bluuebunny/crossref_metadata_2025_split huggingface dataset:
The “Podcast” ECoG dataset for modeling neural activity during natural language comprehension
Authors: Zada Zaid , Nastase Samuel A. , Aubrey Bobbi , Jalon Itamar , Michelmann Sebastian , Wang Haocheng , Hasenfratz Liat , Doyle Werner , Friedman Daniel , Dugan Patricia , Melloni Lucia , Devore Sasha , Flinker Adeen , Devinsky Orrin , Goldstein Ariel , Hasson Uri 
Published: February 2025

AbstractNaturalistic electrocorticography (ECoG) data are a rare but essential resource for studying the brain’s linguistic capabilities. ECoG offers a high temporal resolution suitable for investigating processes at multiple temporal timescales and frequency bands. It also provides broad spatial coverage, often along critical language areas. Here, we share a dataset of nine ECoG participants with 1,330 electrodes listening to a 30-minute audio podcast. The richness of this naturalistic stimulus can be used for various research endeavors, from auditory perception to semantic integration. In addition to the neural data, we extract linguistic features of the stimulus ranging from phonetic information to large language model word embeddings. We use these linguistic features in encoding models that relate stimulus properties to neural activity. Finally, we provide detailed tutorials for preprocessing raw data, extracting stimulus features, and running encoding analyses that can serve as a pedagogical resource or a springboard for new research.
A neuro-immune axis of transcriptomic dysregulation within the subgenual anterior cingulate cortex in schizophrenia
Authors: Smith Rachel L. , Mihalik Agoston , Akula Nirmala , Auluck Pavan K. , Marenco Stefano , Raznahan Armin , Vértes Petra E. , McMahon Francis J. 
Published: February 2025

AbstractMany genes are linked to psychiatric disorders, but genome-wide association studies (GWAS) and differential gene expression (DGE) analyses in post-mortem brain tissue often implicate distinct gene sets. This disconnect impedes therapeutic development, which relies on integrating genetic and genomic insights. We address this issue using a novel multivariate technique that reduces DGE bias by leveraging gene co-expression networks and controlling for confounds such as drug exposure. Deep RNA sequencing was performed in bulk post-mortem sgACC from individuals with bipolar disorder (BD; N=35), major depression (MDD; N=51), schizophrenia (SCZ; N=44), and controls (N=55). Toxicology data dimensionality was reduced using multiple correspondence analysis; case-control gene expression was then analyzed using 1) traditional DGE and 2) group regularized canonical correlation analysis (GRCCA) – a multivariate regression method that accounts for feature interdependence. Gene set enrichment analyses compared results with established neuropsychiatric risk genes, gene ontology pathways, and cell type enrichments. GRCCA revealed a significant association with SCZ (Pperm=0.001; no significant BD or MDD association), and the resulting gene weight vector correlated with DGE SCZ-control t-statistics (R=0.53;P<0.05). Both methods indicated down-regulation of immune and microglial genes and upregulation of ion transport and excitatory neuron genes. However, GRCCA - at both the gene and transcript level - showed stronger enrichments (FDR<0.05). Notably, GRCCA results were enriched for SCZ GWAS-implicated genes (FDR<0.05), while DGE results were not. These findings identify a SCZ-specific sgACC gene expression pattern that highlights SCZ risk genes and implicates neuro-immune pathways, thus demonstrating the utility of multivariate approaches to integrate genetic and genomic signals.
Glucosylceramide induced ectosomes propagate pathogenic α-synuclein in Parkinson’s disease
Authors: Jacquemyn Julie , Mariott Brian , Chang Jinlan , Lee Nathanael Y J , Atonal Luis F. Rubio , Green Ceili , Wong Jeremy , Chik Kennedi , Acevedo-Morantes Claudia , Chen Carol X.-Q. , Nicouleau Michael , You Zhipeng , Deneault Eric , Abdian Narges , Durcan Thomas M. , Jackson Jesse , Ioannou Maria S. 
Published: February 2025

