Every paper, by date: page 144

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 144 of 200: 22 November 2023 to 13 November 2023.

Wednesday, 22 November 2023 (32 papers, 21 on this page)

[32033] doi:10.1038/s41586-023-06758-2 [paper, repository]

Sequential appetite suppression by oral and visceral feedback to the brainstem.

Journal: Nature

Authors' code: mathworks.com/products/matlab (no license)

Status: code verified

[32034] doi:10.1038/s41598-023-46040-z [paper, repository]

Frontoparietal functional connectivity moderates the link between time spent on social media and subsequent negative affect in daily life.

Journal: Scientific reports

Authors' code: cnlab/social_media_brain (no license), dalejn/cleanBib (MIT)

Status: code verified, 12 files readable, 5 matches

[32035] doi:10.1038/s41598-023-46852-z [paper, repository]

Mutant huntingtin confers cell-autonomous phenotypes on Huntington's disease iPSC-derived microglia.

Journal: Scientific reports

Authors' code: hail-is/hail (MIT)

Status: code verified, 1,654 files readable, 3 matches

[32036] doi:10.1038/s42003-023-05553-z [paper, repository]

Phylogenetic comparative analysis of the cerebello-cerebral system in 34 species highlights primate-general expansion of cerebellar crura I-II.

Journal: Communications biology

Authors' code: NevMagi/34primates_cerebellum (Apache-2.0), Zenodo 10054902 (CC-BY-4.0), Zenodo 10054901 (CC-BY-4.0)

Status: code verified, 21 files readable, 15 matches

[32037] doi:10.1080/01658107.2023.2281433 [paper, data]

The Impact of Valsalva Manoeuvres and Exercise on Intracranial Pressure and Cerebrovascular Dynamics in Idiopathic Intracranial Hypertension.

Journal: Neuro-ophthalmology (Aeolus Press)

Status: data only, 1 dataset cited

[32038] doi:10.1091/mbc.e23-07-0269 [paper, repository]

Excess phosphoserine-129 α-synuclein induces synaptic vesicle trafficking and declustering defects at a vertebrate synapse.

Journal: Molecular biology of the cell

Authors' code: jaqulinwallace/MBL-Morgan-Lab-Analysis (no license)

Status: code verified, 5 files readable, 4 matches

[32039] doi:10.1093/psyrad/kkad026 [paper, repository]

Data-driven multimodal fusion: approaches and applications in psychiatric research.

Journal: Psychoradiology

Authors' code: trendscenter.org/software/fit (no license), fsl.fmrib.ox.ac.uk/fsl/fslwiki (no license), rsilva8/MISA (no license), weikanggong/BigFLICA (no license), weikanggong/SuperBigFLICA (no license)

Status: code verified, 113 files readable, 1 match

[32040] doi:10.1098/rsob.230158 [paper, repository]

RNA binding protein AUF1/HNRNPD regulates nuclear export, stability and translation of <i>SNCA</i> transcripts.

Journal: Open biology

Authors' code: doi:10.6084/m9.figshare.c.6902598 (no license)

Status: code found, still to be checked

[32041] doi:10.1098/rsob.230217 [paper, repository]

Cellular and molecular signatures of motherhood in the adult and ageing rat brain.

Journal: Open biology

Authors' code: doi:10.6084/m9.figshare.c.6924508 (no license)

Status: code found, still to be checked

[32042] doi:10.1098/rspb.2023.1749 [paper, repository]

Multiple rod layers increase the speed and sensitivity of vision in nocturnal reef fishes.

Journal: Proceedings. Biological sciences

Authors' code: doi:10.6084/m9.figshare.c.6917874 (no license)

Status: code found, still to be checked

[32043] doi:10.1128/spectrum.02580-23 [paper, repository]

Mouse intestinal microbiome modulation by oral administration of a GABA-producing <i>Bifidobacterium adolescentis</i> strain.

Journal: Microbiology spectrum

Authors' code: ncbi.nlm.nih.gov/bioproject/956357 (no license), ncbi.nlm.nih.gov/biosample (no license)

Status: code verified

[32044] doi:10.1162/imag_a_00032 [paper, repository]

The individualized neural tuning model: Precise and generalizable cartography of functional architecture in individual brains.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: datalad.org (no license), feilong (no license)

Status: code verified

[32045] doi:10.1172/jci.insight.167081 [paper, data]

Quisinostat is a brain-penetrant radiosensitizer in glioblastoma.

Journal: JCI insight

Status: data only, 1 dataset cited

[32046] doi:10.1186/s12915-023-01768-y [paper, data]

Convergent evolution of the sensory pits in and within flatworms.

Journal: BMC biology

Status: data only, 1 dataset cited

[32047] doi:10.1371/journal.pone.0286512 [paper, data]

Sound-encoded faces activate the left fusiform face area in the early blind.

Journal: PloS one

Status: data only, 1 dataset cited

[32048] doi:10.1523/eneuro.0157-23.2023 [paper, repository]

A Network Model of the Modulation of γ Oscillations by NMDA Receptors in Cerebral Cortex.

Journal: eNeuro

Authors' code: modeldb:266508 (no license)

Status: code found, still to be checked

[32049] doi:10.1523/jneurosci.0353-23.2023 [paper]

Prostaglandin E₂ Induces Long-Lasting Inhibition of Noradrenergic Neurons in the Locus Coeruleus and Moderates the Behavioral Response to Stressors.

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

Status: code on request

[32050] doi:10.3389/fbioe.2023.1250102 [paper, repository]

Integrated software for multi-dimensional analysis of motion using tracking, electrophysiology, and sensor signals.

Journal: Frontiers in bioengineering and biotechnology

Authors' code: BoullandLab/MotionAnalyser (GPL-2.0)

Status: code verified, 3 files readable, 8 matches

[32051] doi:10.3390/e25121574 [paper, data]

Interpretability Is in the Mind of the Beholder: A Causal Framework for Human-Interpretable Representation Learning.

Journal: Entropy (Basel, Switzerland)

Status: data only, 1 dataset cited

[32052] doi:10.7554/elife.84897 [paper, repository]

ACC neural ensemble dynamics are structured by strategy prevalence.

Journal: eLife

Authors' code: mathworks.com/matlabcentral/fileexchange (no license)

Status: code found, still to be checked

[32053] doi:10.7717/peerj-cs.1663 [paper, repository]

A novel automated Parkinson's disease identification approach using deep learning and EEG.

Journal: PeerJ. Computer science

Authors' code: supp:PMC10703017/peerj-cs-09-1663-s001.py (no license)

Status: code verified, 1 file readable

Tuesday, 21 November 2023 (22 papers)

[32054] doi:10.1016/j.heliyon.2023.e22536 [paper, data]

Brain tumor feature extraction and edge enhancement algorithm based on U-Net network.

Journal: Heliyon

Status: data only, 1 dataset cited

[32055] doi:10.1016/j.isci.2023.108498 [paper, data]

Simulated vestibular spatial disorientation mouse model under coupled rotation revealing potential involvement of Slc17a6.

Journal: iScience

Status: code on request, 1 dataset cited

[32056] doi:10.1038/s41467-023-43139-9 [paper, repository]

Heterogeneous encoding of temporal stimuli in the cerebellar cortex.

Journal: Nature communications

Authors' code: NarainNeuro/CerebellarHeterogeneity_NC_2023 (no license)

Status: dead link

[32057] doi:10.1038/s41467-023-43293-0 [paper, data]

Small molecule regulators of microRNAs identified by high-throughput screen coupled with high-throughput sequencing.

Journal: Nature communications

Status: data only, 1 dataset cited

[32058] doi:10.1038/s41598-023-45897-4 [paper, repository]

Visual objects approaching the body modulate subsequent somatosensory processing at 4 months of age.

Journal: Scientific reports

Authors' code: OSF jg7xf (no license)

Status: code verified, 5 files readable

[32059] doi:10.1038/s41598-023-47563-1 [paper, repository]

Diffusion MRI anomaly detection in glioma patients.

