bluuebunny/crossref_metadata_2025 huggingface dataset:
Weight index of high-dimensional time-to-event feature selection method
Authors: Bhattacharjee Atanu , Halder Soutik
Published: February 2025

Feature selection in high-dimensional data is challenging, aiming to eliminate irrelevant features and build a robust statistical model that identifies prognostic markers. Our proposed approach introduces a weight function that assigns relevance scores to each feature in the model. This weight function allows us to prioritize features in the dataset, enabling the selection of potential genes based on assigned weights and an updated threshold value. To highlight genes with the greatest variation, the coefficient of variation is integrated into the weight function. In addition, the model considers the proportion of selected factors throughout the iterative process to mitigate selection bias. We evaluate the proposed method using both training and testing datasets, producing a ranked list of filtered gene candidates. To demonstrate the method’s utility, we apply it to a gene expression dataset from the Gene Expression Omnibus, yielding a final selection of 12 features from an initial set of 507. All analyses are conducted in the R programming language. In summary, this method offers a novel approach to feature selection in high-dimensional data, particularly applicable to genomics, proteomics, and transcriptomics datasets used to predict and monitor disease progression. By effectively reducing selection bias, the method supports the creation of reliable statistical models that include valuable prognostic markers.
Paired kernels and truncated Toeplitz operators
Authors: Câmara M. Cristina , Partington Jonathan R.
Published: February 2025

This paper considers paired operators in the context of the Lebesgue Hilbert space

$$L^2$$

L
2

on the unit circle and its subspace, the Hardy space

$$H^2.$$

H
2

.

The kernels of such operators, together with their analytic projections, which are generalizations of Toeplitz kernels, are studied. Inclusion relations between such kernels are considered in detail, and the results are applied to describing the kernels of finite-rank asymmetric truncated Toeplitz operators.
Dictionary-based assessment of European Sustainability Reporting Standard (ESRS) disclosure topics
Authors: Suta Alex , Molnár Péter , Limbach Zétény , Tóth Árpád
Published: February 2025

As the imperative for sustainable business practices and corporate responsibility has grown, the analysis and integration of Environmental, Social, and Governance (ESG) issues into corporate strategies has become a crucial aspect of business strategy. The paper assesses the ESG reporting preparedness of companies in the Central and Eastern European (CEE) region by analyzing their compliance with the European Sustainability Reporting Standards (ESRS). The study assesses the variability in disclosures across ESG pillars and examines their relationship with financial metrics using a test of independence and bootstrapped multiple regression. By employing an automated text analysis methodology on sustainability reports from top-performing companies, including Hungary, the Czech Republic, Poland, Austria, Slovenia, and Romania, the research identifies significant differences in reporting scores across various ESG disclosure topics. The results indicate that Climate Change (E1) scores are higher than those of other topics, suggesting an uneven emphasis on different aspects of sustainability. Furthermore, the analysis reveals that larger companies tend to achieve higher ESG scores, reflecting their greater resources for comprehensive and transparent reporting practices. The research contributes to the understanding of ESG reporting practices in the CEE region and highlights the importance of improvement in sustainability reporting to foster greater transparency and comparability. The findings suggest policy initiatives to encourage balanced reporting across all ESG topics and that companies, particularly smaller ones, could benefit from capacity-building efforts to enhance their reporting capabilities.

Graphical Abstract
Enhancing water sustainability in the Gobi Desert: processes based on IWRM principles
Authors: Purevjav Bolormaa , Klein Bern , Dierkes Julian , Kunz Nadja , Xavier André , McFaul Suzette
Published: February 2025

The mining industry is an important sector that contributes to economic growth and employment creation in Mongolia. Water access, water quality, and community engagement are the major challenges the Mongolian mining industry faces. Integrated Water Resource Management (IWRM) is a holistic water management approach that applies principles of economic efficiency, social equity, and environmental sustainability to ensure water sustainability. A research study was carried out to understand stakeholders’ views and perspectives on IWRM and to identify water use practices, challenges, and barriers in the Gobi Desert mining region. The aim was to identify processes that help to improve access to water in the Gobi Desert region. This research applied a qualitative approach and employed three data collection methods: (1) semi-structured interviews; (2) field observations and (3) documents and academic articles reviews. Research participants were representatives from mining companies, local communities, government, and river basin administrations. In the Gobi Desert region, processes contributing to improving water management are: (1) participatory water monitoring, (2) coal processing plant educational visits, (3) local stakeholders council’s meetings, (4) herder’s well improvement projects, (5) independent water auditing, and (6) water advocacy events. These practices, aligned with the core principles of IWRM provide practical solutions for sustainable water management in mining regions, with the potential for global adaptation.
Preparing future physicians for the gun violence crisis: development of a firearm safety curriculum for medical students during the surgery clerkship
Authors: Hernandez Alexandra E. , Collie Brianna L. , Delamater Jessica , Presser Maxwell , Huerta Carlos T. , Courel Steve C. , Sands Laurence R. , Hui Vanessa W.
Published: February 2025

Purpose

Firearm injuries are a major public health crisis; however, providers are not routinely educated on how to discuss this topic with their patients. To address this gap, a firearm safety curriculum was developed for medical students during their surgery clerkship. Perceptions, knowledge, and preparedness for counseling patients was evaluated before and after dissemination.

