Every paper, by date: page 149

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 149 of 200: 2 October 2023 to 25 September 2023.

Monday, 2 October 2023 (33 papers, 22 on this page)

[33153] doi:10.1038/s41598-023-43565-1 [paper, repository]

Integrating operant behavior and fiber photometry with the open-source python library Pyfiber.

Journal: Scientific reports

Authors' code: inserm-u1215/pyfiber (GPL-3.0)

Status: code verified, 14 files readable, 3 matches

[33154] doi:10.1038/s42003-023-05273-4 [paper, repository]

Task-specific odorant receptor expression in worker antennae indicates that sensory filters regulate division of labor in ants.

Journal: Communications biology

Authors' code: doi:10.17632/yyg46xmph6.3 (no license)

Status: code verified

[33155] doi:10.1038/s42003-023-05304-0 [paper, data]

Myeloid cell deficiency of the inflammatory transcription factor Stat4 protects long-term synaptic plasticity from the effects of a high-fat, high-cholesterol diet.

Journal: Communications biology

Status: data only, 2 datasets cited

[33156] doi:10.1073/pnas.2301207120 [paper]

Molecular determinants for cold adaptation in an Antarctic Na⁺/K⁺-ATPase.

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

Status: code on request

[33157] doi:10.1073/pnas.2302215120 [paper, data]

Architectural experience influences the processing of others' body expressions.

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

Status: data only, 1 dataset cited

[33158] doi:10.1073/pnas.2310820120 [paper, data]

Grid cells in rats deprived of geometric experience during development.

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

Status: data only, 1 dataset cited

[33159] doi:10.1109/tmi.2023.3273158 [paper, repository]

MisMatch: Calibrated Segmentation via Consistency on Differential Morphological Feature Perturbations With Limited Labels.

Journal: IEEE transactions on medical imaging

Authors' code: moucheng2017/MisMatchSSL (no license)

Status: code verified, 46 files readable, 1 match

[33160] doi:10.1172/jci157515 [paper, repository]

Suppression of food intake by Glp1r/Lepr-coexpressing neurons prevents obesity in mouse models.

Journal: The Journal of clinical investigation

Authors' code: ajtomlinson59/-rupp_tomlinson-jclininvest-2023 (no license)

Status: code verified, 8 files readable, 9 matches

[33161] doi:10.1172/jci162120 [paper, data]

Specific quinone reductase 2 inhibitors reduce metabolic burden and reverse Alzheimer's disease phenotype in mice.

Journal: The Journal of clinical investigation

Status: data only, 1 dataset cited

[33162] doi:10.1177/09727531231194399 [paper, data]

Multiomics Approach Reveal Novel Insights in FUS Driven Juvenile Amyotrophic Lateral Sclerosis: A Family Quartet Analysis.

Journal: Annals of neurosciences

Status: data only, 1 dataset cited

[33163] doi:10.1186/s12871-023-02278-8 [paper, data]

Dexmedetomidine modulates neuronal activity of horizontal limbs of diagonal band via α2 adrenergic receptor in mice.

Journal: BMC anesthesiology

Status: data only, 1 dataset cited

[33164] doi:10.1186/s12880-023-01109-z [paper, repository]

Improving MR image quality with a multi-task model, using convolutional losses.

Journal: BMC medical imaging

Authors' code: brudfors/UniRes (MIT), attilasimko/mri-ac (MIT), Zenodo 3749526 (CC-BY-4.0)

Status: code verified, 30 files readable, 3 matches

[33165] doi:10.1186/s12993-023-00220-z [paper, data]

Causal associations between sleep traits and brain structure: a bidirectional Mendelian randomization study.

Journal: Behavioral and brain functions : BBF

Status: data only, 1 dataset cited

[33166] doi:10.1186/s40478-023-01647-1 [paper, data]

Higher angiotensin-converting enzyme 2 (ACE2) levels in the brain of individuals with Alzheimer's disease.

Journal: Acta neuropathologica communications

Status: data only, 4 datasets cited

[33167] doi:10.1371/journal.pcbi.1011506 [paper, repository]

Mouse visual cortex as a limited resource system that self-learns an ecologically-general representation.

Journal: PLoS computational biology

Authors' code: AllenInstitute/AllenSDK (BSD-2-Clause), neuroailab/mouse-vision (no license)

Status: code verified, 1,148 files readable, 23 matches

[33168] doi:10.1371/journal.pcbi.1011523 [paper, repository]

Particle-based simulations reveal two positive feedback loops allow relocation and stabilization of the polarity site during yeast mating.

Journal: PLoS computational biology

Authors' code: guanhighyun/Indecisive-polarity-behavior (no license)

Status: code verified, 2,000 files readable

[33169] doi:10.1371/journal.pcbi.1011529 [paper, repository]

Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning.

Journal: PLoS computational biology

Authors' code: biomedisa/biomedisa (EUPL-1.2)

Status: code verified, 257 files readable, 7 matches

[33170] doi:10.1371/journal.pgen.1010952 [paper, data]

Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency.

Journal: PLoS genetics

Status: data only, 1 dataset cited

[33171] doi:10.1371/journal.pone.0292049 [paper, data]

A topological classifier to characterize brain states: When shape matters more than variance.

Journal: PloS one

Status: data only, 1 dataset cited

[33172] doi:10.2147/cia.s429440 [paper, data]

Rapamycin Responds to Alzheimer's Disease: A Potential Translational Therapy.

Journal: Clinical interventions in aging

Status: data only, 1 dataset cited

[33173] doi:10.3389/fnins.2023.1219133 [paper, data]

Generation of synthetic EEG data for training algorithms supporting the diagnosis of major depressive disorder.

Journal: Frontiers in neuroscience

Status: data only, 2 datasets cited

[33174] doi:10.3389/fresc.2023.1222892 [paper, data]

Finding functionality: Rasch analysis of the Functionality Appreciation Scale in community-dwelling adults in the US.

Journal: Frontiers in rehabilitation sciences

Status: data only, 2 datasets cited

Sunday, 1 October 2023 (47 papers)

[33175] doi:10.1002/trc2.12429 [paper, repository]

SHIP1 therapeutic target enablement: Identification and evaluation of inhibitors for the treatment of late-onset Alzheimer's disease.

Journal: Alzheimer's & dementia (New York, N. Y.)

Authors' code: Zenodo 7231788 (CC-BY-4.0), Zenodo 6208450 (CC-BY-4.0)

Status: empty repository

[33176] doi:10.1007/978-3-031-43999-5_43 [paper, repository]

Unified Brain MR-Ultrasound Synthesis using Multi-Modal Hierarchical Representations.

Journal: Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention

Authors' code: ReubenDo/MHVAE (MIT)

Status: code verified, 11 files readable

[33177] doi:10.1016/j.celrep.2023.113305 [paper, repository]

High-calorie diets uncouple hypothalamic oxytocin neurons from a gut-to-brain satiation pathway via κ-opioid signaling.

