bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal expression pattern of dyslexia susceptibility 1 candidate 1 (DYX1C1) during rat cerebral cortex development
Authors: Zensho Kazumasa , Miyazaki Ikuko , Isse Aika , Misawa Ichika , Masai Kaori , Oka Makio , Tsukahara Hirokazu , Asanuma Masato 
Published: February 2025

Abstract

Background
Developmental dyslexia (DD) is a common learning disorder with significant consequences for affected individuals. Although several candidate genes, including dyslexia susceptibility 1 candidate 1 (DYX1C1), have been implicated in dyslexia, their role in brain development remains unclear. We aimed to elucidate the spatiotemporal expression patterns of DYX1C1 during cerebral cortex development in rats.

Methods
We investigated DYX1C1 expression during cerebral cortex development using rat embryos at various gestational stages (E13.5, 15.5, 17.5 and 20.5) by immunohistochemistry (n = 7 embryos/stage), quantitative real-time PCR (n = 6), and in situ hybridization (n = 11–15).

Results
The DYX1C1-positive cells were predominantly located in the outermost layers of the cortical plate, particularly at E15.5. DYX1C1 mRNA expression peaked at E15.5 and subsequently declined. DYX1C1-positive cells did not co-localize with reelin-positive Cajal-Retzius cells, but co-localized with neuronal markers expressed during development, and had shorter primary cilia than DYX1C1-negative cells.

Conclusions
Our findings highlight the dynamic expression of DYX1C1 in the developing cerebral cortex of rats, implicating its involvement in neurodevelopmental processes. Further investigation of the functional interactions of DYX1C1, particularly its relationship with reelin and its role in cerebrocortical and hippocampal development, may provide insights into the pathophysiology of dyslexia and neurodevelopmental disorders.

Impact

Our study elucidates spatiotemporal expression patterns of endogenous DYX1C1 predominantly in the primitive cortical zone (PCZ), outermost layer of the cortical plate (CP) during cerebral cortex development, particularly peaked at E15.5.

We revealed the spatial relationship between DYX1C1-positive and reelin-expressing Cajal-Retzius (CR) cells, and co-localize with neuronal markers expressed during cerebral cortex development, indicating its contribution to neuronal migration and cortical layer formation.

DYX1C1-positive cells mainly in the PCZ possess shorter primary cilia than DYX1C1-negative cells, suggesting the completion of migration.
STING directly interacts with PAR to promote apoptosis upon acute ionizing radiation-mediated DNA damage
Authors: Sun Yirong , Aliyari Saba R. , Parvatiyar Kislay , Wang Lulan , Zhen Anjie , Sun Wei , Han Xiaobo , Zhang Adele , Kato Ethan , Shi Helen , De Schutter Elena , McBride William H. , French Samuel W. , Cheng Genhong 
Published: February 2025

Abstract
Acute ionizing radiation (IR) causes severe DNA damage, leading to cell cycle arrest, cell death, and activation of the innate immune system. The role and signaling pathway of stimulator of interferon genes (STING) in IR-induced tissue damage and cell death are not well understood. This study revealed that STING is crucial for promoting apoptosis in response to DNA damage caused by acute IR both in vitro and in vivo. STING binds to poly (ADP‒ribose) (PAR) produced by activated poly (ADP‒ribose) polymerase-1 (PARP1) upon IR. Compared with that in WT cells, apoptosis was suppressed in Sting

gt-/gt-
cells. Excessive PAR production by PARP1 due to DNA damage enhances STING phosphorylation, and inhibiting PARP1 reduces cell apoptosis after IR. In vivo, IR-induced crypt cell death was significantly lower in Sting

gt-/gt-
mice or with low-dose PARP1 inhibitor, PJ34, resulting in substantial resistance to abdominal irradiation. STING deficiency or inhibition of PARP1 function can reduce the expression of the proapoptotic gene PUMA, decrease the localization of Bax on the mitochondrial membrane, and thus reduce cell apoptosis. Our findings highlight crucial roles for STING and PAR in the IR-mediated induction of apoptosis, which may have therapeutic implications for controlling radiation-induced apoptosis or acute radiation symptoms.
Direct synthesis of a semiconductive double-helical phosphorus allotrope in a metal-organic framework
Authors: Sapchenko Sergei A. , Belosludov Rodion V. , Vitoria-Irezabal Inigo J. , da Silva Ivan , Chen Xi , Whitehead George F. S. , Maddock John , Natrajan Louise S. , Kippax-Jones Meredydd , Alwis Jayasinghe Dukula De , Bawn Carlo , Polyukhov Daniil M. , Chen Yinlin , Fedin Vladimir P. , Yang Sihai , Schröder Martin 
Published: February 2025

