Every paper, by date: page 152

44,644 papers with a page: 24,189 with their authors' code, 4,955 with code on request, 15,495 with data only. The most recent first, 224 a page. Page 152 of 200: 2 September 2023 to 23 August 2023.

Saturday, 2 September 2023 (10 papers, 2 on this page)

[33825] doi:10.1080/19768354.2023.2250841 [paper, data]

A genomic estimated breeding value-assisted reduction method of single nucleotide polymorphism sets: a novel approach for determining the cutoff thresholds in genome-wide association studies and best linear unbiased prediction.

Journal: Animal cells and systems

Status: data only, 1 dataset cited

[33826] doi:10.3390/s23177614 [paper, data]

Explainable Convolutional Neural Networks for Brain Cancer Detection and Localisation.

Journal: Sensors (Basel, Switzerland)

Status: data only, 1 dataset cited

Friday, 1 September 2023 (54 papers)

[33827] doi:10.1001/jamaneurol.2023.1988 [paper, data]

Mapping Lesion-Related Epilepsy to a Human Brain Network.

Journal: JAMA neurology

Status: data only, 1 dataset cited

[33828] doi:10.1002/dev.22405 [paper, repository]

Early adversity changes the economic conditions of mouse structural brain network organization.

Journal: Developmental psychobiology

Authors' code: OSF evgw5 (no license)

Status: code verified, 6 files readable, 3 matches

[33829] doi:10.1002/jev2.12355 [paper, repository]

Neuron-derived extracellular vesicles contain synaptic proteins, promote spine formation, activate TrkB-mediated signalling and preserve neuronal complexity.

Journal: Journal of extracellular vesicles

Authors' code: Zenodo 1119026 (MIT)

Status: code verified, 949 files readable, 2 matches

[33830] doi:10.1002/pro.4718 [paper, repository]

Two residues determine nicotinic acetylcholine receptor requirement for RIC-3.

Journal: Protein science : a publication of the Protein Society

Authors' code: supp:PMC10443321/PRO-32-e4718-s004.zip (no license)

Status: empty repository

[33831] doi:10.1007/s00406-023-01685-9 [paper, data]

The atypical antidepressant tianeptine confers neuroprotection against oxygen-glucose deprivation.

Journal: European archives of psychiatry and clinical neuroscience

Status: data only, 1 dataset cited

[33832] doi:10.1007/s11060-023-04445-w [paper, data]

Class I HDAC inhibition reduces DNA damage repair capacity of MYC-amplified medulloblastoma cells.

Journal: Journal of neuro-oncology

Status: data only, 1 dataset cited

[33833] doi:10.1016/j.celrep.2023.113070 [paper, repository]

TMEM127 suppresses tumor development by promoting RET ubiquitination, positioning, and degradation.

Journal: Cell reports

Authors' code: broadinstitute/inferCNV (other)

Status: code verified, 82 files readable, 1 match

[33834] doi:10.1016/j.crmeth.2023.100573 [paper, repository]

Three-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics.

Journal: Cell reports methods

Authors' code: SysFate/SysISTD (AGPL-3.0), Zenodo 8180576 (other-open), Zenodo 8180632 (other-open)

Status: code verified, 22 files readable

[33835] doi:10.1016/j.dib.2023.109534 [paper, data]

Dataset for diseases associated with exposure to broflanilide, a novel pesticide, in larval zebrafish (<i>Danio rerio</i>).

Journal: Data in brief

Status: data only, 1 dataset cited

[33836] doi:10.1016/j.isci.2023.107808 [paper, repository]

Decoding hand kinetics and kinematics using somatosensory cortex activity in active and passive movement.

Journal: iScience

Authors' code: AlavieMirfathollahi/S1-COT-Decoding (no license)

Status: code verified, 13 files readable, 5 matches

[33837] doi:10.1016/j.isci.2023.107810 [paper, repository]

Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations.

Journal: iScience

Authors' code: plotly/plotly.py (MIT), fjukstad/gographer (no license), pderdeyn/neural-cyclic-gene-networks (no license)

Status: code verified, 1,535 files readable, 1 match

[33838] doi:10.1016/j.neuron.2023.08.005 [paper, repository]

Active cortical networks promote shunting fast synaptic inhibition in vivo.

Journal: Neuron

Authors' code: swharden/pyABF (MIT), richardjburman (no license)

Status: code verified, 175 files readable, 3 matches

[33839] doi:10.1038/s41380-023-02282-x [paper, repository]

Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes.

Journal: Molecular psychiatry

Authors' code: freeseek/kgp2anc (no license)

Status: code verified, 6 files readable, 2 matches

[33840] doi:10.1038/s41380-023-02296-5 [paper, data]

Neuronal TIMP2 regulates hippocampus-dependent plasticity and extracellular matrix complexity.

Journal: Molecular psychiatry

Status: data only, 1 dataset cited

[33841] doi:10.1038/s41467-023-40998-0 [paper, repository]

Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans.

Journal: Nature communications

Authors' code: SamC873/FUSF_Hydrophone_Scanner (no license), sitiny/mr-to-pct (Apache-2.0), sitiny/BRIC_TUS_Simulation_Tools (GPL-3.0), Zenodo 7110246 (other-open), Zenodo 8027240 (other-open)

Status: code verified, 32 files readable, 7 matches

[33842] doi:10.1038/s41467-023-41027-w [paper, repository]

Neural tuning instantiates prior expectations in the human visual system.

Journal: Nature communications

Authors' code: ReubenRideaux/Neural-tuning-instantiates-prior-expectations-in-the-human-visual-system (no license)

Status: code verified, 5 files readable, 5 matches

[33843] doi:10.1038/s41598-023-40539-1 [paper, data]

Representation of rewards differing in their hedonic valence in the caudate nucleus correlates with the performance in a problem-solving task in dogs (Canis familiaris).

Journal: Scientific reports

Status: data only, 1 dataset cited

[33844] doi:10.1038/s41598-023-40675-8 [paper, data]

Pre-neuronal processing of haptic sensory cues via dispersive high-frequency vibrational modes.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33845] doi:10.1038/s41598-023-40807-0 [paper, repository]

Extracting and visualizing hidden activations and computational graphs of PyTorch models with TorchLens.

Journal: Scientific reports

Authors' code: johnmarktaylor91/torchlens (Apache-2.0), drive.google.com/drive/u (no license), colab.research.google.com/drive/1orjlgzpifvdsvpfqq1lyt3t5hv560sow (no license)

Status: code verified, 2,000 files readable, 2 matches

[33846] doi:10.1038/s41598-023-41613-4 [paper, repository]

Single-trial visually evoked potentials predict both individual choice and market outcomes.

Journal: Scientific reports

Authors' code: john-veillette/eeg-neuroforecasting (no license), Zenodo 6977364 (other-open), john-veillette/mne-ari (BSD-3-Clause)

Status: code verified, 46 files readable, 10 matches

[33847] doi:10.1093/brain/awad075 [paper, data]

Multiomics and machine-learning identify novel transcriptional and mutational signatures in amyotrophic lateral sclerosis.

Journal: Brain : a journal of neurology

Status: data only, 1 dataset cited

[33848] doi:10.1093/brain/awad111 [paper]

Widespread genomic influences on phenotype in Dravet syndrome, a 'monogenic' condition.

Journal: Brain : a journal of neurology

Status: code on request

[33849] doi:10.1093/brain/awad118 [paper, repository]

Spike propagation mapping reveals effective connectivity and predicts surgical outcome in epilepsy.

Journal: Brain : a journal of neurology

Authors' code: mmatarrese/Spike-propagation-reconstruction (no license)

Status: code verified, 7 files readable, 4 matches

[33850] doi:10.1093/brain/awad125 [paper, repository]

Cortical microstructural gradients capture memory network reorganization in temporal lobe epilepsy.

Journal: Brain : a journal of neurology

Authors' code: MICA-MNI/micapipe (GPL-3.0), MICA-MNI/micaopen (GPL-3.0), OSF j532r (no license)

Status: code verified, 392 files readable, 9 matches

[33851] doi:10.1093/cercor/bhad275 [paper]

EEG measurement for the effect of perceptual eye position and eye position training on comitant strabismus.