Journal: Scientific reports

Authors' code: JarekE/Anomaly-detection-in-diffusion-MRI-for-brain-tumor-patients (no license)

Status: code verified, 17 files readable, 2 matches

[32060] doi:10.1038/s41598-023-47627-2 [paper, data]

Extracellular vesicles of human glial cells exert neuroprotective effects via brain miRNA modulation in a rat model of traumatic brain injury.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32061] doi:10.1073/pnas.2306525120 [paper, repository]

Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species.

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

Authors' code: ccluri/metabolic_spiking (GPL-3.0)

Status: code verified, 36 files readable

[32062] doi:10.1080/20008066.2023.2281187 [paper, data]

How does it feel? An exploration of neurobiological and clinical correlates of alexithymia in trauma-exposed police-officers with and without PTSD.

Journal: European journal of psychotraumatology

Status: data only, 1 dataset cited

[32063] doi:10.1080/20008066.2023.2281971 [paper, repository]

The stress-buffering role of friendships in young people with childhood threat experiences: a preliminary report.

Journal: European journal of psychotraumatology

Authors' code: OSF mdfhw (no license)

Status: code verified, 6 files readable, 10 matches

[32064] doi:10.1083/jcb.202305048 [paper, repository]

Sirtuin3 ensures the metabolic plasticity of neurotransmission during glucose deprivation.

Journal: The Journal of cell biology

Authors' code: doi:10.5061/dryad.9p8cz8wn3 (no license)

Status: code verified

[32065] doi:10.1162/imag_a_00034 [paper, data]

FastSurfer-HypVINN: Automated sub-segmentation of the hypothalamus and adjacent structures on high-resolutional brain MRI.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: data only, 4 datasets cited

[32066] doi:10.12688/wellcomeopenres.19187.2 [paper, repository]

Association between circulating inflammatory biomarkers and functional outcome or perihaematomal oedema after ICH: a systematic review & meta-analysis.

Journal: Wellcome open research

Authors' code: Jack-Barrington/ICH_Biomarkers_Meta_Analysis (CC0-1.0), Zenodo 7732800 (CC-BY-4.0), Zenodo 7732801 (CC-BY-4.0)

Status: code verified, 7 files readable, 1 match

[32067] doi:10.1523/eneuro.0111-23.2023 [paper, repository]

A Two-Stage Automatic System for Detection of Interictal Epileptiform Discharges from Scalp Electroencephalograms.

Journal: eNeuro

Authors' code: opop08/scalp_EEG_classification (no license)

Status: code verified, 2 files readable, 2 matches

[32068] doi:10.1523/eneuro.0135-23.2023 [paper, repository]

Reanalysis of EphA3 Knock-In Double Maps in Mouse Suggests That Stochasticity in Topographic Map Formation Acts at the Retina Rather than between Competing Mechanisms at the Colliculus.

Journal: eNeuro

Authors' code: Hjorthmedh/RetinalMap (GPL-2.0)

Status: code verified, 135 files readable, 4 matches

[32069] doi:10.1523/eneuro.0274-23.2023 [paper, repository]

An Integrated Platform for <i>In Vivo</i> Electrophysiology in Spatial Cognition Experiments.

Journal: eNeuro

Authors' code: OSF svtzr (no license)

Status: code verified, 61 files readable, 2 matches

[32070] doi:10.15252/embr.202357269 [paper, data]

The 5:2 diet does not increase adult hippocampal neurogenesis or enhance spatial memory in mice.

Journal: EMBO reports

Status: data only, 1 dataset cited

[32071] doi:10.3390/cells12232668 [paper, data]

Patterns of Gene Expression, Splicing, and Allele-Specific Expression Vary among Macular Tissues and Clinical Stages of Age-Related Macular Degeneration.

Journal: Cells

Status: data only, 2 datasets cited

[32072] doi:10.7554/elife.83645 [paper, repository]

The shared and unique neural correlates of personal semantic, general semantic, and episodic memory.

Journal: eLife

Authors' code: OSF py5k6 (no license)

Status: code verified, 1 file readable

[32073] doi:10.7554/elife.86507 [paper, repository]

Single-cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration.

Journal: eLife

Authors' code: fbnrst/celotto_2023 (no license)

Status: code verified, 2 files readable, 8 matches

[32074] doi:10.7554/elife.91406 [paper, repository]

Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals.

Journal: eLife

Authors' code: wuquan723/Ferret-single-cell-data-from-Matsuzaki-lab (no license)

Status: code verified, 5 files readable, 7 matches

[32075] doi:10.7717/peerj-cs.1684 [paper, repository]

RDET stacking classifier: a novel machine learning based approach for stroke prediction using imbalance data.

Journal: PeerJ. Computer science

Authors' code: supp:PMC10703010/peerj-cs-09-1684-s001.ipynb (no license)

Status: code verified

Monday, 20 November 2023 (33 papers)

[32076] doi:10.1002/alz.13546 [paper, data]

Microglial immunometabolism endophenotypes contribute to sex difference in Alzheimer's disease.

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

Status: data only, 1 dataset cited

[32077] doi:10.1002/hbm.26531 [paper, repository]

The intra-individual reliability of <sup>1</sup> H-MRS measurement in the anterior cingulate cortex across 1 year.

Journal: Human brain mapping

Authors' code: mengyunwang/bbsc (GPL-3.0)

Status: code verified, 106 files readable, 8 matches

[32078] doi:10.1007/s00429-023-02718-8 [paper, repository]

Childhood development of brain white matter myelin: a longitudinal T1w/T2w-ratio study.

Journal: Brain structure & function

Authors' code: ldipnall/Childhood-Development-of-Brain-White-Matter-Myelin-A-Longitudinal-T1w-T2w-ratio-Study (no license)

Status: code verified, 3 files readable, 1 match

[32079] doi:10.1007/s12021-023-09647-1 [paper, repository]

High-Density Exploration of Activity States in a Multi-Area Brain Model.

Journal: Neuroinformatics

Authors' code: davidaquilue/TVBAdEx_ParSweep (no license)

Status: code verified, 6 files readable

[32080] doi:10.1016/j.clinph.2023.11.007 [paper, repository]

Sensory event-related potential morphology predicts age in premature infants.

Journal: Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology

Authors' code: paediatric_neuroimaging/sensory-brain-age-model (no license)

Status: code verified, 6 files readable, 2 matches

[32081] doi:10.1016/j.isci.2023.108497 [paper, data]

FEZ1 participates in human embryonic brain development by modulating neuronal progenitor subpopulation specification and migrations.

Journal: iScience

Status: code on request, 1 dataset cited

[32082] doi:10.1016/j.nbd.2023.106359 [paper, data]

Sex-specific developmental alterations in DYRK1A expression in the brain of a Down syndrome mouse model.

Journal: Neurobiology of disease

Status: data only, 1 dataset cited

[32083] doi:10.1038/s41380-023-02318-2 [paper, repository]

Electroconvulsive therapy-induced volumetric brain changes converge on a common causal circuit in depression.

Journal: Molecular psychiatry

Authors' code: argyelan/publications (MIT)

Status: code verified, 10 files readable

[32084] doi:10.1038/s41467-023-43053-0 [paper, repository]

Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females.

Journal: Nature communications

Authors' code: Zenodo 8398047 (other-open), Zenodo 8395536 (other-open), kyriakisdimitrios/copimmunopd (no license), dii-lih-luxembourg/copimmunopd_clustering (MIT)

Status: code verified, 40 files readable, 7 matches

[32085] doi:10.1038/s41467-023-43131-3 [paper, data]

Mobilization of endocannabinoids by midbrain dopamine neurons is required for the encoding of reward prediction.

Journal: Nature communications

Status: data only, 1 dataset cited

[32086] doi:10.1038/s41467-023-43224-z [paper, data]

Brain-to-gut trafficking of alpha-synuclein by CD11c<sup>+</sup> cells in a mouse model of Parkinson's disease.

Journal: Nature communications

Status: data only, 1 dataset cited

[32087] doi:10.1038/s41467-023-43227-w [paper, repository]

Synaptic mechanisms for associative learning in the cerebellar nuclei.

