Every paper, by date: page 148

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 148 of 200: 12 October 2023 to 2 October 2023.

Thursday, 12 October 2023 (35 papers, 28 on this page)

[32929] doi:10.1016/j.scog.2023.100291 [paper, repository]

Intrusive-like memory errors associate with positive schizotypy.

Journal: Schizophrenia research. Cognition

Authors' code: OSF aj49x (no license)

Status: code verified, 1 file readable, 1 match

[32930] doi:10.1016/j.stemcr.2023.09.012 [paper, repository]

PTBP2 attenuation facilitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes.

Journal: Stem cell reports

Authors' code: fenglabbuf/2023_Zhu_et_al (GPL-3.0)

Status: code verified, 5 files readable, 3 matches

[32931] doi:10.1038/s41467-023-41975-3 [paper, repository]

Widefield imaging of rapid pan-cortical voltage dynamics with an indicator evolved for one-photon microscopy.

Journal: Nature communications

Authors' code: JaegerLab/JEDI-1P-Kv_widefield_imaging_preprocessing_pipeline (MIT), JaegerLab/JEDI-1P_Widefiled_Figures_data (BSD-3-Clause), Zenodo 8209936 (other-open), Zenodo 8209969 (other-open), jaegerlab/jedi-1p_widefield_figures_data (BSD-3-Clause)

Status: code verified, 104 files readable, 10 matches

[32932] doi:10.1038/s41467-023-42055-2 [paper, repository]

Shadow imaging for panoptical visualization of brain tissue in vivo.

Journal: Nature communications

Authors' code: tlambert03/LLSpy (MIT)

Status: code verified, 50 files readable, 2 matches

[32933] doi:10.1038/s41467-023-42083-y [paper, repository]

Large-scale recording of neuronal activity in freely-moving mice at cellular resolution.

Journal: Nature communications

Authors' code: figshare 24076851 (CC-BY-4.0)

Status: code verified, 5 files readable, 3 matches

[32934] doi:10.1038/s41467-023-42094-9 [paper]

HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation.

Journal: Nature communications

Status: code on request

[32935] doi:10.1038/s41593-023-01449-7 [paper, repository]

Behavioral and brain responses to verbal stimuli reveal transient periods of cognitive integration of the external world during sleep.

Journal: Nature neuroscience

Authors' code: OSF gbtjd (no license)

Status: code verified, 3 files readable, 4 matches

[32936] doi:10.1038/s41593-023-01459-5 [paper, repository]

Activity in primate visual cortex is minimally driven by spontaneous movements.

Journal: Nature neuroscience

Authors' code: cortex-lab/phy (BSD-3-Clause), NienborgLab/TalluriKang_et_al_2022 (MIT)

Status: code verified, 222 files readable, 16 matches

[32937] doi:10.1038/s41593-023-01460-y [paper, repository]

The combination of Hebbian and predictive plasticity learns invariant object representations in deep sensory networks.

Journal: Nature neuroscience

Authors' code: fmi-basel/latent-predictive-learning (MIT), fzenke/auryn (GPL-3.0), markummitchell.github.io/engauge-digitizer (no license), Zenodo 8252888 (other-open)

Status: code verified, 352 files readable, 19 matches

[32938] doi:10.1038/s41597-023-02609-x [paper, repository]

Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish.

Journal: Scientific data

Authors' code: BenayounLaboratory/Killifish_RNASeq_2023 (MIT)

Status: code verified, 33 files readable, 7 matches

[32939] doi:10.1038/s41598-023-43193-9 [paper, data]

Consistent effects of the genetics of happiness across the lifespan and ancestries in multiple cohorts.

Journal: Scientific reports

Status: data only, 1 dataset cited

[32940] doi:10.1038/s41598-023-43273-w [paper, repository]

A neural signature of social support mitigates negative emotion.

Journal: Scientific reports

Authors' code: OSF 6qts3 (no license)

Status: code verified, 3 files readable, 2 matches

[32941] doi:10.1073/pnas.2312462120 [paper, repository]

Neural evidence of switch processes during semantic and phonetic foraging in human memory.

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

Authors' code: OSF mf5de (no license)

Status: code verified, 50 files readable, 5 matches

[32942] doi:10.1126/sciadv.ade3300 [paper, repository]

Human voltage-gated Na⁺ and K⁺ channel properties underlie sustained fast AP signaling.

Journal: Science advances

Authors' code: AllenInstitute/MIES (BSD-2-Clause), modeldb:8210 (no license)

Status: code verified, 49 files readable

[32943] doi:10.1126/sciadv.ade4511 [paper, data]

Temporal disparity of action potentials triggered in axon initial segments and distal axons in the neocortex.

Journal: Science advances

Status: data only, 1 dataset cited

[32944] doi:10.1126/sciadv.adf3771 [paper, data]

Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy.

Journal: Science advances

Status: data only, 1 dataset cited

[32945] doi:10.1126/sciadv.adg3754 [paper, repository]

Multi-omic profiling of the developing human cerebral cortex at the single-cell level.

Journal: Science advances

Authors' code: Zenodo 7703253 (other-open), xbendl/singlecell-multiomics-developmental-human-brain (MIT)

Status: code verified, 18 files readable, 21 matches

[32946] doi:10.1126/sciadv.adg3844 [paper, repository]

A cellular resolution atlas of Broca's area.

Journal: Science advances

Authors' code: lens-biophotonics/ZetaStitcher (GPL-3.0), Zenodo 7832049 (other-open), balbasty/biccn-broca-i46 (GPL-3.0)

Status: code verified, 710 files readable, 5 matches

[32947] doi:10.1126/sciadv.adh1914 [paper, repository]

A single-cell multi-omic atlas spanning the adult rhesus macaque brain.

Journal: Science advances

Authors' code: scverse/muon (BSD-3-Clause), Zenodo 7925943 (other-open), Zenodo 7925945 (other-open), Zenodo 7925933 (other-open), Zenodo 7925937 (other-open), Zenodo 7925925 (other-open), cayobiobankresearchunit/macaque-brain-atlas (no license), cayobiobankresearchunit/bbi-sci (other), cayobiobankresearchunit/bbi-sciatac-analyze (other), cayobiobankresearchunit/bbi-dmux (other), cayobiobankresearchunit/bbi-sciatac-demux (other)

Status: code verified, 843 files readable, 40 matches

[32948] doi:10.1126/sciadv.adk3986 [paper, repository]

A marmoset brain cell census reveals regional specialization of cellular identities.

Journal: Science advances

Authors' code: Zenodo 8364941 (other-open), klevando/biccn-strataquest-script (no license)

Status: code verified, 6 files readable

[32949] doi:10.1155/2023/2002855 [paper, data]

Classification of Brain Tumor Images Using CNN.

Journal: Computational intelligence and neuroscience

Status: data only, 1 dataset cited

[32950] doi:10.1242/jeb.245597 [paper, repository]

Comparative morphology of the whiskers and faces of mice (Mus musculus) and rats (Rattus norvegicus).

Journal: The Journal of experimental biology

Authors' code: Zenodo 7992354 (other-open)

Status: code verified, 2 files readable

[32951] doi:10.1371/journal.pcbi.1011509 [paper, repository]

Modeling functional cell types in spike train data.

Journal: PLoS computational biology

Authors' code: zdeblick/ClusteredGLMs (no license)

Status: code verified, 22 files readable, 5 matches

[32952] doi:10.1371/journal.pcbi.1011548 [paper, repository]

Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories.

Journal: PLoS computational biology

Authors' code: ec753/event_based_neuron (no license), modeldb:87284 (no license)

Status: code verified, 61 files readable, 2 matches

[32953] doi:10.1371/journal.pone.0291946 [paper, repository]

U-Net based vessel segmentation for murine brains with small micro-magnetic resonance imaging reference datasets.