Journal: Cerebral cortex (New York, N.Y. : 1991)

Status: code on request

[33852] doi:10.1093/cercor/bhad281 [paper, repository]

DOT1L deletion impairs the development of cortical parvalbumin-expressing interneurons.

Journal: Cerebral cortex (New York, N.Y. : 1991)

Authors' code: Vogel-lab/DOT1L-interneuron-development (no license)

Status: code verified, 4 files readable

[33853] doi:10.1093/cercor/bhad283 [paper]

A comparison of behavioral paradigms assessing spatial memory in tree shrews.

Journal: Cerebral cortex (New York, N.Y. : 1991)

Status: code on request

[33854] doi:10.1093/cercor/bhad289 [paper, data]

The language network is not engaged in object categorization.

Journal: Cerebral cortex (New York, N.Y. : 1991)

Status: data only, 1 dataset cited

[33855] doi:10.1093/g3journal/jkad143 [paper, repository]

An approach for prioritizing candidate genes from RNA-seq using preclinical cocaine self-administration datasets as a test case.

Journal: G3 (Bethesda, Md.)

Authors' code: SexChrLab/RodentAddiction (GPL-3.0)

Status: code verified, 14 files readable, 15 matches

[33856] doi:10.1093/g3journal/jkad183 [paper, repository]

An expanded GCaMP reporter toolkit for functional imaging in Caenorhabditis elegans.

Journal: G3 (Bethesda, Md.)

Authors' code: lu-lab/GCaMP_video_analysis (no license)

Status: code verified, 6 files readable

[33857] doi:10.1093/g3journal/jkad186 [paper, repository]

Identification of a spontaneously arising variant affecting thermotaxis behavior in a recombinant inbred Caenorhabditis elegans line.

Journal: G3 (Bethesda, Md.)

Authors' code: ptmcgrat/sequencer (no license), pysam-developers/pysam (MIT)

Status: code verified, 476 files readable

[33858] doi:10.1093/ijnp/pyad041 [paper, data]

Stress Hormone Dynamics Are Coupled to Brain Serotonin 4 Receptor Availability in Unmedicated Patients With Major Depressive Disorder: A NeuroPharm Study.

Journal: The international journal of neuropsychopharmacology

Status: data only, 9 datasets cited

[33859] doi:10.1093/jamia/ocad135 [paper, repository]

Using artificial intelligence to learn optimal regimen plan for Alzheimer's disease.

Journal: Journal of the American Medical Informatics Association : JAMIA

Authors' code: bioIKEA/Treatment_optimization_AD (no license)

Status: code verified, 404 files readable, 3 matches

[33860] doi:10.1093/molbev/msad181 [paper, repository]

Evolution of Human Brain Left-Right Asymmetry: Old Genes with New Functions.

Journal: Molecular biology and evolution

Authors' code: Jianguo-Wang/BAgenes (no license)

Status: code verified, 3 files readable, 3 matches

[33861] doi:10.1093/nar/gkad604 [paper, repository]

Transcriptome-wide profiling of A-to-I RNA editing by Slic-seq.

Journal: Nucleic acids research

Authors' code: sqhan-whu/A-I_stop (no license)

Status: code verified, 36 files readable, 2 matches

[33862] doi:10.1093/scan/nsad041 [paper, data]

Openness to Experience is associated with neural and performance measures of memory in older adults.

Journal: Social cognitive and affective neuroscience

Status: data only, 1 dataset cited

[33863] doi:10.1093/scan/nsad043 [paper]

Emotion regulation of social pain: double dissociation of lateral prefrontal cortices supporting reappraisal and distraction.

Journal: Social cognitive and affective neuroscience

Status: code on request

[33864] doi:10.1093/scan/nsad045 [paper, data]

Partner similarity and social cognitive traits predict social interaction success among strangers.

Journal: Social cognitive and affective neuroscience

Status: data only, 1 dataset cited

[33865] doi:10.1093/sleep/zsad193 [paper, repository]

Pontine Waves Accompanied by Short Hippocampal Sharp Wave-Ripples During Non-rapid Eye Movement Sleep.

Journal: Sleep

Authors' code: cortex-lab/allenCCF (no license), Sakata-Lab/SleepScore (GPL-3.0)

Status: code verified, 66 files readable

[33866] doi:10.1097/md.0000000000035311 [paper, data]

Pathogenic mechanisms and potential therapeutic targets for Parkinson disease revealed by bioinformatic analysis of necroptosis and immune cell infiltration.

Journal: Medicine

Status: data only, 1 dataset cited

[33867] doi:10.1101/gad.350896.123 [paper, data]

Allelic chromatin structure precedes imprinted expression of <i>Kcnk9</i> during neurogenesis.

Journal: Genes & development

Status: data only, 1 dataset cited

[33868] doi:10.1167/iovs.64.12.18 [paper, repository]

Mechanisms of Extraorbital Lacrimal Gland Aging in Mice: An Integrative Analysis of the Temporal Transcriptome.

Journal: Investigative ophthalmology & visual science

Authors' code: BGI-flexlab/SOAPnuke (GPL-3.0), deweylab/RSEM (GPL-3.0)

Status: code verified, 421 files readable, 1 match

[33869] doi:10.1167/iovs.64.12.27 [paper, data]

Regulation of Axon Guidance by Slit2 and Netrin-1 Signaling in the Lacrimal Gland of Aqp5 Knockout Mice.

Journal: Investigative ophthalmology & visual science

Status: data only, 1 dataset cited

[33870] doi:10.1186/s12864-023-09625-6 [paper, data]

Genome-wide association study of abnormal elevation of ALT in patients exposed to atabecestat.

Journal: BMC genomics

Status: data only, 1 dataset cited

[33871] doi:10.1186/s12929-023-00971-x [paper, repository]

Structural changes in perineuronal nets and their perforating GABAergic synapses precede motor coordination recovery post stroke.

Journal: Journal of biomedical science

Authors' code: supp:PMC10474719/12929_2023_971_MOESM2_ESM.m (no license)

Status: code verified, 1 file readable

[33872] doi:10.1242/dmm.050141 [paper, data]

Glucocorticoid receptor regulates protein chaperone, circadian clock and affective disorder genes in the zebrafish brain.

Journal: Disease models & mechanisms

Status: data only, 1 dataset cited

[33873] doi:10.1371/journal.pbio.3002266 [paper, repository]

Morphological evolution of language-relevant brain areas.

Journal: PLoS biology

Authors' code: gagdiez/chimpanzee-broca (no license), Zenodo 8154437 (other-open)

Status: code verified, 18 files readable

[33874] doi:10.1371/journal.pcbi.1011434 [paper, repository]

A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics.

Journal: PLoS computational biology

Authors' code: RobertaMLo/CRBL (no license), RobertaMLo/CRBL_MF (no license)

Status: code verified, 77 files readable, 12 matches

[33875] doi:10.1371/journal.pone.0291070 [paper, data]

ECG and EEG based detection and multilevel classification of stress using machine learning for specified genders: A preliminary study.

Journal: PloS one

Status: data only, 1 dataset cited

[33876] doi:10.1503/jpn.230065 [paper, data]

Should perception of emotions be classified according to threat detection rather than emotional valence? An updated meta-analysis for a whole-brain atlas of emotional faces processing.

Journal: Journal of psychiatry & neuroscience : JPN

Status: data only, 1 dataset cited

[33877] doi:10.2337/db23-0139 [paper, repository]

Identification of Hypothalamic Glucoregulatory Neurons That Sense and Respond to Changes in Glycemia.

Journal: Diabetes

Authors' code: DeemLab/fiber-photometry (MIT)

Status: code verified, 13 files readable

[33878] doi:10.26508/lsa.202302036 [paper, data]

Alternative oxidase causes cell type- and tissue-specific responses in mutator mice.

Journal: Life science alliance

Status: data only, 1 dataset cited

[33879] doi:10.3390/diagnostics13172840 [paper, repository]

The Diagnostic Accuracy of Artificial Intelligence in Radiological Markers of Normal-Pressure Hydrocephalus (NPH) on Non-Contrast CT Scans of the Brain.

Journal: Diagnostics (Basel, Switzerland)

Authors' code: slundberg/shap (MIT)

Status: code verified, 66 files readable

[33880] doi:10.3390/ijms241713569 [paper, repository]

Spaceflight-Induced Gene Expression Profiles in the Mouse Brain Are Attenuated by Treatment with the Antioxidant BuOE.