Abstract
There remains much ambiguity regarding the structure of red phosphorus. We report the adsorption and photo-polymerisation of P4 molecules encapsulated in an indium(III)-based metal-organic framework to afford a double-helical chain composite comprising of [P8] units. The similarity between the Raman spectrum of bulk red phosphorus and of the metal-organic framework – (P8)n adduct suggests the presence of such helical chains in the structure of amorphous red phosphorus. This provides crystallographic evidence of the structural building blocks of the red phosphorus allotrope stabilized within the pores of a metal-organic host. The (P8)n inclusion compound is an air-stable semiconductor with a band gap of 2.3 eV, which is relevant for gas detection and photo-catalysis. We demonstrate that this phosphorus adduct demonstrates a 10-fold increase in conversion in the oxidation of methyl orange dye compared with the parent metal-organic framework material.
Atypical hippocampal excitatory neurons express and govern object memory
Authors: Kinman Adrienne I. , Merryweather Derek N. , Erwin Sarah R. , Campbell Regan E. , Sullivan Kaitlin E. , Kraus Larissa , Kapustina Margarita , Bristow Brianna N. , Zhang Mingjia Y. , Elder Madeline W. , Wood Sydney C. , Tarik Ali , Kim Esther , Tindall Joshua , Daniels William , Anwer Mehwish , Guo Caiying , Cembrowski Mark S. 
Published: February 2025

Abstract
Classically, pyramidal cells of the hippocampus are viewed as flexibly representing spatial and non-spatial information. Recent work has illustrated distinct types of hippocampal excitatory neurons, suggesting that hippocampal representations and functions may be constrained and interpreted by these underlying cell-type identities. In mice, here we reveal a non-pyramidal excitatory neuron type — the “ovoid” neuron — that is spatially adjacent to subiculum pyramidal cells but differs in gene expression, electrophysiology, morphology, and connectivity. Functionally, novel object encounters drive sustained ovoid neuron activity, whereas familiar objects fail to drive activity even months after single-trial learning. Silencing ovoid neurons prevents non-spatial object learning but leaves spatial learning intact, and activating ovoid neurons toggles novel-object seeking to familiar-object seeking. Such function is doubly dissociable from pyramidal neurons, wherein manipulation of pyramidal cells affects spatial assays but not non-spatial learning. Ovoid neurons of the subiculum thus illustrate selective cell-type-specific control of non-spatial memory and behavioral preference.
High-throughput screening identifies Aurora kinase B as a critical therapeutic target for Merkel cell carcinoma
Authors: Gelb Tara , Garman Khalid A. , Urban Daniel , Coxon Amy , Gryder Berkley , Hill Natasha T. , Miao Lingling , Lee Tobie , Lee Olivia , Chakka Sirisha , Braisted John , Jarvis Jordan E. , Glavin Rachael , Raj Trisha S. , Xiao Ying , Difilippantonio Simone , Wang Amy Q. , Shen Min , Cheng Ken Chih-Chien , Lal-Nag Madhu , Hall Matthew D. , Brownell Isaac 
Published: February 2025