Journal: PloS one

Authors' code: Zenodo 6821322 (other-open), fhooeaist/biss (MPL-2.0)

Status: code verified, 21 files readable, 2 matches

[32954] doi:10.3389/fimmu.2023.1268909 [paper, data]

Vancomycin-induced gut microbial dysbiosis alters enteric neuron-macrophage interactions during a critical period of postnatal development.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[32955] doi:10.3389/fnagi.2023.1239116 [paper, repository]

Genetic background influences the 5XFAD Alzheimer's disease mouse model brain proteome.

Journal: Frontiers in aging neuroscience

Authors' code: edammer/GOparallel (MIT), baderlab.org/genesets (no license)

Status: code verified, 3 files readable, 3 matches

[32956] doi:10.3389/fneur.2023.1271391 [paper, repository]

Association between lactate/albumin ratio and 28-day all-cause mortality in ischemic stroke patients without reperfusion therapy: a retrospective analysis of the MIMIC-IV database.

Journal: Frontiers in neurology

Authors' code: MIT-LCP/mimic-code (MIT)

Status: code verified, 79 files readable, 4 matches

Wednesday, 11 October 2023 (26 papers)

[32957] doi:10.1002/hbm.26503 [paper, repository]

Distinct roles of delta- and theta-band neural tracking for sharpening and predictive coding of multi-level speech features during spoken language processing.

Journal: Human brain mapping

Authors' code: guangtingmai/hbm26503 (no license)

Status: code verified, 16 files readable, 4 matches

[32958] doi:10.1002/hbm.26508 [paper, data]

Neural correlates of temporal recalibration to delayed auditory feedback of active and passive movements.

Journal: Human brain mapping

Status: data only, 1 dataset cited

[32959] doi:10.1016/j.cub.2023.09.047 [paper, repository]

Overestimation in angular path integration precedes Alzheimer's dementia.

Journal: Current biology : CB

Authors' code: Zenodo 8253734 (other-open), Lenakeiz/GenerativeLinearAngularModelPathIntegration (MIT)

Status: code verified, 84 files readable, 9 matches

[32960] doi:10.1038/s41467-023-41877-4 [paper, repository]

A clock-dependent brake for rhythmic arousal in the dorsomedial hypothalamus.

Journal: Nature communications

Authors' code: Zenodo 8298898 (other-open), mfkeles/fpa-with-eeg (no license)

Status: code verified, 48 files readable, 3 matches

[32961] doi:10.1038/s41467-023-42051-6 [paper, data]

Asymmetric gating of a human hetero-pentameric glycine receptor.

Journal: Nature communications

Status: data only, 1 dataset cited

[32962] doi:10.1038/s41467-023-42124-6 [paper, repository]

Revealing invisible cell phenotypes with conditional generative modeling.

Journal: Nature communications

Authors' code: biocompibens/phenexplain (MIT), NVlabs/stylegan2-ada-pytorch (other), Zenodo 8289732 (other-open)

Status: code verified, 64 files readable, 8 matches

[32963] doi:10.1038/s41586-023-06615-2 [paper, repository]

Ultra-fast deep-learned CNS tumour classification during surgery.

Journal: Nature

Authors' code: marcpaga/sturgeon_dev (other), marcpaga/sturgeon (other), Zenodo 8224892 (other-open), Zenodo 8224879 (other-open)

Status: code verified, 111 files readable, 11 matches

[32964] doi:10.1038/s41586-023-06632-1 [paper, repository]

Flexible circuit mechanisms for context-dependent song sequencing.

Journal: Nature

Authors' code: murthylab/MurthyLab_FlySongSegmenter (no license), murthylab (no license)

Status: code verified, 58 files readable, 3 matches

[32965] doi:10.1038/s41598-023-43956-4 [paper, repository]

Blood biomarker-based classification study for neurodegenerative diseases.

Journal: Scientific reports

Authors' code: Zenodo 4483751 (other-open), jackkelly75/thesis_featureselection_ml_code (no license)

Status: code verified, 143 files readable, 5 matches

[32966] doi:10.1038/s41598-023-44093-8 [paper]

Immunoglobulin superfamily member 3 is required for the vagal neural crest cell migration and enteric neuronal network organization.

Journal: Scientific reports

Status: data only

[32967] doi:10.1038/s41598-023-44230-3 [paper, data]

Miniaturization does not change conserved spider anatomy, a case study on spider Rayforstia (Araneae: Anapidae).

Journal: Scientific reports

Status: data only, 1 dataset cited

[32968] doi:10.1038/s41598-023-44293-2 [paper, repository]

The influence of insight on risky decision making and nucleus accumbens activation.

Journal: Scientific reports

Authors' code: MaxiBecker/Insight_Risk_NAcc (MIT)

Status: code verified, 3 files readable, 2 matches

[32969] doi:10.1038/s42003-023-05396-8 [paper, data]

Stress-induced brain responses are associated with BMI in women.

Journal: Communications biology

Status: code on request, 1 dataset cited

[32970] doi:10.1073/pnas.2300255120 [paper, repository]

Distributed feedforward and feedback cortical processing supports human speech production.

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

Authors' code: flinkerlab/DistributedFeedforwardFeedbackProcessing (BSD-3-Clause)

Status: code verified, 74 files readable, 6 matches

[32971] doi:10.1093/psyrad/kkad022 [paper, data]

Visualizing the mind's eye: a future perspective on applications of image reconstruction from brain signals to psychiatry.

Journal: Psychoradiology

Status: data only, 1 dataset cited

[32972] doi:10.1098/rsif.2023.0384 [paper, repository]

Rapid, non-invasive, <i>in vivo</i> measurement of tissue mechanical properties using gravitational loading and a nonlinear virtual fields method.

Journal: Journal of the Royal Society, Interface

Authors' code: OSF b5e6s (no license)

Status: code verified, 2 files readable

[32973] doi:10.1128/msphere.00431-23 [paper, data]

Gut microbiota-associated taurine metabolism dysregulation in a mouse model of Parkinson's disease.

Journal: mSphere

Status: data only, 1 dataset cited

[32974] doi:10.1186/s12974-023-02914-7 [paper, data]

Insulin-degrading enzyme (IDE) as a modulator of microglial phenotypes in the context of Alzheimer's disease and brain aging.

Journal: Journal of neuroinflammation

Status: data only, 6 datasets cited

[32975] doi:10.1242/dmm.050376 [paper, data]

A systematic approach identifies p53-DREAM pathway target genes associated with blood or brain abnormalities.

Journal: Disease models & mechanisms

Status: data only, 1 dataset cited

[32976] doi:10.1371/journal.pone.0284127 [paper, data]

Working memory and attention in choice.

Journal: PloS one

Status: data only, 1 dataset cited

[32977] doi:10.1371/journal.pone.0292666 [paper, data]

Safety and function of programmable ventriculo-peritoneal shunt valves: An in vitro 7 Tesla magnetic resonance imaging study.

Journal: PloS one

Status: data only, 1 dataset cited

[32978] doi:10.3389/fmolb.2023.1252178 [paper, data]

Developmental landscape of computational techniques to explore the potential phytochemicals from <i>Punica granatum</i> peels for their antioxidant activity in Alzheimer's disease.

Journal: Frontiers in molecular biosciences

Status: data only, 4 datasets cited

[32979] doi:10.3390/jimaging9100219 [paper, data]

Evaluating Retinal Disease Diagnosis with an Interpretable Lightweight CNN Model Resistant to Adversarial Attacks.

Journal: Journal of imaging

Status: code on request, 3 datasets cited

[32980] doi:10.3390/s23208386 [paper, data]

EEG and ECG-Based Multi-Sensor Fusion Computing for Real-Time Fatigue Driving Recognition Based on Feedback Mechanism.

Journal: Sensors (Basel, Switzerland)

Status: data only, 2 datasets cited

[32981] doi:10.7554/elife.84122 [paper, repository]

Using multi-modal neuroimaging to characterise social brain specialisation in infants.