Journal: International journal of molecular sciences

Authors' code: ikremsky/Scripts-for-Kremsky-et-al.-GeoMx-DSP-mouse-spaceflight-study (no license)

Status: code verified, 29 files readable, 4 matches

Thursday, 31 August 2023 (26 papers)

[33881] doi:10.1016/j.celrep.2023.113057 [paper]

Cerebellar interneurons control fear memory consolidation via learning-induced HCN plasticity.

Journal: Cell reports

Status: code on request

[33882] doi:10.1016/j.celrep.2023.113058 [paper, data]

System-wide mapping of peptide-GPCR interactions in C. elegans.

Journal: Cell reports

Status: code on request, 1 dataset cited

[33883] doi:10.1038/s41467-023-40812-x [paper]

Purinergic signaling mediates neuroglial interactions to modulate sighs.

Journal: Nature communications

Status: code on request

[33884] doi:10.1038/s41467-023-41032-z [paper, repository]

Birds multiplex spectral and temporal visual information via retinal On- and Off-channels.

Journal: Nature communications

Authors' code: BadenLab/Nature_Comms_paper_23 (no license)

Status: code verified, 17 files readable, 8 matches

[33885] doi:10.1038/s41587-023-01911-8 [paper, repository]

Imaging brain tissue architecture across millimeter to nanometer scales.

Journal: Nature biotechnology

Authors' code: juglab/n2v (BSD-3-Clause), Li-En-Good/VISTA (BSD), danzllab/CATS (AGPL-3.0)

Status: code verified, 150 files readable, 22 matches

[33886] doi:10.1038/s41588-023-01485-w [paper, data]

GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture.

Journal: Nature genetics

Status: data only, 4 datasets cited

[33887] doi:10.1038/s41591-023-02509-y [paper, repository]

Sex differences in brain protein expression and disease.

Journal: Nature medicine

Authors' code: wingolab-org/role_of_sex_in_brain_expression (no license)

Status: code verified, 77 files readable, 1 match

[33888] doi:10.1038/s41594-023-01080-x [paper, repository]

Modulation of GluA2-γ5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2.

Journal: Nature structural & molecular biology

Authors' code: NYUMetabolomics/plz (MIT)

Status: code verified, 18 files readable

[33889] doi:10.1038/s41598-023-41358-0 [paper, data]

The association between working memory precision and the nonlinear dynamics of frontal and parieto-occipital EEG activity.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33890] doi:10.1038/s42003-023-05262-7 [paper, repository]

Leading basic modes of spontaneous activity drive individual functional connectivity organization in the resting human brain.

Journal: Communications biology

Authors' code: arvkevi/kneed (BSD-3-Clause), liaolab-bnu/LeadingModes_rfMRI (no license)

Status: code verified, 16 files readable, 1 match

[33891] doi:10.1038/s43587-023-00469-z [paper, repository]

The integrity of dopaminergic and noradrenergic brain regions is associated with different aspects of late-life memory performance.

Journal: Nature aging

Authors' code: OSF eph9a (no license)

Status: code verified

[33892] doi:10.1101/2023.08.29.555204 [paper, data]

Heterogeneity of synaptic connectivity in the fly visual system

Journal: bioRxiv (preprint)

Status: data only, 2 datasets cited

[33893] doi:10.1186/s11689-023-09498-6 [paper, repository]

Neurogenetic mechanisms of risk for ADHD: Examining associations of polygenic scores and brain volumes in a population cohort.

Journal: Journal of neurodevelopmental disorders

Authors' code: OSF whjuq (no license)

Status: empty repository

[33894] doi:10.1371/journal.pbio.3002239 [paper, repository]

Functional geometry of auditory cortical resting state networks derived from intracranial electrophysiology.

Journal: PLoS biology

Authors' code: Zenodo 8235227 (BSD-3-Clause)

Status: code verified, 44 files readable, 9 matches

[33895] doi:10.1371/journal.pbio.3002271 [paper, repository]

Rapid structural remodeling of peripheral taste neurons is independent of taste cell turnover.

Journal: PLoS biology

Authors' code: Dalston817/ArborTools (CC-BY-NC-SA-4.0), neuromorpho.org/dablefiles/whiddon_krimm (no license)

Status: code verified, 2 files readable

[33896] doi:10.1371/journal.pbio.3002276 [paper, data]

Inhibition of ribosome biogenesis in the epidermis is sufficient to trigger organism-wide growth quiescence independently of nutritional status in C. elegans.

Journal: PLoS biology

Status: data only, 1 dataset cited

[33897] doi:10.1371/journal.pbio.3002277 [paper, repository]

Auditory cortex ensembles jointly encode sound and locomotion speed to support sound perception during movement.

Journal: PLoS biology

Authors' code: figshare 23736831 (CC-BY-4.0)

Status: code verified, 2 files readable

[33898] doi:10.3389/fgene.2023.1181775 [paper, data]

Dysregulation of core neurodevelopmental pathways-a common feature of cancers with perineural invasion.

Journal: Frontiers in genetics

Status: data only, 1 dataset cited

[33899] doi:10.3389/fgene.2023.1236509 [paper, repository]

Interactions between genes involved in physiological dysregulation and axon guidance: role in Alzheimer's disease.

Journal: Frontiers in genetics

Authors' code: UW-GAC/GENESIS (no license)

Status: code verified, 82 files readable, 2 matches

[33900] doi:10.3389/fimmu.2023.1263329 [paper, repository]

Combining single-cell sequencing and spatial transcriptome sequencing to identify exosome-related features of glioblastoma and constructing a prognostic model to identify BARD1 as a potential therapeutic target for GBM patients.

Journal: Frontiers in immunology

Authors' code: carmonalab/UCell (GPL-3.0)

Status: code verified, 19 files readable, 5 matches

[33901] doi:10.3389/fnagi.2023.1212275 [paper, repository]

Identifying Alzheimer's disease and mild cognitive impairment with atlas-based multi-modal metrics.

Journal: Frontiers in aging neuroscience

Authors' code: oxcns.org/aal3.html (no license)

Status: code verified

[33902] doi:10.3389/fnbot.2023.1211570 [paper, repository]

Ring attractor bio-inspired neural network for social robot navigation.

Journal: Frontiers in neurorobotics

Authors' code: jusemat/chimuelo_description (no license), JesusRiveroOrtega/BINNF (no license)

Status: code verified, 4 files readable

[33903] doi:10.3389/fninf.2023.1215261 [paper, repository]

NeuroBridge: a prototype platform for discovery of the long-tail neuroimaging data.

Journal: Frontiers in neuroinformatics

Authors' code: NeuroBridge/NeuroBridge1.0 (other), cambridgeltl/sapbert (MIT)

Status: code verified, 46 files readable, 1 match

[33904] doi:10.3389/fnins.2023.1239009 [paper, data]

Nicotine-mediated effects in neuronal and mouse models of synucleinopathy.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[33905] doi:10.3389/fnsys.2023.1217170 [paper, repository]

Beyond rhythm - a framework for understanding the frequency spectrum of neural activity.

Journal: Frontiers in systems neuroscience

Authors' code: cardin-higley-lab/CBASS (Apache-2.0), Zenodo 8271169 (MIT)

Status: code verified, 155 files readable, 7 matches

[33906] doi:10.3389/fnsys.2023.1222176 [paper, repository]

Differential optogenetic activation of the auditory midbrain in freely moving behaving mice.

Journal: Frontiers in systems neuroscience

Authors' code: Spunc/PsychDetect (GPL-3.0)

Status: code verified, 109 files readable, 3 matches

Wednesday, 30 August 2023 (28 papers)

[33907] doi:10.1002/hbm.26465 [paper, data]

Sex-dependent differences in connectivity patterns are related to episodic memory recall.

Journal: Human brain mapping

Status: data only, 1 dataset cited

[33908] doi:10.1002/hbm.26471 [paper, data]

Denoising brain networks using a fixed mathematical phase change in independent component analysis of magnitude-only fMRI data.

Journal: Human brain mapping

Status: data only, 1 dataset cited

[33909] doi:10.1016/j.ccell.2023.07.010 [paper, repository]

Machine learning identifies experimental brain metastasis subtypes based on their influence on neural circuits.