Abstract
Merkel cell carcinoma (MCC) is a rare, aggressive skin cancer. Most MCCs contain Merkel cell polyomavirus (virus-positive MCC; VP-MCC), and the remaining are virus-negative (VN-MCC). Immune checkpoint inhibitors are the first-line treatment for metastatic MCC, but durable responses are achieved in less than 50% of patients. To identify new treatments, we screen ~4,000 compounds for their ability to reduce MCC viability and demonstrate that VP-MCC and VN-MCC exhibit distinct response profiles. Aurora kinase inhibitors selectively reduce VP-MCC viability, with RNAi screening independently identifying AURKB as an essential gene for MCC survival, especially in VP-MCC. AZD2811, a selective AURKB inhibitor, induces mitotic dysregulation and apoptosis in MCC cells, with greater efficacy in VP-MCC. In mice, AZD2811 nanoparticles inhibit tumor growth and increase survival in both VP-MCC and VN-MCC xenograft models. Overall, our unbiased screens identify AURKB as a promising therapeutic target and AZD2811NP as a potential treatment for MCC.
High-throughput multiplexed serology via the mass-spectrometric analysis of isotopically barcoded beads
Authors: Drainas Alexandros P. , McIlwain David R. , Dallas Alec , Chu Theresa , Delgado-González Antonio , Baron Maya , Angulo-Ibáñez Maria , Trejo Angelica , Bai Yunhao , Hickey John W. , Lu Guolan , Lu Scott , Pineda-Ramirez Jesus , Anglin Khamal , Richardson Eugene T. , Prostko John C. , Frias Edwin , Servellita Venice , Brazer Noah , Chiu Charles Y. , Peluso Michael J. , Martin Jeffrey N. , Wirz Oliver F. , Pham Tho D. , Boyd Scott D. , Kelly J. Daniel , Sage Julien , Nolan Garry P. , Rovira-Clavé Xavier 
Published: February 2025

Abstract
In serology, each sample is typically tested individually, one antigen at a time. This is costly and time consuming. Serology techniques should ideally allow recurrent measurements in parallel in small sample volumes and be inexpensive and fast. Here we show that mass cytometry can be used to scale up multiplexed serology testing by leveraging polystyrene beads uniformly loaded with combinations of stable isotopes. We generated 18,480 unique isotopically barcoded beads to simultaneously detect, in a single tube with 924 serum samples, the levels of immunoglobulins G and M against 19 proteins from SARS-CoV-2 (a total of 36,960 tests in 400 nl of sample volume and 30 μl of reaction volume). As a rapid, high-throughput and cost-effective technique, serology by mass cytometry may contribute to the effective management of public health emergencies originating from infectious diseases.
Aqueous-based recycling of perovskite photovoltaics
Authors: Xiao Xun , Xu Niansheng , Tian Xueyu , Zhang Tiankai , Wang Bingzheng , Wang Xiaoming , Xian Yeming , Lu Chunyuan , Ou Xiangyu , Yan Yanfa , Sun Licheng , You Fengqi , Gao Feng 
Published: February 2025

Abstract
Cumulative silicon photovoltaic (PV) waste highlights the importance of considering waste recycling before the commercialization of emerging PV technologies1,2. Perovskite PVs are a promising next-generation technology3, in which recycling their end-of-life waste can reduce the toxic waste and retain resources4,5. Here we report a low-cost, green-solvent-based holistic recycling strategy to restore all valuable components from perovskite PV waste. We develop an efficient aqueous-based perovskite recycling approach that can also rejuvenate degraded perovskites. We further extend the scope of recycling to charge-transport layers, substrates, cover glasses and metal electrodes. After repeated degradation–recycling processes, the recycled devices show similar efficiency and stability compared with the fresh devices. Our holistic recycling strategy reduces by 96.6% resource depletion and by 68.8% human toxicity (cancer effects) impacts associated with perovskite PVs compared with the landfill treatment. With recycling, the levelized cost of electricity also decreases for both utility-scale and residential systems. This study highlights unique opportunities of perovskite PVs for holistic recycling and paves the way for a sustainable perovskite solar economy.
Learning produces an orthogonalized state machine in the hippocampus
Authors: Sun Weinan , Winnubst Johan , Natrajan Maanasa , Lai Chongxi , Kajikawa Koichiro , Bast Arco , Michaelos Michalis , Gattoni Rachel , Stringer Carsen , Flickinger Daniel , Fitzgerald James E. , Spruston Nelson 
Published: February 2025