Journal: Cell reports

Authors' code: Zenodo 7673205 (other-open), viktormiok/snRNAseq_RiboTagRNAseq-oxytocin (GPL-3.0)

Status: code verified, 12 files readable, 2 matches

[33178] doi:10.1016/j.isci.2023.108116 [paper]

Distinct effects of AMPAR subunit depletion on spatial memory.

Journal: iScience

Status: code on request

[33179] doi:10.1016/j.stem.2023.09.003 [paper, repository]

Tissue morphology influences the temporal program of human brain organoid development.

Journal: Cell stem cell

Authors' code: rosshandler/Structure-Indentity (no license), jboulanger/Organoid_morphology (no license), Zenodo 8322334 (other-open)

Status: code verified, 40 files readable, 21 matches

[33180] doi:10.1016/j.ynstr.2023.100578 [paper]

Pre-COVID brain network topology prospectively predicts social anxiety alterations during the COVID-19 pandemic.

Journal: Neurobiology of stress

Status: code on request

[33181] doi:10.1038/s41598-023-43611-y [paper]

State-dependent modulation of low-threshold-current-regulated dendritic Ca²⁺ response in thalamic reticular neurons with extracellular electric fields.

Journal: Scientific reports

Status: code on request

[33182] doi:10.1042/bsr20231295 [paper, data]

Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1.

Journal: Bioscience reports

Status: code on request, 2 datasets cited

[33183] doi:10.1093/bioinformatics/btad592 [paper, repository]

MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.

Journal: Bioinformatics (Oxford, England)

Authors' code: bo1929/MuDCoD (MIT)

Status: code verified, 13 files readable, 4 matches

[33184] doi:10.1093/brain/awad129 [paper, data]

Regional spreading pattern is associated with clinical phenotype in amyotrophic lateral sclerosis.

Journal: Brain : a journal of neurology

Status: data only, 1 dataset cited

[33185] doi:10.1093/brain/awad132 [paper, repository]

Bumetanide induces post-traumatic microglia-interneuron contact to promote neurogenesis and recovery.

Journal: Brain : a journal of neurology

Authors' code: glichtner/pystackreg (other)

Status: code verified, 28 files readable

[33186] doi:10.1093/brain/awad133 [paper, data]

C-terminal TMEM106B fragments in human brain correlate with disease-associated TMEM106B haplotypes.

Journal: Brain : a journal of neurology

Status: data only, 2 datasets cited

[33187] doi:10.1093/brain/awad142 [paper, data]

Deep brain stimulation alleviates tics in Tourette syndrome via striatal dopamine transmission.

Journal: Brain : a journal of neurology

Status: data only, 1 dataset cited

[33188] doi:10.1093/brain/awad183 [paper, repository]

Lysosomal polygenic risk is associated with the severity of neuropathology in Lewy body disease.

Journal: Brain : a journal of neurology

Authors' code: lpihlstrom/projects (no license)

Status: code verified, 16 files readable

[33189] doi:10.1093/cercor/bhad307 [paper, repository]

Generation and propagation of bursts of activity in the developing basal ganglia.

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

Authors' code: sebbkw/networkbursts2022 (no license)

Status: code verified, 9 files readable, 12 matches

[33190] doi:10.1093/hmg/ddad121 [paper, data]

AAV9-mediated SMN gene therapy rescues cardiac desmin but not lamin A/C and elastin dysregulation in Smn2B/- spinal muscular atrophy mice.

Journal: Human molecular genetics

Status: data only, 1 dataset cited

[33191] doi:10.1093/hmg/ddad125 [paper, data]

Arginine methylation of RNA-binding proteins is impaired in Huntington's disease.

Journal: Human molecular genetics

Status: data only, 2 datasets cited

[33192] doi:10.1093/molbev/msad208 [paper, repository]

Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes.

Journal: Molecular biology and evolution

Authors' code: veg/hyphy-analyses (MIT), peterthorpe5/fish_genome_assembly (no license), LeebanY/Convergent-evolution-of-viviparity-in-Cyprinodontiformes (no license)

Status: code verified, 122 files readable, 23 matches

[33193] doi:10.1093/mtomcs/mfad058 [paper, repository]

Synchrotron X-rays reveal the modes of Fe binding and trace metal storage in the brown algae Laminaria digitata and Ectocarpus siliculosus.

Journal: Metallomics : integrated biometal science

Authors' code: pierrepaleo/spire (no license)

Status: code verified, 38 files readable, 1 match

[33194] doi:10.1093/nar/gkad703 [paper, data]

Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression.

Journal: Nucleic acids research

Status: data only, 1 dataset cited

[33195] doi:10.1093/qjmed/hcad122 [paper, data]

Causal associations and genetic overlap between COVID-19 and intelligence.

Journal: QJM : monthly journal of the Association of Physicians

Status: data only, 2 datasets cited

[33196] doi:10.1093/scan/nsad047 [paper, repository]

Similarity in functional connectome architecture predicts teenage grit.

Journal: Social cognitive and affective neuroscience

Authors' code: Zenodo 7986646 (other-open), humaffectneurolab/stabsim_grit (no license)

Status: code verified, 6 files readable, 3 matches

[33197] doi:10.1093/scan/nsad050 [paper, data]

Unpacking reappraisal: a systematic review of fMRI studies of distancing and reinterpretation.

Journal: Social cognitive and affective neuroscience

Status: data only, 1 dataset cited

[33198] doi:10.1093/scan/nsad051 [paper, repository]

Learning from in-group and out-group models induces separative effects on human mate copying.

Journal: Social cognitive and affective neuroscience

Authors' code: OSF 6h85j (no license)

Status: empty repository

[33199] doi:10.1117/1.nph.10.4.045005 [paper, repository]

It takes two (seconds): decreasing encoding time for two-choice functional near-infrared spectroscopy brain-computer interface communication.

Journal: Neurophotonics

Authors' code: acv132/2seconds2choiceFNIRSBCI (MIT)

Status: code verified, 24 files readable, 9 matches

[33200] doi:10.1117/1.nph.10.4.045006 [paper]

Pulse train gating to improve signal generation for <i>in vivo</i> two-photon fluorescence microscopy.

Journal: Neurophotonics

Status: code on request

[33201] doi:10.1117/1.nph.10.4.045007 [paper]

Depth-sensitive diffuse speckle contrast topography for high-density mapping of cerebral blood flow in rodents.

Journal: Neurophotonics

Status: code on request

[33202] doi:10.1158/1078-0432.ccr-23-0926 [paper]

Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial.