Journal: Cancer cell

Authors' code: osvaldogc/nextpresso1.9.2 (CC-BY-NC-ND-4.0), cnio_bu/varca (no license), Zenodo 7957550 (CC-BY-4.0), Zenodo 7957334 (CC-BY-4.0), cnio_bu/cluster_rnaseq (no license), Zenodo 7963303 (CC-BY-4.0), PridaLab/metast-tree (no license)

Status: code verified, 23 files readable, 8 matches

[33910] doi:10.1016/j.cell.2023.08.009 [paper, repository]

Structural basis for ion selectivity in potassium-selective channelrhodopsins.

Journal: Cell

Authors' code: 3dem/relion (GPL-2.0), keitaroyam/servalcat (MPL-2.0)

Status: code verified, 1,345 files readable, 2 matches

[33911] doi:10.1016/j.devcel.2023.08.017 [paper, data]

Defining the identity and the niches of epithelial stem cells with highly pleiotropic multilineage potency in the human thymus.

Journal: Developmental cell

Status: data only, 1 dataset cited

[33912] doi:10.1016/j.isci.2023.107787 [paper]

Chronic carbon disulfide exposure induces parkinsonian pathology via α-synuclein aggregation and necrosome complex interaction.

Journal: iScience

Status: code on request

[33913] doi:10.1016/j.xcrm.2023.101177 [paper, repository]

Tumor-associated monocytes promote mesenchymal transformation through EGFR signaling in glioma.

Journal: Cell reports. Medicine

Authors' code: theMILOlab/SPATA2 (gnu)

Status: code verified, 79 files readable, 4 matches

[33914] doi:10.1017/gmb.2023.14 [paper, data]

The butyrate-producing and spore-forming bacterial genus <i>Coprococcus</i> as a potential biomarker for neurological disorders.

Journal: Gut microbiome (Cambridge, England)

Status: data only, 1 dataset cited

[33915] doi:10.1021/acs.jmedchem.3c00734 [paper, data]

Pharmacology and Therapeutic Potential of Benzothiazole Analogues for Cocaine Use Disorder.

Journal: Journal of medicinal chemistry

Status: data only, 1 dataset cited

[33916] doi:10.1038/s41467-023-41020-3 [paper, repository]

Critical dynamics arise during structured information presentation within embodied in vitro neuronal networks.

Journal: Nature communications

Authors' code: OSF ncvpq (no license)

Status: code verified, 100 files readable, 4 matches

[33917] doi:10.1038/s41467-023-41025-y [paper, repository]

Acetylcholine modulates the temporal dynamics of human theta oscillations during memory.

Journal: Nature communications

Authors' code: pennmem/pybeh (no license), pennmem/ptsa (GPL-3.0), pennmem/cmlreaders (no license), tgedankien/scopolamine (no license)

Status: code verified, 206 files readable, 2 matches

[33918] doi:10.1038/s41586-023-06459-w [paper, repository]

An orexigenic subnetwork within the human hippocampus.

Journal: Nature

Authors' code: kaijmiller/crp_scripts (GPL-3.0)

Status: code verified, 4 files readable, 3 matches

[33919] doi:10.1038/s41586-023-06465-y [paper, data]

LTP induction by structural rather than enzymatic functions of CaMKII.

Journal: Nature

Status: data only, 1 dataset cited

[33920] doi:10.1038/s41586-023-06478-7 [paper, repository]

Hippocampal representation during collective spatial behaviour in bats.

Journal: Nature

Authors' code: gardner-lab/FinchScope (MIT), gardner-lab/video-capture (MIT)

Status: code verified, 95 files readable, 3 matches

[33921] doi:10.1038/s41598-023-41408-7 [paper, data]

Resting state default mode network is associated with wise advising.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33922] doi:10.1126/sciadv.ade3874 [paper, repository]

Pathway-specific inputs to the superior colliculus support flexible responses to visual threat.

Journal: Science advances

Authors' code: farrowlab/Li-Kuhn-et-al.-2023 (other)

Status: code verified, 64 files readable, 9 matches

[33923] doi:10.1126/sciadv.adg1736 [paper, data]

The neural code for "face cells" is not face-specific.

Journal: Science advances

Status: data only, 2 datasets cited

[33924] doi:10.1155/2023/5602401 [paper, data]

Fecal Microbiota Underlying the Coexistence of Schizophrenia and Multiple Sclerosis in Chinese Patients.

Journal: The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale

Status: data only, 1 dataset cited

[33925] doi:10.1186/s13024-023-00649-w [paper, data]

Amyloid-β (Aβ) immunotherapy induced microhemorrhages are associated with activated perivascular macrophages and peripheral monocyte recruitment in Alzheimer's disease mice.

Journal: Molecular neurodegeneration

Status: data only, 1 dataset cited

[33926] doi:10.1186/s40001-023-01293-2 [paper, data]

Neurological manifestations of SARS-CoV-2: complexity, mechanism and associated disorders.

Journal: European journal of medical research

Status: data only, 2 datasets cited

[33927] doi:10.1523/jneurosci.2307-22.2023 [paper, data]

Dehydroepiandrosterone Sulfate (DHEAS) Is an Endogenous Kv7 Channel Modulator That Reduces Kv7/M-Current Suppression and Inflammatory Pain.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Status: data only, 2 datasets cited

[33928] doi:10.3389/fnagi.2023.1223273 [paper, data]

Transcriptome and methylome of the supraoptic nucleus provides insights into the age-dependent loss of neuronal plasticity.

Journal: Frontiers in aging neuroscience

Status: data only, 1 dataset cited

[33929] doi:10.3389/fnhum.2023.1167786 [paper, repository]

Gray space and default mode network-amygdala connectivity.

Journal: Frontiers in human neuroscience

Authors' code: harri585/grayspace (Unlicense)

Status: code verified, 3 files readable, 2 matches

[33930] doi:10.3389/fonc.2023.1143688 [paper, repository]

Deep-learning and conventional radiomics to predict <i>IDH</i> genotyping status based on magnetic resonance imaging data in adult diffuse glioma.

Journal: Frontiers in oncology

Authors' code: MIC-DKFZ/nnUNet (Apache-2.0)

Status: code verified, 237 files readable, 1 match

[33931] doi:10.3390/ijms241713436 [paper, data]

ERK1/2-Dependent Phosphorylation of GABA_B1(S867/T872), Controlled by CaMKIIβ, Is Required for GABA_B Receptor Degradation under Physiological and Pathological Conditions.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[33932] doi:10.3390/ijms241713484 [paper, data]

Prenatal Alcohol Exposure Impairs the Placenta-Cortex Transcriptomic Signature, Leading to Dysregulation of Angiogenic Pathways.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[33933] doi:10.3390/s23177520 [paper, data]

Functional Connectivity and Feature Fusion Enhance Multiclass Motor-Imagery Brain-Computer Interface Performance.

Journal: Sensors (Basel, Switzerland)

Status: data only, 1 dataset cited

[33934] doi:10.7554/elife.83025 [paper, repository]

Balancing true and false detection of intermittent sensory targets by adjusting the inputs to the evidence accumulation process.

Journal: eLife

Authors' code: annacgeuzebroek/context-dependent-detection (MIT), AnnaCGeuzebroek/Continuous-Behavioural-Modelling (MIT)

Status: code verified, 20 files readable, 23 matches

Tuesday, 29 August 2023 (12 papers)

[33935] doi:10.1007/s12672-023-00765-5 [paper, data]

Caveolin-1 promotes glioma progression and maintains its mitochondrial inhibition resistance.

Journal: Discover oncology

Status: data only, 1 dataset cited

[33936] doi:10.1016/j.isci.2023.107761 [paper]

The selective norepinephrine reuptake inhibitor reboxetine promotes late-stage fracture healing in mice.

Journal: iScience

Status: code on request

[33937] doi:10.1016/j.isci.2023.107765 [paper, repository]

Inhibitory temporo-parietal effective connectivity is associated with explicit memory performance in older adults.

Journal: iScience

Authors' code: bhschott/DCM_MemoryEncoding (no license)

Status: code verified, 24 files readable, 9 matches

[33938] doi:10.1016/j.isci.2023.107773 [paper]

Mechanosensitive accumulation of non-muscle myosin IIB during mitosis requires its translocation activity.