Journal: eLife

Authors' code: maheensiddiqui91/NIRS-EEG (MIT)

Status: code verified, 4 files readable, 1 match

[32982] doi:10.7554/elife.85223 [paper, repository]

Competing neural representations of choice shape evidence accumulation in humans.

Journal: eLife

Authors' code: kalexandriabond/competing-representations-shape-evidence-accumulation (no license)

Status: code verified, 7 files readable, 2 matches

Tuesday, 10 October 2023 (20 papers)

[32983] doi:10.1002/epi4.12834 [paper]

Bilateral ictal EEG is associated with better memory outcome after hippocampal sclerosis surgery.

Journal: Epilepsia open

Status: code on request

[32984] doi:10.1007/s11357-023-00953-9 [paper]

Practice makes imperfect: stronger implicit interference with practice in individuals at high risk of developing Alzheimer's disease.

Journal: GeroScience

Status: code on request

[32985] doi:10.1016/j.dib.2023.109661 [paper, data]

Simultaneous and independent electroencephalography and magnetic resonance imaging: A multimodal neuroimaging dataset.

Journal: Data in brief

Status: data only, 3 datasets cited

[32986] doi:10.1016/j.heliyon.2023.e20639 [paper, data]

Functional clustering of neuronal signals with FMM mixture models.

Journal: Heliyon

Status: data only, 2 datasets cited

[32987] doi:10.1038/s41398-023-02599-9 [paper, repository]

Predicting individual cases of major adolescent psychiatric conditions with artificial intelligence.

Journal: Translational psychiatry

Authors' code: delacylab/integrated_evolutionary_learning (Apache-2.0)

Status: code verified, 26 files readable, 9 matches

[32988] doi:10.1038/s41467-023-41746-0 [paper, repository]

The medial septum controls hippocampal supra-theta oscillations.

Journal: Nature communications

Authors' code: Zenodo 4312494 (CC-BY-4.0), kiralyb/MS_mod_tSC (CC0-1.0), Zenodo 8197408 (other-open), figshare 22060964 (CC-BY-4.0)

Status: code verified, 85 files readable, 37 matches

[32989] doi:10.1073/pnas.2305290120 [paper, repository]

Trajectories through semantic spaces in schizophrenia and the relationship to ripple bursts.

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

Authors' code: matthewnour/verbal_fluency_trajectories (CC-BY-NC-SA-4.0), YunzheLiu/TDLM (no license)

Status: code verified, 360 files readable, 14 matches

[32990] doi:10.1073/pnas.2307508120 [paper, repository]

The adaptive stochasticity hypothesis: Modeling equifinality, multifinality, and adaptation to adversity.

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

Authors' code: DanAkarca/AdaptiveStochasticity (no license)

Status: code verified, 19 files readable, 9 matches

[32991] doi:10.1093/pnasnexus/pgad299 [paper, repository]

Ribosomal dysregulation: A conserved pathophysiological mechanism in human depression and mouse chronic stress.

Journal: PNAS nexus

Authors' code: MEladawi/Ribosome_paper (no license)

Status: code verified, 4 files readable, 2 matches

[32992] doi:10.1186/s12888-023-05243-4 [paper]

A naturalistic study comparing the efficacy of unilateral and bilateral sequential theta burst stimulation in treating major depression - the U-B-D study protocol.

Journal: BMC psychiatry

Status: code on request

[32993] doi:10.1242/bio.060113 [paper, repository]

Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.

Journal: Biology open

Authors' code: Tammimies-Lab/HNRNPUdeficiency-Mastropasqua-et-al (CC0-1.0)

Status: code verified, 10 files readable, 4 matches

[32994] doi:10.1371/journal.pbio.3002324 [paper, repository]

Abstract perceptual choice signals during action-linked decisions in the human brain.

Journal: PLoS biology

Authors' code: OSF ucgk4 (no license)

Status: code verified, 43 files readable, 4 matches

[32995] doi:10.1371/journal.pone.0289461 [paper, data]

Brain and circulating steroids in an electric fish: Relevance for non-breeding aggression.

Journal: PloS one

Status: data only, 1 dataset cited

[32996] doi:10.1371/journal.pone.0292677 [paper, repository]

IPSO-LSTM hybrid model for predicting online public opinion trends in emergencies.

Journal: PloS one

Authors' code: gitee.com/lll0113/ipso-lstm (no license)

Status: code verified, 4 files readable

[32997] doi:10.15252/msb.202311670 [paper, repository]

CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data.

Journal: Molecular systems biology

Authors' code: hkim240/CellNeighborEX (MIT), scverse/scanpy (BSD-3-Clause), scverse/squidpy (BSD-3-Clause), dmcable/spacexr (GPL-3.0), saeyslab/nichenetr (no license), chris-mcginnis-ucsf/DoubletFinder (no license), YuLab-SMU/clusterProfiler (no license)

Status: code verified, 544 files readable, 11 matches

[32998] doi:10.3389/fphys.2023.1248899 [paper, data]

PreEpiSeizures: description and outcomes of physiological data acquisition using wearable devices during video-EEG monitoring in people with epilepsy.

Journal: Frontiers in physiology

Status: data only, 1 dataset cited

[32999] doi:10.3390/cancers15204912 [paper, data]

Intranasal Delivery of Oncolytic Adenovirus XVir-N-31 via Optimized Shuttle Cells Significantly Extends Survival of Glioblastoma-Bearing Mice.

Journal: Cancers

Status: data only, 1 dataset cited

[33000] doi:10.3390/cancers15204920 [paper, data]

Role of Oxidative Stress in Metabolic Reprogramming of Brain Cancer.

Journal: Cancers

Status: data only, 1 dataset cited

[33001] doi:10.3390/toxics11100848 [paper]

Development of an In Vitro Assessment Method for Chemotherapy-Induced Peripheral Neuropathy (CIPN) by Integrating a Microphysiological System (MPS) with Morphological Deep Learning of Soma and Axonal Images.

Journal: Toxics

Status: code on request

[33002] doi:10.7554/elife.83348 [paper, data]

Tyramine and its <i>Amtyr1</i> receptor modulate attention in honey bees (<i>Apis mellifera</i>).

Journal: eLife

Status: data only, 1 dataset cited

Monday, 9 October 2023 (18 papers)

[33003] doi:10.1002/hbm.26489 [paper, data]

Task-dependent spatial processing in the visual cortex.

Journal: Human brain mapping

Status: data only, 1 dataset cited

[33004] doi:10.1038/s41380-023-02285-8 [paper]

Effects of escitalopram on synaptic density in the healthy human brain: a randomized controlled trial.

Journal: Molecular psychiatry

Status: code on request

[33005] doi:10.1038/s41467-023-41891-6 [paper, repository]

Polarized microtubule remodeling transforms the morphology of reactive microglia and drives cytokine release.

Journal: Nature communications

Authors' code: maxadrian/mg-segmentation (GPL-3.0)

Status: empty repository, 2 files readable

[33006] doi:10.1038/s41591-023-02566-3 [paper, data]

Microglia and complement mediate early corticostriatal synapse loss and cognitive dysfunction in Huntington's disease.

Journal: Nature medicine

Status: code on request, 1 dataset cited

[33007] doi:10.1038/s41593-023-01453-x [paper, data]

Activity map of a cortico-cerebellar loop underlying motor planning.

Journal: Nature neuroscience

Status: code on request, 1 dataset cited

[33008] doi:10.1038/s41598-023-43478-z [paper, repository]

A personalized classification of behavioral severity of autism spectrum disorder using a comprehensive machine learning framework.

Journal: Scientific reports

Authors' code: silk1100/behavioralProject (no license)

Status: code verified, 78 files readable, 7 matches

[33009] doi:10.1038/s41598-023-44355-5 [paper, data]

Mass-univariate analysis of scalp ERPs reveals large effects of gaze fixation location during face processing that only weakly interact with face emotional expression.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33010] doi:10.1038/s42003-023-05400-1 [paper]

Task-based activation and resting-state connectivity predict individual differences in semantic capacity for complex semantic knowledge.