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Status: code on request

[33203] doi:10.1162/netn_a_00300 [paper, repository]

The arrow of time of brain signals in cognition: Potential intriguing role of parts of the default mode network.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: decolab/tenet (no license)

Status: dead link

[33204] doi:10.1162/netn_a_00303 [paper, repository]

Comparing individual and group-level simulated neurophysiological brain connectivity using the Jansen and Rit neural mass model.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: multinetlab-amsterdam/projects (MIT)

Status: code verified, 83 files readable, 5 matches

[33205] doi:10.1162/netn_a_00312 [paper, repository]

A parcellation scheme of mouse isocortex based on reversals in connectivity gradients.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: AllenInstitute (no license), satra/mapalign (Apache-2.0), MWolfR/ConnecMap (Apache-2.0)

Status: code verified, 50 files readable, 7 matches

[33206] doi:10.1162/netn_a_00315 [paper, repository]

Optimizing network neuroscience computation of individual differences in human spontaneous brain activity for test-retest reliability.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: ibraindata.com/research/ifnn (no license)

Status: code found, still to be checked

[33207] doi:10.1162/netn_a_00317 [paper, data]

Creativity at rest: Exploring functional network connectivity of creative experts.

Journal: Network neuroscience (Cambridge, Mass.)

Status: data only, 1 dataset cited

[33208] doi:10.1162/netn_a_00318 [paper, repository]

Resolving inter-regional communication capacity in the human connectome.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: neurosynth/neurosynth (MIT), fmilisav/milisav_dyadic_communication (BSD-3-Clause)

Status: code verified, 47 files readable, 16 matches

[33209] doi:10.1162/netn_a_00319 [paper, repository]

Improvements in task performance after practice are associated with scale-free dynamics of brain activity.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: okardan/Practice_Hurst (no license), doi:10.12751/g-node.f87128 (no license)

Status: code verified, 5 files readable

[33210] doi:10.1162/netn_a_00320 [paper, repository]

Functional connectome fingerprinting across the lifespan.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: villeneuvelab/projects (MIT), sihnpy.readthedocs.io (no license)

Status: code verified, 43 files readable, 6 matches

[33211] doi:10.1162/netn_a_00321 [paper, data]

Hierarchical organization of spontaneous co-fluctuations in densely sampled individuals using fMRI.

Journal: Network neuroscience (Cambridge, Mass.)

Status: data only, 1 dataset cited

[33212] doi:10.1162/netn_a_00322 [paper, repository]

A pattern of cognitive resource disruptions in childhood psychopathology.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: enlberman/uchicagoABCDProcessing (no license), enlberman/abcd_enback_bifactor (no license)

Status: code verified, 30 files readable, 5 matches

[33213] doi:10.1162/netn_a_00323 [paper, repository]

Controversies and progress on standardization of large-scale brain network nomenclature.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: OSF 3fzta (no license)

Status: code verified

[33214] doi:10.1167/iovs.64.13.23 [paper, repository]

Achromatopsia-Visual Cortex Stability and Plasticity in the Absence of Functional Cones.

Journal: Investigative ophthalmology & visual science

Authors' code: kendrickkay/alignvolumedata (no license)

Status: code verified, 41 files readable

[33215] doi:10.1167/jov.23.12.6 [paper, repository]

Temporal dynamics of normalization reweighting.

Journal: Journal of vision

Authors' code: bakerdh/normreweight (GPL-3.0), OSF ab3yv (no license)

Status: code verified, 16 files readable, 8 matches

[33216] doi:10.14814/phy2.15730 [paper]

Electrophysiology-aided DBS targeting the ventral intermediate nucleus in an essential tremor patient with MRI-incompatible lead: A case report.

Journal: Physiological reports

Status: code on request

[33217] doi:10.3390/s23198214 [paper, data]

iCanClean Removes Motion, Muscle, Eye, and Line-Noise Artifacts from Phantom EEG.

Journal: Sensors (Basel, Switzerland)

Status: data only, 2 datasets cited

[33218] doi:10.4103/1673-5374.369125 [paper, data]

Characteristics of traumatic brain injury models: from macroscopic blood flow changes to microscopic mitochondrial changes.

Journal: Neural regeneration research

Status: data only, 1 dataset cited

[33219] doi:10.4103/bc.bc_40_23 [paper, data]

Identification of brain endothelial cell-specific genes and pathways in ischemic stroke by integrated bioinformatical analysis.

Journal: Brain circulation

Status: data only, 1 dataset cited

[33220] doi:10.5607/en23021 [paper, data]

Methylation-based Subclassifications of Embryonal Tumor with Multilayered Rosettes in Not Just Pediatric Brains.

Journal: Experimental neurobiology

Status: data only, 1 dataset cited

[33221] doi:10.5812/aapm-139758 [paper, repository]

Evaluation of Intravenous Infusion of Ibuprofen with Paracetamol-Morphine in Pain and Satisfaction of Patients Undergoing Supratentorial Brain Surgery.

Journal: Anesthesiology and pain medicine

Authors' code: ethics.research.ac.ir/proposalcertificateen.php (no license)

Status: code found, still to be checked

Saturday, 30 September 2023 (17 papers)

[33222] doi:10.1016/j.isci.2023.108096 [paper, repository]

Human iPSC modeling recapitulates <i>in vivo</i> sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma.

Journal: iScience

Authors' code: github.ugent.be/ppol/sympatho-adrenergic-differentiation-track (no license)

Status: code verified

[33223] doi:10.1016/j.isci.2023.108102 [paper, repository]

Coherently remapping toroidal cells but not Grid cells are responsible for path integration in virtual agents.

Journal: iScience

Authors' code: CINPLA/spatial-maps (GPL-3.0), Zenodo 8318064 (other-open), bioAI-Oslo/rat-simulator (MIT), Zenodo 8318009 (other-open), bioAI-Oslo/emergent-grid-cells (MIT)

Status: code verified, 90 files readable, 12 matches

[33224] doi:10.1016/j.isci.2023.108107 [paper, repository]

Predicting the efficacy of non-steroidal anti-inflammatory drugs in migraine using deep learning and three-dimensional T1-weighted images.

Journal: iScience

Authors' code: IVisonMed/migraine_mri_dl (no license)

Status: code verified, 3 files readable, 1 match

[33225] doi:10.1016/j.mex.2023.102378 [paper, repository]

Automated preprocessing of 64 channel electroenchephalograms recorded by biosemi instruments.

Journal: MethodsX

Authors' code: Zenodo 8272584 (other-open), kissadamfkut/eeg-preprocess (CC-BY-4.0)

Status: code verified, 20 files readable, 1 match

[33226] doi:10.1016/j.nicl.2023.103520 [paper, repository]

Uncontrolled eating and sensation-seeking partially explain the prediction of future binge drinking from adolescent brain structure.

Journal: NeuroImage. Clinical

Authors' code: RoshanRane/ML_for_IMAGEN (MIT)

Status: code verified, 35 files readable, 6 matches

[33227] doi:10.1038/s41467-023-41686-9 [paper, repository]

Myelination and excitation-inhibition balance synergistically shape structure-function coupling across the human cortex.