Journal: iScience

Status: code on request

[33939] doi:10.1038/s41380-023-02221-w [paper]

Cortical morphology in patients with the deficit and non-deficit syndrome of schizophrenia: a worldwide meta- and mega-analyses.

Journal: Molecular psychiatry

Status: code on request

[33940] doi:10.1038/s41467-023-40903-9 [paper, repository]

Flight trajectory prediction enabled by time-frequency wavelet transform.

Journal: Nature communications

Authors' code: Zenodo 8238768 (Apache-2.0), musdev7/wtftp-model (Apache-2.0)

Status: code verified, 50 files readable, 2 matches

[33941] doi:10.1177/17562864231190298 [paper, repository]

Network topology in brain tumor patients with and without structural epilepsy: a prospective MEG study.

Journal: Therapeutic advances in neurological disorders

Authors' code: gdemarchi (no license)

Status: code verified

[33942] doi:10.1186/s12885-023-11263-w [paper]

Circ_0021350 plays an oncogene role by regulating miR-1207-3p/PIK3R3 in glioblastoma.

Journal: BMC cancer

Status: data only

[33943] doi:10.1523/eneuro.0212-23.2023 [paper, repository]

A Simple, Lightweight, and Low-Cost Customizable Multielectrode Array for Local Field Potential Recordings.

Journal: eNeuro

Authors' code: OSF zxf5t (no license)

Status: empty repository

[33944] doi:10.1523/eneuro.0215-23.2023 [paper, repository]

Hyperpolarization-Activated Cation Channels Shape the Spiking Frequency Preference of Human Cortical Layer 5 Pyramidal Neurons.

Journal: eNeuro

Authors' code: FKSkinnerLab/HumanL5FDG (no license)

Status: code verified, 263 files readable, 8 matches

[33945] doi:10.15252/embr.202356808 [paper, data]

Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function.

Journal: EMBO reports

Status: data only, 1 dataset cited

[33946] doi:10.3389/fphar.2023.1257592 [paper, data]

Successful treatment of lung adenocarcinoma complicated with a rare compound <i>EGFR</i> mutation L833V/H835L using aumolertinib: a case report and literature review.

Journal: Frontiers in pharmacology

Status: data only, 1 dataset cited

Monday, 28 August 2023 (20 papers)

[33947] doi:10.1002/acn3.51879 [paper, repository]

Pupillary dynamics predict long-term outcome in a cohort of acute traumatic brain injury coma patients.

Journal: Annals of clinical and translational neurology

Authors' code: CorbettaLab (no license)

Status: code verified

[33948] doi:10.1007/s10548-023-00983-8 [paper, repository]

Automatic Brain Categorization of Discrete Auditory Emotion Expressions.

Journal: Brain topography

Authors' code: NOCIONS/Letswave6 (no license)

Status: code verified, 1,006 files readable, 2 matches

[33949] doi:10.1007/s12035-023-03587-2 [paper, repository]

Abnormal Brain Protein Abundance and Cross-tissue mRNA Expression in Amyotrophic Lateral Sclerosis.

Journal: Molecular neurobiology

Authors' code: MRCIEU/TwoSampleMR (other)

Status: code verified, 73 files readable, 1 match

[33950] doi:10.1016/j.isci.2023.107755 [paper, repository]

Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol.

Journal: iScience

Authors' code: dviraran/SingleR (GPL-3.0), immunogenomics/harmony (no license), asntech/intervene-shiny (BSD-3-Clause), jlmelville/uwot (GPL-3.0), PF2-pasteur-fr/SARTools (no license), phipsonlab/speckle (GPL-3.0), EskelandLab/Neuralparacet (GPL-3.0), cancell.medisin.uio.no/scatac/hescneurodiffparacet (no license)

Status: code verified, 248 files readable, 17 matches

[33951] doi:10.1016/j.omtm.2023.08.021 [paper]

High-titer AAV disrupts cerebrovascular integrity and induces lymphocyte infiltration in adult mouse brain.

Journal: Molecular therapy. Methods & clinical development

Status: code on request

[33952] doi:10.1016/j.xgen.2023.100399 [paper, repository]

Multiple genes in a single GWAS risk locus synergistically mediate aberrant synaptic development and function in human neurons.

Journal: Cell genomics

Authors' code: thewonlab/H-MAGMA (no license), BenLangmead/bowtie2 (GPL-3.0), macs3-project/MACS (BSD-3-Clause), alexdobin/STAR (MIT), Zenodo 8180188 (other-open), endeneon/vps45_repo (no license)

Status: code verified, 1,076 files readable, 19 matches

[33953] doi:10.1038/s41377-023-01230-2 [paper, repository]

Deep self-learning enables fast, high-fidelity isotropic resolution restoration for volumetric fluorescence microscopy.

Journal: Light, science & applications

Authors' code: Zenodo 6371391 (other-open), peterpark-git/neuroclear (Apache-2.0)

Status: code verified, 62 files readable, 7 matches

[33954] doi:10.1038/s41467-023-40937-z [paper, repository]

Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases.

Journal: Nature communications

Authors' code: nfancy/TSPO_Nature_Comm (no license), Zenodo 82121910 (no license)

Status: code verified, 10 files readable, 5 matches

[33955] doi:10.1038/s41593-023-01413-5 [paper, repository]

Propagation of activity through the cortical hierarchy and perception are determined by neural variability.

Journal: Nature neuroscience

Authors' code: llerussell/STAMovieMaker (no license), Zenodo 8066289 (other-open), Zenodo 8109935 (other-open), packer-lab/popping-off (MIT), priesemann-group/rowland-et-al2023_recurrence (no license)

Status: code verified, 63 files readable, 8 matches

[33956] doi:10.1038/s41598-023-40617-4 [paper]

LAMP1 as a novel molecular biomarker to predict the prognosis of the children with autism spectrum disorder using bioinformatics approaches.

Journal: Scientific reports

Status: data only

[33957] doi:10.1038/s41598-023-40976-y [paper, repository]

Memory capacity and prioritization in female mice.

Journal: Scientific reports

Authors' code: bendor-lab/serial_novel_object (no license)

Status: empty repository

[33958] doi:10.1038/s42003-023-05257-4 [paper, repository]

Neural encoding with unsupervised spiking convolutional neural network.

Journal: Communications biology

Authors' code: KamitaniLab/GenericObjectDecoding (MIT), wang1239435478/Neural-encoding-with-unsupervised-spiking-convolutional-spiking-neural-networks (no license)

Status: code verified, 98 files readable, 3 matches

[33959] doi:10.1073/pnas.2221704120 [paper, repository]

A law of data separation in deep learning.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: avalonstrel/neuralcollapse (MIT), DaDaCheng/Re-equi-sepa (no license), slash0bz/data-separation (no license), kuangliu/pytorch-cifar (MIT), HornHehhf/Equi-Separation (no license)

Status: code verified, 210 files readable, 3 matches

[33960] doi:10.1073/pnas.2304851120 [paper, data]

Differential second messenger signaling via dopamine neurons bidirectionally regulates memory retention.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Status: data only, 1 dataset cited

[33961] doi:10.1371/journal.pcbi.1011395 [paper, repository]

Switching state-space modeling of neural signal dynamics.

Journal: PLoS computational biology

Authors' code: mh105/somata (BSD-3-Clause), Zenodo 7818644 (other-open), mh105/plos_compbiol_switching_paper_analysis (no license)

Status: code verified, 131 files readable, 23 matches

[33962] doi:10.1523/eneuro.0149-23.2023 [paper, repository]

Somatostatin-Expressing Neurons in the Ventral Tegmental Area Innervate Specific Forebrain Regions and Are Involved in Stress Response.

Journal: eNeuro

Authors' code: eLinanin/Anterograde_heatmap (MIT)

Status: code verified, 3 files readable

[33963] doi:10.3389/fnins.2023.1187328 [paper, repository]

Generation of a whole-brain hemodynamic response function and sex-specific differences in cerebral processing of mechano-sensation in mice detected by BOLD fMRI.

