Every paper, by date: page 147

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 147 of 200: 24 October 2023 to 12 October 2023.

Tuesday, 24 October 2023 (16 papers, 2 on this page)

[32705] doi:10.3390/diagnostics13213292 [paper, repository]

Reinforcement-Learning-Based Localization of Hippocampus for Alzheimer's Disease Detection.

Journal: Diagnostics (Basel, Switzerland)

Authors' code: AR13ar/DQN_based_Localization (Apache-2.0)

Status: code verified, 9 files readable, 3 matches

[32706] doi:10.7717/peerj-cs.1599 [paper, repository]

Residual block fully connected DCNN with categorical generalized focal dice loss and its application to Alzheimer's disease severity detection.

Journal: PeerJ. Computer science

Authors' code: supp:PMC10702977/peerj-cs-09-1599-s001.m (no license)

Status: code verified, 1 file readable

Monday, 23 October 2023 (31 papers)

[32707] doi:10.1002/advs.202302333 [paper, repository]

An Ultraflexible Electrode Array for Large-Scale Chronic Recording in the Nonhuman Primate Brain.

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Authors' code: magland/ml_ms4alg (no license)

Status: code verified, 19 files readable, 2 matches

[32708] doi:10.1002/brb3.3212 [paper, data]

Persistent post-COVID headache is associated with suppression of scale-free functional brain dynamics in non-hospitalized individuals.

Journal: Brain and behavior

Status: data only, 1 dataset cited

[32709] doi:10.1007/s00213-023-06479-4 [paper]

Effects of a dissociative drug on fronto-limbic resting-state functional connectivity in individuals with posttraumatic stress disorder: a randomized controlled pilot study.

Journal: Psychopharmacology

Status: code on request

[32710] doi:10.1016/j.cub.2023.09.074 [paper]

Noradrenaline tracks emotional modulation of attention in human amygdala.

Journal: Current biology : CB

Status: code on request

[32711] doi:10.1016/j.dcn.2023.101319 [paper, repository]

Component-specific developmental trajectories of ERP indices of cognitive control in early childhood.

Journal: Developmental cognitive neuroscience

Authors' code: OSF ngmf8 (no license)

Status: code verified, 17 files readable, 7 matches

[32712] doi:10.1016/j.isci.2023.108306 [paper]

Preclinical long-term safety of intraspinal transplantation of human dorsal spinal GABA neural progenitor cells.

Journal: iScience

Status: code on request

[32713] doi:10.1016/j.isci.2023.108307 [paper]

Psychophysical measurement of perceived motion flow of naturalistic scenes.

Journal: iScience

Status: code on request

[32714] doi:10.1016/j.isci.2023.108321 [paper, data]

Mitochondrial metabolism in blood more reliably predicts whole-animal energy needs compared to other tissues.

Journal: iScience

Status: code on request, 2 datasets cited

[32715] doi:10.1016/j.mcpdig.2023.08.009 [paper, repository]

Hemorrhage Evaluation and Detector System for Underserved Populations: HEADS-UP.

Journal: Mayo Clinic proceedings. Digital health

Authors' code: quincy-125/MG-HEADSUP (Apache-2.0)

Status: code verified, 10 files readable

[32716] doi:10.1038/s41467-023-41839-w [paper, repository]

Domain adapted brain network fusion captures variance related to pubertal brain development and mental health.

Journal: Nature communications

Authors' code: dominikkraft/DomAdapt_BrainNetFusion (BSD-3-Clause), Zenodo 8223987 (other-open)

Status: code verified, 22 files readable, 11 matches

[32717] doi:10.1038/s41467-023-42288-1 [paper, repository]

A non-canonical striatopallidal Go pathway that supports motor control.

Journal: Nature communications

Authors' code: figshare 23609595 (CC-BY-4.0)

Status: code verified, 32 files readable, 7 matches

[32718] doi:10.1038/s41467-023-42372-6 [paper, data]

Synapsin condensation controls synaptic vesicle sequestering and dynamics.

Journal: Nature communications

Status: data only, 1 dataset cited

[32719] doi:10.1038/s41598-023-44676-5 [paper]

Superior performance of biofilm versus planktonic Limosilactobacillus reuteri in protection of the intestines and brain in a piglet model of necrotizing enterocolitis.

Journal: Scientific reports

Status: data only

[32720] doi:10.1038/s41598-023-44723-1 [paper, repository]

Attentive pairwise interaction network for AI-assisted clock drawing test assessment of early visuospatial deficits.

Journal: Scientific reports

Authors' code: cccnlab/CDT-API-Network (no license)

Status: code verified, 4 files readable

[32721] doi:10.1038/s41598-023-44891-0 [paper, repository]

Reproducibility of APT-weighted CEST-MRI at 3T in healthy brain and tumor across sessions and scanners.

Journal: Scientific reports

Authors' code: NeuroAI-HD/HD-GLIO (Apache-2.0)

Status: code verified, 9 files readable

[32722] doi:10.1038/s41598-023-45493-6 [paper, repository]

Temporal dynamics of statistical learning in children's song contributes to phase entrainment and production of novel information in multiple cultures.

Journal: Scientific reports

Authors' code: OSF cqmz8 (no license)

Status: code verified, 12 files readable

[32723] doi:10.1038/s42003-023-05440-7 [paper, repository]

Human brain responses are modulated when exposed to optimized natural images or synthetically generated images.

Journal: Communications biology

Authors' code: zijin-gu/NeuroGen (no license), zijin-gu/neural-modulation (no license)

Status: code verified, 25 files readable, 9 matches

[32724] doi:10.1038/s42003-023-05448-z [paper, repository]

A data-driven network decomposition of the temporal, spatial, and spectral dynamics underpinning visual-verbal working memory processes.

Journal: Communications biology

Authors' code: OHBA-analysis/Quinn2018_TaskHMM (MIT)

Status: code verified, 21 files readable, 10 matches

[32725] doi:10.1073/pnas.2310344120 [paper, data]

Activity-induced MeCP2 phosphorylation regulates retinogeniculate synapse refinement.

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

Status: data only, 1 dataset cited

[32726] doi:10.1073/pnas.2313175120 [paper, repository]

Neural signals predict information sharing across cultures.

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

Authors' code: OSF caxfq (no license)

Status: code verified, 4 files readable

[32727] doi:10.1111/jcmm.18001 [paper, repository]

Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1^S858R Schinzel Giedion Syndrome mice.

Journal: Journal of cellular and molecular medicine

Authors' code: Zenodo 8192482 (MIT), ncbi.nlm.nih.gov/geo/query (no license), lasseignelab/230227_JW_Setbp1Manuscript (MIT), Zenodo 8190948 (other-open)

Status: code verified, 112 files readable, 18 matches

[32728] doi:10.1172/jci.insight.172008 [paper, repository]

Locus coeruleus activity while awake is associated with REM sleep quality in older individuals.

Journal: JCI insight

Authors' code: gitlab.uliege.be/cyclotronresearchcentre/public/fasst/lc_oddball_vs_sleep_eeg (no license)

Status: empty repository, 1 file readable

[32729] doi:10.1242/dmm.050200 [paper, data]

Mutation in the FUS nuclear localisation signal domain causes neurodevelopmental and systemic metabolic alterations.

Journal: Disease models & mechanisms

Status: data only, 1 dataset cited

[32730] doi:10.1523/jneurosci.0995-23.2023 [paper, repository]

Rapid Processing of Observed Touch through Social Perceptual Brain Regions: An EEG-fMRI Fusion Study.

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

Authors' code: dianadima/mot_action (no license), haemyleemasson/EEG_experiment (no license)

Status: code verified, 98 files readable, 13 matches

[32731] doi:10.15252/embr.202357176 [paper, data]

Role and mechanism of PVN-sympathetic-adipose circuit in depression and insulin resistance induced by chronic stress.

Journal: EMBO reports

Status: data only, 1 dataset cited

[32732] doi:10.3389/fcell.2023.1147625 [paper, data]

PRELP secreted from mural cells protects the function of blood brain barrier through regulation of endothelial cell-cell integrity.