AbstractIntercellular transmission of α-synuclein contributes to Parkinson’s disease pathology. Yet, the mechanisms of α-synuclein spread are not fully understood. Here, we used live-cell microscopy to examine the impact of Parkinson’s disease associated lipid alterations on α-synuclein release. We discovered that increased glucosylceramides induce ectosome shedding from primary neurons, and from dopaminergic neurons derived from Parkinson’s disease patient iPSCs harboring mutations inGBA1(N370S, L444P and W378G) andLRRK2(G2019S and R1441H) compared to their isogenic control. We show that elevated glucosylceramide similarly increases vesicle release and uptake by other neurons in living mouse brains using 2-photon microscopy. Finally, we show that ectosomes are loaded with pathogenic α-synuclein and lead to the transmission of α-synuclein pathology to neighbouring neurons. These data reveal ectosomes as the predominant route for α-synuclein transmission that can only be appreciated by live-cell imaging technologies.
Hierarchical encoding of natural sounds mixtures in ferret auditory cortex
Authors: Landemard Agnès , Bimbard Célian , Boubenec Yves 
Published: February 2025

AbstractExtracting relevant auditory signals from complex natural scenes is a fundamental challenge for the auditory system. Sounds from multiple sources overlap in time and frequency. In particular, dynamic “fore-ground” sounds are often masked by more stationary “background” sounds. Human auditory cortex exhibits a hierarchical organization where background-invariant representations are progressively enhanced along the processing stream, from primary to non-primary regions. However, we do not know whether this organizational principle is conserved across species and which neural mechanisms drive this invariance. To address these questions, we investigated background invariance in ferret auditory cortex using functional ultrasound imaging (fUSI), which enables large-scale, high-resolution recordings of hemodynamic responses. We measured responses across primary, secondary, and tertiary auditory cortical regions as ferrets passively listened to mixtures of natural sounds and their components in isolation. We found a hierarchical gradient of background invariance, mirroring findings in humans: responses in primary auditory cortex reflected contributions from both foreground and background sounds, while background invariance increased in higher-order auditory regions. Using a spectrotemporal filter-bank model, we found that in ferrets, this hierarchical structure could be largely explained by tuning to low-order acoustic features. However, this model failed to fully account for background invariance in human non-primary auditory cortex, suggesting that additional, higher-order mechanisms are crucial for background segregation in humans.
Optical Pooled Screening for the Discovery of Regulators of the Alternative Lengthening of Telomeres Pathway
Authors: Quintanilla Isabel , Azeroglu Benura , Sagar Md Abdul Kader , Stracker Travis H. , Lazzerini Denchi Eros , Pegoraro Gianluca 
Published: February 2025

AbstractTelomere elongation is essential for the proliferation of cancer cells. Telomere length control is achieved by either the activation of the telomerase enzyme or the recombination-based Alternative Lengthening of Telomeres (ALT) pathway. ALT is active in about 10-15% of human cancers, but its molecular underpinnings remain poorly understood, preventing the discovery of potential novel therapeutic targets. Pooled CRISPR-based functional genomic screens enable the unbiased discovery of molecular factors involved in cancer biology. Recently, Optical Pooled Screens (OPS) have significantly extended the capabilities of pooled functional genomics screens to enable sensitive imaging-based readouts at the single cell level and large scale. To gain a better understanding of the ALT pathway, we developed a novel OPS assay that employs telomeric native DNA FISH (nFISH) as an optical quantitative readout to measure ALT activity. The assay uses standard OPS protocols for library preparation and sequencing. As a critical element, an optimized nFISH protocol is performed before in situ sequencing to maximize the assay performance. We show that the modified nFISH protocol faithfully detects changes in ALT activity upon CRISPR knock-out (KO) of theFANCMandBLMgenes which were previously implicated in ALT. Overall, the OPS-nFISH assay is a reliable method that can provide deep insights into the ALT pathway in a high-throughput format.
Photoinhibition in Mutants of Arabidopsis Deficient in Thylakoid Unsaturation
Authors: Vijayan Perumal , Browse John 
Published: July 2002

Abstract
Thylakoid lipid composition in higher plants is characterized by a high level of fatty acid unsaturation. We have screened four mutants of Arabidopsis that have reduced levels of fatty acid unsaturation. Three of the mutant lines tested, fad5,fad6, and the fad3-2 fad7-2 fad8 triple mutant, were more susceptible to photoinhibition than wild-type Arabidopsis, whereas one mutant, fab1, was indistinguishable from wild type. The fad3-2 fad7-2 fad8triple mutant, which contains no trienoic fatty acids in its thylakoid membranes, was most susceptible to photoinhibition. Detailed investigation of photoinhibition in the triple mutant revealed that the rate of photoinactivation of PSII was the same in wild-type and mutant plants. However, the recovery of photoinactivated PSII was slower infad3-2 fad7-2 fad8, relative to wild type, at all temperatures below 27°C. These results indicate that trienoic fatty acids of thylakoid membrane lipids are required for low-temperature recovery from photoinhibition in Arabidopsis.
Mutagenesis of the Glucose-1-Phosphate-Binding Site of Potato Tuber ADP-Glucose Pyrophosphorylase1
Authors: Fu Yingbin , Ballicora Miguel A. , Preiss Jack 
Published: July 2002