Journal: Frontiers in neuroscience

Authors' code: TheFaberLab/mouse_HRF (no license), TheFaberLab/rat_HRF (no license)

Status: code verified, 4 files readable

[33964] doi:10.3389/fnins.2023.1250991 [paper, data]

Temporal-frequency-phase feature classification using 3D-convolutional neural networks for motor imagery and movement.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[33965] doi:10.3390/cancers15174298 [paper, repository]

Evaluating Physiological MRI Parameters in Patients with Brain Metastases Undergoing Stereotactic Radiosurgery-A Preliminary Analysis and Case Report.

Journal: Cancers

Authors' code: abhogal-lab/seeVR (GPL-3.0)

Status: code verified, 211 files readable, 3 matches

[33966] doi:10.5334/cpsy.94 [paper, repository]

Inferring Trajectories of Psychotic Disorders Using Dynamic Causal Modeling.

Journal: Computational psychiatry (Cambridge, Mass.)

Authors' code: supp:PMC11104383/cpsy-7-1-94-s1.zip (no license)

Status: code verified, 5 files readable, 6 matches

Sunday, 27 August 2023 (5 papers)

[33967] doi:10.1007/s10548-023-01000-8 [paper, repository]

Two-Dimensional Population Receptive Field Mapping of Human Primary Somatosensory Cortex.

Journal: Brain topography

Authors' code: vistalab/vistasoft (no license), ppxma7/pRF_somato_data (no license), Zenodo 1299483 (other-open), justingardner/mrtools (other)

Status: code verified, 3,299 files readable, 10 matches

[33968] doi:10.1111/jcmm.17927 [paper, data]

Identification of T-cell exhaustion-related gene signature for predicting prognosis in glioblastoma multiforme.

Journal: Journal of cellular and molecular medicine

Status: data only, 1 dataset cited

[33969] doi:10.1186/s12974-023-02872-0 [paper, repository]

Cortical superficial siderosis is associated with reactive astrogliosis in cerebral amyloid angiopathy.

Journal: Journal of neuroinflammation

Authors' code: CorinneAuger/cSS-reactive-astrogliosis (no license)

Status: code verified, 64 files readable, 2 matches

[33970] doi:10.1186/s13578-023-01106-3 [paper, data]

Repetitive and compulsive behavior after Early-Life-Pain associated with reduced long-chain sphingolipid species.

Journal: Cell & bioscience

Status: data only, 3 datasets cited

[33971] doi:10.3390/diagnostics13172774 [paper, repository]

A Brain Morphometry Study with Across-Site Harmonization Using a ComBat-Generalized Additive Model in Children and Adolescents.

Journal: Diagnostics (Basel, Switzerland)

Authors' code: rpomponio/neuroHarmonize (MIT)

Status: code verified, 12 files readable, 1 match

Saturday, 26 August 2023 (9 papers)

[33972] doi:10.1016/j.celrep.2023.113026 [paper]

Structure-function analysis of ceTIR-1/hSARM1 explains the lack of Wallerian axonal degeneration in C. elegans.

Journal: Cell reports

Status: code on request

[33973] doi:10.1016/j.celrep.2023.113031 [paper, data]

A comparative analysis of microglial inducible Cre lines.

Journal: Cell reports

Status: data only, 1 dataset cited

[33974] doi:10.1016/j.isci.2023.107738 [paper]

LAT1 (SLC7A5) catalyzes copper(histidinate) transport switching from antiport to uniport mechanism.

Journal: iScience

Status: code on request

[33975] doi:10.1016/j.isci.2023.107750 [paper, repository]

Brain signatures indexing variation in internal processing during perceptual decision-making.

Journal: iScience

Authors' code: OSF ad7zu (no license)

Status: code verified, 13 files readable, 4 matches

[33976] doi:10.1038/s41598-023-40766-6 [paper, repository]

Neuronal diversity can improve machine learning for physics and beyond.

Journal: Scientific reports

Authors' code: nonlinearartificialintelligencelab/diversityNN (no license)

Status: code verified, 15 files readable

[33977] doi:10.1177/0271678x231196989 [paper, repository]

Hemodynamic imaging parameters in brain metastases patients - Agreement between multi-delay ASL and hypercapnic BOLD.

Journal: Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism

Authors' code: JSIERO/ClinicalASL (BSD-3-Clause), Zenodo 6532362 (other-open), abhogal-lab/seevr (GPL-3.0)

Status: code verified, 471 files readable, 14 matches

[33978] doi:10.1177/0271678x231197273 [paper, data]

Progressive reduction in basal ganglia explains and predicts cerebral structural alteration in type 2 diabetes.

Journal: Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism

Status: data only, 6 datasets cited

[33979] doi:10.1186/s12916-023-03023-1 [paper, repository]

Identification and prediction model of placenta-brain axis genes associated with neurodevelopmental delay in moderate and late preterm children.

Journal: BMC medicine

Authors' code: OpenGene/fastp (MIT)

Status: code verified, 68 files readable

[33980] doi:10.3390/s23177440 [paper, repository]

Introducing a New Mobile Electroencephalography System and Evaluating Its Quality in Comparison to Clinical Electroencephalography.

Journal: Sensors (Basel, Switzerland)

Authors' code: neuroinfo-os/dream-machine-eeg (GPL-3.0)

Status: code verified, 2 files readable

Friday, 25 August 2023 (22 papers)

[33981] doi:10.1016/j.bpsgos.2023.08.009 [paper, repository]

Excessive Checking in Obsessive-Compulsive Disorder: Neurochemical Correlates Revealed by 7T Magnetic Resonance Spectroscopy.

Journal: Biological psychiatry global open science

Authors' code: carbocation/falsediscovery (no license)

Status: code verified, 6 files readable

[33982] doi:10.1016/j.isci.2023.107710 [paper]

Role of caveolin-1 in metabolic programming of fetal brain.

Journal: iScience

Status: code on request

[33983] doi:10.1016/j.isci.2023.107715 [paper]

Active shrinkage protects neurons following axonal transection.

Journal: iScience

Status: code on request

[33984] doi:10.1016/j.isci.2023.107716 [paper]

Highly sensitive visual restoration and protection via ectopic expression of chimeric rhodopsin in mice.

Journal: iScience

Status: code on request

[33985] doi:10.1016/j.isci.2023.107718 [paper]

Prelimbic area to lateral hypothalamus circuit drives social aggression.

Journal: iScience

Status: code on request

[33986] doi:10.1016/j.isci.2023.107720 [paper, data]

Playing with your ears: Audio-motor skill learning is sensitive to the lateral relationship between trained hand and ear.

Journal: iScience

Status: code on request, 1 dataset cited

[33987] doi:10.1016/j.xpro.2023.102529 [paper]

Analysis of autophagy deficiency and cytotoxicity in autophagy-deficient human embryonic stem cell-derived neurons.

Journal: STAR protocols

Status: code on request

[33988] doi:10.1017/neu.2023.44 [paper, repository]

Structural impairment in superficial and deep white matter in schizophrenia.

Journal: Acta neuropsychiatrica

Authors' code: pnlbwh/dMRIharmonization (other)

Status: code verified, 36 files readable, 1 match

[33989] doi:10.1038/s41366-023-01370-w [paper, repository]

A randomized controlled trial investigating the effect of liraglutide on self-reported liking and neural responses to food stimuli in participants with obesity.

Journal: International journal of obesity (2005)

Authors' code: munoztd0/mouthpiecegusto (GPL-3.0), evapool/GLP1_Pleasure (no license)

Status: code verified, 63 files readable, 5 matches

[33990] doi:10.1038/s41467-023-40512-6 [paper, repository]

Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging.

Journal: Nature communications

Authors' code: lingjunli-research/Automatic-MSI-Spectra-Extraction (MIT)

Status: code verified, 3 files readable, 1 match

[33991] doi:10.1038/s41467-023-40744-6 [paper, repository]

Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection.

Journal: Nature communications

Authors' code: Shians/CellBench (GPL-3.0), broadinstitute/Tangram (BSD-3-Clause), RubD/Giotto (MIT), tabdelaal/spage (MIT), quon-titative-biology/scProjection (MIT), Zenodo 8173396 (other-open)

Status: code verified, 228 files readable, 5 matches

[33992] doi:10.1038/s41467-023-40927-1 [paper, data]

Microglial REV-ERBα regulates inflammation and lipid droplet formation to drive tauopathy in male mice.