Abstract
Cognitive maps confer animals with flexible intelligence by representing spatial, temporal and abstract relationships that can be used to shape thought, planning and behaviour. Cognitive maps have been observed in the hippocampus1, but their algorithmic form and learning mechanisms remain obscure. Here we used large-scale, longitudinal two-photon calcium imaging to record activity from thousands of neurons in the CA1 region of the hippocampus while mice learned to efficiently collect rewards from two subtly different linear tracks in virtual reality. Throughout learning, both animal behaviour and hippocampal neural activity progressed through multiple stages, gradually revealing improved task representation that mirrored improved behavioural efficiency. The learning process involved progressive decorrelations in initially similar hippocampal neural activity within and across tracks, ultimately resulting in orthogonalized representations resembling a state machine capturing the inherent structure of the task. This decorrelation process was driven by individual neurons acquiring task-state-specific responses (that is, ‘state cells’). Although various standard artificial neural networks did not naturally capture these dynamics, the clone-structured causal graph, a hidden Markov model variant, uniquely reproduced both the final orthogonalized states and the learning trajectory seen in animals. The observed cellular and population dynamics constrain the mechanisms underlying cognitive map formation in the hippocampus, pointing to hidden state inference as a fundamental computational principle, with implications for both biological and artificial intelligence.
High-resolution traffic flow data from the urban traffic control system in Glasgow
Authors: Li Yue , Zhao Qunshan , Wang Mingshu 
Published: February 2025

Abstract
Traffic flow data has been used in various disciplines, including geography, transportation, urban planning, and public health. However, existing datasets often have limitations such as low spatiotemporal resolution and inconsistent quality due to data collection methods and the need for an adequate data cleaning process. This paper introduces a long-term traffic flow dataset at an intra-city scale with high spatio-temporal granularity. The dataset covers the Glasgow City Council area for four consecutive years spanning the COVID-19 pandemic, from October 2019 to September 2023, providing comprehensive temporal and spatial coverage. Such detailed information facilitates diverse applications, including traffic dynamic analysis, traffic management, infrastructure planning, and urban environment improvement. Also, it provides a valuable dataset to understand traffic flow change during a once-in-a-lifetime pandemic event.
Lower cardiorespiratory fitness is associated with an altered gut microbiome. The Study of Health in Pomerania (SHIP)
Authors: Markus Marcello Ricardo Paulista , Weiss Frank-Ulrich , Hertel Johannes , Weiss Stefan , Rühlemann Malte , Bang Corinna , Franke Andre , Völker Uwe , Homuth Georg , Kocher Thomas , Völzke Henry , Lerch Markus M. , Ittermann Till , Felix Stephan Burkhard , Ewert Ralf , Bahls Martin , Dörr Marcus , Frost Fabian 
Published: February 2025

Abstract
Sedentarism is characterized by low levels of physical activity, a risk factor for obesity and cardio-metabolic diseases. It can also adversely affect the composition and diversity of the gut microbiome which may result in harmful consequences for human health. While cardiorespiratory fitness (CRF) is inversely and independently associated with cardiovascular risk factors and diseases and all-cause mortality, the relationship between low CRF and the gut microbiome is not well known. A total of 3,616 individuals from two independent population-based cohorts of the Study of Health in Pomerania (SHIP-START and SHIP-TREND) performed standardized, symptom-limited cardiopulmonary exercise testing (CPET) and had faecal samples collected to determine gut microbiota profiles (16S rRNA gene sequencing). We analysed cross-sectional associations of CRF with the gut microbiome composition controlling for confounding factors. Lower CRF was associated with reduced microbial diversity, loss of beneficial short-chain fatty acid producing bacteria (i.e. Butyricoccus, Coprococcus, unclassified Ruminococcaceae or Lachnospiraceae) and an increase in opportunistic pathogens such as Escherichia/Shigella, or Citrobacter. Decreased cardiorespiratory performance was associated with a gut microbiota pattern that has been previously related to a proinflammatory state. These associations were independent of body weight or glycemic control.
Connectomic analysis of taste circuits in Drosophila
Authors: Walker Sydney R. , Peña-Garcia Marco , Devineni Anita V. 
Published: February 2025

Abstract
Our sense of taste is critical for regulating food consumption. The fruit fly Drosophila represents a highly tractable model to investigate mechanisms of taste processing, but taste circuits beyond sensory neurons are largely unidentified. Here, we use a whole-brain connectome to investigate the organization of Drosophila taste circuits. We trace pathways from four populations of sensory neurons that detect different taste modalities and project to the subesophageal zone (SEZ), the primary taste region of the fly brain. We find that second-order taste neurons are primarily located within the SEZ and largely segregated by taste modality, whereas third-order neurons have more projections outside the SEZ and more overlap between modalities. Taste projections out of the SEZ innervate regions implicated in feeding, olfactory processing, and learning. We analyze interconnections within and between taste pathways, characterize modality-dependent differences in taste neuron properties, identify other types of inputs onto taste pathways, and use computational simulations to relate neuronal connectivity to predicted activity. These studies provide insight into the architecture of Drosophila taste circuits.
Prediction of intrinsic and extraneous cognitive load with oculometric and biometric indicators
Authors: Ekin Merve , Krejtz Krzysztof , Duarte Carlos , Duchowski Andrew T. , Krejtz Izabela 
Published: February 2025

