bluuebunny/crossref_metadata_2025_split huggingface dataset:
A vectorial code for semantics in human hippocampus
Authors: Franch Melissa , Mickiewicz Elizabeth A. , Belanger James L. , Chericoni Assia , Chavez Ana G. , Katlowitz Kalman A. , Mathura Raissa , Bartoli Eleonora , Kemmer Suzanne , Piantadosi Steven T. , Provenza Nicole R. , Watrous Andrew J. , Sheth Sameer A. , Hayden Benjamin Y. 
Published: February 2025

ABSTRACTAs we listen to speech, our brains actively compute the meaning of individual words. Inspired by the success of large language models (LLMs), we hypothesized that the brain employs vectorial coding principles, such that meaning is reflected in distributed activity of single neurons. We recorded responses of hundreds of neurons in the human hippocampus, which has a well-established role in semantic coding, while participants listened to narrative speech. We find encoding of contextual word meaning in the simultaneous activity of neurons whose individual selectivities span multiple unrelated semantic categories. Like embedding vectors in semantic models, distance between neural population responses correlates with semantic distance; however, this effect was only observed in contextual embedding models (like BERT) and was reversed in non-contextual embedding models (like Word2Vec), suggesting that the semantic distance effect depends critically on contextualization. Moreover, for the subset of highly semantically similar words, even contextual embedders showed an inverse correlation between semantic and neural distances; we attribute this pattern to the noise-mitigating benefits of contrastive coding. Finally, in further support for the critical role of context, we find that range of neural responses covaries with lexical polysemy. Ultimately, these results support the hypothesis that semantic coding in the hippocampus follows vectorial principles.
Hematologic, Immunologic and Outcome Characteristics of Severe acute respiratory syndrome 2 (SARS-COV-2) among People Living with HIV in Eastern Uganda: A Retrospective Study
Authors: Otaala Timothy , Opito Ronald , Mugisha Kenneth , Oryokot Bonniface , Bakashaba Baker , Esabu Moses , Nbidde Susan Nabadda , Watmon Benedicto , Etolu Wilson , Lubaale Moses Yovani , Olupot-Olupot Peter 
Published: February 2025

AbstractIntroductionGlobally People Living with HIV (PLWHIV) are prone to severe opportunistic infections with Coronavirus disease of 2019 (COVID-19) inclusive. Dual infection of HIV and COVID-19 could complicate the clinical outcomes of these patients. This study sought to determine hematologic, immunologic, virologic and outcome characteristics of people with HIV and COVID-19 co-infections in two Mbale and Soroti Regional Referral Hospitals in Eastern Uganda.MethodsA retrospective review of medical records of PLHIV and contracted COVID-19 virus was conducted in two large regional referral hospitals in Eastern Uganda using a data abstraction tool. Data was captured using Kobo collect toolbox, downloaded in Microsoft Excel and analyzed using STATA version 15.0. Descriptive statistics was reported as frequencies and proportions, while contingency and comparisons were done at the bivariate level analysis. The penalized logistic regression was conducted at multivariate level to establish the factors associated with COVID-19 severity among PLHIV.ResultsA total of 100 patient records had 38%(n=38) of individuals aged 40-50 years and 62%(n=62) females. Most patients (6 in 10) were peasants with 79%(n=79) having low-income levels. Other than HIV, 3 out of 10 patients had comorbidities. Also, 30 had haematological records, of which 9 (30%) had leucocytosis and 3, leucopoenia. Further, 67% had immunologic records, of which 22 (33%) had CD4 counts <200 cells/mm3. Only 22% of patients had viral load results, of which 8 (36) were unsuppressed. Nineteen percent (19/100) patients had severe COVID-19 and 14% (14/100) died. Socio-demographic factors significantly associated with severe COVID-19 outcomes were being male (P=0.026) and having other comorbidities (P<0.001).ConclusionA significant proportion of PLHIV co-infected with COVID-19 had abnormal hematological and virological status possibly due to varying socio-demographic characteristics. Clinical outcomes of HIV and COVID-19 co-infection may therefore vary depending on an interplay between host factors, viral factors, and comorbidities.
Ambient temperature structural studies of Penicillin-binding Protein 2a ofMethicillin-Resistant Staphylococcus aureuswith XFELs and synchrotrons
Authors: Grieco Alice , Quereda-Moraleda Isabel , Botha Sabine , Dörner Katerina , Schmidt Christina , Han Huijong , Vakili Mohammad , Schulz Joachim , Koua Faisal , de Wijn Raphael , Kharitonov Konstantin , Round Adam , Bielecki Johan , Kupitz Christopher , Lisova Stella , Schleissner Pamela , Sierra Ray , Mariani Valerio , Basu Shibom , Orlans Julien , Rose Samuel , de Sanctis Daniele , Gee Leland B. , Bean Richard , Mobashery Shahriar , Chang Mayland , Hermoso Juan A. , Martin-Garcia Jose Manuel 
Published: February 2025