Journal: Nature communications

Authors' code: BroRobin/SynMechCN (no license)

Status: code verified, 54 files readable, 12 matches

[32088] doi:10.1038/s41467-023-43271-6 [paper]

Dopamine receptor activation regulates reward expectancy signals during cognitive control in primate prefrontal neurons.

Journal: Nature communications

Status: code on request

[32089] doi:10.1038/s41559-023-02249-9 [paper, repository]

Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish.

Journal: Nature ecology & evolution

Authors' code: figshare 23805702 (CC-BY-4.0)

Status: code verified, 3 files readable, 7 matches

[32090] doi:10.1038/s41592-023-02059-8 [paper, repository]

Multi-layered maps of neuropil with segmentation-guided contrastive learning.

Journal: Nature methods

Authors' code: google-research/connectomics (Apache-2.0), Zenodo 5539913 (other-open), seung-lab/kimimaro (GPL-3.0)

Status: code verified, 189 files readable, 9 matches

[32091] doi:10.1038/s41593-023-01490-6 [paper, repository]

Facemap: a framework for modeling neural activity based on orofacial tracking.

Journal: Nature neuroscience

Authors' code: janelia-idf/bias (Apache-2.0), mouseland/facemap (GPL-3.0)

Status: code verified, 176 files readable, 14 matches

[32092] doi:10.1038/s41597-023-02645-7 [paper, repository]

Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases.

Journal: Scientific data

Authors' code: bsmn/bsmn-pipeline (no license), Zenodo 4321679 (other-open), apuapaquola/pyslavseq (no license), PatrickJReed/Longboard (MIT)

Status: code verified, 113 files readable, 4 matches

[32093] doi:10.1038/s42003-023-05548-w [paper, repository]

Omics data integration suggests a potential idiopathic Parkinson's disease signature.

Journal: Communications biology

Authors' code: gitlab.lcsb.uni.lu/dvb/zagare_2022 (Apache-2.0)

Status: code verified, 14 files readable, 5 matches

[32094] doi:10.1038/s42003-023-05566-8 [paper, repository]

Auditory inputs modulate intrinsic neuronal timescales during sleep.

Journal: Communications biology

Authors' code: duodenum96/sleep_paper (GPL-3.0), Zenodo 10080607 (CC-BY-4.0)

Status: code verified, 22 files readable, 2 matches

[32095] doi:10.1073/pnas.2306275120 [paper, repository]

Machine-guided discovery of a real-world rogue wave model.

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

Authors' code: dionhaefner/rogue-wave-discovery (MIT)

Status: code verified, 14 files readable, 9 matches

[32096] doi:10.1111/acel.14044 [paper, data]

Integrative multi-omics analysis reveals the critical role of the PBXIP1 gene in Alzheimer's disease.

Journal: Aging cell

Status: data only, 2 datasets cited

[32097] doi:10.1161/jaha.123.032689 [paper, data]

Contribution of the <i>APOE</i> Genotype to Cognitive Impairment in Individuals With <i>NOTCH3</i> Cysteine-Altering Variants.

Journal: Journal of the American Heart Association

Status: data only, 1 dataset cited

[32098] doi:10.1186/s12915-023-01738-4 [paper, data]

Tissue-specific temperature dependence of RNA editing levels in zebrafish.

Journal: BMC biology

Status: data only, 1 dataset cited

[32099] doi:10.12688/wellcomeopenres.19591.2 [paper, repository]

Predictive Clinical Neuroscience Portal (PCNportal): instant online access to research-grade normative models for clinical neuroscientists.

Journal: Wellcome open research

Authors' code: amarquand/PCNtoolkit (GPL-3.0), Zenodo 7708367 (no license), predictive-clinical-neuroscience/PCNportal (GPL-3.0), Zenodo 5207839 (no license), saigerutherford/evidence_embracing_nm (no license)

Status: code verified, 149 files readable, 4 matches

[32100] doi:10.1371/journal.pbio.3002389 [paper, repository]

The murine meninges acquire lymphoid tissue properties and harbour autoreactive B cells during chronic Trypanosoma brucei infection.

Journal: PLoS biology

Authors' code: Zenodo 7814657 (CC-BY-4.0), Zenodo 10018598 (CC-BY-4.0), Zenodo 18188236 (CC-BY-4.0), Zenodo 18188237 (CC-BY-4.0)

Status: code verified, 7 files readable, 7 matches

[32101] doi:10.1371/journal.pbio.3002399 [paper, repository]

Item-specific neural representations during human sleep support long-term memory.

Journal: PLoS biology

Authors' code: OSF bw94f (no license)

Status: code verified, 15 files readable, 4 matches

[32102] doi:10.1371/journal.pcbi.1011208 [paper, repository]

Overcoming chemotherapy resistance in low-grade gliomas: A computational approach.

Journal: PLoS computational biology

Authors' code: ThibDelo/LGG_resistance (no license), Zenodo 8387519 (other-open), Zenodo 8387520 (other-open)

Status: code verified, 87 files readable, 12 matches

[32103] doi:10.1371/journal.ppat.1011350 [paper, repository]

Oligodendrocyte-derived IL-33 functions as a microglial survival factor during neuroinvasive flavivirus infection.

Journal: PLoS pathogens

Authors' code: OberstLab (no license)

Status: code verified

[32104] doi:10.1523/eneuro.0095-23.2023 [paper, data]

A Somatosensory Computation That Unifies Limbs and Tools.

Journal: eNeuro

Status: data only, 1 dataset cited

[32105] doi:10.15252/embj.2023115030 [paper, data]

Mechanistic basis of ligand efficacy in the calcium-activated chloride channel TMEM16A.

Journal: The EMBO journal

Status: data only, 2 datasets cited

[32106] doi:10.18632/aging.205220 [paper, data]

Identification of tryptophan metabolism-related genes in immunity and immunotherapy in Alzheimer's disease.

Journal: Aging

Status: data only, 1 dataset cited

[32107] doi:10.3389/fmed.2023.1172767 [paper, data]

Deep learning-based magnetic resonance image segmentation technique for application to glioma.

Journal: Frontiers in medicine

Status: data only, 2 datasets cited

[32108] doi:10.3390/ijms242216509 [paper, data]

MiR-138-5p Upregulation during Neuronal Maturation Parallels with an Increase in Neuronal Survival.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Sunday, 19 November 2023 (1 paper)

[32109] doi:10.1016/j.nbas.2023.100101 [paper, data]

Urine-derived cells from the aged donor for the 2D/3D modeling of neural cells via iPSCs.

Journal: Aging brain

Status: data only, 1 dataset cited

Saturday, 18 November 2023 (12 papers)

[32110] doi:10.1016/j.celrep.2023.113471 [paper]

Co-transmitting interneurons in the mouse olfactory bulb regulate olfactory detection and discrimination.

Journal: Cell reports

Status: code on request

[32111] doi:10.1016/j.jbc.2023.105475 [paper]

Antisense oligonucleotides targeting the miR-29b binding site in the GRN mRNA increase progranulin translation.

Journal: The Journal of biological chemistry

Status: data only

[32112] doi:10.1038/s41398-023-02643-8 [paper, repository]

Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure.

Journal: Translational psychiatry

Authors' code: biobakery/kneaddata (MIT), heliosdrm/pwr (GPL-3.0)

Status: code verified, 48 files readable, 1 match

[32113] doi:10.1038/s41467-023-43213-2 [paper, repository]

A primate nigrostriatal atlas of neuronal vulnerability and resilience in a model of Parkinson's disease.

Journal: Nature communications

Authors' code: leitang607/Parkinson_disease (no license)

Status: code verified, 16 files readable, 8 matches

[32114] doi:10.1038/s41467-023-43298-9 [paper, repository]

On-tissue dataset-dependent MALDI-TIMS-MS² bioimaging.