Journal: Frontiers in cell and developmental biology

Status: data only, 1 dataset cited

[32733] doi:10.3389/fmolb.2023.1250335 [paper, repository]

Primary cilia-mediated regulation of microglial secretion in Alzheimer's disease.

Journal: Frontiers in molecular biosciences

Authors' code: indrops/indrops (no license), choelab/Fronties-in-molecular-bioscience-2023 (no license)

Status: code verified, 17 files readable, 13 matches

[32734] doi:10.3389/fpsyt.2023.1293663 [paper, repository]

The pleiotropic contribution of genes in dopaminergic and serotonergic pathways to addiction and related behavioral traits.

Journal: Frontiers in psychiatry

Authors' code: bulik/ldsc (GPL-3.0)

Status: code verified, 27 files readable, 2 matches

[32735] doi:10.3390/biom13101562 [paper, data]

Untargeted Lipidomic Approach for Studying Different Nervous System Tissues of the Murine Model of Krabbe Disease.

Journal: Biomolecules

Status: data only, 2 datasets cited

[32736] doi:10.3390/s23208654 [paper, repository]

GPU Implementation of the Improved CEEMDAN Algorithm for Fast and Efficient EEG Time-Frequency Analysis.

Journal: Sensors (Basel, Switzerland)

Authors' code: EEGLab-Pannon (no license), EEGLab-Pannon/CEEMDAN-GPU (MIT)

Status: code verified, 10 files readable, 2 matches

[32737] doi:10.7554/elife.84596 [paper, data]

Transcriptional control of motor pool formation and motor circuit connectivity by the LIM-HD protein Isl2.

Journal: eLife

Status: data only, 1 dataset cited

Sunday, 22 October 2023 (1 paper)

[32738] doi:10.3390/ijms242015454 [paper, data]

Activation of the TNF-α-Necroptosis Pathway in Parvalbumin-Expressing Interneurons of the Anterior Cingulate Cortex Contributes to Neuropathic Pain.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Saturday, 21 October 2023 (10 papers)

[32739] doi:10.1002/cam4.6627 [paper]

Warburg effect-related risk scoring model to assess clinical significance and immunity characteristics of glioblastoma.

Journal: Cancer medicine

Status: data only

[32740] doi:10.1007/s12021-023-09644-4 [paper, repository]

Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space.

Journal: Neuroinformatics

Authors' code: ntimonid/Population_Integrator (MIT)

Status: code verified, 22 files readable, 7 matches

[32741] doi:10.1016/j.isci.2023.108241 [paper, repository]

Astrocyte's self-repairing characteristics improve working memory in spiking neuronal networks.

Journal: iScience

Authors' code: Research-lab-KUMS/working-memory-with-self-repairing (MIT)

Status: code verified, 23 files readable, 4 matches

[32742] doi:10.1016/j.jlr.2023.100463 [paper, data]

Sialidase NEU3 action on GM1 ganglioside is neuroprotective in GM1 gangliosidosis.

Journal: Journal of lipid research

Status: data only, 1 dataset cited

[32743] doi:10.1038/s41467-023-42441-w [paper, repository]

Continuous multiplexed population representations of task context in the mouse primary visual cortex.

Journal: Nature communications

Authors' code: golshanilab/AttentionTask (no license), CSNLWigner/mouse-v1-context (no license), CSNLWigner/mouse-v1-context-movement (no license)

Status: code verified, 51 files readable, 23 matches

[32744] doi:10.1038/s41467-023-42505-x [paper, data]

Soluble TREM2 ameliorates tau phosphorylation and cognitive deficits through activating transgelin-2 in Alzheimer's disease.

Journal: Nature communications

Status: data only, 2 datasets cited

[32745] doi:10.1038/s41525-023-00376-7 [paper, repository]

Rare predicted loss of function alleles in Bassoon (BSN) are associated with obesity.

Journal: NPJ genomic medicine

Authors' code: rgcgithub.github.io/regenie (no license)

Status: code verified

[32746] doi:10.1038/s41531-023-00591-0 [paper, repository]

Expanding causal genes for Parkinson's disease via multi-omics analysis.

Journal: NPJ Parkinson's disease

Authors' code: bogdanlab/focus (GPL-3.0)

Status: code verified, 17 files readable, 1 match

[32747] doi:10.1038/s41598-023-45420-9 [paper, data]

A novel non-invasive efficient photography-based technique for length measuring and individual identification of seahorses.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32748] doi:10.3390/s23208621 [paper, repository]

Accelerometric Classification of Resting and Postural Tremor Amplitude.

Journal: Sensors (Basel, Switzerland)

Authors' code: OSF mp5ha (no license)

Status: code verified, 11 files readable

Friday, 20 October 2023 (27 papers)

[32749] doi:10.1007/s10618-023-00979-9 [paper, repository]

Somtimes: self organizing maps for time series clustering and its application to serious illness conversations.

Journal: Data mining and knowledge discovery

Authors' code: pypi.org/project/somtimes (no license), ali-javed/somtimes (MIT)

Status: code verified, 8 files readable, 2 matches

[32750] doi:10.1016/j.crneur.2023.100113 [paper, repository]

Apnea of prematurity induces short and long-term development-related transcriptional changes in the murine cerebellum.

Journal: Current research in neurobiology

Authors' code: ma-riviere/DE-AoP-23 (CC-BY-4.0), Zenodo 8139284 (CC-BY-4.0)

Status: code verified, 32 files readable, 1 match

[32751] doi:10.1016/j.dib.2023.109708 [paper, data]

Large-scale annotation dataset for fetal head biometry in ultrasound images.

Journal: Data in brief

Status: data only, 3 datasets cited

[32752] doi:10.1016/j.isci.2023.108270 [paper]

Fucoxanthin ameliorates traumatic brain injury by suppressing the blood-brain barrier disruption.

Journal: iScience

Status: code on request

[32753] doi:10.1016/j.jbc.2023.105371 [paper, data]

Using CRISPR-Cas9/phosphoproteomics to identify substrates of calcium/calmodulin-dependent kinase 2δ.

Journal: The Journal of biological chemistry

Status: data only, 1 dataset cited

[32754] doi:10.1016/j.xpro.2023.102478 [paper, repository]

Mapping Kenyon cell inputs in Drosophila using dye electroporation.

Journal: STAR protocols

Authors' code: ishanigan/hayashi-et-al-2022 (no license)

Status: code verified, 7 files readable

[32755] doi:10.1038/s41467-023-42203-8 [paper, data]

American crows that excel at tool use activate neural circuits distinct from less talented individuals.

Journal: Nature communications

Status: data only, 1 dataset cited

[32756] doi:10.1038/s41467-023-42231-4 [paper]

Dynamic neural representations of memory and space during human ambulatory navigation.

Journal: Nature communications

Status: code on request

[32757] doi:10.1038/s41467-023-42371-7 [paper, repository]

Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups.

Journal: Nature communications

Authors' code: bioinfo-pf-curie/RNA-seq (CECILL-2.1), bourdeautlab/LobonIglesias2023 (no license)

Status: code verified, 50 files readable, 22 matches

[32758] doi:10.1038/s41598-023-43264-x [paper, data]

Excitatory stimulation of the ventromedial prefrontal cortex reduces cognitive gambling biases via improved feedback learning.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32759] doi:10.1093/evlett/qrad049 [paper, repository]

Heritable variation in thermal profiles is associated with reproductive success in the world's largest bird.

Journal: Evolution letters

Authors' code: abumadsen/thermal-images-ostrich (no license)

Status: code verified, 2 files readable

[32760] doi:10.1109/access.2023.3326412 [paper, repository]

Non-Stationary Dynamic Mode Decomposition.

Journal: IEEE access : practical innovations, open solutions

Authors' code: learning-2-learn/nsdmd (no license)

Status: code verified, 20 files readable, 3 matches

[32761] doi:10.1126/sciadv.adh8313 [paper, data]

Tunable hydrogel viscoelasticity modulates human neural maturation.