Methods

All second-year medical students enrolled in the surgery core clerkship from March 2023 to March 2024 were included. The curriculum consists of a 30-min didactic presentation discussing gun violence with techniques to identify and counsel at-risk patients followed by a 30-min, interactive case-based discussion where students simulate counseling strategies. Pre- and post-session surveys included a 5-point Likert scale to evaluate efficacy of the curriculum. Paired student’s t test was conducted to compare pre- and post-survey responses.

Results

Of the 249 students, 54.6% % were female, 50.9% were White, and mean age was 25 ± 2 years. While 91.9% of students responded that they had never owned a gun, 37.8% had lived in a home where a gun was present, and 48.2% had fired a gun before. Only 24.7% of students had previously taken a gun-safety course, and 15.4% received training on counseling patients on firearm safety. One hundred thirty three students completed both pre- and post-session surveys for analysis. After the course, students had higher agreement on the importance of physician’s roles and responsibilities in patient education on firearm safety, and students felt more prepared to counsel patients. Knowledge of patient risk factors for firearm injury increased significantly from students being able to identify 1.4 ± 1.1 risk factors correctly on pre-test to identifying 2.6 ± 1.6 risk factors correctly on post-test (t(64) = − 5.6, p < 0.01).

Conclusion

The firearm safety curriculum is a simple and effective tool that augments students’ knowledge and understanding of gun violence, as well as prepares them to counsel patients on firearm safety. This curriculum can be widely implemented as an important intervention to equip future physicians with the necessary tools to help address the firearm crisis in the United States.
Digital transformation and financing constraints: evidence from Chinese manufacturing multinational enterprises
Authors: Bo Lan , Li Haoyu , Zhang Shijin , Tang Ruize
Published: February 2025

In light of recent global economic uncertainties and technological advancements, it has become crucial to build new competitive advantages for Chinese manufacturing enterprises in the international arena, with the impact of their digital transformation efforts being particularly significant. This research addresses a pressing need to understand how digital transformation can be strategically utilized to overcome financial barriers for Chinese manufacturing multinational enterprises. Using data from Shanghai and Shenzhen A-share listed companies between 2011 and 2023, the study reveals that digital transformation can effectively ease financial constraints faced by these manufacturing multinational enterprises through reducing information asymmetry and enhancing innovation capability. Moreover, the depth of the internationalization strategy enhances the positive effects of digital transformation on financing constraints, whereas a broader international presence tends to substitute these benefits. Additional analysis shows that digital transformation as a whole, irrespective of the specific focus area, effectively alleviates financing constraints, delivering consistent benefits across all continents. Notably, compared to non-multinational Chinese manufacturing firms, multinational manufacturing companies experience a greater alleviation of financing constraints through digital transformation. The study concludes that digital transformation is a vital tool for reducing financial barriers in multinational manufacturing firms. These findings will contribute to the broader discourse on digitalization in emerging markets and offer practical implications for business strategy and financial management in the digital age.
CBENet: contextual and boundary-enhanced network for oil spill detection via microwave remote sensing
Authors: Di Mengmeng , Di Xinnan , Xiao Huiyao , Gao Ying , Li Yongqing
Published: February 2025

In microwave remote sensing images, oil spills are generally distributed at various scales with blurry boundaries. To accurately detect variable oil spills from microwave remote sensing images, especially from synthetic aperture radar (SAR) images, we developed a contextual and boundary-enhanced network (CBENet) for oil spill detection from SAR observation images. The CBENet employs an encoder-decoder architecture that includes an encoder, a contextual fusion module, and a decoder. The encoder-decoder architecture intrinsically captures both global and local features of oil spills through the downsampling and upsampling processes inherent to the framework. The contextual fusion module enhances the contextual feature fusion using parallel dilated convolution branches. Furthermore, the utilization of a boundary-enhanced loss function further improves detection by focusing on the precise identification of oil spill boundaries. These properties strengthen the CBENet to effectively detect oil spills with blurry boundaries. The effectiveness of the CBENet has been validated through comprehensive empirical experiments including qualitative and quantitative evaluations. Comparative analyses demonstrate that CBENet outperforms several state-of-the-art detection models, significantly enhancing oil spill detection accuracy from SAR observation images.
Tungstate intercalated Mg-Al layered double hydroxide and its derived mixed metal oxide: preparation, characterization, and investigation of optical, electrical, and dielectric properties
Authors: Lahkale Redouane , Sabbar Elmouloudi
Published: February 2025

