nanomedicine products. Finally, we examine the primary reasons for the historical neglect in translating sex-specific wound healing research into clinical practice and propose strategic solutions. By tackling these issues, the article advocates advanced treatment frameworks that could significantly improve healing outcomes for individuals of all sexes, thereby optimizing both efficacy and inclusivity in chronic wound management.
Quality assurance in lung cancer screening
Authors: Taib Adnan G , Au-Yong Iain T H , Nair Arjun , Devaraj Anand , Chen Yan , Baldwin David R
Published: November 2024

The effectiveness of screening programmes is critically dependent on the accuracy of the screening test. Where this relies on clinical expertise, there is an imperative to assure that the level of expertise meets expected standards. In cancer screening involving images, the focus is on the reader. Auditing of results is fraught with difficulty because of the time taken to accumulate enough data with confirmed outcomes to identify underperformance before any harm is done. Late recognition can lead to the need for reanalysis and recall of screening participants with loss of confidence in the programme. External quality assurance (EQA) is a method that enables clinical expertise to be tested rapidly by using test datasets with confirmed clinical outcome. In the UK, the breast cancer screening programme has had EQA in place for over 30 years. This article describes the development of the first EQA process in lung cancer screening, using the experience gained from running the breast cancer EQA, and the proposed future developments.
Social work, personalisation, and the : A Bourdieusian analysis
Authors: Bark Harry
Published: November 2024

This article considers the role of social work in English social care within the context of the Care Act 2014 and related policy agendas. This is achieved through a theoretical analysis of English social care policy and legislation rooted in the work of Pierre Bourdieu. Having been contextualized in the consolidation of neoliberal hegemony in Britain, particular focus is given to social care reforms stemming from the 2010–2015 Coalition Government, including the implementation of the Care Act 2014 and its associated personalisation principles. Utilizing Pierre Bourdieu’s concepts of ‘habitus’, ‘field’, and ‘capital’, social care policy and reform is viewed as embodying an ongoing ideological shift in the ways in which the state, and its social care professions, are envisaged as functioning and interacting with its citizens. From this, the role of social work in English social care is considered in relation to policy agendas underpinning the Care Act 2014 and more recent policy reviews and proposals. This article concludes by drawing on Bourdieu’s notion of ‘hysteresis’ to conceptualize a profession facing a complex negotiation of its skills and values within destabilizing political, economic, and ideological framings of practice.
The emerging field of non-invasive brain stimulation in Alzheimer’s disease
Authors: Koch Giacomo , Altomare Daniele , Benussi Alberto , Bréchet Lucie , Casula Elias P , Dodich Alessandra , Pievani Michela , Santarnecchi Emiliano , Frisoni Giovanni B
Published: November 2024

Treating cognitive impairment is a holy grail of modern clinical neuroscience. In the past few years, non-invasive brain stimulation is increasingly emerging as a therapeutic approach to ameliorate performance in patients with cognitive impairment and as an augmentation approach in persons whose cognitive performance is within normal limits. In patients with Alzheimer’s disease, better understanding of brain connectivity and function has allowed for the development of different non-invasive brain stimulation protocols. Recent studies have shown that transcranial stimulation methods enhancing brain plasticity with several modalities have beneficial effects on cognitive functions. Amelioration has been shown in preclinical studies on behaviour of transgenic mouse models for Alzheimer’s pathology and in clinical studies with variable severity of cognitive impairment. While the field is still grappling with issues related to the standardization of target population, frequency, intensity, treatment duration and stimulated region, positive outcomes have been reported on cognitive functions and on markers of brain pathology. Here we review the most encouraging protocols based on repetitive transcranial magnetic stimulation, transcranial direct current stimulation, transcranial alternating current stimulation, visual-auditory stimulation, photobiomodulation and transcranial focused ultrasound, which have demonstrated efficacy to enhance cognitive functions or slow cognitive decline in patients with Alzheimer’s disease. Beneficial non-invasive brain stimulation effects on cognitive functions are associated with the modulation of specific brain networks. The most promising results have been obtained targeting key hubs of higher-level cognitive networks, such as the frontal-parietal network and the default mode network. The personalization of stimulation parameters according to individual brain features sheds new light on optimizing non-invasive brain stimulation protocols for future applications.