AbstractPenicillin-binding protein 2a (PBP2a) is a transpeptidase responsible for the β-lactam resistance in methicillin-resistantStaphylococcus aureus(MRSA), posing significant challenges to antibiotic therapy. PBP2a’s unique structural features, including its highly flexible active site and allosteric regulation, enable it to maintain catalytic activity even in the presence of β-lactam antibiotics. Despite extensive characterization using cryogenic crystallography, key questions remain about its dynamic properties and conformational changes under near-physiological conditions. Room-temperature crystallography methods, particularly serial femtosecond X-ray crystallography (SFX) at XFELs, provide a powerful approach to capture these dynamics. Unlike cryogenic conditions that can constrain protein flexibility, SFX enables the study of conformational variability and interaction networks closer to physiological states. Here, we present the first room-temperature structures of PBP2a obtained using SFX to uncover insights into the enzyme’s flexibility, allosteric communication, and catalytic mechanisms. These findings are built upon optimized large-scale production and crystallization protocols for PBP2a, ensuring high-quality microcrystals suitable for SFX data collection. The room-temperature structures reveal novel interaction patterns, including unique salt bridge networks and dynamic structural elements absent in cryogenic studies. Furthermore, comparative analyses highlight how environmental conditions influence the conformational states of PBP2a, providing new perspectives on its resistance mechanisms. By integrating structural data from EuXFEL and LCLS, this study not only enhances our understanding of PBP2a’s functional dynamics but also underscores the value of room-temperature crystallography in studying antibiotic resistance. These insights could guide the design of next-generation β-lactam antibiotics capable of overcoming PBP2a-mediated resistance.
A spatial transcriptomics atlas of live donors reveals unique zonation patterns in the healthy human liver
Authors: Yakubovsky Oran , Afriat Amichay , Egozi Adi , Halpern Keren Bahar , Barkai Tal , Harnik Yotam , Kohanim Yael Korem , Novoselsky Roy , Golani Ofra , Goliand Inna , Addadi Yoseph , Kedmi Merav , Keren-Shaul Hadas , Fellus-Alyagor Liat , Hirsch Dana , Mayer Chen , Pery Ron , Pencovich Niv , Taner Timucin , Nachmany Ido , Itzkovitz Shalev 
Published: February 2025

AbstractReconstructing gene expression atlases for human tissues is challenging due to limited access to healthy samples from live donors. Neurologically deceased donors often show ischemic changes, while tissues near diseased regions may have altered gene expression. The liver, with its unique regenerative capacity, allows analysis from live healthy donors (LHDs). Using spatial transcriptomics (Visum, Visium HD and MERFISH), we analyzed 16 liver samples: eight from young LHDs and eight from patients with liver pathology, sampling ‘adjacent normal’ tissue. LHD livers displayed significant gene expression differences from ‘adjacent normal’ tissues. Hepatocytes exhibited marked zonation along the porto-central axis of liver lobules, with key functions pericentrally shifted compared to other mammals. Our atlas identified dynamic programs in early steatotic hepatocytes, showing transitions from lipid uptake in low-lipid regions to insulin hypersensitivity in high-lipid regions. This study presents a spatial gene expression reference for the healthy human liver and insights into hepatocyte adaptations in steatosis.
Emergent modularity in large language models: Insights from aphasia simulations
Authors: Wang Chengcheng , Fan Zhiyu , Han Zaizhu , Bi Yanchao , Li Jixing 
Published: February 2025