Journal: Nature communications

Authors' code: pfotiad/SFC_Nature_Comm_2023 (MIT)

Status: code verified, 25 files readable, 26 matches

[33228] doi:10.1038/s41467-023-41755-z [paper, data]

Neural mechanisms for the localization of unexpected external motion.

Journal: Nature communications

Status: code on request, 2 datasets cited

[33229] doi:10.1038/s41467-023-41803-8 [paper, repository]

Phase information is conserved in sparse, synchronous population-rate-codes via phase-to-rate recoding.

Journal: Nature communications

Authors' code: danielmk/tempotron (MIT), barisckuru/phase-to-rate (MIT), Zenodo 8278084 (other-open), danielmk/phase-to-rate (MIT)

Status: code verified, 456 files readable, 14 matches

[33230] doi:10.1038/s41467-023-41897-0 [paper, repository]

PET-measured human dopamine synthesis capacity and receptor availability predict trading rewards and time-costs during foraging.

Journal: Nature communications

Authors' code: angmirian/Foraging_Dopamine_2023 (no license), Zenodo 8283106 (other-open)

Status: code verified, 8 files readable, 7 matches

[33231] doi:10.1038/s41598-023-43444-9 [paper, repository]

The simplified Kirchhoff network model (SKNM): a cell-based reaction-diffusion model of excitable tissue.

Journal: Scientific reports

Authors' code: Zenodo 8340201 (CC-BY-4.0)

Status: code verified, 5 files readable, 5 matches

[33232] doi:10.1038/s41598-023-43690-x [paper, data]

Genetic contributions to brain serotonin transporter levels in healthy adults.

Journal: Scientific reports

Status: code on request, 9 datasets cited

[33233] doi:10.1186/s12974-023-02906-7 [paper, data]

Unbiased multitissue transcriptomic analysis reveals complex neuroendocrine regulatory networks mediated by spinal cord injury-induced immunodeficiency.

Journal: Journal of neuroinflammation

Status: data only, 7 datasets cited

[33234] doi:10.1186/s12974-023-02907-6 [paper, data]

Receptor-interacting protein kinase 2 (RIPK2) profoundly contributes to post-stroke neuroinflammation and behavioral deficits with microglia as unique perpetrators.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[33235] doi:10.3390/brainsci13101396 [paper, repository]

Within-Person Modulation of Neural Networks following Interoceptive Awareness Training through Mindful Awareness in Body-Oriented Therapy (MABT): A Pilot Study.

Journal: Brain sciences

Authors' code: OSF ctqrh (no license)

Status: code verified, 25 files readable, 6 matches

[33236] doi:10.3390/ijms241914769 [paper]

Metabolomic Signatures of Alzheimer's Disease Indicate Brain Region-Specific Neurodegenerative Progression.

Journal: International journal of molecular sciences

Status: code on request

[33237] doi:10.3390/nu15194227 [paper, repository]

Dissecting the Association between Gut Microbiota and Brain Structure Change Rate: A Two-Sample Bidirectional Mendelian Randomization Study.

Journal: Nutrients

Authors' code: alexa-kur/miQTL_cookbook (no license)

Status: code verified, 15 files readable

[33238] doi:10.3390/s23198192 [paper, data]

Deep Multi-Branch CNN Architecture for Early Alzheimer's Detection from Brain MRIs.

Journal: Sensors (Basel, Switzerland)

Status: data only, 1 dataset cited

Friday, 29 September 2023 (23 papers)

[33239] doi:10.1002/dad2.12468 [paper, repository]

Leveraging longitudinal diffusion MRI data to quantify differences in white matter microstructural decline in normal and abnormal aging.

Journal: Alzheimer's & dementia (Amsterdam, Netherlands)

Authors' code: VUMC-VMAC/Tractography_Templates (no license)

Status: code verified, 1 file readable

[33240] doi:10.1002/hbm.26498 [paper, repository]

Oxytocin enhances the triangular association among behavior, resting-state, and task-state functional connectivity.

Journal: Human brain mapping

Authors' code: andlab-um/OT-cpm (no license)

Status: code verified, 4 files readable, 2 matches

[33241] doi:10.1016/j.celrep.2023.113160 [paper]

Analysis of proteome-wide degradation dynamics in ALS SOD1 iPSC-derived patient neurons reveals disrupted VCP homeostasis.

Journal: Cell reports

Status: code on request

[33242] doi:10.1016/j.celrep.2023.113162 [paper]

Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state.

Journal: Cell reports

Status: code on request

[33243] doi:10.1016/j.cub.2023.09.011 [paper, data]

Theta-band phase locking during encoding leads to coordinated entorhinal-hippocampal replay.

Journal: Current biology : CB

Status: code on request, 1 dataset cited

[33244] doi:10.1016/j.isci.2023.108098 [paper]

The role of HIF-1α/HO-1 pathway in hippocampal neuronal ferroptosis in epilepsy.

Journal: iScience

Status: code on request

[33245] doi:10.1016/j.ynirp.2023.100186 [paper, repository]

Pairing explainable deep learning classification with clustering to uncover effects of schizophrenia upon whole brain functional network connectivity dynamics.

Journal: Neuroimage. Reports

Authors' code: cae67/Relevance_Clustering (no license)

Status: code verified, 1 file readable, 5 matches

[33246] doi:10.1038/s41380-023-02269-8 [paper]

Dysfunctional serotonergic neuron-astrocyte signaling in depressive-like states.

Journal: Molecular psychiatry

Status: code on request

[33247] doi:10.1038/s41467-023-41710-y [paper, repository]

Photostimulation of brain lymphatics in male newborn and adult rodents for therapy of intraventricular hemorrhage.

Journal: Nature communications

Authors' code: HUST-LAB/MLV-diameter (no license)

Status: code verified, 1 file readable, 2 matches

[33248] doi:10.1038/s41467-023-41715-7 [paper, repository]

Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation.

Journal: Nature communications

Authors' code: bcbio/bcbio-nextgen (MIT), YannVRB/Visium-SOR-mouse (no license)

Status: code verified, 323 files readable, 5 matches

[33249] doi:10.1038/s41537-023-00394-5 [paper]

Finding normal-to-better neurocognitive indexes in individuals with schizotypal traits using a social role task.

Journal: Schizophrenia (Heidelberg, Germany)

Status: code on request

[33250] doi:10.1073/pnas.2305071120 [paper, data]

Local extracellular K&lt;sup&gt;+&lt;/sup&gt; in cortex regulates norepinephrine levels, network state, and behavioral output.

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

Status: data only, 1 dataset cited

[33251] doi:10.1111/jcmm.17960 [paper, repository]

Identification of immune-related hub genes and construction of an immune-related gene prognostic index for low-grade glioma.