Journal: Science advances

Status: data only, 1 dataset cited

[32762] doi:10.1186/s12915-023-01730-y [paper, data]

The BAF chromatin remodeling complex licenses planarian stem cells access to ectodermal and mesodermal cell fates.

Journal: BMC biology

Status: data only, 7 datasets cited

[32763] doi:10.1186/s40478-023-01656-0 [paper, data]

Modelling TDP-43 proteinopathy in Drosophila uncovers shared and neuron-specific targets across ALS and FTD relevant circuits.

Journal: Acta neuropathologica communications

Status: data only, 1 dataset cited

[32764] doi:10.1186/s40658-023-00584-1 [paper]

Optimization of Q.Clear reconstruction for dynamic <sup>18</sup>F PET imaging.

Journal: EJNMMI physics

Status: code on request

[32765] doi:10.1371/journal.pbio.3002328 [paper, repository]

A Drosophila glial cell atlas reveals a mismatch between transcriptional and morphological diversity.

Journal: PLoS biology

Authors' code: AustinSeroka/2022_stage17_glia (no license), VilFernandesLab/2022_DrosophilaGlialAtlas (no license)

Status: code verified, 10 files readable, 19 matches

[32766] doi:10.1371/journal.pone.0292518 [paper, repository]

The effects of prior exposure to prism lenses on de novo motor skill learning.

Journal: PloS one

Authors' code: OSF 8crqa (no license)

Status: code verified, 1 file readable

[32767] doi:10.1371/journal.pone.0292926 [paper, data]

In depth characterization of midbrain organoids derived from wild type iPSC lines.

Journal: PloS one

Status: data only, 1 dataset cited

[32768] doi:10.1371/journal.pone.0293031 [paper, data]

CONcreTEXT norms: Concreteness ratings for Italian and English words in context.

Journal: PloS one

Status: data only, 3 datasets cited

[32769] doi:10.21769/bioprotoc.4854 [paper, repository]

Princeton RAtlas: A Common Coordinate Framework for Fully cleared, Whole <i>Rattus norvegicus</i> Brains.

Journal: Bio-protocol

Authors' code: emilyjanedennis/PRA (MIT), superelastix/simpleelastix (Apache-2.0)

Status: code verified, 239 files readable

[32770] doi:10.3389/fmicb.2023.1229783 [paper, repository]

Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice.

Journal: Frontiers in microbiology

Authors' code: groups.google.com/g/anvio (no license), cfarkas/annotate_my_genomes (MIT), christophergandrud/networkD3 (no license)

Status: code verified, 46 files readable

[32771] doi:10.3389/fneur.2023.1253398 [paper, repository]

Case report: Analysis of a gene variant and prenatal diagnosis in a family with megalencephalic leukoencephalopathy with subcortical cysts.

Journal: Frontiers in neurology

Authors' code: deepmind/alphafold (Apache-2.0)

Status: code verified, 101 files readable

[32772] doi:10.3389/fnhum.2023.1239105 [paper, repository]

Optimized high-definition tDCS in patients with skull defects and skull plates.

Journal: Frontiers in human neuroscience

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

Status: code verified, 2,000 files readable, 1 match

[32773] doi:10.3390/e25101469 [paper, repository]

Diffusion Probabilistic Modeling for Video Generation.

Journal: Entropy (Basel, Switzerland)

Authors' code: saulzhang/video_prediction_zoo (MIT), Harrypotterrrr/DVD-GAN (no license), buggyyang/RVD (no license)

Status: code verified, 91 files readable, 5 matches

[32774] doi:10.3390/s23208607 [paper, data]

Analysis of Connectome Graphs Based on Boundary Scale.

Journal: Sensors (Basel, Switzerland)

Status: data only, 1 dataset cited

[32775] doi:10.7554/elife.85175 [paper, repository]

Two human brain systems micro-structurally associated with obesity.

Journal: eLife

Authors' code: ucam-department-of-psychiatry/UKB (GPL-3.0)

Status: code verified, 38 files readable, 1 match

Thursday, 19 October 2023 (32 papers)

[32776] doi:10.1016/j.celrep.2023.113252 [paper, repository]

APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.

Journal: Cell reports

Authors' code: ADNetworksPPG/YH_NK01_APOE4_HMGB1_paper (MIT), Zenodo 8309839 (other-open)

Status: code verified, 84 files readable, 16 matches

[32777] doi:10.1016/j.neuron.2023.09.022 [paper, repository]

Radial astrocyte synchronization modulates the visual system during behavioral-state transitions.

Journal: Neuron

Authors' code: Zenodo 8345236 (other-open), Zenodo 8345249 (other-open), zebrain-lab/Toolbox-Romano-et-al (GPL-3.0), zebrain-lab/Optogenetics (no license), zebrain-lab/BaumerRecord (no license)

Status: code verified, 154 files readable, 6 matches

[32778] doi:10.1016/j.neuron.2023.09.035 [paper, repository]

A frontopolar-temporal circuit determines the impact of social information in macaque decision making.

Journal: Neuron

Authors' code: alimahmoodia/Monkey-Social-Information-Use (no license), stnava.github.io/ants (no license)

Status: code verified

[32779] doi:10.1038/s41467-023-42052-5 [paper, repository]

Frontal cortex activity during the production of diverse social communication calls in marmoset monkeys.

Journal: Nature communications

Authors' code: Zenodo 8242611 (CC-BY-4.0)

Status: code verified, 44 files readable, 4 matches

[32780] doi:10.1038/s41467-023-42141-5 [paper, repository]

Ketamine's acute effects on negative brain states are mediated through distinct altered states of consciousness in humans.

Journal: Nature communications

Authors' code: WilliamsPanLab/Ketamine-FEET-Mediation (no license)

Status: code verified, 13 files readable, 5 matches

[32781] doi:10.1038/s41467-023-42362-8 [paper]

Adrenergic modulation of melanocortin pathway by hunger signals.

Journal: Nature communications

Status: code on request

[32782] doi:10.1038/s41467-023-42416-x [paper, data]

Ligand activation mechanisms of human KCNQ2 channel.

Journal: Nature communications

Status: data only, 16 datasets cited

[32783] doi:10.1038/s41531-023-00586-x [paper, data]

Dopaminergic denervation and associated MRI microstructural changes in the nigrostriatal projection in early Parkinson's disease patients.

Journal: NPJ Parkinson's disease

Status: data only, 1 dataset cited

[32784] doi:10.1038/s41556-023-01247-0 [paper, repository]

A MEC-2/stomatin condensate liquid-to-solid phase transition controls neuronal mechanotransduction during touch sensing.

Journal: Nature cell biology

Authors' code: gitlab.icfo.net/rheo/tweezers/droplets (no license)

Status: code verified, 9 files readable, 2 matches

[32785] doi:10.1038/s41593-023-01456-8 [paper, repository]

Non-invasive temporal interference electrical stimulation of the human hippocampus.

Journal: Nature neuroscience

Authors' code: gitlab.eps.surrey.ac.uk/nemo/ti-paper (no license), gitlab.eps.surrey.ac.uk/nemo/facenametask (no license)

Status: code found, still to be checked

[32786] doi:10.1038/s41593-023-01457-7 [paper, repository]

Noninvasive theta-burst stimulation of the human striatum enhances striatal activity and motor skill learning.

Journal: Nature neuroscience

Authors' code: Zenodo 8252501 (CC-BY-4.0)

Status: code verified

[32787] doi:10.1038/s41593-023-01461-x [paper, repository]

The rat frontal orienting field dynamically encodes value for economic decisions under risk.

Journal: Nature neuroscience

Authors' code: erlichlab/risk-fof-ppc-2023 (no license)

Status: code verified, 37 files readable, 26 matches

[32788] doi:10.1038/s41597-023-02614-0 [paper, repository]

A comparison of neuroelectrophysiology databases.