Journal: Nature communications

Authors' code: mzmine/mzmine3 (MIT), mzmine.github.io/mzmine_documentation (no license), SteffenHeu/simsef_py (MIT), Zenodo 8009939 (other-open)

Status: code verified, 2,010 files readable, 9 matches

[32115] doi:10.1038/s41540-023-00317-1 [paper, repository]

Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE.

Journal: NPJ systems biology and applications

Authors' code: jameslu01/TDNODE (MIT)

Status: code verified, 35 files readable, 23 matches

[32116] doi:10.1038/s41598-023-47410-3 [paper, repository]

Aberrations in temporal dynamics of cognitive processing induced by Parkinson's disease and Levodopa.

Journal: Scientific reports

Authors' code: AIRLab-Sharif/Parkinson-PAC (no license)

Status: code verified, 26 files readable

[32117] doi:10.1038/s41598-023-47420-1 [paper, data]

A novel subject-wise dictionary learning approach using multi-subject fMRI spatial and temporal components.

Journal: Scientific reports

Status: code on request, 1 dataset cited

[32118] doi:10.1186/s13321-023-00773-1 [paper, repository]

BBB-PEP-prediction: improved computational model for identification of blood-brain barrier peptides using blending position relative composition specific features and ensemble modeling.

Journal: Journal of cheminformatics

Authors' code: ansar390/bbb-pep-prediction (CC0-1.0)

Status: code verified, 8 files readable, 4 matches

[32119] doi:10.1186/s40708-023-00211-w [paper]

Explainability of random survival forests in predicting conversion risk from mild cognitive impairment to Alzheimer's disease.

Journal: Brain informatics

Status: code on request

[32120] doi:10.3390/ijms242216474 [paper, data]

Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[32121] doi:10.3390/ph16111626 [paper, data]

URB937 Prevents the Development of Mechanical Allodynia in Male Rats with Trigeminal Neuralgia.

Journal: Pharmaceuticals (Basel, Switzerland)

Status: data only, 1 dataset cited

Friday, 17 November 2023 (30 papers)

[32122] doi:10.1007/s11060-023-04508-y [paper, data]

The long non-coding RNA OTX2-AS1 promotes tumor growth and predicts response to BCL-2 inhibition in medulloblastoma.

Journal: Journal of neuro-oncology

Status: data only, 3 datasets cited

[32123] doi:10.1016/j.dcn.2023.101326 [paper, repository]

Developmental coupling of brain iron and intrinsic activity in infants during the first 150 days.

Journal: Developmental cognitive neuroscience

Authors' code: ndar.nih.gov (no license)

Status: code found, still to be checked

[32124] doi:10.1016/j.heliyon.2023.e22431 [paper, data]

Patient-specific warning of epileptic seizure upon shapelets features.

Journal: Heliyon

Status: data only, 1 dataset cited

[32125] doi:10.1016/j.molmet.2023.101837 [paper, repository]

Short-term consumption of highly processed diets varying in macronutrient content impair the sense of smell and brain metabolism in mice.

Journal: Molecular metabolism

Authors' code: NeethuVenugopal/videocrop (no license)

Status: code verified, 4 files readable

[32126] doi:10.1016/j.neuron.2023.10.024 [paper, repository]

Reorganization of adolescent prefrontal cortex circuitry is required for mouse cognitive maturation.

Journal: Neuron

Authors' code: denisecailab/ezTrack (GPL-3.0)

Status: code verified, 9 files readable

[32127] doi:10.1016/j.xpro.2023.102722 [paper, repository]

Protocol for dissecting cascade computational components in neural networks of a visual system.

Journal: STAR protocols

Authors' code: jiankliu/STNMF-SNN (no license)

Status: code verified, 33 files readable, 11 matches

[32128] doi:10.1016/j.ynstr.2023.100589 [paper, data]

Imbalanced glucocorticoid and mineralocorticoid stress hormone receptor function has sex-dependent and independent regulatory effects in the mouse hippocampus.

Journal: Neurobiology of stress

Status: data only, 1 dataset cited

[32129] doi:10.1038/s41398-023-02648-3 [paper, repository]

Transcriptomic analysis reveals mitochondrial pathways associated with distinct adolescent behavioral phenotypes and stress response.

Journal: Translational psychiatry

Authors' code: uc-r.github.io/pca (no license), uc-r.github.io/kmeans_clustering (no license)

Status: code verified

[32130] doi:10.1038/s41467-023-43062-z [paper, repository]

Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations.

Journal: Nature communications

Authors' code: samtools/samtools (MIT), broadinstitute/gatk (Apache-2.0), python.org/downloads (no license), dreichlab/eig (BSD-3-Clause), Kahle-Lab/VOGM (no license)

Status: code verified, 2,195 files readable, 11 matches

[32131] doi:10.1038/s41467-023-43292-1 [paper, repository]

GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21.

Journal: Nature communications

Authors' code: changhuizhong/GitCode (no license)

Status: code verified, 1 file readable, 2 matches

[32132] doi:10.1038/s41598-023-47136-2 [paper, data]

Inferring individual evaluation criteria for reaching trajectories with obstacle avoidance from EEG signals.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32133] doi:10.1080/15592294.2023.2276425 [paper, data]

Analysis of the interplay between MeCP2 and histone H1 during <i>in vitro</i> differentiation of human ReNCell neural progenitor cells.

Journal: Epigenetics

Status: data only, 2 datasets cited

[32134] doi:10.1101/2023.11.16.567403 [paper, repository]

Non-destructive X-ray tomography of brain tissue ultrastructure

Journal: bioRxiv (preprint)

Authors' code: Zenodo 16364653 (MIT), cboschp/ptychostainedtissue (MIT), Zenodo 17233854 (MIT), Zenodo 16364654 (MIT)

Status: code verified, 148 files readable

[32135] doi:10.1117/1.jbo.28.11.116502 [paper, repository]

Multiplane HiLo microscopy with speckle illumination and non-local means denoising.

Journal: Journal of biomedical optics

Authors' code: biomicroscopy/NLM-HiLo (MIT)

Status: code verified, 10 files readable

[32136] doi:10.1126/sciadv.adf8764 [paper, data]

Leukotriene A4 hydrolase inhibition improves age-related cognitive decline via modulation of synaptic function.

Journal: Science advances

Status: data only, 2 datasets cited

[32137] doi:10.1162/imag_a_00031 [paper, repository]

A 7T interleaved fMRS and fMRI study on visual contrast dependency in the human brain.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: mrshub/mm-consensus-data-collection (BSD-3-Clause)

Status: empty repository, 2 files readable

[32138] doi:10.1186/s12888-023-05351-1 [paper, repository]

Effect of aerobic exercise on brain metabolite profiles in the mouse models of methamphetamine addiction: LC-MS-based metabolomics study.

Journal: BMC psychiatry

Authors' code: pan.baidu.com/s/1npdoyfwttxdczxxtlyjysa (no license)

Status: code verified

[32139] doi:10.1186/s12906-023-04247-7 [paper, data]

Brazilian green propolis prevent Alzheimer's disease-like cognitive impairment induced by amyloid beta in mice.

Journal: BMC complementary medicine and therapies

Status: data only, 1 dataset cited

[32140] doi:10.1186/s12974-023-02913-8 [paper, data]

Cytokine enrichment in deep cerebellar nuclei is contributed by multiple glial populations and linked to reduced amyloid plaque pathology.

Journal: Journal of neuroinflammation

Status: data only, 2 datasets cited

[32141] doi:10.1186/s12974-023-02939-y [paper, data]

Ly6C-high monocytes alleviate brain injury in experimental subarachnoid hemorrhage in mice.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[32142] doi:10.1186/s13054-023-04731-z [paper, repository]

Relationship between the shape of intracranial pressure pulse waveform and computed tomography characteristics in patients after traumatic brain injury.

Journal: Critical care (London, England)

Authors' code: CMataczynski/ICP_NN (no license)

Status: code verified, 27 files readable

[32143] doi:10.1186/s13229-023-00577-y [paper]

Increased cerebral lactate levels in adults with autism spectrum disorders compared to non-autistic controls: a magnetic resonance spectroscopy study.