Journal: Journal of cellular and molecular medicine

Authors' code: sooc-how-Feng/LGG-subtypes (no license)

Status: dead link

[33252] doi:10.1126/sciadv.adg1894 [paper, repository]

HAVOC: Small-scale histomic mapping of cancer biodiversity across large tissue distances using deep neural networks.

Journal: Science advances

Authors' code: codido.co (no license), diamandislabii/faust-feature-vectors-2019 (no license), diamandislabii/havoc (GPL-3.0), Zenodo 3234829 (CC-BY-4.0), colab.research.google.com/drive/1gx7gxtbibf5iny0rel7qktm-oamv4w6s (no license), doi:10.5061/dryad.zs7h44jf9 (no license)

Status: code verified, 17 files readable, 2 matches

[33253] doi:10.1155/2023/3320211 [paper, repository]

Production of Highly Uniform Midbrain Organoids from Human Pluripotent Stem Cells.

Journal: Stem cells international

Authors' code: taynaud/python-louvain (BSD-3-Clause)

Status: code verified, 8 files readable

[33254] doi:10.1177/0271678x231204769 [paper]

Similarity between structural and proxy estimates of brain connectivity.

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

Status: code on request

[33255] doi:10.1186/s12014-023-09426-9 [paper, data]

A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors.

Journal: Clinical proteomics

Status: data only, 4 datasets cited

[33256] doi:10.1186/s13059-023-03037-1 [paper, data]

A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial-temporal regulation of histone arginine methylation in neurodevelopment.

Journal: Genome biology

Status: data only, 1 dataset cited

[33257] doi:10.3389/fnins.2023.1269100 [paper, data]

EFF_D_SVM: a robust multi-type brain tumor classification system.

Journal: Frontiers in neuroscience

Status: data only, 2 datasets cited

[33258] doi:10.3390/brainsci13101386 [paper, repository]

The Challenge of Diffusion Magnetic Resonance Imaging in Cerebral Palsy: A Proposed Method to Identify White Matter Pathways.

Journal: Brain sciences

Authors' code: scilus/tractoflow (other), scilus/noddi_flow (MIT), scilus/rbx_flow (MIT), scilus/scilpy (MIT), surfer.nmr.mgh.harvard.edu (no license), scilus/freesurfer_flow (MIT), scilus/tractometry_flow (no license)

Status: code verified, 611 files readable, 6 matches

[33259] doi:10.3390/brainsci13101389 [paper, data]

Age-Specific Effects of Visual Feature Binding.

Journal: Brain sciences

Status: data only, 1 dataset cited

[33260] doi:10.3892/mmr.2023.13107 [paper, data]

circ_0000018 downregulation peripherally ameliorates neuroprotection against acute ischemic stroke through the miR‑871/BCL2L11 axis.

Journal: Molecular medicine reports

Status: data only, 1 dataset cited

[33261] doi:10.7554/elife.86175 [paper, repository]

The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid.

Journal: eLife

Authors' code: doi:10.5061/dryad.573n5tbc2 (no license)

Status: code verified

Thursday, 28 September 2023 (28 papers)

[33262] doi:10.1007/s00426-023-01872-2 [paper, data]

The tool effect is lower in older adults with or without cognitive impairments than in young adults.

Journal: Psychological research

Status: data only, 1 dataset cited

[33263] doi:10.1016/j.cell.2023.08.034 [paper, repository]

Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells.

Journal: Cell

Authors' code: deriverylab/GPU_registration (GPL-3.0), deriverylab/GPU_wavelet_a_trous (no license), deriverylab/3D_array_colocalization (no license), Zenodo 8357466 (other-open), jdmanton/lsfm_tools (no license)

Status: code verified, 35 files readable, 7 matches

[33264] doi:10.1016/j.isci.2023.108069 [paper, repository]

GABAergic signaling shapes multiple aspects of <i>Drosophila</i> courtship motor behavior.

Journal: iScience

Authors' code: FlyCourtship/FlySongSegmenter (no license)

Status: code verified, 99 files readable

[33265] doi:10.1016/j.nicl.2023.103519 [paper, repository]

Subregional analysis of striatum iron in Parkinson's disease and rapid eye movement sleep behaviour disorder.

Journal: NeuroImage. Clinical

Authors' code: AlanKuurstra/qsm_sstv (no license)

Status: code verified, 4 files readable

[33266] doi:10.1016/j.xcrm.2023.101208 [paper]

Shared GABA transmission pathology in dopamine agonist- and antagonist-induced dyskinesia.

Journal: Cell reports. Medicine

Status: code verified

[33267] doi:10.1038/s41467-023-40948-w [paper, data]

A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease.

Journal: Nature communications

Status: data only, 1 dataset cited

[33268] doi:10.1038/s41467-023-41723-7 [paper, data]

Estrogen receptor beta in astrocytes modulates cognitive function in mid-age female mice.

Journal: Nature communications

Status: data only, 1 dataset cited

[33269] doi:10.1038/s41467-023-41749-x [paper, data]

Thalamocortical control of cell-type specificity drives circuits for processing whisker-related information in mouse barrel cortex.

Journal: Nature communications

Status: data only, 2 datasets cited

[33270] doi:10.1038/s41525-023-00370-z [paper, data]

SLCO5A1 and synaptic assembly genes contribute to impulsivity in juvenile myoclonic epilepsy.

Journal: NPJ genomic medicine

Status: data only, 1 dataset cited

[33271] doi:10.1038/s41551-023-01095-1 [paper, data]

In-ear integrated sensor array for the continuous monitoring of brain activity and of lactate in sweat.

Journal: Nature biomedical engineering

Status: data only, 1 dataset cited

[33272] doi:10.1038/s41592-023-01969-x [paper, repository]

Learning single-cell perturbation responses using neural optimal transport.

Journal: Nature methods

Authors' code: TissueMAPS (no license), ebi.ac.uk/biostudies/arrayexpress (no license)

Status: code verified

[33273] doi:10.1038/s41592-023-01998-6 [paper, repository]

D-LMBmap: a fully automated deep-learning pipeline for whole-brain profiling of neural circuitry.

Journal: Nature methods

Authors' code: lmbneuron/D-LMBmap (no license)

Status: code verified, 282 files readable, 15 matches

[33274] doi:10.1038/s41592-023-02017-4 [paper, repository]

A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening.

Journal: Nature methods

Authors' code: xinhe-lab/GSFA (MIT), xinhe-lab/GSFA_paper (no license)

Status: code verified, 81 files readable, 22 matches

[33275] doi:10.1038/s41592-023-02029-0 [paper, repository]

Deep learning-driven adaptive optics for single-molecule localization microscopy.

Journal: Nature methods

Authors' code: HuanglabPurdue/DL-AO (no license)

Status: code verified, 13 files readable, 5 matches

[33276] doi:10.1038/s41598-023-40852-9 [paper, data]

A neural marker of the human face identity familiarity effect.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33277] doi:10.1073/pnas.2211179120 [paper, repository]

Human-like scene interpretation by a guided counterstream processing.