AbstractRecent large language models (LLMs) have demonstrated remarkable proficiency in complex linguistic tasks and have been shown to share certain computational principles with human language processing. However, whether LLMs’ internal components perform distinct functions, like semantic and syntactic processing in human language systems, remains unclear. Here, we systematically disrupted components of LLMs to simulate the behavioral profiles of aphasia—a disorder characterized by specific language deficits resulting from brain injury. Our findings showed that lesioning specific components of LLMs could replicate behaviors characteristic of different aphasia subtypes. Notably, while semantic deficits as those observed in Wernicke’s and Conduction aphasia, were relatively straightforward to simulate, reproducing syntactic and lexical impairments, as seen in Broca’s and Anomic aphasia, proved more challenging. Together, these results highlight both parallels and discrepancies between emergent modularity in LLMs and the human language system, providing new insights into how information is represented and processed in artificial and biological intelligence.
Subthreshold electric fields bidirectionally modulate neurotransmitter release through axon polarization
Authors: Aberra Aman S. , Miles Madelyn W. , Hoppa Michael B. 
Published: February 2025

1.SUMMARYSubthreshold electric fields modulate brain activity and demonstrate potential in several therapeutic applications. Electric fields are known to generate heterogenous membrane polarization within neurons due to their complex morphologies. While the effects of somatic and dendritic polarization in postsynaptic neurons have been characterized, the functional consequences of axonal polarization on neurotransmitter release from the presynapse are unknown. Here, we combined noninvasive optogenetic indicators of voltage, calcium and neurotransmitter release to study the subcellular response within single neurons to subthreshold electric fields. We first captured the detailed spatiotemporal polarization profile produced by uniform electric fields within individual neurons. Small polarization of presynaptic boutons produces rapid and powerful modulation of neurotransmitter release, with the direction – facilitation or inhibition – depending on the direction of polarization. We determined that subthreshold electric fields drive this effect by rapidly altering the number of synaptic vesicles participating in neurotransmission, producing effects which resemble short-term plasticity akin to presynaptic homeostatic plasticity. These results provide key insights into the mechanisms of subthreshold electric fields at the cellular level.Abstract Figure
Perinatal environmental enrichment affects murine neonates’ brain structure before their active engagement with environment
Authors: Kaller Malte S. , Ligneul Clémence , Allemang-Grand Rylan , Zhang Tie Yuan , Ellegood Jacob , Meaney Michael , Lerch Jason P. 
Published: February 2025

AbstractEarly life experiences shape individuals. Environmental enrichment, an experimental paradigm used to study the effect of increased environmental complexity and novelty in animal models, has long been recognised for its broad effect on nervous system function and behaviour. In adult rodents, structural changes in the brain due to enriched environments are well documented, notably in the hippocampus. However, the effect of environmental enrichment on the developing brain during early life is not well understood. This study aims to investigate how environmental enrichment affects brain development during the critical perinatal period, and how such effects compare to those observed during adulthood.We use high-resolution MRI to measure the brain structure of mouse neonates at postnatal day 7, born either in an enriched or a standard environment. We show that rodents exhibit brain structure differences as early as postnatal day 7. However, the regional changes observed differ from those in adulthood: hippocampal changes are limited, but changes in the hindbrain, the dorsal striatum, and the medial habenula are strong.Given the lack of direct interaction between neonates and the environment at P7, we hypothesised that maternal care may mediate these effects. We show that maternal care differs between enriched and standard environments, that maternal care correlates with brain structure changes in the neonates, and that maternal care and enriched environment affect brain structure similarly. This suggests that early changes in brain structure due to environmental enrichment are at least partly mediated by maternal care. This study provides novel insight into the differential effect of enriched environment on early brain development in rodents.
Strong amplification of quantitative genetic variation under a balance between mutation and fluctuating stabilizing selection
Authors: Bertram Jason , Shafiei Zahra 
Published: February 2025