Journal: Molecular autism

Status: code on request

[32144] doi:10.1186/s40478-023-01679-7 [paper, data]

Molecular and functional profiling of chemotolerant cells unveils nucleoside metabolism-dependent vulnerabilities in medulloblastoma.

Journal: Acta neuropathologica communications

Status: data only, 1 dataset cited

[32145] doi:10.1371/journal.pcbi.1011567 [paper, repository]

Information-theoretic analyses of neural data to minimize the effect of researchers' assumptions in predictive coding studies.

Journal: PLoS computational biology

Authors' code: pwollstadt/retinogeniculate_synapse (other), Zenodo 8310751 (other-open), Zenodo 7750021 (other-open)

Status: code verified, 87 files readable, 6 matches

[32146] doi:10.2196/47445 [paper, data]

Artificial Intelligence-Based Methods for Integrating Local and Global Features for Brain Cancer Imaging: Scoping Review.

Journal: JMIR medical informatics

Status: data only, 1 dataset cited

[32147] doi:10.3389/fneur.2023.1266828 [paper, repository]

Psychometric evaluation and reference values for the German Postconcussion Symptom Inventory (PCSI-SR8) in children aged 8-12 years.

Journal: Frontiers in neurology

Authors' code: mzeldovich (no license)

Status: code verified

[32148] doi:10.3390/cancers15225460 [paper, data]

Current Knowledge about the Peritumoral Microenvironment in Glioblastoma.

Journal: Cancers

Status: data only, 1 dataset cited

[32149] doi:10.3390/ncrna9060072 [paper, data]

Ethanol- and PARP-Mediated Regulation of Ribosome-Associated Long Non-Coding RNA (lncRNA) in Pyramidal Neurons.

Journal: Non-coding RNA

Status: data only, 1 dataset cited

[32150] doi:10.7554/elife.84951 [paper, repository]

Neuroimaging and behavioral evidence that violent video games exert no negative effect on human empathy for pain and emotional reactivity to violence.

Journal: eLife

Authors' code: OSF yx423 (no license)

Status: code verified, 2 files readable

[32151] doi:10.7554/elife.89338 [paper, repository]

Single-cell RNAseq analysis of spinal locomotor circuitry in larval zebrafish.

Journal: eLife

Authors' code: JimmyKelly-bio/Single-cell-RNA-seq-analysis-of-spinal-locomotor-circuitry-in-larval-zebrafish (no license)

Status: code verified, 2 files readable, 17 matches

Thursday, 16 November 2023 (36 papers)

[32152] doi:10.1007/s00204-023-03627-9 [paper, data]

Transcriptome analysis of the cerebral cortex of acrylamide-exposed wild-type and IL-1β-knockout mice.

Journal: Archives of toxicology

Status: data only, 1 dataset cited

[32153] doi:10.1016/j.brs.2023.11.005 [paper, repository]

Resting-state background features demonstrate multidien cycles in long-term EEG device recordings.

Journal: Brain stimulation

Authors' code: penn-cnt/RNS_processing_toolbox (no license), wojemann/multidien-cycle-biomarkers (no license)

Status: code verified, 30 files readable, 1 match

[32154] doi:10.1016/j.isci.2023.108451 [paper, data]

Sbp2l contributes to oligodendrocyte maturation through translational control in Tcf7l2 signaling.

Journal: iScience

Status: code on request, 1 dataset cited

[32155] doi:10.1016/j.isci.2023.108476 [paper]

Optimal inhaled oxygen and carbon dioxide concentrations for post-cardiac arrest cerebral reoxygenation and neurological recovery.

Journal: iScience

Status: code on request

[32156] doi:10.1016/j.neuron.2023.10.016 [paper, repository]

Internal-state-dependent control of feeding behavior via hippocampal ghrelin signaling.

Journal: Neuron

Authors' code: MacAskillLab (no license)

Status: code verified

[32157] doi:10.1016/j.nicl.2023.103544 [paper, repository]

A deep learning analysis of stroke onset time prediction and comparison to DWI-FLAIR mismatch.

Journal: NeuroImage. Clinical

Authors' code: prediction2020/dwi-flair-mismatch (no license)

Status: code verified, 110 files readable, 3 matches

[32158] doi:10.1016/j.stemcr.2023.10.014 [paper]

A novel human iPSC model of COL4A1/A2 small vessel disease unveils a key pathogenic role of matrix metalloproteinases.

Journal: Stem cell reports

Status: code on request

[32159] doi:10.1016/j.xpro.2023.102725 [paper]

Protocol for generating embedding-free brain organoids enriched with oligodendrocytes.

Journal: STAR protocols

Status: code on request

[32160] doi:10.1038/s41398-023-02631-y [paper, repository]

Magnetic seizure therapy and electroconvulsive therapy increase aperiodic activity.

Journal: Translational psychiatry

Authors' code: voytekresearch/ect-mst (no license)

Status: code verified, 12 files readable, 6 matches

[32161] doi:10.1038/s41398-023-02634-9 [paper, repository]

Clinical EEG slowing induced by electroconvulsive therapy is better described by increased frontal aperiodic activity.

Journal: Translational psychiatry

Authors' code: voytekresearch/smith_ect (no license)

Status: code verified, 16 files readable, 6 matches

[32162] doi:10.1038/s41398-023-02650-9 [paper]

High state boredom vastly affects psychiatric inpatients and predicts their treatment duration.

Journal: Translational psychiatry

Status: code on request

[32163] doi:10.1038/s41467-023-42746-w [paper, data]

A toolbox of astrocyte-specific, serotype-independent adeno-associated viral vectors using microRNA targeting sequences.

Journal: Nature communications

Status: data only, 1 dataset cited

[32164] doi:10.1038/s41467-023-42931-x [paper, repository]

Online conversion of reconstructed neural morphologies into standardized SWC format.

Journal: Nature communications

Authors' code: hub.docker.com/r/neuromorpho (no license), neuromorpho/xyz2swc (MIT), Zenodo 8429036 (other-open)

Status: code verified, 764 files readable, 4 matches

[32165] doi:10.1038/s41467-023-43150-0 [paper, data]

Mesenchymal stromal cells alleviate depressive and anxiety-like behaviors via a lung vagal-to-brain axis in male mice.

Journal: Nature communications

Status: data only, 2 datasets cited

[32166] doi:10.1038/s41467-023-43218-x [paper, repository]

Topographic axonal projection at single-cell precision supports local retinotopy in the mouse superior colliculus.

Journal: Nature communications

Authors' code: figshare 24158658 (CC-BY-4.0)

Status: code verified, 6 files readable

[32167] doi:10.1038/s41467-023-43237-8 [paper, repository]

Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape.

Journal: Nature communications

Authors' code: doi:10.6084/m9.figshare.c.6858271.v1 (no license), TheWebMonks/meshmonk (Apache-2.0), figshare 7649024 (Apache-2.0), immunogenomics/cov-ldsc (other), Atkinson-Lab/Tractor (MIT)

Status: code verified, 617 files readable, 3 matches

[32168] doi:10.1038/s41467-023-43242-x [paper, data]

Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype.

Journal: Nature communications

Status: data only, 1 dataset cited

[32169] doi:10.1038/s41587-023-01977-4 [paper, data]

Generation of locus coeruleus norepinephrine neurons from human pluripotent stem cells.

Journal: Nature biotechnology

Status: data only, 1 dataset cited

[32170] doi:10.1038/s41593-023-01484-4 [paper, data]

Cryo-EM of Aβ fibrils from mouse models find tg-APP<sub>ArcSwe</sub> fibrils resemble those found in patients with sporadic Alzheimer's disease.

Journal: Nature neuroscience

Status: data only, 1 dataset cited

[32171] doi:10.1038/s43588-023-00544-w [paper, repository]

Predictive analyses of regulatory sequences with EUGENe.