Layered double hydroxides intercalated with tungstate ions ([WO4]2–) are among the anionic clays with interesting applications due to the physicochemical properties of the element tungsten. Their transformation by calcination into the corresponding derived mixed metal oxides should modify their properties. In view of this, the aim of this study is to compare the light absorption behavior of tungstate intercalated Mg-Al layered double hydroxide (LDH) with that of its derived mixed metal oxide (MMO), as well as their electrical and dielectric properties. The LDH precursor was prepared successfully by the co-precipitation method at pH 10, while MMO was obtained by calcining LDH at 723 K. Subsequently, LDH and MMO were characterized by X-ray diffraction and analyzed by thermal gravimetric analysis/differential thermal analysis and Raman spectroscopy. The electrical response, modeled by an equivalent circuit, was found to be intimately dependent on the structures of LDH and MMO, while the light absorption behavior is mainly due to the presence of the distorted [WO4]2– and the tetragonal MgWO4 in LDH and MMO, respectively. In addition, MMO showed an improvement in the dielectric properties through the large decrease in the dielectric loss tangent and electrical conductivity. However, LDH exhibited greater absorption coefficients in the ultraviolet region with a lower optical energy gap compared with its derived MMO, resulting in energy gaps of 4.23 and 4.35 eV for LDH and MMO, respectively. Results revealed that calcining LDH to form MMO fails to improve light absorption, but does improve the dielectric behavior, which makes possible the use of LDH as a shielding material against UV light and MMO for energy storage applications.
Reflections on the future of African universities
Authors: Falola Toyin
Published: February 2025

Jeremiah O. Arowosegbe’s essay ‘African universities and the challenge of postcolonial development’ sheds significant light on political and economic influences, freedom within academia, and the role of these institutions within wider socio-political contexts. I want to endorse some of his proposals and make additional suggestions to comprehend the complexities and potential directions of African universities.
Beyond crisis: African universities’ global presence before and after structural adjustment
Authors: Ivaska Andrew
Published: February 2025

I want to say what a privilege it is to be invited to comment on Jeremiah Arowosegbe’s article ‘African universities and the challenge of postcolonial development’. First and foremost, this is because Arowosegbe’s piece is exactly the kind of intervention we need more of: passionately written, politically engaged commentaries on the state of African universities today by scholars based on the continent who are invested in charting the best way forward for their institutions. African universities have been in a kind of Janus-faced state for at least the last decade, if not longer. On the one hand, institutions with records of having been among the world’s most exciting universities of the 1960s and 1970s – Makerere, Ibadan, Dar es Salaam – have had to endure a near total, decades-long collapse driven by austerity programmes imposed by the International Monetary Fund (IMF) and forced on African states from the 1980s. This is a crisis that undoubtably lingers – indeed, Arowosegbe makes it his focus – and these universities have had to struggle not to be entirely defined by this story of lack and of failure. On the other hand, some of these institutions (including those named above) have come through the fire of this collapse and have emerged with new life that cannot be reduced to mere tendrils. On the contrary: the continent’s top dozen or so universities are today producing students who will very likely become the world’s next generation of humanists, social scientists and hard scientists focused on Africa, and beyond too. The pipeline for this present generation of students often now runs from undergraduate and master’s programmes in Africa, to top doctoral programmes in North America and Europe, to these students being the most competitive candidates for the mini-boom (relatively speaking) in tenure-track positions in disciplinary scholarship and pedagogy focused on Africa. Amidst a more general withering of the humanities in globally northern universities, African and Black Studies constitute a partial exception to the dying throes of higher education as we know it and are part of a laudable and long overdue diversification of the field. Adding to the reconfiguration of African Studies’ landscape of labour, the dramatic shortage of viable jobs in North America and the UK is making the job market for graduates of the world’s top PhD programmes a truly global one that includes Africa prominently. Not since the 1960s have we seen the prospect of top African universities being realistically able to attract new scholars trained in the global North to base themselves in Africa – a potential boon to African universities (even if one that remains more in potentia than realized).
Reconstructing the future: taking ownership of copyright in Africa
Authors: Diawara Mamadou
Published: February 2025

What is the state of copyright in Africa today, when specialists in the field, notably in the USA, are sounding the alarm? Taking as its starting point a right that emerged in the West in the twilight of the nineteenth century, this article examines the ways in which copyright is discussed, established and experienced in sub-Saharan Africa. It questions the relevance of the vocabulary used and asks how Africa can be made intelligible in the context of a heterogeneous world. Since the 1990s, international organizations have promoted and imposed the economic notion of material goods, inventing a new tradition. The result is a heritage, the commons, that is reduced to a resource divorced from any historical or social context. How can we go beyond these rights, which are a source of a ‘promise economy’ for creators, to promote imprescriptible and inalienable human rights? How can experienced creators resist copyright that takes them back to the Middle Ages?
Meteorology, weather and war in South East Asia: Malaya c.1940–1960
Authors: Williamson Fiona
Published: February 2025

This article interrogates the positioning of British colonial meteorology in Malaysia and Singapore from the 1940s to 1960. This period spanned a global conflict and an internecine war, effecting profound sociopolitical changes from which neither Malaysia nor Singapore would emerge the same. The meteorological services were essential to Britain’s armed conflicts, providing vital weather information to the army, navy and, especially, the air forces, as well as supporting the aviation and shipping industry often in difficult and dangerous circumstances. This article argues that British military policy in South East Asia and the specific concerns of the colonial government in Malaya directly commanded the meteorological agenda on the ground during this period, with a secondary but significant impact on tropical climate and weather research. It thus addresses the interplay of science, colonialism and military interest from the perspective of a region that has featured little in the history of science.
Employment Rights Bill – What Does it Mean for Employers?
Authors: Cordran Bob
Published: February 2025