Journal: Communications biology

Status: code on request

[33011] doi:10.1073/pnas.2216942120 [paper, repository]

Different roles of response covariability and its attentional modulation in the sensory cortex and posterior parietal cortex.

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

Authors' code: herrlich10/mripy (MIT), doi:10.6084/m9.figshare.c.6230499.v1 (no license)

Status: code verified, 70 files readable, 3 matches

[33012] doi:10.1073/pnas.2307584120 [paper, repository]

Predicting the attention of others.

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

Authors' code: KirstensGitHub/predicting_attention (no license)

Status: code verified, 362 files readable, 4 matches

[33013] doi:10.1073/pnas.2309843120 [paper, data]

Adaptor protein-3 produces synaptic vesicles that release phasic dopamine.

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

Status: data only, 1 dataset cited

[33014] doi:10.1111/eva.13570 [paper, repository]

Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivore <i>Lynx lynx</i> (Linnaeus, 1758).

Journal: Evolutionary applications

Authors' code: Enricobazzi/Local_adaptation_Eurasian_lynx (no license)

Status: code verified, 33 files readable, 21 matches

[33015] doi:10.1162/imag_a_00020 [paper, data]

Test-retest reliability of the human connectome: An OPM-MEG study.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: code on request, 2 datasets cited

[33016] doi:10.3389/fbioe.2023.1251195 [paper, data]

Accelerating the in vitro emulation of Alzheimer's disease-associated phenotypes using a novel 3D blood-brain barrier neurosphere co-culture model.

Journal: Frontiers in bioengineering and biotechnology

Status: data only, 1 dataset cited

[33017] doi:10.3390/genes14101921 [paper, data]

Genome Sequencing of Consanguineous Family Implicates Ubiquitin-Specific Protease 53 (&lt;i&gt;USP53&lt;/i&gt;) Variant in Psychosis/Schizophrenia: Wild-Type Expression in Murine Hippocampal CA 1-3 and Granular Dentate with AMPA Synapse Interactions.

Journal: Genes

Status: data only, 1 dataset cited

[33018] doi:10.3390/s23198330 [paper]

Classifying Tremor Dominant and Postural Instability and Gait Difficulty Subtypes of Parkinson's Disease from Full-Body Kinematics.

Journal: Sensors (Basel, Switzerland)

Status: code on request

[33019] doi:10.3390/s23198341 [paper, data]

3D Ultrasonic Brain Imaging with Deep Learning Based on Fully Convolutional Networks.

Journal: Sensors (Basel, Switzerland)

Status: data only, 1 dataset cited

[33020] doi:10.7717/peerj.16172 [paper, data]

The gray matter atrophy and related network changes occur in the higher cognitive region rather than the primary sensorimotor cortex after spinal cord injury.

Journal: PeerJ

Status: data only, 1 dataset cited

Sunday, 8 October 2023 (4 papers)

[33021] doi:10.1016/j.jadohealth.2023.08.033 [paper]

Risk Assessment of Maladaptive Behaviors in Adolescents: Nutrition, Screen Time, Prenatal Exposure, Childhood Adversities - Adolescent Brain Cognitive Development Study.

Journal: The Journal of adolescent health : official publication of the Society for Adolescent Medicine

Status: code on request

[33022] doi:10.1080/19336950.2023.2253102 [paper, data]

Overlap in synaptic neurological condition susceptibility pathways and the neural pannexin 1 interactome revealed by bioinformatics analyses.

Journal: Channels (Austin, Tex.)

Status: data only, 2 datasets cited

[33023] doi:10.1111/cpr.13558 [paper, repository]

Integration of human organoids single-cell transcriptomic profiles and human genetics repurposes critical cell type-specific drug targets for severe COVID-19.

Journal: Cell proliferation

Authors' code: mayunlong89/scHuman_organoids_COVID19 (no license), x-burner-ux/scDrugHunter (other)

Status: code verified, 12 files readable, 2 matches

[33024] doi:10.3390/brainsci13101428 [paper, data]

Towards Environment-Aware Fall Risk Assessment: Classifying Walking Surface Conditions Using IMU-Based Gait Data and Deep Learning.

Journal: Brain sciences

Status: data only, 1 dataset cited

Saturday, 7 October 2023 (9 papers)

[33025] doi:10.1016/j.ebiom.2023.104820 [paper, repository]

Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data.

Journal: EBioMedicine

Authors' code: taehojo/c-SWAT (no license)

Status: code verified, 4 files readable, 3 matches

[33026] doi:10.1016/j.ymthe.2023.10.003 [paper, repository]

Transplanted human neural stem cells rescue phenotypes in zQ175 Huntington's disease mice and innervate the striatum.

Journal: Molecular therapy : the journal of the American Society of Gene Therapy

Authors' code: yjzhang/split-seq-pipeline (MIT)

Status: code verified, 14 files readable

[33027] doi:10.1038/s41467-023-41750-4 [paper, repository]

Ketamine evoked disruption of entorhinal and hippocampal spatial maps.

Journal: Nature communications

Authors' code: daharoni/Miniscope_DAQ_Software (MIT), fordanic/image-registration (GPL-3.0), GiocomoLab/Masuda_et_al_2023 (GPL-3.0), Zenodo 7903214 (other-open)

Status: code verified, 577 files readable, 21 matches

[33028] doi:10.1038/s41467-023-41926-y [paper, repository]

Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas.

Journal: Nature communications

Authors' code: lh3/varcmp (no license)

Status: code verified, 8 files readable

[33029] doi:10.1038/s41467-023-42088-7 [paper, data]

Immediate neural impact and incomplete compensation after semantic hub disconnection.

Journal: Nature communications

Status: code on request, 2 datasets cited

[33030] doi:10.1038/s41467-023-42117-5 [paper, data]

Open structure and gating of the Arabidopsis mechanosensitive ion channel MSL10.

Journal: Nature communications

Status: data only, 1 dataset cited

[33031] doi:10.1038/s41598-023-43488-x [paper, repository]

Adaptive structure evolution and biologically plausible synaptic plasticity for recurrent spiking neural networks.

Journal: Scientific reports

Authors' code: braincog-x/brain-cog (Apache-2.0)

Status: code verified, 545 files readable, 2 matches

[33032] doi:10.1038/s41598-023-43547-3 [paper, data]

A phenomenological model of whole brain dynamics using a network of neural oscillators with power-coupling.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33033] doi:10.1186/s13229-023-00570-5 [paper, repository]

EEG functional connectivity in infants at elevated familial likelihood for autism spectrum disorder.

Journal: Molecular autism

Authors' code: lina-usc/asd_infants_eeg_con_paper (MIT)

Status: code verified, 13 files readable, 8 matches

Friday, 6 October 2023 (35 papers)

[33034] doi:10.1007/s00415-023-12015-3 [paper, data]

The value of routine blood work-up in clinical stratification and prognosis of patients with amyotrophic lateral sclerosis.

Journal: Journal of neurology

Status: data only, 1 dataset cited

[33035] doi:10.1016/j.cell.2023.09.004 [paper, repository]

Generative replay underlies compositional inference in the hippocampal-prefrontal circuit.

Journal: Cell

Authors' code: schwartenbeckph/Generative-Replay (no license), YunzheLiu/TDLM (no license)

Status: code verified, 61 files readable, 5 matches

[33036] doi:10.1016/j.isci.2023.108140 [paper]

Amplitude- and frequency-dependent activation of layer II/III neurons by intracortical microstimulation.

Journal: iScience

Status: code on request

[33037] doi:10.1016/j.isci.2023.108152 [paper]

FUS-dependent microRNA deregulations identify TRIB2 as a druggable target for ALS motor neurons.