Journal: Nature computational science

Authors' code: ML4GLand/EUGENe (MIT), eugene-tools.readthedocs.io (no license), ML4GLand/EUGENe_paper (CC0-1.0), ML4GLand/SeqData (MIT), ML4GLand/SeqDatasets (MIT), ML4GLand/SeqPro (MIT), ml4gland/tutorials (CC-BY-4.0), ml4gland/use_cases (no license), ML4GLand/SeqExplainer (MIT), tobjores/synthetic-promoter-designs-enabled-by-a-comprehensive-analysis-of-plant-core-promoters (no license), Zenodo 8169774 (CC-BY-4.0), Zenodo 8357440 (other-open), Zenodo 8357432 (other-open)

Status: code verified, 534 files readable, 22 matches

[32172] doi:10.1186/s12916-023-03128-7 [paper, data]

Mood, Activity Participation, and Leisure Engagement Satisfaction (MAPLES): results from a randomised controlled pilot feasibility trial for low mood in acquired brain injury.

Journal: BMC medicine

Status: data only, 1 dataset cited

[32173] doi:10.1186/s12920-023-01728-z [paper, repository]

Perampanel effectiveness in treating ROGDI-related Kohlschütter-Tönz syndrome: first reported case in China and literature review.

Journal: BMC medical genomics

Authors' code: karlnicholas/GeneDoc (no license)

Status: code verified, 223 files readable

[32174] doi:10.1186/s12964-023-01335-6 [paper, data]

Epigenetic-focused CRISPR/Cas9 screen identifies (absent, small, or homeotic)2-like protein (ASH2L) as a regulator of glioblastoma cell survival.

Journal: Cell communication and signaling : CCS

Status: data only, 1 dataset cited

[32175] doi:10.1186/s13024-023-00673-w [paper, repository]

Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons.

Journal: Molecular neurodegeneration

Authors' code: HaoGroup-ProtContLib (no license)

Status: code verified

[32176] doi:10.1186/s13063-023-07720-3 [paper]

Detailed statistical analysis plan for a secondary Bayesian analysis of the SafeBoosC-III trial: a multinational, randomised clinical trial assessing treatment guided by cerebral oximetry monitoring versus usual care in extremely preterm infants.

Journal: Trials

Status: code on request

[32177] doi:10.1186/s41747-023-00389-y [paper, data]

Brainstem anatomy with 7-T MRI: in vivo assessment and ex vivo comparison.

Journal: European radiology experimental

Status: data only, 2 datasets cited

[32178] doi:10.1242/dev.202068 [paper, repository]

Accurate staging of chick embryonic tissues via deep learning of salient features.

Journal: Development (Cambridge, England)

Authors' code: aleju/imgaug (MIT), ianbgroves/chick_embryo_DCNN_classifier (no license), ianbgroves/chick_embryonic_classifier (no license)

Status: code verified, 174 files readable, 3 matches

[32179] doi:10.1371/journal.pone.0285652 [paper, repository]

Songbird mesostriatal dopamine pathways are spatially segregated before the onset of vocal learning.

Journal: PloS one

Authors' code: OSF h78b4 (no license)

Status: code verified, 2 files readable, 1 match

[32180] doi:10.1371/journal.pone.0294612 [paper, data]

Anethole attenuates motor dysfunctions, striatal neuronal activity deficiency and blood brain barrier permeability by decreasing striatal α-synuclein and oxidative stress in rotenone-induced Parkinson's disease of male rats.

Journal: PloS one

Status: data only, 1 dataset cited

[32181] doi:10.26508/lsa.202302237 [paper]

Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposure.

Journal: Life science alliance

Status: data only

[32182] doi:10.3389/fimmu.2023.1237016 [paper, data]

PolySialic acid-nanoparticles inhibit macrophage mediated inflammation through Siglec agonism: a potential treatment for age related macular degeneration.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[32183] doi:10.3389/fmicb.2023.1287271 [paper, data]

<i>Bacteroides vulgatus</i> alleviates dextran sodium sulfate-induced colitis and depression-like behaviour by facilitating gut-brain axis balance.

Journal: Frontiers in microbiology

Status: data only, 1 dataset cited

[32184] doi:10.3389/fncel.2023.1182493 [paper, data]

S-SCAM is essential for synapse formation.

Journal: Frontiers in cellular neuroscience

Status: data only, 1 dataset cited

[32185] doi:10.3390/ijms242216396 [paper, data]

Identification of CDK1, PBK, and CHEK1 as an Oncogenic Signature in Glioblastoma: A Bioinformatics Approach to Repurpose Dapagliflozin as a Therapeutic Agent.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[32186] doi:10.3390/metabo13111153 [paper]

Diffuse Optical Monitoring of Cerebral Hemodynamics and Oxygen Metabolism during and after Cardiopulmonary Bypass: Hematocrit Correction and Neurological Vulnerability.

Journal: Metabolites

Status: code on request

[32187] doi:10.7554/elife.85706 [paper, repository]

Dynamics and maintenance of categorical responses in primary auditory cortex during task engagement.

Journal: eLife

Authors' code: rupeshjnu/A1-Category (GPL-3.0)

Status: code verified, 24 files readable, 4 matches

Wednesday, 15 November 2023 (25 papers)

[32188] doi:10.1007/s00424-023-02871-3 [paper, repository]

Amyloid plaques and normal ageing have differential effects on microglial Ca&lt;sup&gt;2+&lt;/sup&gt; activity in the mouse brain.

Journal: Pflugers Archiv : European journal of physiology

Authors' code: AttwellLab/Microglia (MIT), AttwellLab/MyelinCalcium (MIT), AttwellLab (no license)

Status: code verified, 16 files readable, 2 matches

[32189] doi:10.1016/j.crmeth.2023.100645 [paper, repository]

SpaceWalker enables interactive gradient exploration for spatial transcriptomics data.

Journal: Cell reports methods

Authors' code: alleninstitute/abc_atlas_access (BSD-2-Clause), Zenodo 10017490 (CC-BY-4.0), ManiVaultStudio/SpaceWalker (LGPL-3.0)

Status: code verified, 519 files readable, 1 match

[32190] doi:10.1038/s41467-023-42390-4 [paper, data]

Nucleolar reorganization after cellular stress is orchestrated by SMN shuttling between nuclear compartments.

Journal: Nature communications

Status: data only, 1 dataset cited

[32191] doi:10.1038/s41467-023-42642-3 [paper, repository]

Hippocampal firing fields anchored to a moving object predict homing direction during path-integration-based behavior.

Journal: Nature communications

Authors' code: kevin-allen/ktan (GPL-3.0), Mrymna/Jazi_et.al_2023_noInt (no license), Zenodo 8356898 (other-open)

Status: code verified, 65 files readable, 17 matches

[32192] doi:10.1038/s41467-023-42964-2 [paper, repository]

Altered corollary discharge signaling in the auditory cortex of a mouse model of schizophrenia predisposition.

Journal: Nature communications

Authors' code: torfisigurdsson/22q11CDPaper (no license), Zenodo 8414756 (other-open)

Status: code verified, 2 files readable, 5 matches

[32193] doi:10.1038/s41586-023-06720-2 [paper, repository]

Embryo-scale reverse genetics at single-cell resolution.

Journal: Nature

Authors' code: bbi-lab/bbi-dmux (other), bbi-lab/bbi-sci (other), cole-trapnell-lab/sdg-zfish (MIT)

Status: code verified, 68 files readable, 16 matches

[32194] doi:10.1080/20008066.2023.2272477 [paper, repository]

Posttraumatic growth EEG neuromarkers: translational neural comparisons with resilience and PTSD in trauma-exposed healthy adults.

Journal: European journal of psychotraumatology

Authors' code: jnvandermeer/nf-rtime-preview (GPL-2.0)

Status: code verified, 368 files readable, 3 matches

[32195] doi:10.1093/noajnl/vdad151 [paper, data]

Structural connectome-based predictive modeling of cognitive deficits in treated glioma patients.

Journal: Neuro-oncology advances

Status: data only, 1 dataset cited

[32196] doi:10.1098/rsif.2023.0428 [paper, repository]

Cortex-driven cytoplasmic flows in elongated cells: fluid mechanics and application to nuclear transport in <i>Drosophila</i> embryos.