Journal: Scientific data

Authors' code: ome/ome-zarr-py (BSD-2-Clause), bioimagesuiteweb.github.io/webapp (no license), kitware.github.io/itk-vtk-viewer (no license)

Status: code verified, 48 files readable

[32789] doi:10.1038/s41598-023-44405-y [paper, data]

Distinct neural representations during a brain-machine interface and manual reaching task in motor cortex, prefrontal cortex, and striatum.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32790] doi:10.1038/s41598-023-44426-7 [paper, data]

Neuroprotective potential of intranasally delivered L-myc immortalized human neural stem cells in female rats after a controlled cortical impact injury.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32791] doi:10.1038/s41746-023-00940-6 [paper]

A real-world clinical validation for AI-based MRI monitoring in multiple sclerosis.

Journal: NPJ digital medicine

Status: code on request

[32792] doi:10.1073/pnas.2305460120 [paper, repository]

Fully-primed slowly-recovering vesicles mediate presynaptic LTP at neocortical neurons.

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

Authors' code: HallermannLab/2023_PNAS (no license)

Status: code verified, 37 files readable

[32793] doi:10.1093/braincomms/fcad279 [paper, repository]

Assessment of white matter hyperintensity severity using multimodal magnetic resonance imaging.

Journal: Brain communications

Authors' code: CoBrALab/WMH_Signal_AD_OParent_2023 (no license), rmarkello/pyls (GPL-2.0)

Status: code verified, 42 files readable, 9 matches

[32794] doi:10.1101/2023.10.18.23297200 [paper, repository]

DNAm scores for serum GDF15 and NT-proBNP levels associate with a range of traits affecting the body and brain

Journal: medRxiv (preprint)

Authors' code: Zenodo 6801458 (CC-BY-4.0)

Status: code verified

[32795] doi:10.1186/s12987-023-00473-w [paper, data]

Proteomic interrogation of the meninges reveals the molecular identities of structural components and regional distinctions along the CNS axis.

Journal: Fluids and barriers of the CNS

Status: data only, 2 datasets cited

[32796] doi:10.1242/bio.060151 [paper]

Spatial transcriptomics map of the embryonic mouse brain - a tool to explore neurogenesis.

Journal: Biology open

Status: data only

[32797] doi:10.1371/journal.pgen.1010961 [paper, repository]

The parenting hub of the hypothalamus is a focus of imprinted gene action.

Journal: PLoS genetics

Authors' code: MJHiggs/IG-Single-Cell-Enrichment (no license)

Status: code verified, 22 files readable, 2 matches

[32798] doi:10.1371/journal.pone.0288909 [paper, repository]

Protocol of the Budapest sleep, experiences, and traits study: An accessible resource for understanding associations between daily experiences, individual differences, and objectively measured sleep.

Journal: PloS one

Authors' code: Zenodo 7799130 (CC-BY-4.0)

Status: code verified

[32799] doi:10.1371/journal.pone.0292866 [paper, data]

Reliable retrieval is intrinsically rewarding: Recency, item difficulty, study session memory, and subjective confidence predict satisfaction in word-pair recall.

Journal: PloS one

Status: data only, 1 dataset cited

[32800] doi:10.1523/eneuro.0328-23.2023 [paper, repository]

YAEL: Your Advanced Electrode Localizer.

Journal: eNeuro

Authors' code: beauchamplab/rave (no license)

Status: code verified, 18 files readable

[32801] doi:10.3389/fcell.2023.1270892 [paper, data]

Transcriptome analysis reveals genes associated with stem cell activation by physical exercise in the dentate gyrus of aged p16Ink4a knockout mice.

Journal: Frontiers in cell and developmental biology

Status: data only, 1 dataset cited

[32802] doi:10.3389/fnins.2023.1209398 [paper, repository]

Auditory and reward structures reflect the pleasure of musical expectancies during naturalistic listening.

Journal: Frontiers in neuroscience

Authors' code: benjaminpgold/auditory-reward-pleasure-of-musical-expectancies (no license)

Status: code verified, 4 files readable, 6 matches

[32803] doi:10.3389/fnins.2023.1240209 [paper, data]

Sex linked behavioral and hippocampal transcriptomic changes in mice with cell-type specific <i>Egr1</i> loss.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[32804] doi:10.3389/fphar.2023.1270443 [paper, repository]

Simulating clinical trials for model-informed precision dosing: using warfarin treatment as a use case.

Journal: Frontiers in pharmacology

Authors' code: DavAug/mipd-warfarin (no license)

Status: code verified, 64 files readable, 14 matches

[32805] doi:10.3390/ijms242015339 [paper, data]

Cultured Mesenchymal Cells from Nasal Turbinate as a Cellular Model of the Neurodevelopmental Component of Schizophrenia Etiology.

Journal: International journal of molecular sciences

Status: code on request, 1 dataset cited

[32806] doi:10.7554/elife.69205 [paper, repository]

Mechanical vibration patterns elicit behavioral transitions and habituation in crawling <i>Drosophila</i> larvae.

Journal: eLife

Authors' code: supp:PMC10586805/elife-69205-code1.zip (no license)

Status: code verified, 1 file readable

[32807] doi:10.7554/elife.83196 [paper, repository]

Motor actions are spatially organized in motor and dorsal premotor cortex.

Journal: eLife

Authors' code: OSF 7sgbe (no license)

Status: code verified, 72 files readable, 3 matches

Wednesday, 18 October 2023 (24 papers)

[32808] doi:10.1002/hbm.26517 [paper, repository]

Test-retest reliability and predictive utility of a macroscale principal functional connectivity gradient.

Journal: Human brain mapping

Authors' code: haririlab/publications (no license)

Status: code verified, 5 files readable, 3 matches

[32809] doi:10.1002/hbm.26518 [paper, repository]

Revisiting deficits in threat and safety appraisal in obsessive-compulsive disorder.

Journal: Human brain mapping

Authors' code: clinical-brain-networks/OCDbaseline_public (MIT)

Status: code verified, 43 files readable, 7 matches

[32810] doi:10.1007/s12975-023-01189-7 [paper, repository]

Intracerebral Administration of a Novel Self-Assembling Peptide Hydrogel Is Safe and Supports Cell Proliferation in Experimental Intracerebral Haemorrhage.

Journal: Translational stroke research

Authors' code: uva-peirce-cottler-lab/public_REAVER (BSD-3-Clause)

Status: code verified, 90 files readable, 2 matches

[32811] doi:10.1016/j.isci.2023.108240 [paper, repository]

Functional sophistication in human escape.

Journal: iScience

Authors' code: bachlab/vrthreat (GPL-3.0)

Status: code verified, 22 files readable, 9 matches

[32812] doi:10.1016/j.isci.2023.108243 [paper]

Changes in neuropeptide large dense core vesicle trafficking dynamics contribute to adaptive responses to a systemic homeostatic challenge.

Journal: iScience

Status: code on request

[32813] doi:10.1016/j.isci.2023.108244 [paper, repository]

A common spectrum underlying brain disorders across lifespan revealed by deep learning on brain networks.

Journal: iScience

Authors' code: mianxinliu/mahgcn-code (no license), Jfortin1/ComBatHarmonization (no license), MICA-MNI/BrainSpace (BSD-3-Clause)

Status: code verified, 164 files readable, 6 matches

[32814] doi:10.1016/j.omtm.2023.101140 [paper]

Molecular and functional correction of a deep intronic splicing mutation in <i>CFTR</i> by CRISPR-Cas9 gene editing.

Journal: Molecular therapy. Methods & clinical development

Status: code on request

[32815] doi:10.1021/acsomega.3c05769 [paper, data]

Transcript-Level In Silico Analysis of Alzheimer's Disease-Related Gene Biomarkers and Their Evaluation with Bioactive Flavonoids to Explore Therapeutic Interactions.

Journal: ACS omega

Status: data only, 1 dataset cited

[32816] doi:10.1038/s41586-023-06623-2 [paper, repository]

Clinical trial links oncolytic immunoactivation to survival in glioblastoma.

Journal: Nature

Authors' code: OSF ybcg7 (no license)

Status: code verified, 39 files readable, 11 matches

[32817] doi:10.1038/s41598-023-44782-4 [paper]

Quantitative analysis of prion disease using an AI-powered digital pathology framework.