Journal: iScience

Status: code on request

[33038] doi:10.1016/j.isci.2023.108154 [paper]

Memory ability and retention performance relate differentially to sleep depth and spindle type.

Journal: iScience

Status: code on request

[33039] doi:10.1016/j.isci.2023.108164 [paper, data]

Dissecting the daily feeding pattern: Peripheral CLOCK/CYCLE generate the feeding/fasting episodes and neuronal molecular clocks synchronize them.

Journal: iScience

Status: data only, 1 dataset cited

[33040] doi:10.1016/j.isci.2023.108166 [paper, repository]

Single-cell profiling of glial cells from the mouse amygdala under opioid dependent and withdrawal states.

Journal: iScience

Authors' code: timflutre/trimmomatic (no license), alexdobin/STAR (MIT)

Status: code verified, 367 files readable

[33041] doi:10.1016/j.nicl.2023.103523 [paper, data]

Network connectivity and local transcriptomic vulnerability underpin cortical atrophy progression in Parkinson's disease.

Journal: NeuroImage. Clinical

Status: data only, 1 dataset cited

[33042] doi:10.1038/s41398-023-02614-z [paper, repository]

Melatonin alleviates depression-like behaviors and cognitive dysfunction in mice by regulating the circadian rhythm of AQP4 polarization.

Journal: Translational psychiatry

Authors' code: RWParsons/circacompare (other)

Status: code verified, 15 files readable

[33043] doi:10.1038/s41467-023-41547-5 [paper, repository]

Activity-dependent organization of prefrontal hub-networks for associative learning and signal transformation.

Journal: Nature communications

Authors' code: AbstractGeek/CategoricalScatterplot (MIT), jp.mathworks.com/matlabcentral/fileexchange (no license), hanshuting/graph_ensemble (GPL-3.0), darikoneil/Identification-of-Pattern-Completion-Neurons (GPL-3.0)

Status: code verified, 263 files readable, 7 matches

[33044] doi:10.1038/s41514-023-00119-z [paper, data]

Developing cognitive workload and performance evaluation models using functional brain network analysis.

Journal: npj aging

Status: data only, 1 dataset cited

[33045] doi:10.1038/s41598-023-43152-4 [paper, data]

Seasonal variations of functional connectivity of human brains.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33046] doi:10.1038/s41598-023-43794-4 [paper, data]

Dissociating different temporal stages of emotional word processing by feature-based attention.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33047] doi:10.1038/s41598-023-44183-7 [paper, data]

Deconvolution reveals cell-type-specific transcriptomic changes in the aging mouse brain.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33048] doi:10.1073/pnas.2300258120 [paper, data]

Structure-based design of nanobodies that inhibit seeding of Alzheimer's patient-extracted tau fibrils.

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

Status: data only, 1 dataset cited

[33049] doi:10.1080/19768354.2023.2266006 [paper, data]

Compensatory enhancement of paternal care in maternally neglected mice family.

Journal: Animal cells and systems

Status: data only, 1 dataset cited

[33050] doi:10.1101/2023.10.05.561097 [paper, data]

An integrated transcriptomic cell atlas of human neural organoids

Journal: bioRxiv (preprint)

Status: data only, 2 datasets cited

[33051] doi:10.1111/acel.14005 [paper, data]

Use of ³¹ P magnetisation transfer magnetic resonance spectroscopy to measure ATP changes after 670 nm transcranial photobiomodulation in older adults.

Journal: Aging cell

Status: data only, 1 dataset cited

[33052] doi:10.1126/sciadv.adh0183 [paper, data]

Chronic stress hinders sensory axon regeneration via impairing mitochondrial cristae and OXPHOS.

Journal: Science advances

Status: data only, 1 dataset cited

[33053] doi:10.1126/sciadv.adh0974 [paper, repository]

Multifunctional fibers enable modulation of cortical and deep brain activity during cognitive behavior in macaques.

Journal: Science advances

Authors' code: doi:10.5061/dryad.zkh1893ft (no license), igarwood/NHP_fibers (no license), Zenodo 8151158 (MIT)

Status: code verified, 71 files readable, 6 matches

[33054] doi:10.1126/sciadv.adi1480 [paper, repository]

SpikingJelly: An open-source machine learning infrastructure platform for spike-based intelligence.

Journal: Science advances

Authors' code: fangwei123456/spikingjelly (Apache-2.0), Zenodo 8310901 (CC-BY-4.0)

Status: code verified, 513 files readable, 19 matches

[33055] doi:10.1162/imag_a_00021 [paper, repository]

Family income is not significantly associated with T1w/T2w ratio in the Human Connectome Project in Development.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: dgweissman/hcpd_adversity (GPL-3.0)

Status: code verified, 13 files readable, 5 matches

[33056] doi:10.1162/imag_a_00022 [paper, repository]

The impact of quality control on cortical morphometry comparisons in autism.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: sbedford0/FSQC (GPL-3.0), Qoala-T/QC (BSD-3-Clause)

Status: code verified, 33 files readable, 9 matches

[33057] doi:10.1186/s10194-023-01670-6 [paper, repository]

Increased MRI-based Brain Age in chronic migraine patients.

Journal: The journal of headache and pain

Authors' code: rafaloz/MigraineBA (no license)

Status: code verified, 8 files readable, 8 matches

[33058] doi:10.1186/s12885-023-11418-9 [paper, data]

Epigenomic perturbation of novel EGFR enhancers reduces the proliferative and invasive capacity of glioblastoma and increases sensitivity to temozolomide.

Journal: BMC cancer

Status: data only, 1 dataset cited

[33059] doi:10.1186/s12974-023-02915-6 [paper, repository]

Nisin a probiotic bacteriocin mitigates brain microbiome dysbiosis and Alzheimer's disease-like neuroinflammation triggered by periodontal disease.

Journal: Journal of neuroinflammation

Authors' code: figshare 22586137 (CC-BY-4.0)

Status: code verified

[33060] doi:10.1523/eneuro.0474-22.2023 [paper, repository]

Lateralization and Time-Course of Cortical Phonological Representations during Syllable Production.

Journal: eNeuro

Authors' code: GuentherLab/ecog-clust-paper-code (no license)

Status: code verified, 1,325 files readable, 14 matches

[33061] doi:10.3389/fnins.2023.1132088 [paper, data]

Modality-specific brain representations during automatic processing of face, voice and body expressions.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[33062] doi:10.3389/fnins.2023.1212791 [paper, data]

Physiological and cognitive changes after treatments of cyclophosphamide, methotrexate, and fluorouracil: implications of the gut microbiome and depressive-like behavior.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[33063] doi:10.3389/fnins.2023.1241919 [paper, data]

An experimental platform for stochastic analyses of single serotonergic fibers in the mouse brain.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[33064] doi:10.3389/fphys.2023.1231793 [paper, data]

Cortical oxygen extraction fraction using quantitative BOLD MRI and cerebral blood flow during vasodilation.

Journal: Frontiers in physiology

Status: data only, 1 dataset cited

[33065] doi:10.3389/fvets.2023.1239965 [paper]

A body map of super-enhancers and their function in pig.

Journal: Frontiers in veterinary science

Status: data only

[33066] doi:10.3390/molecules28196956 [paper, data]

The Effect of Abamectin on Locusta Migratoria Neurosecretory Cells and Mid Gut, Using Ultrastructure Examination, Oxidative Stress Study, and In-Silico Molecular Docking.

Journal: Molecules (Basel, Switzerland)

Status: data only, 1 dataset cited

[33067] doi:10.7554/elife.86833 [paper, repository]

Diminishing neuronal acidification by channelrhodopsins with low proton conduction.

Journal: eLife

Authors' code: figshare 24121323 (CC-BY-4.0), figshare 24121317 (CC-BY-4.0), figshare 24121305 (CC-BY-4.0), figshare 24121302 (CC-BY-4.0)

Status: empty repository

[33068] doi:10.7717/peerj.16261 [paper, data]

Neural drive and motor unit characteristics after anterior cruciate ligament reconstruction: implications for quadriceps weakness.