Journal: Journal of the Royal Society, Interface

Authors' code: Zenodo 8398819 (CC-BY-4.0)

Status: code verified, 23 files readable, 4 matches

[32197] doi:10.1098/rspb.2023.1945 [paper, repository]

Early life adversity jointly regulates body-mass index and working memory development.

Journal: Proceedings. Biological sciences

Authors' code: OSF ezscm (no license), doi:10.6084/m9.figshare.c.6902614 (no license)

Status: code verified, 11 files readable, 8 matches

[32198] doi:10.1101/2023.11.15.565967 [paper, data]

Creation of de novo cryptic splicing for ALS/FTD precision medicine

Journal: bioRxiv (preprint)

Status: data only, 1 dataset cited

[32199] doi:10.1126/sciadv.adj3906 [paper, repository]

Reconstructing visual illusory experiences from human brain activity.

Journal: Science advances

Authors' code: bvlc/caffe (BSD-2-Clause), KamitaniLab/DeepImageReconstruction (no license), Zenodo 10037569 (CC-BY-4.0), KamitaniLab/IllusionReconstruction (no license)

Status: code verified, 465 files readable, 12 matches

[32200] doi:10.1152/jn.00275.2023 [paper, repository]

Revisiting a classical theory of sensory specificity: assessing consistency and stability of thermosensitive spots.

Journal: Journal of neurophysiology

Authors' code: iezqrom/publication-thermal-spots-quality-location-inconsistent (no license), Zenodo 10091459 (CC-BY-4.0)

Status: code verified, 28 files readable

[32201] doi:10.1162/imag_a_00030 [paper]

High sensitivity mapping of brain-wide functional networks in awake mice using simultaneous multi-slice fUS imaging.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: code on request

[32202] doi:10.1186/s12859-023-05535-2 [paper, repository]

PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery.

Journal: BMC bioinformatics

Authors' code: wu-lab/pathexpsurv (no license)

Status: code verified, 6 files readable, 1 match

[32203] doi:10.1186/s12864-023-09778-4 [paper, repository]

Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections.

Journal: BMC genomics

Authors' code: RNAdetective/Congenital_CMV-ZIKV_infections (MPL-2.0)

Status: code verified, 2 files readable

[32204] doi:10.1186/s12916-023-03146-5 [paper, repository]

The effects of creatine supplementation on cognitive performance-a randomised controlled study.

Journal: BMC medicine

Authors' code: OSF xpwkc (no license)

Status: code verified, 1 file readable

[32205] doi:10.1186/s13059-023-03092-8 [paper, data]

Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein.

Journal: Genome biology

Status: data only, 1 dataset cited

[32206] doi:10.1186/s13195-023-01345-z [paper, data]

Neuronal transcriptome, tau and synapse loss in Alzheimer's knock-in mice require prion protein.

Journal: Alzheimer's research & therapy

Status: data only, 1 dataset cited

[32207] doi:10.15252/embr.202357164 [paper, data]

Trained immunity induced by high-salt diet impedes stroke recovery.

Journal: EMBO reports

Status: data only, 2 datasets cited

[32208] doi:10.3389/fneur.2023.1254290 [paper, data]

Migraine and major depression: localizing shared genetic susceptibility in different cell types of the nervous systems.

Journal: Frontiers in neurology

Status: data only, 1 dataset cited

[32209] doi:10.3389/fnins.2023.1278096 [paper]

Modulation of prefrontal couplings by prior belief-related responses in ventromedial prefrontal cortex.

Journal: Frontiers in neuroscience

Status: code on request

[32210] doi:10.3389/fnrgo.2023.1273810 [paper, data]

Workload-dependent hemispheric asymmetries during the emotion-cognition interaction: a close-to-naturalistic fNIRS study.

Journal: Frontiers in neuroergonomics

Status: data only, 2 datasets cited

[32211] doi:10.3389/fpsyg.2023.1198691 [paper, data]

Combining contour and region for closed boundary extraction of a shape.

Journal: Frontiers in psychology

Status: data only, 1 dataset cited

[32212] doi:10.7554/elife.88567 [paper, repository]

Combined transcranial magnetic stimulation and electroencephalography reveals alterations in cortical excitability during pain.

Journal: eLife

Authors' code: nahian92/tms_eeg_preprocessing (GPL-3.0)

Status: code verified, 3 files readable, 2 matches

Tuesday, 14 November 2023 (22 papers)

[32213] doi:10.1007/s00330-023-10414-8 [paper, repository]

Brain age predicted using graph convolutional neural network explains neurodevelopmental trajectory in preterm neonates.

Journal: European radiology

Authors' code: bigting84/Brain-Age-Prediction (no license)

Status: code verified, 6 files readable, 1 match

[32214] doi:10.1016/j.cub.2023.10.039 [paper]

Melanopsin enhances image persistence.

Journal: Current biology : CB

Status: code on request

[32215] doi:10.1016/j.isci.2023.108437 [paper]

Multimodal integration for Barrett's esophagus.

Journal: iScience

Status: code on request

[32216] doi:10.1016/j.isci.2023.108442 [paper, repository]

<i>Tsc2</i> coordinates neuroprogenitor differentiation.

Journal: iScience

Authors' code: vshanka23/tsc_scrna_feliciano (no license)

Status: code verified, 4 files readable, 1 match

[32217] doi:10.1016/j.isci.2023.108443 [paper, data]

Chronic AMPK inactivation slows SHH medulloblastoma progression by inhibiting mTORC1 signaling and depleting tumor stem cells.

Journal: iScience

Status: code on request, 1 dataset cited

[32218] doi:10.1016/j.isci.2023.108457 [paper]

Neural alpha oscillations index context-driven perception of ambiguous vowel sequences.

Journal: iScience

Status: code on request

[32219] doi:10.1016/j.omtm.2023.101158 [paper]

Anti-tau intrabodies: From anti-tau immunoglobulins to the development of functional scFv intrabodies.

Journal: Molecular therapy. Methods & clinical development

Status: code on request

[32220] doi:10.1038/s41419-023-06196-y [paper, data]

The long noncoding RNA nHOTAIRM1 is necessary for differentiation and activity of iPSC-derived spinal motor neurons.

Journal: Cell death & disease

Status: data only, 1 dataset cited

[32221] doi:10.1038/s41467-023-43158-6 [paper, repository]

CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.

Journal: Nature communications

Authors' code: broadinstitute/picard (MIT), kimpenn/chex-seq (no license), kimpenn/chex-analysis (MPL-2.0), Zenodo 8399820 (MPL-2.0), Zenodo 8399827 (MPL-2.0)

Status: code verified, 853 files readable, 27 matches

[32222] doi:10.1038/s41467-023-43252-9 [paper, repository]

Superior colliculus bidirectionally modulates choice activity in frontal cortex.

Journal: Nature communications

Authors' code: NuoLiLabBCM/ThomasYangEtAL2023NC (MIT)

Status: code verified, 60 files readable, 20 matches

[32223] doi:10.1038/s41698-023-00475-9 [paper, repository]

Hyperspectral imaging benchmark based on machine learning for intraoperative brain tumour detection.

Journal: NPJ precision oncology

Authors' code: HIRIS-Lab/InvivoBrainHSI-Benchmark (Apache-2.0)

Status: code verified, 11 files readable, 5 matches

[32224] doi:10.1038/s42003-023-05518-2 [paper]

On the functional brain networks involved in tool-related action understanding.

Journal: Communications biology

Status: code on request

[32225] doi:10.1038/s42003-023-05522-6 [paper, repository]

Multisensory input modulates memory-guided spatial navigation in humans.

Journal: Communications biology

Authors' code: OSF u47mj (no license)

Status: code verified, 2 files readable, 1 match

[32226] doi:10.1073/pnas.2306279120 [paper, repository]

Causal evidence for a coordinated temporal interplay within the language network.