The Employment Rights Bill was published in October 2024. In this article, Bob Cordran, an Employment Partner at Memery Crystal, takes a look at the key reforms at the heart of it.
Expert consensus on the prevention and treatment of enamel demineralization in orthodontic treatment
Authors: Xia Lunguo , Zhou Chenchen , Mei Peng , Jin Zuolin , He Hong , Wang Lin , Bai Yuxing , Chen Lili , Li Weiran , Wang Jun , Hu Min , Song Jinlin , Cao Yang , Liu Yuehua , Hou Benxiang , Wei Xi , Niu Lina , Lu Haixia , Ma Wensheng , Wang Peijun , Zhang Guirong , Guo Jie , Li Zhihua , Lu Haiyan , Ren Liling , Xu Linyu , Wu Xiuping , Lu Yanqin , Hu Jiangtian , Yue Lin , Zhang Xu , Fang Bing
Published: February 2025

Abstracts

Enamel demineralization, the formation of white spot lesions, is a common issue in clinical orthodontic treatment. The appearance of white spot lesions not only affects the texture and health of dental hard tissues but also impacts the health and aesthetics of teeth after orthodontic treatment. The prevention, diagnosis, and treatment of white spot lesions that occur throughout the orthodontic treatment process involve multiple dental specialties. This expert consensus will focus on providing guiding opinions on the management and prevention of white spot lesions during orthodontic treatment, advocating for proactive prevention, early detection, timely treatment, scientific follow-up, and multidisciplinary management of white spot lesions throughout the orthodontic process, thereby maintaining the dental health of patients during orthodontic treatment.
Porphyromonas gingivalis potentiates stem-like properties of oral squamous cell carcinoma by modulating SCD1-dependent lipid synthesis via NOD1/KLF5 axis
Authors: Zang Wenli , Geng Fengxue , Liu Junchao , Wang Zengxu , Zhang Shuwei , Li Yuchao , Lu Ze , Pan Yaping
Published: February 2025

Cancer stem cells (CSCs) are widely acknowledged as primary mediators to the initiation and progression of tumors. The association between microbial infection and cancer stemness has garnered considerable scholarly interest in recent years. Porphyromonas gingivalis (P. gingivalis) is increasingly considered to be closely related to the development of oral squamous cell carcinoma (OSCC). Nevertheless, the role of P. gingivalis in the stemness of OSCC cells remains uncertain. Herein, we showed that P. gingivalis was positively correlated with CSC markers expression in human OSCC specimens, promoted the stemness and tumorigenicity of OSCC cells, and enhanced tumor formation in nude mice. Mechanistically, P. gingivalis increased lipid synthesis in OSCC cells by upregulating the expression of stearoyl-CoA desaturase 1 (SCD1) expression, a key enzyme involved in lipid metabolism, which ultimately resulted in enhanced acquisition of stemness. Moreover, SCD1 suppression attenuated P. gingivalis-induced stemness of OSCC cells, including CSCs markers expression, sphere formation ability, chemoresistance, and tumor growth, in OSCC cells both in vitro and in vivo. Additionally, upregulation of SCD1 in P. gingivalis-infected OSCC cells was associated with the expression of KLF5, and that was modulated by P. gingivalis-activated NOD1 signaling. Taken together, these findings highlight the importance of SCD1-dependent lipid synthesis in P. gingivalis-induced stemness acquisition in OSCC cells, suggest that the NOD1/KLF5 axis may play a key role in regulating SCD1 expression and provide a molecular basis for targeting SCD1 as a new option for attenuating OSCC cells stemness.
Neonatal microbiome in the multiomics era: development and its impact on long-term health
Authors: Neu Josef , Stewart Christopher J.
Published: February 2025

The neonatal microbiome has been the focus of considerable research over the past two decades and studies have added fascinating information in terms of early microbial patterns and how these relate to various disease processes. One difficulty with the interpretation of these relationships is that such data is associative and provides little in terms of proof of causality or the underpinning mechanisms. Integrating microbiome data with other omics such as the proteome, inflammatory mediators, and the metabolome is an emerging approach to address this gap. Here we discuss these omics, their integration, and how they can be applied to improve our understanding, treatment, and prevention of disease.

Impact

This review introduces the concept of multiomics in neonatology and how emerging technologies can be integrated improve understanding, treatment, and prevention of disease.

We highlight considerations for performing multiomic research in neonates and the need for validation in separate cohorts and/or relevant model systems.

We summarise how the use of multiomics is expanding and lay out steps to bring this to the clinic to enable precision medicine.
Dental careers: findings of a national dental workforce survey
Authors: Clark Megan , McGregor Ailsa , Khairuddin Aina Najwa Mohd , Smith Malcolm , Gallagher Jennifer E.
Published: February 2025

Aim To explore dentists' experiences of their professional careers and job satisfaction within the United Kingdom (UK) workforce.

Methods A cross-sectional survey of the national dentist workforce was conducted using an online questionnaire, informed by previous research. The anonymous online survey was conducted between February and May 2021, with ethical approval, via national gatekeeper institutions, and promoted through social media. Statistical analysis of the data was performed in SPSS.