Journal: Scientific reports

Status: code on request

[32818] doi:10.1038/s42003-023-05430-9 [paper, data]

Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice.

Journal: Communications biology

Status: data only, 1 dataset cited

[32819] doi:10.1098/rsob.230215 [paper, repository]

Temperature activated transient receptor potential ion channels from Antarctic fishes.

Journal: Open biology

Authors' code: doi:10.6084/m9.figshare.c.6858595 (no license)

Status: code found, still to be checked

[32820] doi:10.1159/000534669 [paper, data]

Chronic Stress Exacerbates Hyperglycemia-Induced Affective Symptoms in Male Mice.

Journal: Neuroimmunomodulation

Status: data only, 1 dataset cited

[32821] doi:10.1213/ane.0000000000006746 [paper, data]

Dynamic Nomogram for Predicting the Risk of Perioperative Neurocognitive Disorders in Adults.

Journal: Anesthesia and analgesia

Status: data only, 1 dataset cited

[32822] doi:10.1371/journal.pcbi.1011555 [paper, repository]

A recurrent neural network model of prefrontal brain activity during a working memory task.

Journal: PLoS computational biology

Authors' code: epiwek/retrocueing_RNN (CC0-1.0), OSF g6m7t (no license)

Status: code verified, 43 files readable, 30 matches

[32823] doi:10.1371/journal.pone.0293123 [paper, repository]

Machine learning with optimization to create medicine intake schedules for Parkinson's disease patients.

Journal: PloS one

Authors' code: supp:PMC10584128/pone.0293123.s002.zip (no license)

Status: code verified, 14 files readable, 5 matches

[32824] doi:10.1523/eneuro.0005-23.2023 [paper, repository]

Pupil Size Is Sensitive to Low-Level Stimulus Features, Independent of Arousal-Related Modulation.

Journal: eNeuro

Authors' code: elimerriam/pupilArousal (no license), Zenodo 1299497 (other-open), justingardner/mgl (GPL-2.0)

Status: code verified, 737 files readable, 3 matches

[32825] doi:10.3389/fnagi.2023.1225816 [paper]

Bayesian workflow for the investigation of hierarchical classification models from tau-PET and structural MRI data across the Alzheimer's disease spectrum.

Journal: Frontiers in aging neuroscience

Status: code on request

[32826] doi:10.3389/fnetp.2023.1242505 [paper, repository]

Time-varying information measures: an adaptive estimation of information storage with application to brain-heart interactions.

Journal: Frontiers in network physiology

Authors' code: YuriAntonacci/Time-VaryingIS (no license)

Status: code verified, 6 files readable, 4 matches

[32827] doi:10.3389/fnhum.2023.1251690 [paper, data]

Methods for motion artifact reduction in online brain-computer interface experiments: a systematic review.

Journal: Frontiers in human neuroscience

Status: data only, 1 dataset cited

[32828] doi:10.3390/biology12101344 [paper, repository]

Protein-Protein Interaction Network Extraction Using Text Mining Methods Adds Insight into Autism Spectrum Disorder.

Journal: Biology

Authors' code: lnezamuldeen/PPI_creation_models (no license)

Status: dead link

[32829] doi:10.3390/cells12202483 [paper, data]

Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma.

Journal: Cells

Status: data only, 1 dataset cited

[32830] doi:10.3390/healthcare11202763 [paper, data]

Artificial Cognition for Detection of Mental Disability: A Vision Transformer Approach for Alzheimer's Disease.

Journal: Healthcare (Basel, Switzerland)

Status: data only, 1 dataset cited

[32831] doi:10.3390/ijms242015313 [paper, data]

Expression Pattern of Trace Amine-Associated Receptors during Differentiation of Human Pluripotent Stem Cells to Dopaminergic Neurons.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Tuesday, 17 October 2023 (30 papers)

[32832] doi:10.1002/hbm.26511 [paper, data]

Integration and segregation manifolds in the brain ensure cognitive flexibility during tasks and rest.

Journal: Human brain mapping

Status: data only, 1 dataset cited

[32833] doi:10.1002/hbm.26512 [paper, repository]

Morphological connectivity differences in Alzheimer's disease correlate with gene transcription and cell-type.

Journal: Human brain mapping

Authors' code: brainsmash.readthedocs.io (no license)

Status: code verified

[32834] doi:10.1002/jmri.29078 [paper, repository]

Total and Regional Brain Volumes in Fetuses With Congenital Heart Disease.

Journal: Journal of magnetic resonance imaging : JMRI

Authors' code: hub.docker.com/r/fetalsvrtk (no license)

Status: code verified

[32835] doi:10.1016/j.celrep.2023.113241 [paper]

Loss of succinyl-CoA synthetase in mouse forebrain results in hypersuccinylation with perturbed neuronal transcription and metabolism.

Journal: Cell reports

Status: code on request

[32836] doi:10.1016/j.celrep.2023.113253 [paper]

Probing cerebral malaria inflammation in 3D human brain microvessels.

Journal: Cell reports

Status: code on request

[32837] doi:10.1016/j.celrep.2023.113276 [paper, repository]

Somatic structural variation signatures in pediatric brain tumors.

Journal: Cell reports

Authors' code: Illumina/manta (GPL-3.0), guru-yang/Meerkat (no license), dellytools/delly (BSD-3-Clause), arq5x/bedtools2 (MIT)

Status: code verified, 822 files readable, 3 matches

[32838] doi:10.1016/j.isci.2023.108227 [paper, data]

AKAP150 from nucleus accumbens dopamine D1 and D2 receptor-expressing medium spiny neurons regulates morphine withdrawal.

Journal: iScience

Status: code on request, 1 dataset cited

[32839] doi:10.1038/s41420-023-01677-7 [paper, data]

Neuronal RBM5 modulates cell signaling responses to traumatic and hypoxic-ischemic injury in a sex-dependent manner.

Journal: Cell death discovery

Status: data only, 7 datasets cited

[32840] doi:10.1038/s41467-023-42176-8 [paper, data]

Neural deficits in a mouse model of PACS1 syndrome are corrected with PACS1- or HDAC6-targeting therapy.

Journal: Nature communications

Status: data only, 1 dataset cited

[32841] doi:10.1038/s41467-023-42227-0 [paper, data]

O-GlcNAcylation regulates neurofilament-light assembly and function and is perturbed by Charcot-Marie-Tooth disease mutations.

Journal: Nature communications

Status: data only, 1 dataset cited

[32842] doi:10.1038/s41467-023-42315-1 [paper, repository]

Thalamic nucleus reuniens coordinates prefrontal-hippocampal synchrony to suppress extinguished fear.

Journal: Nature communications

Authors' code: marenlab/HPC-PL-Coupling-in-Context-Extinction-Retrieval (no license)

Status: code verified, 20 files readable, 3 matches

[32843] doi:10.1038/s41467-023-42380-6 [paper, data]

Human thalamic low-frequency oscillations correlate with expected value and outcomes during reinforcement learning.

Journal: Nature communications

Status: code on request, 1 dataset cited

[32844] doi:10.1038/s41598-023-44322-0 [paper]

MRI-based multivariate gray matter volumetric distance for predicting motor symptom progression in Parkinson's disease.

Journal: Scientific reports

Status: code on request

[32845] doi:10.1038/s41598-023-44772-6 [paper, repository]

Dopamine D1-like receptors modulate synchronized oscillations in the hippocampal-prefrontal-amygdala circuit in contextual fear.

Journal: Scientific reports

Authors' code: OSF km2s7 (no license)

Status: code verified, 60 files readable, 3 matches

[32846] doi:10.1038/s41598-023-44871-4 [paper, data]

Females exhibit smaller volumes of brain activation and lower inter-subject variability during motor tasks.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32847] doi:10.1073/pnas.2304085120 [paper, repository]

Modeling naturalistic face processing in humans with deep convolutional neural networks.