Journal: Nature communications

Status: data only, 3 datasets cited

[33993] doi:10.1038/s41467-023-40985-5 [paper, repository]

A frontal transcallosal inhibition loop mediates interhemispheric balance in visuospatial processing.

Journal: Nature communications

Authors' code: zhoupc/CNMF_E (GPL-3.0)

Status: code verified, 266 files readable

[33994] doi:10.1038/s42003-023-05231-0 [paper, repository]

Role of interneuron subtypes in controlling trial-by-trial output variability in the neocortex.

Journal: Communications biology

Authors' code: michaelglh/MotifNet (no license)

Status: code verified, 18 files readable

[33995] doi:10.1093/braincomms/fcad229 [paper, data]

Pathway-specific polygenic scores for Alzheimer's disease are associated with changes in brain structure in younger and older adults.

Journal: Brain communications

Status: data only, 1 dataset cited

[33996] doi:10.1126/sciadv.ade1755 [paper, repository]

Modular architecture facilitates noise-driven control of synchrony in neuronal networks.

Journal: Science advances

Authors' code: Zenodo 7962283 (other-open), Priesemann-Group/stimulating_modular_cultures (no license)

Status: code verified, 56 files readable, 7 matches

[33997] doi:10.1152/ajpheart.00362.2023 [paper, repository]

Dual effects of the small-conductance Ca²⁺-activated K⁺ current on human atrial electrophysiology and Ca²⁺-driven arrhythmogenesis: an in silico study.

Journal: American journal of physiology. Heart and circulatory physiology

Authors' code: elegrandi.wixsite.com/grandilab/downloads (no license), drgrandilab (no license)

Status: code verified

[33998] doi:10.1186/s13244-023-01487-6 [paper]

An active learning approach to train a deep learning algorithm for tumor segmentation from brain MR images.

Journal: Insights into imaging

Status: code on request

[33999] doi:10.1371/journal.pcbi.1011139 [paper, repository]

Rapid memory encoding in a recurrent network model with behavioral time scale synaptic plasticity.

Journal: PLoS computational biology

Authors' code: PanYe87/BTSP-Based-Learning (MIT)

Status: code verified, 29 files readable, 4 matches

[34000] doi:10.1523/eneuro.0134-23.2023 [paper, repository]

Rapid Audiovisual Integration Guides Predictive Actions.

Journal: eNeuro

Authors' code: mike-lawrence/ez (no license)

Status: code verified, 15 files readable

[34001] doi:10.3389/fcimb.2023.1215205 [paper, data]

Hydrogel-based 3D human iPSC-derived neuronal culture for the study of rabies virus infection.

Journal: Frontiers in cellular and infection microbiology

Status: data only, 1 dataset cited

[34002] doi:10.3389/fnins.2023.1133086 [paper, repository]

Fiber-orientation independent component of R₂* obtained from single-orientation MRI measurements in simulations and a post-mortem human optic chiasm.

Journal: Frontiers in neuroscience

Authors' code: quantitative-mri-and-in-vivo-histology/r2s_iso_estimation (MIT)

Status: code verified, 15 files readable, 8 matches

Thursday, 24 August 2023 (36 papers)

[34003] doi:10.1002/hbm.26461 [paper, repository]

Mapping the macrostructure and microstructure of the in vivo human hippocampus using diffusion MRI.

Journal: Human brain mapping

Authors' code: khanlab/hippunfold (MIT), Bradley-Karat/Hippo_Macro_Micro (no license), Zenodo 7837990 (other-open), bradley-karat/hippo_spin_testing (no license)

Status: code verified, 86 files readable, 4 matches

[34004] doi:10.1002/hbm.26464 [paper, data]

Lifespan neurodegeneration of the human brain in multiple sclerosis.

Journal: Human brain mapping

Status: data only, 3 datasets cited

[34005] doi:10.1002/hbm.26470 [paper]

Distributed attribute representation in the superior parietal lobe during probabilistic decision-making.

Journal: Human brain mapping

Status: code on request

[34006] doi:10.1007/s00330-023-10078-4 [paper, data]

Automated, fast, robust brain extraction on contrast-enhanced T1-weighted MRI in presence of brain tumors: an optimized model based on multi-center datasets.

Journal: European radiology

Status: data only, 1 dataset cited

[34007] doi:10.1007/s00429-023-02692-1 [paper, repository]

Altered corpus callosum structure in adolescents with cerebral palsy: connection to gait and balance.

Journal: Brain structure & function

Authors' code: tjrantal/javaMSE (GPL)

Status: code verified, 14 files readable

[34008] doi:10.1016/j.celrep.2023.113037 [paper, repository]

Single-nucleus RNA sequencing of developing superior colliculus identifies neuronal diversity and candidate mediators of circuit assembly.

Journal: Cell reports

Authors' code: ParkLabMiami/snRNAseq-developing-superior-colliculus (no license), Zenodo 8061024 (CC-BY-4.0)

Status: code verified, 10 files readable, 23 matches

[34009] doi:10.1038/s41420-023-01612-w [paper, data]

Targeting ANXA7/LAMP5-mTOR axis attenuates spinal cord injury by inhibiting neuronal apoptosis via enhancing autophagy in mice.

Journal: Cell death discovery

Status: data only, 1 dataset cited

[34010] doi:10.1038/s41467-023-40816-7 [paper, repository]

Circadian clock regulator Bmal1 gates axon regeneration via Tet3 epigenetics in mouse sensory neurons.

Journal: Nature communications

Authors' code: shenlab-sinai/NGS-Data-Charmer (no license)

Status: code verified, 6 files readable

[34011] doi:10.1038/s41467-023-40861-2 [paper, data]

Human forebrain organoid-based multi-omics analyses of PCCB as a schizophrenia associated gene linked to GABAergic pathways.

Journal: Nature communications

Status: data only, 1 dataset cited

[34012] doi:10.1038/s41598-023-37508-z [paper, repository]

Accurate sex prediction of cisgender and transgender individuals without brain size bias.

Journal: Scientific reports

Authors' code: juaml/sex_prediction_vbm (no license)

Status: code verified, 73 files readable, 9 matches

[34013] doi:10.1038/s41598-023-40324-0 [paper, repository]

Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally.

Journal: Scientific reports

Authors' code: RHReynolds/RNAseqProcessing (no license)

Status: code verified, 17 files readable, 5 matches

[34014] doi:10.1038/s41598-023-40683-8 [paper, repository]

Cross-species comparative analysis of single presynapses.

Journal: Scientific reports

Authors' code: tpjoe/SynTOF2021 (no license), elo-nsrb/SynTOF_Cross-species_analysis (no license), Zenodo 5606203 (MIT)

Status: code verified, 51 files readable, 5 matches

[34015] doi:10.1038/s41598-023-40896-x [paper]

Transport pathways and kinetics of cerebrospinal fluid tracers in mouse brain observed by dynamic contrast-enhanced MRI.

Journal: Scientific reports

Status: code on request

[34016] doi:10.1038/s42003-023-05199-x [paper, repository]

Dynamic expectations: Behavioral and electrophysiological evidence of sub-second updates in reward predictions.

Journal: Communications biology

Authors' code: Zenodo 8048382 (CC-BY-4.0)

Status: code verified, 13 files readable, 2 matches

[34017] doi:10.1085/jgp.202213263 [paper, data]

Mitochondrial morphology governs ATP production rate.

Journal: The Journal of general physiology

Status: data only, 1 dataset cited

[34018] doi:10.1093/braincomms/fcad224 [paper, repository]

Elevated representational similarity of voluntary action and inhibition in Tourette syndrome.

Journal: Brain communications

Authors' code: OSF 94ybj (no license), marsbar-toolbox.github.io/index.html (no license), OSF 6yknx (no license), brainder.org/2011/09 (no license)

Status: code verified, 5 files readable

[34019] doi:10.1113/jp284503 [paper]

Two motor neuron synergies, invariant across ankle joint angles, activate the triceps surae during plantarflexion.

Journal: The Journal of physiology

Status: code on request

[34020] doi:10.1186/s12859-023-05444-4 [paper, repository]

Sensitivity of CNN image analysis to multifaceted measurements of neurite growth.