Results Of the 1,240 respondents, 875 had completed 96% of the questionnaire, including providing demographic details, and were included for analysis. Almost half (46%) reported their career was ‘not as envisaged'. A majority (58%) of dentists reported that their career plans had changed and 40.2% reported planning on changing careers. Significant associations were found between an individual's career plan trajectories (‘as envisaged', ‘changed plan' and ‘planning on changing') and sex, ethnicity, job satisfaction, primary role settings, country qualification was obtained and duration of working experience. Men were significantly more likely to report their career was as envisaged. Job satisfaction was higher for those whose careers were as envisaged and had no plans for future changes.

Conclusions Careers were not necessarily as envisaged, with over half of the dentists surveyed changing their career plans over their working life. There was greater satisfaction among those whose careers were envisaged and had experienced career progression..
GWAS meta-analysis of psoriasis identifies new susceptibility alleles impacting disease mechanisms and therapeutic targets
Authors: Dand Nick , Stuart Philip E. , Bowes John , Ellinghaus David , Nititham Joanne , Saklatvala Jake R. , Teder-Laving Maris , Thomas Laurent F. , Traks Tanel , Uebe Steffen , Assmann Gunter , Baudry David , Behrens Frank , Billi Allison C. , Brown Matthew A. , Burkhardt Harald , Capon Francesca , Chung Raymond , Curtis Charles J. , Duckworth Michael , Ellinghaus Eva , FitzGerald Oliver , Gerdes Sascha , Griffiths Christopher E. M. , Gulliver Susanne , Helliwell Philip S. , Ho Pauline , Hoffmann Per , Holmen Oddgeir L. , Huang Zhi-ming , Hveem Kristian , Jadon Deepak , Köhm Michaela , Kraus Cornelia , Lamacchia Céline , Lee Sang Hyuck , Ma Feiyang , Mahil Satveer K. , McHugh Neil , McManus Ross , Modalsli Ellen H. , Nissen Michael J. , Nöthen Markus , Oji Vinzenz , Oksenberg Jorge R. , Patrick Matthew T. , Perez White Bethany E. , Ramming Andreas , Rech Jürgen , Rosen Cheryl , Sarkar Mrinal K. , Schett Georg , Schmidt Börge , Tejasvi Trilokraj , Traupe Heiko , Voorhees John J. , Wacker Eike Matthias , Warren Richard B. , Wasikowski Rachael , Weidinger Stephan , Wen Xiaoquan , Zhang Zhaolin ,   BSTOP study group, Burden A. David , Smith Catherine H. , Brown Sara J. , Dand Nick , Mahil Satveer K. , McAteer Helen , Schofield Julia , Siebert Stefan ,   Estonian Biobank research team, Metspalu Andres , Milani Lili , Nelis Mari , Barton Anne , Chandran Vinod , Esko Tõnu , Foerster John , Franke Andre , Gladman Dafna D. , Gudjonsson Johann E. , Gulliver Wayne , Hüffmeier Ulrike , Kingo Külli , Kõks Sulev , Liao Wilson , Løset Mari , Mägi Reedik , Nair Rajan P. , Rahman Proton , Reis André , Smith Catherine H. , Di Meglio Paola , Barker Jonathan N. , Tsoi Lam C. , Simpson Michael A. , Elder James T.
Published: February 2025

Psoriasis is a common, debilitating immune-mediated skin disease. Genetic studies have identified biological mechanisms of psoriasis risk, including those targeted by effective therapies. However, the genetic liability to psoriasis is not fully explained by variation at robustly identified risk loci. To refine the genetic map of psoriasis susceptibility we meta-analysed 18 GWAS comprising 36,466 cases and 458,078 controls and identified 109 distinct psoriasis susceptibility loci, including 46 that have not been previously reported. These include susceptibility variants at loci in which the therapeutic targets IL17RA and AHR are encoded, and deleterious coding variants supporting potential new drug targets (including in STAP2, CPVL and POU2F3). We conducted a transcriptome-wide association study to identify regulatory effects of psoriasis susceptibility variants and cross-referenced these against single cell expression profiles in psoriasis-affected skin, highlighting roles for the transcriptional regulation of haematopoietic cell development and epigenetic modulation of interferon signalling in psoriasis pathobiology.
Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm
Authors: Kshirsagar Meghana , Meller Artur , Humphreys Ian R. , Sledzieski Samuel , Xu Yixi , Dodhia Rahul , Horvitz Eric , Berger Bonnie , Bowman Gregory R. , Ferres Juan Lavista , Baker David , Baek Minkyung
Published: February 2025

The majority of proteins must form higher-order assemblies to perform their biological functions, yet few machine learning models can accurately and rapidly predict the symmetry of assemblies involving multiple copies of the same protein chain. Here, we address this gap by finetuning several classes of protein foundation models, to predict homo-oligomer symmetry. Our best model named Seq2Symm, which utilizes ESM2, outperforms existing template-based and deep learning methods achieving an average AUC-PR of 0.47, 0.44 and 0.49 across homo-oligomer symmetries on three held-out test sets compared to 0.24, 0.24 and 0.25 with template-based search. Seq2Symm uses a single sequence as input and can predict at the rate of ~80,000 proteins/hour. We apply this method to 5 proteomes and ~3.5 million unlabeled protein sequences, showing its promise to be used in conjunction with downstream computationally intensive all-atom structure generation methods such as RoseTTAFold2 and AlphaFold2-multimer. Code, datasets, model are available at: https://github.com/microsoft/seq2symm.
Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency
Authors: Solovyov Alexander , Behr Julie M. , Hoyos David , Banks Eric , Drong Alexander W. , Thornlow Bryan , Zhong Jimmy Z. , Garcia-Rivera Enrique , McKerrow Wilson , Chu Chong , Arisdakessian Cedric , Zaller Dennis M. , Kamihara Junne , Diao Liyang , Fromer Menachem , Greenbaum Benjamin D.
Published: February 2025