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

Authors' code: deepinsight/insightface (no license), GUO-Jiahui/face_DCNN (MIT)

Status: code verified, 1,742 files readable, 2 matches

[32848] doi:10.1073/pnas.2304933120 [paper, data]

Vestibular CCK signaling drives motion sickness-like behavior in mice.

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

Status: data only, 1 dataset cited

[32849] doi:10.1073/pnas.2306475120 [paper, repository]

Sexual differentiation of neural mechanisms of stress sensitivity during puberty.

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

Authors' code: bctrainorlab/behavioral_quantification (no license)

Status: dead link

[32850] doi:10.1093/braincomms/fcad270 [paper]

EEG microstate quantifiers and state space descriptors during anaesthesia in patients with postoperative delirium: a descriptive analysis.

Journal: Brain communications

Status: code on request

[32851] doi:10.1101/2023.10.17.562714 [paper, data]

Binge feeding-induced Olfactory Cortex Suppression Reduces Satiation

Journal: bioRxiv (preprint)

Status: data only, 2 datasets cited

[32852] doi:10.1111/cns.14480 [paper]

Fine-grained features characterize hippocampal and amygdaloid change pattern in Parkinson's disease and discriminate cognitive-deficit subtype.

Journal: CNS neuroscience & therapeutics

Status: code on request

[32853] doi:10.1162/imag_a_00023 [paper, repository]

Automated motion artifact detection in early pediatric diffusion MRI using a convolutional neural network.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: jmweaver-uw/infQC_pub (MIT)

Status: code verified, 5 files readable, 3 matches

[32854] doi:10.1186/s12888-023-05223-8 [paper, repository]

Mindfulness-based real-time fMRI neurofeedback: a randomized controlled trial to optimize dosing for depressed adolescents.

Journal: BMC psychiatry

Authors' code: pab2163/mindful_brain_project (no license), gablab/murfi2 (Apache-2.0)

Status: code verified, 425 files readable, 17 matches

[32855] doi:10.1186/s12938-023-01164-1 [paper, repository]

Deep learning based on susceptibility-weighted MR sequence for detecting cerebral microbleeds and classifying cerebral small vessel disease.

Journal: Biomedical engineering online

Authors' code: Huatsing-Lau/CSVD-CMBs-Detection-and-Classification (no license)

Status: code verified, 57 files readable, 4 matches

[32856] doi:10.1186/s12974-023-02902-x [paper, repository]

Voltammetry in the spleen assesses real-time immunomodulatory norepinephrine release elicited by autonomic neurostimulation.

Journal: Journal of neuroinflammation

Authors' code: mgerber000/SpleenFSCV (Apache-2.0)

Status: code verified, 46 files readable, 2 matches

[32857] doi:10.1371/journal.pone.0292316 [paper, data]

MEG correlates of speech planning in simple vs. interactive picture naming in children and adults.

Journal: PloS one

Status: data only, 1 dataset cited

[32858] doi:10.3389/fnins.2023.1224721 [paper, repository]

Is increased activation in the fusiform face area to Greebles a result of appropriate expertise training or caused by Greebles' face likeness?

Journal: Frontiers in neuroscience

Authors' code: OSF 5tm9v (no license)

Status: code verified, 1 file readable

[32859] doi:10.3389/fonc.2023.1238607 [paper, data]

Tracking tumor evolution during the first-line treatment in brain glioma <i>via</i> serial profiling of cell-free tumor DNA from tumor <i>in situ</i> fluid.

Journal: Frontiers in oncology

Status: data only, 1 dataset cited

[32860] doi:10.3390/diagnostics13203234 [paper, data]

Efficient Skip Connections-Based Residual Network (ESRNet) for Brain Tumor Classification.

Journal: Diagnostics (Basel, Switzerland)

Status: data only, 2 datasets cited

[32861] doi:10.3758/s13423-023-02377-0 [paper, repository]

C-SMB 2.0: Integrating over 25 years of motor sequencing research with the Discrete Sequence Production task.

Journal: Psychonomic bulletin & review

Authors' code: OSF hmpnc (no license)

Status: empty repository

Monday, 16 October 2023 (24 papers)

[32862] doi:10.1016/j.cell.2023.09.013 [paper, data]

Serotonin reduction in post-acute sequelae of viral infection.

Journal: Cell

Status: code on request, 6 datasets cited

[32863] doi:10.1016/j.isci.2023.108220 [paper, repository]

<i>Pcdh19</i> mediates olfactory sensory neuron coalescence during postnatal stages and regeneration.

Journal: iScience

Authors' code: maths.usyd.edu.au/u/yingxinl (no license)

Status: code verified

[32864] doi:10.1016/j.isci.2023.108222 [paper, repository]

Controlling morpho-electrophysiological variability of neurons with detailed biophysical models.

Journal: iScience

Authors' code: doi:10.7910/dvn/fgwmuf (no license), Zenodo 8220287 (CC-BY-4.0), Zenodo 8269363 (CC-BY-4.0), Zenodo 8136124 (other-open), BlueBrain/emodel-generalisation (CC-BY-4.0), pypi.org/project/emodel-generalisation (no license), bluebrain/bluepyopt (GPL-3.0), bluebrain/sscxemodelexamples (CC-BY-4.0)

Status: code verified, 687 files readable, 5 matches

[32865] doi:10.1016/j.nbd.2023.106328 [paper, data]

Feed-forward metabotropic signaling by Cav1 Ca&lt;sup&gt;2+&lt;/sup&gt; channels supports pacemaking in pedunculopontine cholinergic neurons.

Journal: Neurobiology of disease

Status: data only, 1 dataset cited

[32866] doi:10.1038/s41467-023-41752-2 [paper, repository]

Initial conditions combine with sensory evidence to induce decision-related dynamics in premotor cortex.

Journal: Nature communications

Authors' code: gamaleldin/CFR (no license), murraylab/PsychRNN (MIT), machenslab/dPCA (MIT), chand-lab/Dynamics2023 (no license)

Status: code verified, 780 files readable, 14 matches

[32867] doi:10.1038/s41467-023-42202-9 [paper, repository]

Descending GABAergic pathway links brain sugar-sensing to peripheral nociceptive gating in Drosophila.

Journal: Nature communications

Authors' code: bigwww.epfl.ch/thevenaz/stackreg (no license)

Status: code verified

[32868] doi:10.1038/s41537-023-00403-7 [paper]

Aberrant sense of agency induced by delayed prediction signals in schizophrenia: a computational modeling study.

Journal: Schizophrenia (Heidelberg, Germany)

Status: code on request

[32869] doi:10.1038/s41593-023-01442-0 [paper, repository]

Model metamers reveal divergent invariances between biological and artificial neural networks.

Journal: Nature neuroscience

Authors' code: jenellefeather/model_metamers_pytorch (MIT), jenellefeather/chcochleagram (MIT), Zenodo 8373260 (other-open)

Status: code verified, 389 files readable, 26 matches

[32870] doi:10.1038/s41593-023-01455-9 [paper, repository]

Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain.

Journal: Nature neuroscience

Authors' code: YiZhang-lab/PFC-MERFISH (MIT), Zenodo 8247763 (other-open)

Status: code verified, 38 files readable, 10 matches

[32871] doi:10.1038/s41598-023-44645-y [paper, repository]

Brain-computer interface for robot control with eye artifacts for assistive applications.

Journal: Scientific reports

Authors' code: KK4r4s/BCI-TIAGo-Control-with-EEG-Using-Eye-Artifacts (Apache-2.0)

Status: code verified, 146 files readable, 4 matches

[32872] doi:10.1038/s41598-023-44763-7 [paper, data]

Detection and classification of adult epilepsy using hybrid deep learning approach.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32873] doi:10.1073/pnas.2311131120 [paper, repository]

Ciliary localization of a light-activated neuronal GPCR shapes behavior.

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

Authors' code: Zenodo 8411217 (CC-BY-4.0)

Status: code verified, 6 files readable, 2 matches

[32874] doi:10.1136/bmjopen-2023-073378 [paper, repository]

<b>B</b>rain connectivity-guided, Optimised theta burst transcranial magnetic stimulation to improve Central Pain Modulation in knee Osteoarthritis Pain (BoostCPM): protocol of a pilot randomised clinical trial in a secondary care setting in the UK.