AbstractLysine (Lys)-195 in the homotetrameric ADP-glucose pyrophosphorylase (ADPGlc PPase) fromEscherichia coli was shown previously to be involved in the binding of the substrate glucose-1-phosphate (Glc-1-P). This residue is highly conserved in the ADPGlc PPase family. Site-directed mutagenesis was used to investigate the function of this conserved Lys residue in the large and small subunits of the heterotetrameric potato (Solanum tuberosum) tuber enzyme. The apparent affinity for Glc-1-P of the wild-type enzyme decreased 135- to 550-fold by changing Lys-198 of the small subunit to arginine, alanine, or glutamic acid, suggesting that both the charge and the size of this residue influence Glc-1-P binding. These mutations had little effect on the kinetic constants for the other substrates (ATP and Mg2+ or ADP-Glc and inorganic phosphate), activator (3-phosphoglycerate), inhibitor (inorganic phosphate), or on the thermal stability. Mutagenesis of the corresponding Lys (Lys-213) in the large subunit had no effect on the apparent affinity for Glc-1-P by substitution with arginine, alanine, or glutamic acid. A double mutant, SK198RLK213R, was also obtained that had a 100-fold reduction of the apparent affinity for Glc-1-P. The data indicate that Lys-198 in the small subunit is directly involved in the binding of Glc-1-P, whereas they appear to exclude a direct role of Lys-213 in the large subunit in the interaction with this substrate.
Interaction of Osmotic Stress, Temperature, and Abscisic Acid in the Regulation of Gene Expression in Arabidopsis
Authors: Xiong Liming , Ishitani Manabu , Zhu Jian-Kang 
Published: July 2002

Abstract
The impact of simultaneous environmental stresses on plants and how they respond to combined stresses compared with single stresses is largely unclear. By using a transgene (RD29A-LUC) consisting of the firefly luciferase coding sequence (LUC) driven by the stress-responsive RD29A promoter, we investigated the interactive effects of temperature, osmotic stress, and the phytohormone abscisic acid (ABA) in the regulation of gene expression in Arabidopsis seedlings. Results indicated that both positive and negative interactions exist among the studied stress factors in regulating gene expression. At a normal growth temperature (22°C), osmotic stress and ABA act synergistically to induce the transgene expression. Low temperature inhibits the response to osmotic stress or to combined treatment of osmotic stress and ABA, whereas low temperature and ABA treatments are additive in inducing transgene expression. Although high temperature alone does not activate the transgene, it significantly amplifies the effects of ABA and osmotic stress. The effect of multiple stresses in the regulation ofRD29A-LUC expression in signal transduction mutants was also studied. The results are discussed in the context of cold and osmotic stress signal transduction pathways.
Microsomal Electron Transfer in Higher Plants: Cloning and Heterologous Expression of NADH-Cytochromeb5Reductase from Arabidopsis
Authors: Fukuchi-Mizutani Masako , Mizutani Masaharu , Tanaka Yoshikazu , Kusumi Takaaki , Ohta Daisaku 
Published: July 2002

Abstract
AtCBR, a cDNA encoding NADH-cytochrome (Cyt)b5 reductase, and AtB5-A and AtB5-B, two cDNAs encoding Cyt b5, were isolated from Arabidopsis. The primary structure deduced from the AtCBR cDNA was 40% identical to those of the NADH-Cyt b5reductases of yeast and mammals. A recombinant AtCBR protein prepared using a baculovirus system exhibited typical spectral properties of NADH-Cyt b5 reductase and was used to study its electron-transfer activity. The recombinant NADH-Cytb5 reductase was functionally active and displayed strict specificity to NADH for the reduction of a recombinant Cyt b5 (AtB5-A), whereas no Cytb5 reduction was observed when NADPH was used as the electron donor. Conversely, a recombinant NADPH-Cyt P450 reductase of Arabidopsis was able to reduce Cytb5 with NADPH but not with NADH. To our knowledge, this is the first evidence in higher plants that both NADH-Cyt b5 reductase and NADPH-Cyt P450 reductase can reduce Cyt b5 and have clear specificities in terms of the electron donor, NADH or NADPH, respectively. This substrate specificity of the two reductases is discussed in relation to the NADH- and NADPH-dependent activities of microsomal fatty acid desaturases.
Winter Survival of Transgenic Alfalfa Overexpressing Superoxide Dismutase1
Authors: McKersie Bryan D. , Bowley Stephen R. , Jones Kim S. 
Published: July 2002