AbstractThe observation of high heritability in most quantitative traits has been a long-standing puzzle. There is a general consensus that simple models of quantitative genetic variation, which are mostly founded on the assumption of mutation-selection balance in a constant environment, have failed to explain high heritability. To make matters worse, the reasons for failure are unknown, leaving little to guide future model developments. Here we revisit this puzzle by taking the canonical Latter-Bulmer model and relaxing the assumption of perfect environmental stasis. Instead we assume that the trait optimum changes slowly but steadily in a random walk (specifically, an Ornstein-Uhlenbeck process), similar to standard models used for phylogenetic comparative methods. We show that our model behaves qualitatively differently to its stationary optimum counterpart even though the optimum only changes slowly. This is the result of a feedback between the adaptation rate and selection coefficient fluctuations. The heritability predictions resulting from this feedback are more consistent with observations and also less sensitive to evolutionary parameters than the classical LB model. We derive a simple formula to predict genetic variation under random walk optimum fluctuations which helps to explain some of our counter-intuitive results and which should be useful for understanding the potential influence of fluctuations in future work. Since the feedback driving our results should also occur in more complex models e.g. with multiple traits, we argue that environmental change has been an essential biological ingredient missing in previous mutation-selection balance models of quantitative trait heritability.
The morphology and small subunit rDNA gene phylogeny of the novel goniomonad genusEbisugoniomonasand two novelPoseidogoniomonasspecies
Authors: Zavadska Daryna , Sachs Maria , Arndt Hartmut , Richter Daniel J. 
Published: February 2025

AbstractGoniomonads are heterotrophic representatives of Cryptista, sister lineage to the phototrophic Cryptists. Goniomonads are morphologically and genetically diverse, comprising nine genera described so far. Besides morphologically described genera, SSU rDNA sequencing data has revealed the existence of at least one more monophyletic genus-level lineage within goniomonads, as well as more novel species within the described genera. Furthermore, the diversity of SSU rDNA sequences within goniomonads is not fully investigated, and addition of novel sequences can be crucial for understanding the evolution and diversity of goniomonads and for providing a basis for taxonomic descriptions. The morphological data record available for goniomonads is relatively limited: many cellular features remain undescribed, or described only for a few isolates.In this study, we describe the new genus and speciesEbisugoniomonas hispanican. gen. n. sp., and two novel species withinPoseidogoniomonas:P. posteriocircusn. sp. andP. zopfkaesiformisn. sp. We report a range of observations on the cellular features of goniomonads: periplast plate arrangement pattern and intracellular structures. We also update the SSU rDNA phylogeny of goniomonads by adding sequences from novel isolates and environmental DNA studies.Several sequences recovered from novel isolates and environmental DNA datasets likely represent highly divergent lineages of goniomonads in the SSU rDNA phylogeny.
Fisher’s information matrix approach for Fourier features physics-informed neural networks for two-dimensional local time-fractional anomalous diffusion equations with nonlinear thermal diffusivity
Authors: Jha Navnit , Mallik Ekansh 
Published: February 2025

Purpose
This study aims to explore the influence of Fourier-feature enhanced physics-informed neural networks (PINNs) on effectively solving two-dimensional local time-fractional anomalous diffusion equations with nonlinear thermal diffusivity. By tackling the shortcomings of conventional numerical methods in managing fractional derivatives and nonlinearities, this research addresses a significant gap in the literature regarding efficient solution strategies for complex diffusion processes.

Design/methodology/approach
This study uses a quantitative methodology featuring a feed-forward neural network architecture combined with a Fourier feature layer. Automatic differentiation is implemented to ensure precise gradient calculations for fractional derivatives. The effectiveness of the proposed approach is showcased through numerical simulations across various sub-diffusion and super-diffusion scenarios, with fractal space parameters adjusted to examine behavior. In addition, the training process is assessed using the Fisher information matrix to analyze the loss landscape.

Findings
The results demonstrate that the Fourier-feature enhanced PINNs effectively capture the dynamics of the anomalous diffusion equation, achieving greater solution accuracy than traditional methods. The analysis using the Fisher information matrix underscores the importance of hyperparameter tuning in optimizing network performance. These findings support the hypothesis that Fourier features improve the model’s capacity to represent complex solution behaviors, providing the relationship between model architecture and diffusion dynamics.