Journal: BMJ open

Authors' code: SPMIC-UoN (no license)

Status: code verified

[32875] doi:10.1177/13674935231205041 [paper, repository]

Establishing priorities in child health: Giving parents and youth a voice.

Journal: Journal of child health care : for professionals working with children in the hospital and community

Authors' code: OSF ajkmp (no license)

Status: empty repository

[32876] doi:10.1186/s13059-023-03066-w [paper, repository]

Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue.

Journal: Genome biology

Authors' code: bioconductor.org/packages/treg (no license), lieberinstitute/10xpilot_snrnaseq-human (Artistic-2.0), LieberInstitute/TREG_paper (no license), LieberInstitute/TREG (no license), Zenodo 5149046 (other-open)

Status: code verified, 168 files readable, 16 matches

[32877] doi:10.1186/s13059-023-03079-5 [paper, repository]

The evolution and mutational robustness of chromatin accessibility in Drosophila.

Journal: Genome biology

Authors' code: LiZhaoLab/DL_ATAC (no license), Zenodo 8381363 (other-open)

Status: code verified, 34 files readable, 6 matches

[32878] doi:10.1371/journal.pcbi.1011571 [paper, repository]

Establishing brain states in neuroimaging data.

Journal: PLoS computational biology

Authors' code: allavailablepubliccode/Phase (no license)

Status: code verified, 2 files readable, 2 matches

[32879] doi:10.1371/journal.pone.0292808 [paper, repository]

Characterization of spatiotemporal dynamics of binary and graded tonic pain in humans using intracranial recordings.

Journal: PloS one

Authors' code: Rolston-Lab/LeGUI (GPL-3.0)

Status: code verified, 1,196 files readable, 2 matches

[32880] doi:10.15252/embj.2022113213 [paper, data]

Morphogenesis and development of human telencephalic organoids in the absence and presence of exogenous extracellular matrix.

Journal: The EMBO journal

Status: code on request, 1 dataset cited

[32881] doi:10.3389/fneur.2023.1247532 [paper, repository]

Ecological validity of a deep learning algorithm to detect gait events from real-life walking bouts in mobility-limiting diseases.

Journal: Frontiers in neurology

Authors' code: neurogeriatricskiel/mobilised (no license)

Status: code verified, 12 files readable, 2 matches

[32882] doi:10.3390/cells12202461 [paper]

lncRNA Sequencing Reveals Neurodegeneration-Associated FUS Mutations Alter Transcriptional Landscape of iPS Cells That Persists in Motor Neurons.

Journal: Cells

Status: data only

[32883] doi:10.7554/elife.52599 [paper, repository]

Hierarchical temporal prediction captures motion processing along the visual pathway.

Journal: eLife

Authors' code: JesseLivezey/gabor_fit (MIT), ox-ang/hierarchical_temporal_prediction (no license), sacadena/Cadena2019PlosCB (CC-BY-NC-ND-4.0), webstorms/stacktp (MIT), webstorms/neuralpred (MIT)

Status: code verified, 72 files readable, 7 matches

[32884] doi:10.7554/elife.83930 [paper, repository]

Flexible coding of time or distance in hippocampal cells.

Journal: eLife

Authors' code: doi:10.5061/dryad.ngf1vhhxp (no license), derdikman/Abramson_code (MIT)

Status: code verified, 19 files readable, 6 matches

[32885] doi:10.7554/elife.85786 [paper, repository]

Pynapple, a toolbox for data analysis in neuroscience.

Journal: eLife

Authors' code: pynapple-org/pynapple-paper-2023 (GPL-3.0), pynapple-org/pynapple (MIT), peyrachelab/pynacollada (GPL-3.0)

Status: code verified, 118 files readable, 4 matches

Sunday, 15 October 2023 (2 papers)

[32886] doi:10.1016/j.dib.2023.109659 [paper, repository]

Transcriptome dataset of light-dependent expression in the early onset retinal degeneration model, <i>Mcoln1^-/-</i> mouse.

Journal: Data in brief

Authors' code: daehwankimlab.github.io/hisat2 (no license), JonathanGM70/Mcoln1- (no license)

Status: code verified, 1 file readable

[32887] doi:10.1016/j.dib.2023.109669 [paper, data]

Single dose intranasal oxytocin administration: Data from healthy younger and older adults.

Journal: Data in brief

Status: data only, 3 datasets cited

Saturday, 14 October 2023 (12 papers)

[32888] doi:10.1002/hbm.26483 [paper]

dcSBM: A federated constrained source-based morphometry approach for multivariate brain structure mapping.

Journal: Human brain mapping

Status: code on request

[32889] doi:10.1002/hbm.26510 [paper, repository]

Aberrant degree centrality profiles during rumination in major depressive disorder.

Journal: Human brain mapping

Authors' code: XiaoChenPhD/Jia_2023 (GPL-3.0)

Status: code verified, 9 files readable, 2 matches

[32890] doi:10.1016/j.celrep.2023.113244 [paper]

α-Synuclein-dependent increases in PIP5K1γ drive inositol signaling to promote neurotoxicity.

Journal: Cell reports

Status: code on request

[32891] doi:10.1016/j.dcn.2023.101314 [paper, repository]

Structural and functional connectome relationships in early childhood.

Journal: Developmental cognitive neuroscience

Authors' code: yoonmihong/SCFC (no license)

Status: code verified, 6 files readable, 4 matches

[32892] doi:10.1016/j.ebiom.2023.104835 [paper, repository]

Uncovering distinct progression patterns of tau deposition in progressive supranuclear palsy using [¹⁸F]Florzolotau PET imaging and subtype/stage inference algorithm.

Journal: EBioMedicine

Authors' code: ucl-pond/pySuStaIn (MIT)

Status: code verified, 19 files readable, 2 matches

[32893] doi:10.1016/j.isci.2023.108214 [paper, repository]

Detection and annotation of transposable element insertions and deletions on the human genome using nanopore sequencing.

Journal: iScience

Authors' code: Zenodo 8375338 (other-open), lh3/minimap2 (MIT), eldariont/svim (GPL-3.0), tjiangHIT/cuteSV (MIT), philres/ngmlr (MIT), fritzsedlazeck/Sniffles (MIT), ChaissonLab/LRA (other), benoukraflab/NanoVar (GPL-3.0), fritzsedlazeck/SURVIVOR (MIT), pysam-developers/pysam (MIT), ruanjue/wtdbg2 (GPL-3.0), javiercguard/tenanoporepipeline (no license)

Status: code verified, 987 files readable, 3 matches

[32894] doi:10.1016/j.nicl.2023.103530 [paper, repository]

Borderline shades: Morphometric features predict borderline personality traits but not histrionic traits.

Journal: NeuroImage. Clinical

Authors' code: neurolabusc/surf-ice (BSD-2-Clause)

Status: code verified, 45 files readable

[32895] doi:10.1038/s41467-023-42322-2 [paper, data]

KDM2B regulates hippocampal morphogenesis by transcriptionally silencing Wnt signaling in neural progenitors.

Journal: Nature communications

Status: data only, 1 dataset cited

[32896] doi:10.1038/s41597-023-02603-3 [paper, data]

Assessment of Surgical Tasks Using Neuroimaging Dataset (ASTaUND).

Journal: Scientific data

Status: data only, 2 datasets cited

[32897] doi:10.1038/s41598-023-44656-9 [paper]

Copper metabolism-related Genes in entorhinal cortex for Alzheimer's disease.

Journal: Scientific reports

Status: data only

[32898] doi:10.1093/pnasnexus/pgad337 [paper, repository]

Recursive neural programs: A differentiable framework for learning compositional part-whole hierarchies and image grammars.