Journal: PeerJ

Status: data only, 1 dataset cited

Thursday, 5 October 2023 (29 papers)

[33069] doi:10.1016/j.isci.2023.108130 [paper]

LRRK2 G2019S promotes astrocytic inflammation induced by oligomeric α-synuclein through NF-κB pathway.

Journal: iScience

Status: code on request

[33070] doi:10.1016/j.isci.2023.108138 [paper, repository]

Scn2a insufficiency alters spontaneous neuronal Ca²⁺ activity in somatosensory cortex during wakefulness.

Journal: iScience

Authors' code: doi:10.5061/dryad.83bk3j9z2 (no license), Zenodo 8411680 (GPL-3.0)

Status: code verified

[33071] doi:10.1016/j.stemcr.2023.09.005 [paper, data]

Rare intercellular material transfer as a confound to interpreting inner retinal neuronal transplantation following internal limiting membrane disruption.

Journal: Stem cell reports

Status: code on request, 1 dataset cited

[33072] doi:10.1038/s41380-023-02281-y [paper, repository]

Astrocytic β-catenin signaling via TCF7L2 regulates synapse development and social behavior.

Journal: Molecular psychiatry

Authors' code: Neuroinflab/pyEcoHAB (LGPL-2.1)

Status: code verified, 39 files readable, 2 matches

[33073] doi:10.1038/s41398-023-02615-y [paper, repository]

Dynamic functional connectivity changes associated with psychiatric traits and cognitive deficits in Cushing's disease.

Journal: Translational psychiatry

Authors' code: psywalkeryanxy/paper_CD_ICA (no license)

Status: code verified, 4 files readable

[33074] doi:10.1038/s41467-023-41928-w [paper, repository]

Fluorescent sensors for imaging of interstitial calcium.

Journal: Nature communications

Authors' code: Zenodo 8355596 (other-open), griesbecklabbiotoolsforbioimaging/valiente-et-al (no license)

Status: code verified, 6 files readable

[33075] doi:10.1038/s41562-023-01706-6 [paper, repository]

Hippocampal neurons code individual episodic memories in humans.

Journal: Nature human behaviour

Authors' code: figshare 14905317 (CC-BY-4.0)

Status: code verified

[33076] doi:10.1038/s41593-023-01452-y [paper, repository]

Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition.

Journal: Nature neuroscience

Authors' code: mcvickerlab/sn_cocaine_rats (MIT)

Status: code verified, 2,000 files readable

[33077] doi:10.1038/s41598-023-43715-5 [paper, repository]

Effects of MRI scanner manufacturers in classification tasks with deep learning models.

Journal: Scientific reports

Authors' code: xmuyzz/3D-CNN-PyTorch (MIT), rkushol/Effects-of-MRI-scanner-manufacturer (MIT), rpomponio/neuroHarmonize (MIT), Jfortin1/ComBatHarmonization (no license)

Status: code verified, 53 files readable, 5 matches

[33078] doi:10.1073/pnas.2204700120 [paper, data]

Endothelial deletion of EPH receptor A4 alters single-cell profile and Tie2/Akap12 signaling to preserve blood-brain barrier integrity.

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

Status: data only, 1 dataset cited

[33079] doi:10.1126/science.adi0576 [paper]

Hormone-mediated neural remodeling orchestrates parenting onset during pregnancy.

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

Status: code on request

[33080] doi:10.1186/s12917-023-03732-y [paper, data]

Application of metagenomics for diagnosis of broilers displaying neurological symptoms.

Journal: BMC veterinary research

Status: data only, 1 dataset cited

[33081] doi:10.1186/s12993-023-00218-7 [paper, repository]

Multivariate multiscale entropy (mMSE) as a tool for understanding the resting-state EEG signal dynamics: the spatial distribution and sex/gender-related differences.

Journal: Behavioral and brain functions : BBF

Authors' code: is-umk/complexity (GPL-3.0)

Status: code verified, 9 files readable, 1 match

[33082] doi:10.1186/s13054-023-04655-8 [paper, data]

The spectrum of sepsis-associated encephalopathy: a clinical perspective.

Journal: Critical care (London, England)

Status: data only, 6 datasets cited

[33083] doi:10.1186/s40001-023-01291-4 [paper, data]

Resveratrol: a potential medication for the prevention and treatment of varicella zoster virus-induced ischemic stroke.

Journal: European journal of medical research

Status: data only, 1 dataset cited

[33084] doi:10.1242/dev.201871 [paper, repository]

Mapping oto-pharyngeal development in a human inner ear organoid model.

Journal: Development (Cambridge, England)

Authors' code: slowkow/ggrepel (GPL-3.0), Koehler-Lab/Inner_Ear_Organoid_Developmental_Atlas (no license), Zenodo 8363670 (CC-BY-4.0)

Status: code verified, 106 files readable, 19 matches

[33085] doi:10.1371/journal.pcbi.1010508 [paper, repository]

Circadian distribution of epileptiform discharges in epilepsy: Candidate mechanisms of variability.

Journal: PLoS computational biology

Authors' code: imarinelli/Marinelli_PLOSCB2022 (no license)

Status: code verified, 14 files readable

[33086] doi:10.1371/journal.pntd.0011657 [paper]

Zika virus diversity in mice is maintained during early vertical transmission from placenta to fetus, but reduced in fetal bodies and brains at late stages of infection.

Journal: PLoS neglected tropical diseases

Status: data only

[33087] doi:10.1371/journal.pone.0290326 [paper, repository]

Common knowledge processing patterns in networks of different systems.

Journal: PloS one

Authors' code: zalandoresearch/fashion-mnist (MIT)

Status: code verified, 14 files readable

[33088] doi:10.1371/journal.pone.0291275 [paper, repository]

Foveal feedback in perceptual processing: Contamination of neural representations and task difficulty effects.

Journal: PloS one

Authors' code: OSF t4yf2 (no license)

Status: empty repository

[33089] doi:10.18632/aging.205084 [paper, data]

Novel diagnostic biomarkers of oxidative stress, immunological characterization and experimental validation in Alzheimer's disease.

Journal: Aging

Status: data only, 1 dataset cited

[33090] doi:10.3389/fnagi.2023.1258315 [paper, repository]

Neuroimaging and serum biomarkers of neurodegeneration and neuroplasticity in Parkinson's disease patients treated by intermittent theta-burst stimulation over the bilateral primary motor area: a randomized, double-blind, sham-controlled, crossover trial study.

Journal: Frontiers in aging neuroscience

Authors' code: CunninghamLab/TMSAnalysisToolBox (GPL-3.0)

Status: code verified, 285 files readable, 3 matches

[33091] doi:10.3389/fnbot.2023.1269848 [paper, repository]

Embodied bidirectional simulation of a spiking cortico-basal ganglia-cerebellar-thalamic brain model and a mouse musculoskeletal body model distributed across computers including the supercomputer Fugaku.

Journal: Frontiers in neurorobotics

Authors' code: Zenodo 3763356 (GPL-2.0), numericalbrainorg/CppRosBridge_demo (MIT)

Status: code verified, 8 files readable

[33092] doi:10.3389/fncel.2023.1275771 [paper, data]

Time-course adaptive changes in hippocampal transcriptome and synaptic function induced by simulated microgravity associated with cognition.

Journal: Frontiers in cellular neuroscience

Status: data only, 1 dataset cited

[33093] doi:10.3389/fnins.2023.1229509 [paper, repository]

Patients with type 1 diabetes and albuminuria have a reduced brain glycolytic capability that is correlated with brain atrophy.

Journal: Frontiers in neuroscience

Authors' code: MarkVestergaard/PCMCalculator (MIT), MarkVestergaard/SBOCalculator (MIT)

Status: code verified, 6 files readable, 5 matches

[33094] doi:10.3389/fnmol.2023.1258823 [paper, data]

Type 2 cytokines sensitize human sensory neurons to itch-associated stimuli.