Somatic mobilization of LINE-1 (L1) has been implicated in cancer etiology. We analyzed a recent TCGA data release comprised of nearly 5000 pan-cancer paired tumor-normal whole-genome sequencing (WGS) samples and ~9000 tumor RNA samples. We developed TotalReCall an improved algorithm and pipeline for detection of L1 retrotransposition (RT), finding high correlation between L1 expression and “RT burden” per sample. Furthermore, we mathematically model the dual regulatory roles of p53, where mutations in TP53 disrupt regulation of both L1 expression and retrotransposition. We found those with Li-Fraumeni Syndrome (LFS) heritable TP53 pathogenic and likely pathogenic variants bear similarly high L1 activity compared to matched cancers from patients without LFS, suggesting this population be considered in attempts to target L1 therapeutically. Due to improved sensitivity, we detect over 10 genes beyond TP53 whose mutations correlate with L1, including ATRX, suggesting other, potentially targetable, mechanisms underlying L1 regulation in cancer remain to be discovered.
Rare genetic associations with human lifespan in UK Biobank are enriched for oncogenic genes
Authors: Park Junyoung , Peña-Tauber Andrés , Talozzi Lia , Greicius Michael D. , Le Guen Yann
Published: February 2025

Human lifespan is shaped by genetic and environmental factors. To enable precision health, understanding how genetic variants influence mortality is essential. We conducted a survival analysis in European ancestry participants of the UK Biobank, using age-at-death (N=35,551) and last-known-age (N=358,282). The associations identified were predominantly driven by cancer. We found lifespan-associated loci (APOE, ZSCAN23) for common variants and six genes where burden of loss-of-function variants were linked to reduced lifespan (TET2, ATM, BRCA2, CKMT1B, BRCA1, ASXL1). Additionally, eight genes with pathogenic missense variants were associated with reduced lifespan (DNMT3A, SF3B1, TET2, PTEN, SOX21, TP53, SRSF2, RLIM). Many of these genes are involved in oncogenic pathways and clonal hematopoiesis. Our findings highlight the importance of understanding genetic factors driving the most prevalent causes of mortality at a population level, highlighting the potential of early genetic testing to identify germline and somatic variants increasing one’s susceptibility to cancer and/or early death.
The complex structure of aquatic food webs emerges from a few assembly rules
Authors: García-Oliva Ovidio , Wirtz Kai
Published: February 2025

Food-web theory assumes that larger-bodied predators generally select larger prey. This allometric rule fails to explain a considerable fraction of trophic links in aquatic food webs. Here we show that food-web constraints result in guilds of predators that vary in size but have specialized on prey of the same size, and that the distribution of such specialist guilds explains about one-half of the food-web structure. We classified 517 pelagic species into five predator functional groups. Most of these follow three prey selection strategies: a guild following the allometric rule whereby larger predators eat larger prey and two guilds of specialists that prefer either smaller or larger prey than predicted by the allometric rule. Such coexistence of non-specialist and specialist guilds independent from taxa or body size points towards structural principles behind ecological complexity. We show that the pattern describes >90% of observed linkages in 218 food webs in 18 aquatic ecosystems worldwide. The pattern can be linked to eco-evolutionary constraints to prey exploitation and provides a blueprint for more effective food-web models.
Persistence of davemaoite at lower-mantle conditions
Authors: Wang Lin , Miyajima Nobuyoshi , Wang Fei , Katsura Tomoo
Published: February 2025

The lower mantle occupies over half of Earth’s volume, and accordingly, its mineralogy is crucial in determining the structure and dynamics of Earth. Davemaoite, the calcium silicate perovskite, was believed to coexist with bridgmanite in the lower mantle and is considered essential for understanding the chemical evolution and dynamics of Earth’s lower mantle. However, the presence of davemaoite is challenged due to the potential for high calcium silicate solubility in bridgmanite. Here we use an ultrahigh-pressure multi-anvil technique to show experimentally that the calcium solubility in bridgmanite is insufficient to eliminate davemaoite under mantle conditions, including typical mantle pressure, temperature and chemical compositions. We conclude that davemaoite has been stable in Earth’s lower mantle since its formation. Due to the limited calcium solubility in bridgmanite, davemaoite-enriched domains are expected at the core–mantle boundary. These domains could serve as the principal reservoir for incompatible elements in the lower mantle and may be the source for some ocean island basalts. Furthermore, our study offers an explanation for the observed large low-shear-wave-velocity provinces at the bottom of the lower mantle. These provinces may consist of davemaoite-enriched materials crystallized from basal magma ocean in early Earth history.
Rapid brain tumor classification from sparse epigenomic data
Authors: Brändl Björn , Steiger Mara , Kubelt Carolin , Rohrandt Christian , Zhu Zhihan , Evers Maximilian , Wang Gaojianyong , Schuldt Bernhard , Afflerbach Ann-Kristin , Wong Derek , Lum Amy , Halldorsson Skarphedinn , Djirackor Luna , Leske Henning , Magadeeva Svetlana , Smičius Romualdas , Quedenau Claudia , Schmidt Nils O. , Schüller Ulrich , Vik-Mo Einar O. , Proescholdt Martin , Riemenschneider Markus J. , Zadeh Gelareh , Ammerpohl Ole , Yip Stephen , Synowitz Michael , van Bömmel Alena , Kretzmer Helene , Müller Franz-Josef
Published: February 2025