Journal: PNAS nexus

Authors' code: FishAres/RNP6 (no license)

Status: code verified, 43 files readable

[32899] doi:10.1117/1.nph.10.4.045003 [paper]

Cerebrovascular reactivity to carbon dioxide tension in newborns: data from combined time-resolved near-infrared spectroscopy and diffuse correlation spectroscopy.

Journal: Neurophotonics

Status: code on request

Friday, 13 October 2023 (22 papers)

[32900] doi:10.1002/exp.20220133 [paper, repository]

Spatial transcriptomic analysis of the mouse brain following chronic social defeat stress.

Journal: Exploration (Beijing, China)

Authors' code: SpatialTranscriptomicsResearch/st_spot_detector (MIT), satijalab/seurat (other), MarcElosua/SPOTlight (GPL-3.0)

Status: code verified, 212 files readable, 5 matches

[32901] doi:10.1038/s41467-023-41919-x [paper, data]

Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication.

Journal: Nature communications

Status: data only, 2 datasets cited

[32902] doi:10.1038/s41467-023-42091-y [paper, repository]

Developmental atlas of phase-amplitude coupling between physiologic high-frequency oscillations and slow waves.

Journal: Nature communications

Authors' code: kaz1126/MI_HFO (no license), Zenodo 8267570 (other-open)

Status: code verified, 4 files readable

[32903] doi:10.1038/s41467-023-42164-y [paper, data]

Structural insights into the allosteric inhibition of P2X4 receptors.

Journal: Nature communications

Status: data only, 1 dataset cited

[32904] doi:10.1038/s41598-023-43706-6 [paper, repository]

Differential diagnosis of neurodegenerative dementias with the explainable MRI based machine learning algorithm MUQUBIA.

Journal: Scientific reports

Authors' code: neugrid2.eu (no license)

Status: code verified

[32905] doi:10.1038/s41598-023-43785-5 [paper, repository]

Associations between the circumstances and severity of head impacts in men's university ice hockey.

Journal: Scientific reports

Authors' code: Zenodo 7847675 (CC-BY-4.0)

Status: empty repository

[32906] doi:10.1038/s41598-023-44250-z [paper, repository]

Neural mechanisms underlying interindividual differences in intergenerational sustainable behavior.

Journal: Scientific reports

Authors' code: processmacro.org/download.html (no license)

Status: dead link

[32907] doi:10.1038/s41598-023-44517-5 [paper, repository]

Exploring the performance of implicit neural representations for brain image registration.

Journal: Scientific reports

Authors' code: BrainImageAnalysis/INRsRegExp (MIT)

Status: code verified, 9 files readable, 3 matches

[32908] doi:10.1038/s42003-023-05356-2 [paper]

Human-specific evolutionary markers linked to foetal neurodevelopment modulate brain surface area in schizophrenia.

Journal: Communications biology

Status: code on request

[32909] doi:10.1073/pnas.2306990120 [paper]

Hemispheric asymmetry in cortical thinning reflects intrinsic organization of the neurotransmitter systems and homotopic functional connectivity.

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

Status: code on request

[32910] doi:10.1073/pnas.2309331120 [paper, data]

The <i>Drosophila</i> blood-brain barrier regulates sleep via Moody G protein-coupled receptor signaling.

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

Status: data only, 1 dataset cited

[32911] doi:10.1126/science.adf5357 [paper, repository]

Single-cell DNA methylation and 3D genome architecture in the human brain.

Journal: Science (New York, N.Y.)

Authors' code: hq-1.gitbook.io/mc (no license), jksr/human-brain-atlas-code (no license), zhoujt1994.github.io/schicluster (no license)

Status: code verified, 6 files readable, 3 matches

[32912] doi:10.1186/s12859-023-05513-8 [paper, repository]

lifex-ep: a robust and efficient software for cardiac electrophysiology simulations.

Journal: BMC bioinformatics

Authors' code: Zenodo 8085266 (other-at), coin-or/ADOL-C (GPL-2.0), opencollab/arpack-ng (BSD-3-Clause), gitlab.inria.fr/scotch/scotch (no license)

Status: code verified, 1,101 files readable

[32913] doi:10.1186/s12880-023-01103-5 [paper, repository]

DeepHipp: accurate segmentation of hippocampus using 3D dense-block based on attention mechanism.

Journal: BMC medical imaging

Authors' code: CSuperlei/DeepHipp (no license)

Status: code verified, 16 files readable, 1 match

[32914] doi:10.1371/journal.pcbi.1011554 [paper, repository]

Short-term neuronal and synaptic plasticity act in synergy for deviance detection in spiking networks.

Journal: PLoS computational biology

Authors' code: kernfel/plasticity-synergy-deviance-detection (MIT), Zenodo 8333172 (other-open)

Status: code verified, 67 files readable, 3 matches

[32915] doi:10.1371/journal.pgen.1010989 [paper, data]

Investigating trait variability of gene co-expression network architecture in brain by controlling for genomic risk of schizophrenia.

Journal: PLoS genetics

Status: data only, 1 dataset cited

[32916] doi:10.1523/eneuro.0026-23.2023 [paper, data]

Distinguishing Fine Structure and Summary Representation of Sound Textures from Neural Activity.

Journal: eNeuro

Status: data only, 1 dataset cited

[32917] doi:10.3389/fimmu.2023.1128476 [paper, data]

Extracellular proteins as potential biomarkers in Sepsis-related cerebral injury.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[32918] doi:10.3389/fncom.2023.1269019 [paper, data]

Computational assessment of visual coding across mouse brain areas and behavioural states.

Journal: Frontiers in computational neuroscience

Status: data only, 1 dataset cited

[32919] doi:10.3389/fneur.2023.1209941 [paper, repository]

Verbal memory depends on structural hippocampal subfield volume.

Journal: Frontiers in neurology

Authors' code: surfer.nmr.mgh.harvard.edu/fswiki/hippocampalsubfields (no license)

Status: code verified

[32920] doi:10.3389/fnins.2023.1200373 [paper, repository]

Tree representations of brain structural connectivity via persistent homology.

Journal: Frontiers in neuroscience

Authors' code: phuchonguyen/brain-topology (no license)

Status: code verified, 27 files readable, 11 matches

[32921] doi:10.3389/fnins.2023.1275959 [paper, data]

The TMEM106B T186S coding variant increases neurite arborization and synaptic density in primary hippocampal neurons.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

Thursday, 12 October 2023 (35 papers, 7 on this page)

[32922] doi:10.1002/alz.13502 [paper, repository]

Alzheimer's disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Authors' code: Zenodo 7802699 (no license)

Status: code verified

[32923] doi:10.1002/brb3.3272 [paper, repository]

Hands off, brain off? A meta-analysis of neuroimaging data during active and passive driving.

Journal: Brain and behavior

Authors' code: neurolabusc/surf-ice (BSD-2-Clause)

Status: code verified, 45 files readable

[32924] doi:10.1007/s11682-023-00803-4 [paper, repository]

Causality methods to study the functional connectivity in brain networks: the basal ganglia - thalamus causal interactions.

Journal: Brain imaging and behavior

Authors' code: jakobrunge/tigramite (GPL-3.0)

Status: code verified, 109 files readable, 6 matches

[32925] doi:10.1016/j.bbi.2023.10.006 [paper, repository]

The role of the Toll like receptor 4 signaling in sex-specific persistency of depression-like behavior in response to chronic stress.

Journal: Brain, behavior, and immunity

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

Status: code verified, 6 files readable

[32926] doi:10.1016/j.isci.2023.108184 [paper]

<i>O</i>-GlcNAcylation regulates OTX2's proteostasis.

Journal: iScience

Status: code on request

[32927] doi:10.1016/j.isci.2023.108187 [paper]

Neural oscillations and speech processing at birth.

Journal: iScience

Status: code on request

[32928] doi:10.1016/j.nicl.2023.103529 [paper, repository]

Impact of follow ups, time interval and study duration in diffusion &amp; myelin MRI clinical study in MS.

Journal: NeuroImage. Clinical

Authors' code: scilus (no license)

Status: code verified

Also: by category, author, journal, institution, tool or dataset; the search; the DOI lookup for any paper read, with or without a page.