Abstract
To test the hypothesis that enhanced tolerance of oxidative stress would improve winter survival, two clones of alfalfa (Medicago sativa) were transformed with a Mn-superoxide dismutase (Mn-SOD) targeted to the mitochondria or to the chloroplast. Although Mn-SOD activity increased in most primary transgenic plants, both cytosolic and chloroplastic forms of Cu/Zn-SOD had lower activity in the chloroplast SOD transgenic plants than in the nontransgenic plants. In a field trial at Elora, Ontario, Canada, the survival and yield of 33 primary transgenic and control plants were compared. After one winter most transgenic plants had higher survival rates than control plants, with some at 100%. Similarly, some independent transgenic plants had twice the herbage yield of the control plants. Prescreening the transgenic plants for SOD activity, vigor, or freezing tolerance in the greenhouse was not effective in identifying individual transgenic plants with improved field performance. Freezing injury to leaf blades and fibrous roots, measured by electrolyte leakage from greenhouse-grown acclimated plants, indicated that the most tolerant were only 1°C more freezing-tolerant than alfalfa clone N4. There were no differences among transgenic and control plants for tetrazolium staining of field-grown plants at any freezing temperature. Therefore, although many of the transgenic plants had higher winter survival rates and herbage yield, there was no apparent difference in primary freezing injury, and therefore, the trait is not associated with a change in the primary site of freezing injury.
Isolation, Chromosomal Localization, and Differential Expression of Mitochondrial Manganese Superoxide Dismutase and Chloroplastic Copper/Zinc Superoxide Dismutase Genes in Wheat1
Authors: Wu Guohai , Wilen Ronald W. , Robertson Albert J. , Gusta Lawrence V. 
Published: July 2002

Abstract
Superoxide dismutase (SOD) gene expression was investigated to elucidate its role in drought and freezing tolerance in spring and winter wheat (Triticum aestivum). cDNAs encoding chloroplastic Cu/ZnSODs and mitochondrial MnSODs were isolated from wheat. MnSOD and Cu/ZnSOD genes were mapped to the long arms of the homologous group-2 and -7 chromosomes, respectively. Northern blots indicated that MnSOD genes were drought inducible and decreased after rehydration. In contrast, Cu/ZnSOD mRNA was not drought inducible but increased after rehydration. In both spring and winter wheat seedlings exposed to 2°C, MnSOD transcripts attained maximum levels between 7 and 49 d. Transcripts of Cu/ZnSOD mRNA were detected sooner in winter than in spring wheat; however, they disappeared after 21 d of acclimation. Transcripts of both classes of SOD genes increased during natural acclimation in both spring and winter types. Exposure of fully hardened plants to three nonlethal freeze-thaw cycles resulted in Cu/Zn mRNA accumulation; however, MnSOD mRNA levels declined in spring wheat but remained unchanged in winter wheat. The results of the dehydration and freeze-thaw-cycle experiments suggest that winter wheat has evolved a more effective stress-repair mechanism than spring wheat.
The Localization and Expression of the Class II Starch Synthases of Wheat1
Authors: Li Zhongyi , Chu Xiusheng , Mouille Gregory , Yan Liuling , Kosar-Hashemi Behjat , Hey Sandra , Napier Johnathan , Shewry Peter , Clarke Bryan , Appels Rudi , Morell Matthew K. , Rahman Sadequr 
Published: July 2002

AbstractThe starch granules of hexaploid wheat (Triticum aestivum) contain a group of three proteins known as SGP-1 (starch granule protein-1) proteins, which have apparent molecular masses of 100, 108, and 115 kD. The nature and role of these proteins has not been defined previously. We demonstrate that these polypeptides are starch synthases that are present in both the starch granule and the soluble fraction at the early stages of wheat endosperm development, but that are exclusively granule bound at mid and late endosperm development. A partial cDNA clone encoding a fragment of the 100-kD protein was obtained by screening a wheat endosperm cDNA expression library using monoclonal antibodies. Three classes of cDNA were subsequently isolated from a wheat endosperm cDNA library by nucleic acid hybridization and were shown to encode the 100-, 108-, and 115-kD proteins. The cDNA sequences are highly homologous to class II starch synthases and have the highest homology with the maize SSIIa (starch synthase IIa) gene. mRNA for the SGP-1 proteins was detected in the leaf, pre-anthesis florets, and endosperm of wheat and is highly expressed in the leaf and in the grain during the early to mid stages of development. We discuss the roles of the SGP-1 proteins in starch biosynthesis in wheat.
Coordinate Changes in Carbon Partitioning and Plastidial Metabolism during the Development of Oilseed Rape Embryos
Authors: Eastmond Peter J. , Rawsthorne Stephen 
Published: July 2002