Although the intraoperative molecular diagnosis of the approximately 100 known brain tumor entities described to date has been a goal of neuropathology for the past decade, achieving this within a clinically relevant timeframe of under 1 h after biopsy collection remains elusive. Advances in third-generation sequencing have brought this goal closer, but established machine learning techniques rely on computationally intensive methods, making them impractical for live diagnostic workflows in clinical applications. Here we present MethyLYZR, a naive Bayesian framework enabling fully tractable, live classification of cancer epigenomes. For evaluation, we used nanopore sequencing to classify over 200 brain tumor samples, including 10 sequenced in a clinical setting next to the operating room, achieving highly accurate results within 15 min of sequencing. MethyLYZR can be run in parallel with an ongoing nanopore experiment with negligible computational overhead. Therefore, the only limiting factors for even faster time to results are DNA extraction time and the nanopore sequencer’s maximum parallel throughput. Although more evidence from prospective studies is needed, our study suggests the potential applicability of MethyLYZR for live molecular classification of nervous system malignancies using nanopore sequencing not only for the neurosurgical intraoperative use case but also for other oncologic indications and the classification of tumors from cell-free DNA in liquid biopsies.
CETD, a global compound events detection and visualisation toolbox and dataset
Authors: Yin Cong , Ting Mingfang , Kornhuber Kai , Horton Radley M. , Yang Yaping , Jiang Yelin
Published: February 2025

Compound events (CEs) are attracting increased attention due to their significant societal and ecological impacts. However, their inherent complexity can pose challenges for climate scientists and practitioners, highlighting the need for a more approachable and intuitive framework for detecting and visualising CEs. Here, we introduce the Compound Events Toolbox and Dataset (CETD), which provides the first integrated, interactive, and extensible platform for CE detection and visualisation. Employing observations, reanalysis, and model simulations, CETD can quantify the frequency, duration, and severity of multiple CE types: multivariate, sequential, and concurrent events. It can analyse CEs often linked to severe impacts on human health, wildfires, and air pollution, such as hot-dry, wet-windy, and hot-dry-stagnation events. To validate the performance of CETD, we conduct statistical analyses for several high-impact events, such as the 2019 Australian wildfires and the 2022 European heatwaves. The accessibility and extensibility of CETD will benefit the broader community by enabling them to better understand and prepare for the risks and challenges posed by CEs in a warming world.
Experimental and numerical investigation to optimise liquid desiccant system for advanced air conditioning
Authors: Shivaprasad K. V. , Roy Sumit , Giampieri Alessandro , Smallbone Andrew , Roskilly Anthony Paul
Published: February 2025

This study aims to experimentally demonstrate a liquid desiccant systems effectiveness by using thermo-chemical fluid, such as aqueous solution of calcium chloride. This study evaluated the effect of operating temperatures on air properties (temperature, relative humidity, and moisture content) and system effectiveness by varying air flow rates. The system’s functionality was influenced by the operational temperature and air flow rate, and the dehumidification effectiveness was higher at low operating temperatures and low airflow rates. An ANN metamodel-based control strategy is also proposed for implementation in hybrid thermo-chemical networks with the help of system performance data and real-time data. The suggested ANN model’s results were validated using a variety of measuring techniques, including the RMSE, MAPE, correlation (R), and coefficient of determination (R2). The proposed ANN analysis achieved an excellent correlation between predicted and experimentally measured data.
Multi-modal Language models in bioacoustics with zero-shot transfer: a case study
Authors: Miao Zhongqi , Elizalde Benjamin , Deshmukh Soham , Kitzes Justin , Wang Huaming , Dodhia Rahul , Ferres Juan Lavista
Published: February 2025