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

Authors' code: OSF tb58w (no license)

Status: empty repository

[32227] doi:10.1073/pnas.2307935120 [paper, repository]

Matrix Product Belief Propagation for reweighted stochastic dynamics over graphs.

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

Authors' code: stecrotti/MatrixProductBP.jl (Apache-2.0)

Status: code verified, 65 files readable, 5 matches

[32228] doi:10.1073/pnas.2309227120 [paper, repository]

Rapid and signal crowdedness-robust in situ sequencing through hybrid block coding.

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

Authors' code: huanglab111/sprint-seq (no license)

Status: code verified, 58 files readable

[32229] doi:10.21105/joss.05268 [paper, repository]

spiketools: a Python package for analyzing single-unit neural activity.

Journal: Journal of open source software

Authors' code: Zenodo 10076024 (Apache-2.0), spiketools/spiketools (Apache-2.0)

Status: code verified, 243 files readable

[32230] doi:10.3389/fnins.2023.1238941 [paper, repository]

Altered neural encoding of vowels in noise does not affect behavioral vowel discrimination in gerbils with age-related hearing loss.

Journal: Frontiers in neuroscience

Authors' code: Zenodo 10370064 (lgpl-3.0-or-later), Zenodo 10370063 (lgpl-3.0-or-later)

Status: code verified, 42 files readable, 5 matches

[32231] doi:10.3389/fnins.2023.1243409 [paper, data]

Effortful and effortless training of executive functions improve brain multiple demand system activities differently: an activation likelihood estimation meta-analysis of functional neuroimaging studies.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[32232] doi:10.7554/elife.87081 [paper, repository]

Human skeletal muscle organoids model fetal myogenesis and sustain uncommitted PAX7 myogenic progenitors.

Journal: eLife

Authors' code: satijalab.org/seurat (no license), cole-trapnell-lab.github.io/monocle3 (no license)

Status: code verified

[32233] doi:10.7554/elife.87691 [paper, repository]

Mesotrode chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice.

Journal: eLife

Authors' code: OSF 67p3s (no license), OSF ke6fg (no license)

Status: code verified, 8 files readable

[32234] doi:10.7554/elife.89766 [paper, data]

Cue- versus reward-encoding basolateral amygdala projections to nucleus accumbens.

Journal: eLife

Status: data only, 1 dataset cited

Monday, 13 November 2023 (25 papers, 22 on this page)

[32235] doi:10.1002/brb3.3327 [paper]

Benefits of a mosaic approach for assessing cortical atrophy in individual multiple sclerosis patients.

Journal: Brain and behavior

Status: code on request

[32236] doi:10.1007/s41999-023-00880-0 [paper]

Trends in frailty in brain tumor care during the COVID-19 pandemic in a nationwide hospital network in Germany.

Journal: European geriatric medicine

Status: code on request

[32237] doi:10.1017/s2633903x23000247 [paper, repository]

A spatial statistical framework for the parametric study of fiber networks: Application to fibronectin deposition by normal and activated fibroblasts.

Journal: Biological imaging

Authors' code: aigrapa/ECM-fiber-graph (no license)

Status: code verified, 82 files readable, 2 matches

[32238] doi:10.1038/s41380-023-02314-6 [paper, repository]

The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment.

Journal: Molecular psychiatry

Authors' code: Susuqu/scRNAseq_flydrug (MIT)

Status: code verified, 5 files readable, 6 matches

[32239] doi:10.1038/s41467-023-42553-3 [paper]

Change detection in the primate auditory cortex through feedback of prediction error signals.

Journal: Nature communications

Status: code on request

[32240] doi:10.1038/s41467-023-42876-1 [paper, data]

Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson's disease mouse model.

Journal: Nature communications

Status: data only, 1 dataset cited

[32241] doi:10.1038/s41593-023-01480-8 [paper, repository]

The APOE-R136S mutation protects against APOE4-driven Tau pathology, neurodegeneration and neuroinflammation.

Journal: Nature neuroscience

Authors' code: gladstone-institutes/YH_MN01_NatureNeuroscience_paper (MIT), Zenodo 8368715 (other-open)

Status: code verified, 86 files readable, 23 matches

[32242] doi:10.1038/s41593-023-01485-3 [paper, repository]

Meta-reinforcement learning via orbitofrontal cortex.

Journal: Nature neuroscience

Authors' code: ryhattori/MetaRL-PRL (MIT), Zenodo 8368718 (other-open)

Status: code verified, 6 files readable, 2 matches

[32243] doi:10.1038/s41598-023-47107-7 [paper, data]

Utilizing deep learning via the 3D U-net neural network for the delineation of brain stroke lesions in MRI image.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32244] doi:10.1038/s42003-023-05483-w [paper, repository]

A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo.

Journal: Communications biology

Authors' code: figshare 24093942 (CC-BY-4.0)

Status: code verified, 116 files readable, 8 matches

[32245] doi:10.1038/s42003-023-05488-5 [paper, repository]

A glutamate-gated chloride channel as the mite-specific target-site of dicofol and other diphenylcarbinol acaricides.

Journal: Communications biology

Authors' code: rmclarklab/BSA (MIT)

Status: code verified, 4 files readable

[32246] doi:10.1038/s43587-023-00519-6 [paper, data]

Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology.

Journal: Nature aging

Status: code on request, 2 datasets cited

[32247] doi:10.1186/s12916-023-03153-6 [paper, repository]

Cardiovascular events and venous thromboembolism after primary malignant or non-malignant brain tumour diagnosis: a population matched cohort study in Wales (United Kingdom).

Journal: BMC medicine

Authors' code: OSF 3fmy5 (no license)

Status: empty repository

[32248] doi:10.1186/s13018-023-04352-w [paper]

Network pharmacology and experimental validation methods to reveal the active compounds and hub targets of Curculigo orchioides Gaertn in rheumatoid arthritis.

Journal: Journal of orthopaedic surgery and research

Status: data only

[32249] doi:10.1186/s13072-023-00522-6 [paper, data]

Differential usage of DNA modifications in neurons, astrocytes, and microglia.

Journal: Epigenetics & chromatin

Status: data only, 10 datasets cited

[32250] doi:10.1186/s13195-023-01335-1 [paper]

Divergent brain regional atrophy and associated fiber disruption in amnestic and non-amnestic MCI.

Journal: Alzheimer's research & therapy

Status: code on request

[32251] doi:10.1371/journal.pcbi.1011027 [paper, repository]

Repetitive transcranial magnetic stimulation (rTMS) triggers dose-dependent homeostatic rewiring in recurrent neuronal networks.

Journal: PLoS computational biology

Authors' code: swathianil/homeostatic_structural_plasticity_rTMS (MIT)

Status: code verified, 9 files readable, 2 matches

[32252] doi:10.2196/48210 [paper, data]

Using Wearable Devices and Speech Data for Personalized Machine Learning in Early Detection of Mental Disorders: Protocol for a Participatory Research Study.

Journal: JMIR research protocols

Status: data only, 1 dataset cited

[32253] doi:10.3389/fnbeh.2023.1289407 [paper, data]

Quantitative and qualitative sex difference in habenula-induced inhibition of midbrain dopamine neurons in the rat.

Journal: Frontiers in behavioral neuroscience

Status: data only, 1 dataset cited

[32254] doi:10.3389/fnhum.2023.1215291 [paper, data]

Transcriptional changes in the rat brain induced by repetitive transcranial magnetic stimulation.

Journal: Frontiers in human neuroscience

Status: data only, 1 dataset cited

[32255] doi:10.3389/fnhum.2023.1277539 [paper, repository]

Encoding of continuous perceptual choices in human early visual cortex.

Journal: Frontiers in human neuroscience

Authors' code: RiccardoBarb/GPR_fMRI (GPL-3.0)

Status: code verified, 71 files readable, 16 matches

[32256] doi:10.3389/fpsyt.2023.1266770 [paper, data]

Lower cortical thickness and increased brain aging in adults with cocaine use disorder.

Journal: Frontiers in psychiatry

Status: data only, 2 datasets cited

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