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

Authors' code: liavassif/BU-TD (no license)

Status: code verified, 15 files readable, 2 matches

[33278] doi:10.1159/000534249 [paper, data]

Olfactory Bulbs in Arthritis Model Mouse Persistently Express Interleukin-6 before the Onset of Arthritis: Relationship to Food Intake.

Journal: Neuroimmunomodulation

Status: data only, 1 dataset cited

[33279] doi:10.1186/s12859-023-05482-y [paper, repository]

A robust approach to 3D neuron shape representation for quantification and classification.

Journal: BMC bioinformatics

Authors' code: matlabbaltam/Neuron-Morphology (no license)

Status: code verified, 69 files readable, 1 match

[33280] doi:10.1371/journal.pcbi.1011484 [paper, repository]

A role for cortical interneurons as adversarial discriminators.

Journal: PLoS computational biology

Authors' code: KordingLab/adversarial-wake-sleep (no license)

Status: code verified, 8 files readable, 3 matches

[33281] doi:10.1371/journal.pone.0291832 [paper, data]

Is there an influence of perceptual or cognitive impairment on complex sentence processing in hearing aid users?

Journal: PloS one

Status: data only, 1 dataset cited

[33282] doi:10.3389/fdgth.2023.1184919 [paper, repository]

Understanding the performance and reliability of NLP tools: a comparison of four NLP tools predicting stroke phenotypes in radiology reports.

Journal: Frontiers in digital health

Authors' code: CogStack/CogStack-SemEHR (Apache-2.0)

Status: code verified, 118 files readable, 1 match

[33283] doi:10.3389/fncel.2023.1256184 [paper, data]

Identification of immune-related biomarkers in peripheral blood of schizophrenia using bioinformatic methods and machine learning algorithms.

Journal: Frontiers in cellular neuroscience

Status: data only, 1 dataset cited

[33284] doi:10.3389/fnhum.2023.1147352 [paper, repository]

Changes in the superior longitudinal fasciculus and anterior thalamic radiation in the left brain are associated with developmental dyscalculia.

Journal: Frontiers in human neuroscience

Authors' code: OSF c2bng (no license)

Status: empty repository

[33285] doi:10.3389/fphar.2023.1140656 [paper, repository]

A pilot study of cerebral metabolism and serotonin 5-HT_2A receptor occupancy in rats treated with the psychedelic tryptamine DMT in conjunction with the MAO inhibitor harmine.

Journal: Frontiers in pharmacology

Authors' code: OSF dn8fy (no license)

Status: code verified, 11 files readable, 1 match

[33286] doi:10.3390/e25101393 [paper, repository]

Complexity Synchronization of Organ Networks.

Journal: Entropy (Basel, Switzerland)

Authors' code: Korosh137/MDEA (no license)

Status: code verified, 1 file readable, 1 match

[33287] doi:10.3390/ijms241914670 [paper, data]

Hyperinsulinemia Impairs Clathrin-Mediated Endocytosis of the Insulin Receptor and Activation of Endothelial Nitric Oxide Synthase in Brain Endothelial Cells.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[33288] doi:10.3390/ijms241914689 [paper, repository]

Recent Advances in High-Content Imaging and Analysis in iPSC-Based Modelling of Neurodegenerative Diseases.

Journal: International journal of molecular sciences

Authors' code: StemCellMetab/Mitochondrial-membranepotential (no license), thayerlab/ASIA-pipelines (no license), StemCellMetab/Mitochondrial-membrane-potential (no license)

Status: code verified, 3 files readable

[33289] doi:10.3390/s23198136 [paper, repository]

One Definition to Join Them All: The N-Spherical Solution for the EEG Lead Field.

Journal: Sensors (Basel, Switzerland)

Authors' code: rbruna/eeg-spheres (GPL-3.0)

Status: code verified, 10 files readable

Wednesday, 27 September 2023 (34 papers)

[33290] doi:10.1002/hbm.26447 [paper, repository]

Denoising task-related fMRI: Balancing noise reduction against signal loss.

Journal: Human brain mapping

Authors' code: coghill-painlab/preproc_comparison (no license)

Status: code verified, 5 files readable, 4 matches

[33291] doi:10.1007/s12035-023-03631-1 [paper]

Identification of lncRNA-miRNA-mRNA Networks in the Lenticular Nucleus Region of the Brain Contributes to Hepatolenticular Degeneration Pathogenesis and Therapy.

Journal: Molecular neurobiology

Status: data only

[33292] doi:10.1016/j.isci.2023.108047 [paper, repository]

Pretrial predictors of conflict response efficacy in the human prefrontal cortex.

Journal: iScience

Authors' code: abherman99/pretrial_RT_prediction (no license)

Status: code verified, 3 files readable, 2 matches

[33293] doi:10.1016/j.isci.2023.108048 [paper, repository]

Identifying new players in structural synaptic plasticity through <i>dArc1</i> interrogation.

Journal: iScience

Authors' code: mhammell-laboratory/TEtranscripts (GPL-3.0), usadellab/Trimmomatic (GPL-3.0), alexdobin/star (MIT)

Status: code verified, 500 files readable

[33294] doi:10.1016/j.isci.2023.108082 [paper]

Metformin inhibits inflammatory response and endoplasmic reticulum stress to improve hypothalamic aging in obese mice.

Journal: iScience

Status: code on request

[33295] doi:10.1021/acs.bioconjchem.3c00347 [paper, data]

Self-Adjuvanting TLR7/8 Agonist and Fentanyl Hapten Co-Conjugate Achieves Enhanced Protection against Fentanyl Challenge.

Journal: Bioconjugate chemistry

Status: data only, 1 dataset cited

[33296] doi:10.1038/s41467-023-40749-1 [paper, repository]

Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit assembly.

Journal: Nature communications

Authors' code: nbviewer.org/github/scverse (no license)

Status: dead link

[33297] doi:10.1038/s41467-023-40939-x [paper, data]

Tomography of memory engrams in self-organizing nanowire connectomes.

Journal: Nature communications

Status: data only, 2 datasets cited

[33298] doi:10.1038/s41467-023-41046-7 [paper]

An all 2D bio-inspired gustatory circuit for mimicking physiology and psychology of feeding behavior.

Journal: Nature communications

Status: code on request

[33299] doi:10.1038/s41467-023-41635-6 [paper, data]

Evolution of schooling drives changes in neuroanatomy and motion characteristics across predation contexts in guppies.

Journal: Nature communications

Status: data only, 1 dataset cited

[33300] doi:10.1038/s41467-023-41648-1 [paper, repository]

Time-dependent memory transformation in hippocampus and neocortex is semantic in nature.