Abstract
Measurements of metabolic fluxes in whole embryos and isolated plastids have revealed major changes in the pathways of carbon utilization during cotyledon filling by oilseed rape (Brassica napus L.) embryos. In the early cotyledon stage (stage A), embryos used sucrose (Suc) predominantly for starch synthesis. Plastids isolated from these embryos imported glucose-6-phosphate (Glc-6-P) and partitioned it to starch and fatty acids synthesis and to the oxidative pentose phosphate pathway in the ratio of 2:1:1 on a hexose basis. Of the substrates tested, Glc-6-P gave the highest rates of fatty acid synthesis by the plastids and pyruvate was used weakly. By the mid- to late-cotyledon stage (stage C), oil accumulation by the embryos was rapid, as was their utilization of Suc for oil synthesis in vitro. Plastids from C-stage embryos differed markedly from those of stage-A embryos: (a) pyruvate uptake and utilization for fatty acid synthesis increased by respectively 18- and 25-fold; (b) Glc-6-P partitioning was predominantly to the oxidative pentose phosphate pathway (respective ratios of 1:1:3); and (c) the rate of plastidial fatty acid synthesis more than doubled. This increased rate of fatty synthesis was dependent upon the increase in pyruvate uptake and was mediated through the induction of a saturable transporter activity.
Sensing of Osmotic Pressure Changes in Tomato Cells
Authors: Felix Georg , Regenass Martin , Boller Thomas 
Published: July 2002

Abstract
Cells of tomato (Lycopersicon esculentum) growing in suspension gradually depleted their culture medium and caused a steady decrease in its osmolality. When confronted with a sudden change in medium osmolality (a hypo-osmotic or hyperosmotic shock), respectively, these cells responded with volume changes and stress symptoms such as rapid extracellular alkalinization, efflux of K+-ions, and induction of 1-aminocyclopropane-1-carboxylate synthase acid, the key enzyme of ethylene biosynthesis. This array of stress symptoms is well known from cultured plant cells treated with microbial elicitors. Compared with elicitor treatment, induction of responses by hyperosmotic shock was slow and occurred only after increases of approximately 200,000 Pa in osmotic pressure. In contrast, hypo-osmotic shock induced responses without measurable lag and faster than elicitor treatments. Measurable medium alkalinization was induced when medium osmolality was reduced by as little as approximately 10 mosmol, a change corresponding to only approximately 0.2 bar in osmotic pressure. Like treatment with elicitors, hypo-osmotic shock induced specific changes in protein phosphorylations as demonstrated by in vivo labeling with [33P]orthophosphate. Exposure of cells to consecutive up- and down-shifts in medium osmolality showed that sensing of osmotic changes occurred within seconds, whereas adaptation to new osmotic conditions proceeded over hours. In conclusion, suspension-cultured plant cells display rapid, easily measurable macroscopic responses to osmotic shock and provide an interesting model system to study osmoregulation, a key process in plant growth and development.
Cell Division Activity during Apical Hook Development
Authors: Raz Vered , Koornneef Maarten 
Published: July 2002

Abstract
Growth during plant development is predominantly governed by the combined activities of cell division and cell elongation. The relative contribution of both activities controls the growth of a tissue. A fast change in growth is exhibited at the apical hypocotyl of etiolated seedlings where cells grow at different rates to form a hook-like structure, which is traditionally assumed to result from differential cell elongation. Using new tools we show asymmetric distribution of cell division during early stages of hook development. Cell divisions in the apical hook were predominantly found in subepidermal layers during an early step of hook development, but were absent in mutants exhibiting a hookless phenotype. In addition, during exaggeration of hook curvature, which is mediated by ethylene, a rapid change in the combined activities of cell division and cell elongation was detected. Our results indicate a fast change in cell division activity during apical hook development. We suggest that cell division together with cell elongation contributes to apical hook growth. Our results emphasize the change in the relative contribution of cell division and cell elongation in a fast growing structure like the apical hook.