Originality/value
This research presents a novel approach to solving fractional anomalous diffusion equations through Fourier-feature enhanced PINNs. The results contribute to the advancement of computational methods in areas such as thermal engineering, materials science and biological diffusion modeling, while also providing a foundation for future investigations into training dynamics within neural networks.
Rethinking work, with the pandemic disruption: metatheorizing with world hypotheses and systems changes
Authors: Ing David , Nousala Susu 
Published: February 2025

PurposeAs economies have reopened after the COVID-19 pandemic, resumption of pre-pandemic normalcy in work has not been uniform. For each worker and leader, an essential question is whether the world of work has changed irreversibly, or if prior careers and business models can be resumed. A philosophical inquiry into theories of the world of work provides a framing that separates everyday changes from systems changes.Design/methodology/approachA metatheoretical approach to world theories from 1942 is revisited. Attention is drawn to systems of knowledge along the dimensions of analytic-deductive treatments, and dispersive-integrative treatments. Socio-Technical Systems relate to Organicism, and Socio-Ecological Systems relate to Contextualism. Reworking a processual philosophy, an alternative World Hypothesis is proposed.Findings(Con)texturalism-dyadicism reframes causal texture theory as (1) rhythmic pacing; (2) dyadic diachrony; and (3) transformative reifying. New insights into the effects with the onset and passing of the pandemic disruption are gained.Research limitations/implicationsUpdating systems theories of socio-technical and socio-ecological perspectives invokes a post-colonial constructivist philosophy that appreciates roots in American pragmatism, ecological anthropology, and Chinese philosophy of science. The emphasis of systems rhythms prioritizes a processual orientation, compatible with a yinyang material-immaterial onto-epistemology.Practical implicationsAs the world recovers from the disruptions of the COVID-19 pandemic, the changed nature of work is only one of many aspects that been altered. Systems perspectives both of parts inside an organization (i.e. socio-technical individuals in groups) and wholes alongside other wholes (i.e. socio-ecological groups co-responding with their (con)textures) are not independent, but interrelated. Disruption of work systems may result in only incremental adaptation for some, with transformative shifts in world theory for others. Recognizing that organizations change from within, persistent pathologies may be diagnosed.Originality/valueSystems theories of work from the 1960s were based on pragmatism from the 1940s. The metatheoretical contextualism of Stephen C. Pepper is complemented by a 21st century constructivist philosophy that is post-colonial and non-anthropocentric. Reifying organizational systems theories for audiences founded on a Western philosophy of science requires extended explanations bridging over to a non-Western (i.e. Classical Chinese) lineage.
“Everything, everywhere, all at once”: the role of accounting and reporting in achieving sustainable development goals
Authors: Kaur Amanpreet , Argento Daniela , Sharma Umesh , Soobaroyen Teerooven 
Published: February 2025

PurposeThe purpose of this paper is to highlight and compare insights from research conducted in the field of accounting and reporting for Sustainable Development Goals (SDGs) in the public, not-for-profit and hybrid sectors. It is also an introduction to the special issue on “Sustainability Accounting and Reporting for Sustainable Development Goals (SDGs): Progress, Challenges, and Future Research Agenda”.Design/methodology/approachThis paper reviews the findings and reflections in the academic literature on developments in the SDG accounting and reporting practices across public, not-for-profit and hybrid sectors globally.FindingsThe findings of the review indicate that SDG accounting and reporting practices of public, not-for-profit and hybrid sectors are still in their infancy. Considerable political and organisational barriers hinder the achievement of SDGs. Nonetheless, aligning local and global goals, engaging stakeholders effectively and implementing robust progress monitoring and review systems can facilitate a meaningful engagement with the SDGs. The special issue articles offer decision-makers valuable insights on the factors enabling the adoption and implementation of SDGs.Originality/valueThis paper contributes to the ongoing discussions on the role of accounting and reporting processes within public, not-for-profit and hybrid sectors in advancing the achievement of SDGs.