Journal: Nature communications

Authors' code: Zenodo 8363230 (other-open), Zenodo 836230 (CC-BY-4.0), valentinakrenz/semanticmemorytransformation (no license)

Status: code verified, 10 files readable, 7 matches

[33301] doi:10.1038/s41467-023-41722-8 [paper, repository]

A phylogenetically-conserved axis of thalamocortical connectivity in the human brain.

Journal: Nature communications

Authors' code: StuartJO/ThalamicGradients (no license)

Status: code verified, 144 files readable, 35 matches

[33302] doi:10.1038/s41467-023-41730-8 [paper, data]

Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex.

Journal: Nature communications

Status: data only, 1 dataset cited

[33303] doi:10.1038/s41531-023-00576-z [paper]

Grey-matter correlates of empathy in 4-Repeat Tauopathies.

Journal: NPJ Parkinson's disease

Status: code on request

[33304] doi:10.1038/s41586-023-06564-w [paper, repository]

Assembloid CRISPR screens reveal impact of disease genes in human neurodevelopment.

Journal: Nature

Authors' code: dmorgens/castle (no license)

Status: empty repository, 1 file readable

[33305] doi:10.1038/s41586-023-06569-5 [paper, repository]

Spatial atlas of the mouse central nervous system at molecular resolution.

Journal: Nature

Authors' code: wanglab-broad/mCNS-atlas (no license)

Status: code verified, 167 files readable, 8 matches

[33306] doi:10.1038/s42003-023-05355-3 [paper, repository]

Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats.

Journal: Communications biology

Authors' code: Zhang-lab/Rat_Brain_Meth (no license), Zenodo 8170364 (CC-BY-4.0)

Status: code verified, 29 files readable

[33307] doi:10.1093/bioadv/vbad127 [paper, data]

VISTA: visualizing the spatial transcriptome of the <i>C.elegans</i> nervous system.

Journal: Bioinformatics advances

Status: data only, 1 dataset cited

[33308] doi:10.1093/nsr/nwad256 [paper]

Brain circuits for retching-like behavior.

Journal: National science review

Status: code on request

[33309] doi:10.1097/rmr.0000000000000307 [paper, repository]

Locally Low-Rank Denoising of Multi-Echo Functional MRI Data With Application in Resting-State Analysis.

Journal: Topics in magnetic resonance imaging : TMRI

Authors' code: candes.su.domains/software/sure (no license)

Status: code verified

[33310] doi:10.1101/lm.053834.123 [paper, repository]

Hippocampal memory reactivation during sleep is correlated with specific cortical states of the retrosplenial and prefrontal cortices.

Journal: Learning & memory (Cold Spring Harbor, N.Y.)

Authors' code: shizhaoliu/memory (no license), 410pfeliciano/data_replay_coordination_to_rtc_pfc_states (no license)

Status: code verified, 16 files readable, 5 matches

[33311] doi:10.1126/sciadv.adi6888 [paper, data]

Reconstructing the origin and early evolution of the snake brain.

Journal: Science advances

Status: data only, 1 dataset cited

[33312] doi:10.1128/spectrum.00176-23 [paper, data]

The impact of Parkinson's disease-associated gut microbiota on the transcriptome in &lt;i&gt;Drosophila&lt;/i&gt;.

Journal: Microbiology spectrum

Status: data only, 1 dataset cited

[33313] doi:10.1186/s12859-023-05495-7 [paper, repository]

A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder.

Journal: BMC bioinformatics

Authors' code: pcdslab/ASD-DiagNet (GPL-3.0)

Status: code verified, 3 files readable

[33314] doi:10.1186/s12974-023-02899-3 [paper, data]

Glycolytic shift during West Nile virus infection provides new therapeutic opportunities.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[33315] doi:10.1371/journal.pone.0291200 [paper, repository]

TumorDetNet: A unified deep learning model for brain tumor detection and classification.

Journal: PloS one

Authors' code: kaggle.com/abhranta/brain-tumor-detection-mri (no license), kaggle.com/navoneel/brain-mri-images-for-brain-tumor-detection (no license), kaggle.com/alifrahman/modiified (no license), kaggle.com/umarsiddiqui9/bttypes (no license), kaggle.com/sartajbhuvaji/brain-tumor-classification-mri (no license)

Status: dead link

[33316] doi:10.1371/journal.pone.0291528 [paper, data]

Brain activation by a VR-based motor imagery and observation task: An fMRI study.

Journal: PloS one

Status: data only, 1 dataset cited

[33317] doi:10.3389/fmolb.2023.1254834 [paper, data]

Comparative assessment of Alzheimer's disease-related biomarkers in plasma and neuron-derived extracellular vesicles: a nested case-control study.

Journal: Frontiers in molecular biosciences

Status: data only, 1 dataset cited

[33318] doi:10.3389/fncel.2023.1253446 [paper, repository]

Homosynaptic plasticity induction causes heterosynaptic changes at the unstimulated neighbors in an induction pattern and location-specific manner.

Journal: Frontiers in cellular neuroscience

Authors' code: Zenodo 7871541 (other-open)

Status: code verified, 2 files readable

[33319] doi:10.3389/fninf.2023.1251023 [paper, data]

Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN.

Journal: Frontiers in neuroinformatics

Status: data only, 1 dataset cited

[33320] doi:10.3389/fnins.2023.1223226 [paper, repository]

A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology.

Journal: Frontiers in neuroscience

Authors' code: yuqitiancivm/neuroncounting (MIT)

Status: code verified, 11 files readable, 3 matches

[33321] doi:10.3390/bioengineering10101132 [paper, data]

TGF-β and SHH Regulate Pluripotent Stem Cell Differentiation into Brain Microvascular Endothelial Cells in Generating an In Vitro Blood-Brain Barrier Model.

Journal: Bioengineering (Basel, Switzerland)

Status: data only, 1 dataset cited

[33322] doi:10.3390/biomimetics8060456 [paper, repository]

Numerical Reconstruction of Cyclist Impact Accidents: Can Helmets Protect the Head-Neck of Cyclists?

Journal: Biomimetics (Basel, Switzerland)

Authors' code: lstc.com (no license)

Status: code verified

[33323] doi:10.3390/ijms241914648 [paper, data]

Gibbs Energy and Gene Expression Combined as a New Technique for Selecting Drug Targets for Inhibiting Specific Protein-Protein Interactions.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Tuesday, 26 September 2023 (36 papers)

[33324] doi:10.1002/hbm.26490 [paper, repository]

Estimation of fMRI responses related to epileptic discharges using Bayesian hierarchical modeling.

Journal: Human brain mapping

Authors' code: zhengchencai/HierarchicalBayesianEEGfMRI (BSD-3-Clause)

Status: code verified, 5 files readable

[33325] doi:10.1002/hbm.26492 [paper]

Are we really targeting and stimulating DLPFC by placing transcranial electrical stimulation (tES) electrodes over F3/F4?