Automatically detecting sound events with Artificial Intelligence (AI) has become increas- ingly popular in the field of bioacoustics, ecoacoustics, and soundscape ecology, particularly for wildlife monitoring and conservation. Conventional methods predominantly employ supervised learning techniques that depend on substantial amounts of manually annotated bioacoustic data. However, manual annotation in bioacoustics is tremendously resource- intensive in terms of both human labor and financial resources, and it requires considerable domain expertise. Moreover, the supervised learning framework limits the application scope to predefined categories within a closed setting. The recent advent of Multi-Modal Language Models has markedly enhanced the versatility and possibilities within the realm of AI appli- cations, as this technique addresses many of the challenges that inhibit the deployment of AI in real-world applications. In this paper, we explore the potential of Multi-Modal Language Models in the context of bioacoustics through a case study. We aim to showcase the potential and limitations of Multi-Modal Language Models in bioacoustic applications. In our case study, we applied an Audio-Language Model–—a type of Multi-Modal Language Model that aligns language with audio / sound recording data—–named CLAP (Contrastive Language–Audio Pretraining) to eight bioacoustic benchmarks covering a wide variety of sounds previously unfamiliar to the model. We demonstrate that CLAP, after simple prompt engineering, can effectively recognize group-level categories such as birds, frogs, and whales across the benchmarks without the need for specific model fine-tuning or additional training, achieving a zero-shot transfer recognition performance comparable to supervised learning baselines. Moreover, we show that CLAP has the potential to perform tasks previously unattainable with supervised bioacoustic approaches, such as estimating relative distances and discovering unknown animal species. On the other hand, we also identify limitations of CLAP, such as the model’s inability to recognize fine-grained species-level categories and the reliance on manually engineered text prompts in real-world applications.
Improving ALS detection and cognitive impairment stratification with attention-enhanced deep learning models
Authors: Xia Yuqing , Gregory Jenna M. , Waldron Fergal M. , Spence Holly , Vallejo Marta
Published: February 2025

Amyotrophic lateral sclerosis (ALS) is a fatal neurological disease marked by motor deterioration and cognitive decline. Early diagnosis is challenging due to the complexity of sporadic ALS and the lack of a defined risk population. In this study, we developed Miniset-DenseSENet, a convolutional neural network combining DenseNet121 with a Squeeze-and-Excitation attention mechanism, using 190 autopsy brain images from the Gregory Laboratory at the University of Aberdeen. The model distinguishes controls, ALS patients with no cognitive impairment, and ALS patients with cognitive impairment (ALS-frontotemporal dementia) with 97.37% accuracy, addressing a significant challenge in overlapping neurodegenerative disorders involving TDP-43 proteinopathy. Miniset-DenseSENet outperformed other transfer learning models, achieving a sensitivity of 1 and specificity of 0.95. These findings suggest that integrating transfer learning and attention mechanisms into neuroimaging can enhance diagnostic accuracy, enabling earlier ALS detection and improving patient stratification. This model has the potential to guide clinical decisions and support personalied therapeutic strategies.
Prebiotic formation of thioesters via cyclic anhydrides as a key step in the emergence of metabolism
Authors: El Qami Abdelkarim , Hilari Jorge Isaac , Blandin Véronique , Gayraud Oscar , Milet Anne , Vallée Yannick
Published: February 2025

Thioesters are high-energy derivatives of carboxylic acids that are essential in the functioning of today’s living cells. Their central role argues in favor of their early introduction in the abiotic reaction network which led to the emergence of life on Earth. We propose that the first thioesters appeared during the establishment of the reverse tricarboxylic acid (rTCA) cycle, an effective metabolic cycle for the synthesis of organic molecules from CO2. Most of the acids in this cycle are 1,4-diacids. We show that the formation of a cyclic anhydride from aqueous solutions of succinic or citric acid is possible using drying conditions over silica, as it could happen in an evaporating pond. When these 1,4-diacids are dried in the presence of thiols, thioesters are obtained. Our experimental and theoretical results demonstrate that analogs of succinyl-CoA and citryl-CoA, thioesters from the rTCA cycle, can be produced. Such a process highlights the importance of 1,4-diacids, which would have been introduced in the metabolism then under construction because of their ability to form anhydrides and to be activated in the absence of triphosphates or of any other activating agent. At its beginning, the rTCA cycle should therefore be interpreted mainly as a “1,4-diacid cycle”.
Characteristics of wetting behavior under unloading in natural granite residual soil
Authors: Yin Song , Huang Jianing , Li Xinming , Sun Yuzhou , Li Yuru , Zhang Xianwei
Published: February 2025

Excavation of foundation pits induces stress release in the soil, leading to deformation driven by the redistribution of internal stresses and particle adjustment. Rainfall infiltration further increases soil water content, weakening particle bonding through the dissolution of cementing agents, and inducing additional wetting deformation. However, there has only been limited experimental research examining the deformation behavior of soil under the coupled effects of unloading and wetting, especially in water-rich excavation conditions, where these factors interact dynamically. This study systematically investigates the coupled effects of unloading and wetting on the deformation behavior of natural granite residual soil (GRS) through triaxial tests. The results reveal that the interaction between unloading and wetting amplifies soil deformation, with significant non-linear dependencies on confining pressure and saturation levels. The stress–strain curves of natural GRS under unloading path exhibit strain-hardening behavior, and the vertical wetting deformation decreases with increasing saturation. Furthermore, the study identifies pronounced anisotropic wetting deformation, with tensile wetting deformation significantly exceeding compressive wetting deformation under equivalent stress states. This anisotropy diminishes with increasing confining pressure, highlighting the stress-dependency of wetting deformation behavior. The hyperbolic model shows a larger wetting deformation than the linear model, underscoring its practical significance in designing safer excavation strategies under coupled unloading and wetting conditions. These findings provide a foundation for improving deformation prediction and risk management in geotechnical engineering.