Abstract
This study focused on the prediction of intrinsic and extraneous cognitive load using eye-tracking metrics, heart rate variability, and galvanic skin response. Intrinsic cognitive load is associated with the inherent complexity of the mental task, whereas extraneous cognitive load is related to the distracting and unrelated elements in the task. Thirty-three participants (aged
$$21.24 \pm 3.51$$
) performed different levels of mental calculations to induce intrinsic cognitive load in the first task and a visual search task to manipulate extraneous cognitive load in the second task. During both tasks, participants’ eye movements, heart rate, and galvanic skin response were continuously recorded. Participants’ working memory was controlled. Subjective cognitive load was also assessed following each experimental task. A discriminant model, consisting of oculo- and bio-metric indicators, could discriminate between cognitive loads (intrinsic vs.extraneous) and levels (low vs.high). In particular, average fixation duration, average saccade amplitude, and
$$\mathscr {K}$$
coefficient each have an impact on the model. In addition, task difficulty may be distinguished by the Low-High Index of Pupillary Activity (LHIPA) and heart rate variability.
Phase transition, structural stability and electrical properties of V or Mn doped ZnSe composites under high pressure
Authors: Liu Tao , Huang Yuxuan , Wang Shixia , Wang Yalin , Cheng Ping , Wu Jia 
Published: February 2025

Abstract
The structural parameters and enthalpies of pure ZnSe and different concentrations of V/Mn:ZnSe at high pressures were calculated using the first principles calculation method based on density functional theory. The lattice constants and bond lengths of all the systems decrease under pressure, and the respective phase transition pressures are obtained from the enthalpy-pressure relationship curves, which show that V/Mn elemental doping reduces the phase transition pressure of ZnSe, and the phase transition pressure further decreases with the increase of the doping concentration. The doping formation energies and the elastic constant criterion at atmospheric and high pressures confirm the structural stability of all the systems within the pressures of this study, and the pugh ratio confirms that they are all ductile structures.The results of electrical properties study show that at atmospheric pressure, all V:ZnSe systems have metallic properties, and a metal to semiconductor transition occurs at high pressure when the doping concentration is 12.5%. However, the Mn:ZnSe systems are semiconductors at both atmospheric and high pressures. Pressure significantly influences the degeneracy and position of the impurity bands: the impurity bands of V:ZnSe move toward higher energy under pressure, while the impurity bands of the Mn:ZnSe system shift toward lower energy. The element doping concentration also affects the d orbital degeneracy of V/Mn:ZnSe under atmospheric pressure, the degeneracy of V/Mn-d orbital decreases with the increase in doping concentration. Under high pressure, the degeneracy of the V/Mn-d orbital decreases further when the doping concentration is 3.13%, but the degeneracy is enhanced when the doping concentration is 6.25 and 12.5%. Doping can effectively change the phase transition pressure of ZnSe, and the pressure can effectively modulate the properties of this material.
Collective chemo-mechanical oscillations and cluster waves in communicating colloids
Authors: Göth Nils , Dzubiella Joachim 
Published: February 2025

Abstract
Communication and feedback are crucial for the self-organization and the emergent viscoelastic behavior of life-like soft matter systems. However, the specific effects of communication between the individual components on their properties, interactions, and collective dynamics are not fully understood. Here, we report on two-dimensional Brownian dynamics simulations of catalytically active, non-motile hydrogel colloids with explicit resolution of chemical signaling clouds and chemo-mechanical feedback through a size-dependent permeability for the fuel. In particular, we investigate how their spatiotemporal structure and dynamical behavior depend on the communication magnitude and the colloid density. We discover a diverse range of nonequilibrium structures and active phases, including transitions from uncorrelated to synchronized oscillations and the emergence of elastic cluster waves for increasing chemo-mechanical coupling. Our findings highlight microscopic physical principles behind communication-driven cooperativity and could inform the design of active soft matter systems with adaptive functionalities.