Journal: Frontiers in molecular neuroscience

Status: data only, 1 dataset cited

[33095] doi:10.3390/diagnostics13193133 [paper, repository]

Video Analysis of Small Bowel Capsule Endoscopy Using a Transformer Network.

Journal: Diagnostics (Basel, Switzerland)

Authors' code: syupoh/VWCE-Net (no license)

Status: code verified, 325 files readable

[33096] doi:10.3390/ijms241914926 [paper, repository]

Transcriptional Dysregulation and Impaired Neuronal Activity in <i>FMR1</i> Knock-Out and Fragile X Patients' iPSC-Derived Models.

Journal: International journal of molecular sciences

Authors' code: Zenodo 3875777 (CC-BY-4.0), Zenodo 3738330 (CC-BY-4.0)

Status: empty repository

[33097] doi:10.7554/elife.88124 [paper, repository]

Thalamic regulation of ocular dominance plasticity in adult visual cortex.

Journal: eLife

Authors' code: heimel/inVivoTools (GPL-2.0), OSF dbhgw (no license)

Status: code verified, 1,789 files readable, 2 matches

Wednesday, 4 October 2023 (27 papers)

[33098] doi:10.1002/hbm.26497 [paper, repository]

Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods.

Journal: Human brain mapping

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

Status: code verified, 108 files readable, 1 match

[33099] doi:10.1002/hbm.26506 [paper, repository]

Pre-movement event-related potentials and multivariate pattern of EEG encode action outcome prediction.

Journal: Human brain mapping

Authors' code: OSF 3qfxb (no license)

Status: empty repository

[33100] doi:10.1002/hbm.26507 [paper, data]

Decreased beta-band activity in left supramarginal gyrus reflects cognitive decline: Evidence from a large clinical dataset in patients with dementia.

Journal: Human brain mapping

Status: data only, 2 datasets cited

[33101] doi:10.1007/s11538-023-01206-8 [paper, repository]

An Adaptive Generalized Leaky Integrate-and-Fire Model for Hippocampal CA1 Pyramidal Neurons and Interneurons.

Journal: Bulletin of mathematical biology

Authors' code: modeldb:267598 (no license), live-papers.brainsimulation.eu (no license)

Status: code verified

[33102] doi:10.1007/s12035-023-03673-5 [paper, data]

Identification of Regulatory Elements in Primary Sensory Neurons Involved in Trauma-Induced Neuropathic Pain.

Journal: Molecular neurobiology

Status: data only, 1 dataset cited

[33103] doi:10.1016/j.dcn.2023.101310 [paper, repository]

Neural evidence for procedural automatization during cognitive development: Intraparietal response to changes in very-small addition problem-size increases with age.

Journal: Developmental cognitive neuroscience

Authors' code: BBL-lab/BBL-batch-system (no license)

Status: code verified, 131 files readable, 8 matches

[33104] doi:10.1016/j.heliyon.2023.e20625 [paper, data]

Early detection of Parkinson's disease: Systematic analysis of the influence of the eyes on quantitative biomarkers in resting state electroencephalography.

Journal: Heliyon

Status: data only, 1 dataset cited

[33105] doi:10.1016/j.jbc.2023.105319 [paper, data]

A PrP EGFR signaling axis controls neural stem cell senescence through modulating cellular energy pathways.

Journal: The Journal of biological chemistry

Status: data only, 1 dataset cited

[33106] doi:10.1016/j.patter.2023.100855 [paper, repository]

A universal workflow for creation, validation, and generalization of detailed neuronal models.

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

Authors' code: BlueBrain/SSCxEModelExamples (CC-BY-4.0), Zenodo 8220219 (CC-BY-4.0)

Status: code verified, 113 files readable, 8 matches

[33107] doi:10.1038/s41586-023-06606-3 [paper, repository]

Bridging two insect flight modes in evolution, physiology and robophysics.

Journal: Nature

Authors' code: agilesystemslab/synch_asynch_sim (no license)

Status: code verified, 21 files readable

[33108] doi:10.1038/s41597-023-02583-4 [paper, repository]

The R package for DICOM to brain imaging data structure conversion.

Journal: Scientific data

Authors' code: bidsconvertr/bidsconvertr (GPL-3.0), bidsconvertr.github.io/usage_notes (no license), Zenodo 8252451 (other-open), wulms/bidsconvertr (GPL-3.0)

Status: code verified, 42 files readable, 15 matches

[33109] doi:10.1111/joa.13961 [paper, data]

The Fuzzy planar cell polarity protein (FUZ), necessary for primary cilium formation, is essential for pituitary development.

Journal: Journal of anatomy

Status: data only, 3 datasets cited

[33110] doi:10.1159/000534343 [paper, data]

Long-Term Acetylcholinesterase Depletion Alters the Levels of Key Synaptic Proteins while Maintaining Neuronal Markers in the Aging Zebrafish (Danio rerio) Brain.

Journal: Gerontology

Status: data only, 1 dataset cited

[33111] doi:10.1186/s12915-023-01709-9 [paper, repository]

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta.

Journal: BMC biology

Authors' code: Zenodo 7267763 (CC-BY-4.0)

Status: code verified, 1 file readable, 3 matches

[33112] doi:10.1186/s12974-023-02908-5 [paper, data]

Cortistatin deficiency reveals a dysfunctional brain endothelium with impaired gene pathways, exacerbated immune activation, and disrupted barrier integrity.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[33113] doi:10.1371/journal.pone.0291305 [paper, repository]

Genetics of vegetarianism: A genome-wide association study.

Journal: PloS one

Authors' code: saigegit.github.io/saige-doc (no license)

Status: code verified

[33114] doi:10.1371/journal.pone.0291631 [paper, data]

Federated learning based futuristic biomedical big-data analysis and standardization.

Journal: PloS one

Status: data only, 1 dataset cited

[33115] doi:10.1371/journal.pone.0292342 [paper, data]

Blue light exposure-dependent improvement in robustness of circadian rest-activity rhythm in aged rats.

Journal: PloS one

Status: data only, 1 dataset cited

[33116] doi:10.15252/emmm.202318144 [paper, repository]

Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma.

Journal: EMBO molecular medicine

Authors' code: wgiese/zebrafish_xenograft_analysis (MIT), ega-archive.org/studies/egas00001007481 (no license)

Status: code verified, 31 files readable, 8 matches

[33117] doi:10.3389/fneur.2023.1258116 [paper, repository]

SWADESH: a multimodal multi-disease brain imaging and neuropsychological database and data analytics platform.

Journal: Frontiers in neurology

Authors' code: rii-mango/Papaya (BSD-3-Clause)

Status: code verified, 74 files readable, 2 matches

[33118] doi:10.3389/fnins.2023.1236876 [paper, data]

Distribution of corpora amylacea in the human midbrain: using synchrotron radiation phase-contrast microtomography, high-field magnetic resonance imaging, and histology.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[33119] doi:10.3389/fnmol.2023.1223798 [paper]

Effect of methanol fixation on single-cell RNA sequencing of the murine dentate gyrus.

Journal: Frontiers in molecular neuroscience

Status: data only

[33120] doi:10.3390/diagnostics13193121 [paper, repository]

Functional FDG-PET: Measurement of Task Related Neural Activity in Humans-A Compartment Model Approach and Comparison to fMRI.

Journal: Diagnostics (Basel, Switzerland)

Authors' code: fil.ion.ucl.ac.uk/spm/software (no license)

Status: code verified

[33121] doi:10.3758/s13428-023-02199-x [paper, repository]

The open toolbox for behavioral research.

Journal: Behavior research methods

Authors' code: gitlab.ruhr-uni-bochum.de/ikn/otbr (CC-BY-SA-4.0)

Status: code verified, 147 files readable, 7 matches

[33122] doi:10.7554/elife.86837 [paper, repository]

A theory of hippocampal theta correlations accounting for extrinsic and intrinsic sequences.