Journal: BMC bioinformatics

Authors' code: Mullans/NeuriteNet (Apache-2.0)

Status: code verified, 16 files readable, 11 matches

[34021] doi:10.1186/s12993-023-00215-w [paper]

Enhancement of dynamic visual acuity using transcranial alternating current stimulation with gamma burst entrained on alpha wave troughs.

Journal: Behavioral and brain functions : BBF

Status: code on request

[34022] doi:10.1242/dev.201651 [paper, data]

Neurogenesis redirects β-catenin from adherens junctions to the nucleus to promote axonal growth.

Journal: Development (Cambridge, England)

Status: data only, 2 datasets cited

[34023] doi:10.1371/journal.pbio.3002257 [paper, data]

Phytosterols reverse antiretroviral-induced hearing loss, with potential implications for cochlear aging.

Journal: PLoS biology

Status: data only, 1 dataset cited

[34024] doi:10.1371/journal.pone.0285683 [paper, repository]

Segmenting white matter hyperintensities on isotropic three-dimensional Fluid Attenuated Inversion Recovery magnetic resonance images: Assessing deep learning tools on a Norwegian imaging database.

Journal: PloS one

Authors' code: MartinRovang/WMH_segmentation (no license)

Status: code verified, 70 files readable, 4 matches

[34025] doi:10.1371/journal.pone.0289956 [paper, data]

Temporal characterization of hyaluronidases after peripheral nerve injury.

Journal: PloS one

Status: data only, 1 dataset cited

[34026] doi:10.1371/journal.pone.0290446 [paper, repository]

BCI-Walls: A robust methodology to predict if conscious EEG changes can be detected in the presence of artefacts.

Journal: PloS one

Authors' code: researchdata.gla.ac.uk/1258 (no license), Zenodo 7852162 (GPL-2.0), berndporr/bci_wall_analysis (GPL-3.0)

Status: code verified, 20 files readable, 3 matches

[34027] doi:10.1523/jneurosci.0625-23.2023 [paper, repository]

Multimodal Imaging for Validation and Optimization of Ion Channel-Based Chemogenetics in Nonhuman Primates.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Authors' code: minamimoto-lab/2023-Hori-PSAMPSEM (no license)

Status: code verified, 8 files readable

[34028] doi:10.3389/fendo.2023.1241019 [paper, data]

Unraveling the periprandial changes in brain serotonergic activity and its correlation with food intake-related neuropeptides in rainbow trout <i>Oncorhynchus mykiss</i>.

Journal: Frontiers in endocrinology

Status: data only, 1 dataset cited

[34029] doi:10.3389/fgene.2023.1218408 [paper]

Pan-glioma analyses reveal species- and tumor-specific regulation of neuron-glioma synapse genes by lncRNAs.

Journal: Frontiers in genetics

Status: data only

[34030] doi:10.3389/fnbeh.2023.1239463 [paper, repository]

Transcranial direct current stimulation (tDCS) over the orbitofrontal cortex reduces delay discounting.

Journal: Frontiers in behavioral neuroscience

Authors' code: andypotatohy/roast (GPL-3.0)

Status: code verified, 2,000 files readable

[34031] doi:10.3389/fncom.2023.1215824 [paper, repository]

Exploring spiking neural networks: a comprehensive analysis of mathematical models and applications.

Journal: Frontiers in computational neuroscience

Authors' code: Rao-Sanaullah/A-Comprehensive-Analysis-of-Mathematical-Models-and-Applications (MIT)

Status: code verified, 42 files readable, 12 matches

[34032] doi:10.3389/fnins.2023.1233416 [paper, data]

The PyMVPA BIDS-App: a robust multivariate pattern analysis pipeline for fMRI data.

Journal: Frontiers in neuroscience

Status: data only, 3 datasets cited

[34033] doi:10.3389/fnrgo.2023.1216440 [paper, data]

AMBER: advancing multimodal brain-computer interfaces for enhanced robustness-A dataset for naturalistic settings.

Journal: Frontiers in neuroergonomics

Status: data only, 1 dataset cited

[34034] doi:10.3389/fpsyt.2023.1247714 [paper, data]

MicroRNA expression profiles of stress susceptibility and resilience in the prelimbic and infralimbic cortex of rats after single prolonged stress.

Journal: Frontiers in psychiatry

Status: data only, 1 dataset cited

[34035] doi:10.3390/biom13091298 [paper]

TRIM6: An Upregulated Biomarker with Prognostic Significance and Immune Correlations in Gliomas.

Journal: Biomolecules

Status: data only

[34036] doi:10.3390/biomedicines11092370 [paper, repository]

Automatic Detection and Classification of Epileptic Seizures from EEG Data: Finding Optimal Acquisition Settings and Testing Interpretable Machine Learning Approach.

Journal: Biomedicines

Authors' code: bi-dac.com (no license)

Status: code found, still to be checked

[34037] doi:10.7554/elife.83187 [paper, repository]

Inferential eye movement control while following dynamic gaze.

Journal: eLife

Authors' code: OSF g9bzt (no license)

Status: code verified, 4 files readable, 1 match

[34038] doi:10.7717/peerj-cs.1490 [paper, repository]

Classification of Alzheimer's disease stages from magnetic resonance images using deep learning.

Journal: PeerJ. Computer science

Authors' code: MoraRubio/alzheimer-stages-dl (GPL-3.0)

Status: code verified, 5 files readable, 2 matches

Wednesday, 23 August 2023 (23 papers, 10 on this page)

[34039] doi:10.1016/j.heliyon.2023.e19096 [paper, data]

Evaluating circulating soluble markers of endothelial dysfunction and risk factors associated with PE: A multicentre longitudinal case control study in northern Ghana.

Journal: Heliyon

Status: data only, 1 dataset cited

[34040] doi:10.1016/j.isci.2023.107453 [paper]

Melodic intonation therapy for non-fluent aphasia after stroke: A clinical pilot study on behavioral and DTI findings.

Journal: iScience

Status: code on request

[34041] doi:10.1038/s41586-023-06377-x [paper, repository]

A high-performance speech neuroprosthesis.

Journal: Nature

Authors' code: fwillett/speechBCI (no license)

Status: code verified, 799 files readable

[34042] doi:10.1038/s41597-023-02437-z [paper, repository]

A natural language fMRI dataset for voxelwise encoding models.

Journal: Scientific data

Authors' code: alexhuth/sensimetrics_filter (MIT), Zenodo 8208839 (MIT), huthlab/deep-fmri-dataset (MIT)

Status: code verified, 23 files readable, 9 matches

[34043] doi:10.1038/s41597-023-02458-8 [paper, repository]

An open-access dataset of naturalistic viewing using simultaneous EEG-fMRI.

Journal: Scientific data

Authors' code: NathanKlineInstitute/NATVIEW_EEGFMRI (CC-BY-SA-4.0), Zenodo 4623809 (CC-BY-4.0)

Status: code verified, 20 files readable, 9 matches

[34044] doi:10.1038/s41597-023-02471-x [paper, repository]

A large-scale fMRI dataset for the visual processing of naturalistic scenes.

Journal: Scientific data

Authors' code: BNUCNL/NOD-fmri (MIT), edickie/ciftify (MIT)

Status: code verified, 85 files readable, 16 matches

[34045] doi:10.1038/s41598-023-40278-3 [paper, repository]

Neural superstatistics for Bayesian estimation of dynamic cognitive models.

Journal: Scientific reports

Authors' code: bayesflow-org/Neural-Superstatistics (MIT)

Status: code verified, 45 files readable, 17 matches

[34046] doi:10.1038/s41598-023-40879-y [paper, data]

miRNA profiling as a complementary diagnostic tool for amyotrophic lateral sclerosis.

Journal: Scientific reports

Status: data only, 1 dataset cited

[34047] doi:10.1038/s41746-023-00904-w [paper, repository]

Explainable deep learning approach for extracting cognitive features from hand-drawn images of intersecting pentagons.

Journal: NPJ digital medicine

Authors' code: stasaki/PentaMind (BSD-3-Clause)

Status: code verified, 9 files readable, 4 matches

[34048] doi:10.1088/1361-6560/ace306 [paper, repository]

A minimum assumption approach to MEG sensor array design.

Journal: Physics in medicine and biology

Authors' code: andreyzhd/MEGSim (GPL-3.0)

Status: code verified, 31 files readable, 6 matches

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