Journal: eLife

Authors' code: yyhhoi/directionalnet (MIT)

Status: code verified, 37 files readable, 8 matches

[33123] doi:10.7554/elife.90431 [paper, data]

Optogenetic activation of visual thalamus generates artificial visual percepts.

Journal: eLife

Status: data only, 1 dataset cited

[33124] doi:10.7759/cureus.46456 [paper, data]

Autosomal Dominant Intellectual Development Disorder-6 (MRD6) Without Seizures Linked to a De Novo Mutation in the grin2b Gene Revealed by Exome Sequencing: A Case Report of a Moroccan Child.

Journal: Cureus

Status: data only, 1 dataset cited

Tuesday, 3 October 2023 (17 papers)

[33125] doi:10.1002/hbm.26454 [paper, data]

Semantic-specific and domain-general mechanisms for integration and update of contextual information.

Journal: Human brain mapping

Status: data only, 1 dataset cited

[33126] doi:10.1002/hbm.26472 [paper]

Identifying canonical and replicable multi-scale intrinsic connectivity networks in 100k+ resting-state fMRI datasets.

Journal: Human brain mapping

Status: code on request

[33127] doi:10.1016/j.celrep.2023.113188 [paper]

Melanocortin-3 receptor expression in AgRP neurons is required for normal activation of the neurons in response to energy deficiency.

Journal: Cell reports

Status: code on request

[33128] doi:10.1038/s41398-023-02597-x [paper, repository]

Long-term effects of prenatal infection on the human brain: a prospective multimodal neuroimaging study.

Journal: Translational psychiatry

Authors' code: ajsuleri/prenatal_infection_multimodal_imaging (GPL-3.0)

Status: code verified, 6 files readable, 13 matches

[33129] doi:10.1038/s41398-023-02600-5 [paper, data]

Effects of vortioxetine on hippocampal-related cognitive impairment induced in rats by androgen deprivation as a model of prostate cancer treatment.

Journal: Translational psychiatry

Status: data only, 1 dataset cited

[33130] doi:10.1038/s41598-023-43686-7 [paper, repository]

Differential gene expression analysis based on linear mixed model corrects false positive inflation for studying quantitative traits.

Journal: Scientific reports

Authors' code: tangjiji199645/LMM_DGE_Pipeline (no license)

Status: code verified, 3 files readable

[33131] doi:10.1117/1.nph.10.4.045001 [paper]

Quantitative hemodynamic imaging: a method to correct the effects of optical properties on laser speckle imaging.

Journal: Neurophotonics

Status: code on request

[33132] doi:10.1186/s12885-023-11433-w [paper, data]

ARPC5 acts as a potential prognostic biomarker that is associated with cell proliferation, migration and immune infiltrate in gliomas.

Journal: BMC cancer

Status: data only, 1 dataset cited

[33133] doi:10.1186/s13059-023-03068-8 [paper, repository]

CEGA: a method for inferring natural selection by comparative population genomic analysis across species.

Journal: Genome biology

Authors' code: ChenHuaLab/CEGA (GPL-2.0), Zenodo 8360249 (GPL-2.0)

Status: code verified, 8 files readable

[33134] doi:10.1186/s13195-023-01311-9 [paper, data]

Identification of methylation-regulated genes modulating microglial phagocytosis in hyperhomocysteinemia-exacerbated Alzheimer's disease.

Journal: Alzheimer's research & therapy

Status: data only, 1 dataset cited

[33135] doi:10.1186/s13578-023-01120-5 [paper, data]

Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer's disease brains.

Journal: Cell & bioscience

Status: code on request, 1 dataset cited

[33136] doi:10.12688/f1000research.129923.2 [paper, repository]

Brain-localized CD4 and CD8 T cells perform correlated random walks and not Levy walks.

Journal: F1000Research

Authors' code: DhruvPatel5701/TcellsInBrain (MIT)

Status: code verified, 16 files readable, 1 match

[33137] doi:10.1371/journal.pbio.3002269 [paper, repository]

Inferred Attractiveness: A generalized mechanism for sexual selection that can maintain variation in traits and preferences over time.

Journal: PLoS biology

Authors' code: OSF r673j (no license)

Status: code verified, 17 files readable

[33138] doi:10.1371/journal.pone.0291978 [paper, data]

Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene.

Journal: PloS one

Status: data only, 2 datasets cited

[33139] doi:10.3389/fimmu.2023.1250055 [paper, data]

Uncovering the neuroprotective effect of vitamin B12 in pneumococcal meningitis: insights into its pleiotropic mode of action at the transcriptional level.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[33140] doi:10.3389/fnut.2023.1257472 [paper, data]

A mixture of Nordic berries improves cognitive function, metabolic function and alters the gut microbiota in C57Bl/6J male mice.

Journal: Frontiers in nutrition

Status: data only, 1 dataset cited

[33141] doi:10.3390/cells12192399 [paper, data]

In Cerebellar Atrophy of 12-Month-Old ATM-Null Mice, Transcriptome Upregulations Concern Most Neurotransmission and Neuropeptide Pathways, While Downregulations Affect Prominently Itpr1, Usp2 and Non-Coding RNA.

Journal: Cells

Status: data only, 1 dataset cited

Monday, 2 October 2023 (33 papers, 11 on this page)

[33142] doi:10.1002/cne.25539 [paper, data]

A multifaceted architectural framework of the mouse claustrum complex.

Journal: The Journal of comparative neurology

Status: data only, 1 dataset cited

[33143] doi:10.1016/j.isci.2023.108110 [paper]

Microglial P2X4 receptors are essential for spinal neurons hyperexcitability and tactile allodynia in male and female neuropathic mice.

Journal: iScience

Status: code on request

[33144] doi:10.1016/j.isci.2023.108113 [paper]

Regional variation in the organization and connectivity of the first synapse in the primate night vision pathway.

Journal: iScience

Status: code on request

[33145] doi:10.1016/j.xpro.2023.102623 [paper, repository]

Protocol to investigate the neural basis for copulation posture of Drosophila using a closed-loop real-time optogenetic system.

Journal: STAR protocols

Authors' code: Zenodo 7780536 (other-open), mjskay/ARTool (GPL), toshi-ara/brunnermunzel (no license)

Status: code verified, 34 files readable, 2 matches

[33146] doi:10.1038/s41398-023-02611-2 [paper, data]

CHD8 regulates gut epithelial cell function and affects autism-related behaviors through the gut-brain axis.

Journal: Translational psychiatry

Status: data only, 1 dataset cited

[33147] doi:10.1038/s41467-023-41881-8 [paper, data]

PIWI-interacting RNA expression regulates pathogenesis in a Caenorhabditis elegans model of Lewy body disease.

Journal: Nature communications

Status: data only, 2 datasets cited

[33148] doi:10.1038/s41592-023-02034-3 [paper, data]

Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration.

Journal: Nature methods

Status: data only, 11 datasets cited

[33149] doi:10.1038/s41593-023-01443-z [paper, repository]

Multilevel visual motion opponency in Drosophila.

Journal: Nature neuroscience

Authors' code: gin.g-node.org/gammer/ammer_et_al_2023 (no license), doi:10.12751/g-node.7v3pe6 (no license)

Status: code verified

[33150] doi:10.1038/s41597-023-02563-8 [paper, data]

Author Correction: Single-nucleus profiling of adult mice sub-ventricular zone after blast-related traumatic brain injury.

Journal: Scientific data

Status: data only, 1 dataset cited

[33151] doi:10.1038/s41598-023-43073-2 [paper, data]

Comparison of virtual reality to physical box and blocks on cortical an neuromuscualar activations in young adults.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33152] doi:10.1038/s41598-023-43526-8 [paper, data]

Movement-related tactile gating in blindness.

Journal: Scientific reports

Status: code on request, 1 dataset cited

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