Journal: Human brain mapping

Status: code on request

[33326] doi:10.1007/s00415-023-11998-3 [paper, data]

Dystonia and Parkinsonism in COA7-related disorders: expanding the phenotypic spectrum.

Journal: Journal of neurology

Status: data only, 1 dataset cited

[33327] doi:10.1007/s10548-023-01006-2 [paper, repository]

Complexity Measures for EEG Microstate Sequences: Concepts and Algorithms.

Journal: Brain topography

Authors' code: Frederic-vW/eeg_microstates (MIT), Frederic-vW/potts-complexity (no license), plus-microstate/toolbox (GPL-3.0)

Status: code verified, 323 files readable, 4 matches

[33328] doi:10.1016/j.celrep.2023.113175 [paper]

Microenvironmental stiffness induces metabolic reprogramming in glioblastoma.

Journal: Cell reports

Status: code on request

[33329] doi:10.1016/j.isci.2023.108052 [paper, repository]

Defective phagocytosis leads to neurodegeneration through systemic increased innate immune signaling.

Journal: iScience

Authors' code: McCallLabBU/neurodegeneration_vacuole_quantification (no license)

Status: code verified, 4 files readable

[33330] doi:10.1016/j.isci.2023.108056 [paper]

Absence of Embigin accelerates hearing loss and causes sub-viability, brain and heart defects in C57BL/6N mice due to interaction with <i>Cdh23</i>^<i>ahl</i>.

Journal: iScience

Status: code on request

[33331] doi:10.1016/j.molmet.2023.101811 [paper]

Deletion of Ascl1 in pancreatic β-cells improves insulin secretion, promotes parasympathetic innervation, and attenuates dedifferentiation during metabolic stress.

Journal: Molecular metabolism

Status: data only

[33332] doi:10.1016/j.omtm.2023.101122 [paper]

Awake intracerebroventricular delivery and safety assessment of oligonucleotides in a large animal model.

Journal: Molecular therapy. Methods & clinical development

Status: code on request

[33333] doi:10.1016/j.xpro.2023.102618 [paper]

Harvesting mouse suprachiasmatic nucleus by vibrating microtome for diurnal transcriptome analysis.

Journal: STAR protocols

Status: code on request

[33334] doi:10.1038/s41467-023-41435-y [paper, data]

Natural product P57 induces hypothermia through targeting pyridoxal kinase.

Journal: Nature communications

Status: data only, 1 dataset cited

[33335] doi:10.1038/s41467-023-41677-w [paper, repository]

Patient-specific models link neurotransmitter receptor mechanisms with motor and visuospatial axes of Parkinson's disease.

Journal: Nature communications

Authors' code: neuropm-lab/svd_pls (no license)

Status: code verified, 4 files readable, 2 matches

[33336] doi:10.1038/s41467-023-41689-6 [paper, repository]

Neurophysiological signatures of cortical micro-architecture.

Journal: Nature communications

Authors' code: netneurolab/shafiei_megdynamics (BSD-3-Clause), thomasyeolab/cbig (MIT), Zenodo 8258832 (other-open)

Status: code verified, 2,026 files readable, 7 matches

[33337] doi:10.1038/s41467-023-41711-x [paper, repository]

Ictogenesis proceeds through discrete phases in hippocampal CA1 seizures in mice.

Journal: Nature communications

Authors' code: Zenodo 8274424 (CC-BY-4.0)

Status: code verified, 19 files readable, 5 matches

[33338] doi:10.1038/s41467-023-41744-2 [paper, data]

Social memory deficit caused by dysregulation of the cerebellar vermis.

Journal: Nature communications

Status: data only, 1 dataset cited

[33339] doi:10.1038/s41467-023-41745-1 [paper, repository]

Feedforward attentional selection in sensory cortex.

Journal: Nature communications

Authors' code: westerberg-science/attentional-capture-code (no license), Zenodo 8163978 (other-open)

Status: code verified, 4 files readable

[33340] doi:10.1038/s41598-023-42802-x [paper, repository]

Deepfake smiles matter less-the psychological and neural impact of presumed AI-generated faces.

Journal: Scientific reports

Authors' code: OSF xymz8 (no license), OSF 7mj8f (no license)

Status: code verified, 4 files readable, 5 matches

[33341] doi:10.1038/s41598-023-42961-x [paper, repository]

Non-inferiority of deep learning ischemic stroke segmentation on non-contrast CT within 16-hours compared to expert neuroradiologists.

Journal: Scientific reports

Authors' code: SophieOstmeier/UncertainSmallEmpty (Apache-2.0), SophieOstmeier/StrokeAnalyzer (Apache-2.0)

Status: code verified, 11 files readable

[33342] doi:10.1038/s41598-023-43327-z [paper, data]

Putative photosensitivity in internal light organs (organs of Pesta) of deep-sea sergestid shrimps.

Journal: Scientific reports

Status: data only, 1 dataset cited

[33343] doi:10.1038/s42003-023-05361-5 [paper, repository]

Cortical temporal integration can account for limits of temporal perception: investigations in the binaural system.

Journal: Communications biology

Authors' code: Ravinderjit-S/DynamicBinauralProcessing (BSD-3-Clause), Zenodo 8098476 (other-open)

Status: code verified, 110 files readable, 8 matches

[33344] doi:10.1073/pnas.2305292120 [paper, repository]

Hippocampal activity predicts contextual misattribution of false memories.

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

Authors' code: memory.psych.upenn.edu/data (no license)

Status: code found, still to be checked

[33345] doi:10.1162/imag_a_00019 [paper, repository]

Dual-encoded magnetization transfer and diffusion imaging and its application to tract-specific microstructure mapping.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: TardifLab/mt-diff (no license)

Status: code verified, 30 files readable, 8 matches

[33346] doi:10.1186/s12864-023-09678-7 [paper, data]

De novo assembly and annotation of the singing mouse genome.

Journal: BMC genomics

Status: data only, 1 dataset cited

[33347] doi:10.1371/journal.pone.0291029 [paper, data]

Functional characterization of a single nucleotide polymorphism associated with Alzheimer's disease in a hiPSC-based neuron model.

Journal: PloS one

Status: data only, 1 dataset cited

[33348] doi:10.1371/journal.pone.0291771 [paper, data]

Are there dedicated neural mechanisms for imitation? A study of grist and mills.

Journal: PloS one

Status: data only, 1 dataset cited

[33349] doi:10.1523/eneuro.0148-23.2023 [paper, repository]

A Deep Learning Approach for Neuronal Cell Body Segmentation in Neurons Expressing GCaMP Using a Swin Transformer.

Journal: eNeuro

Authors' code: stephenbaek/cell-transformer (Apache-2.0)

Status: code verified, 461 files readable, 1 match

[33350] doi:10.3389/fneur.2023.1249429 [paper, data]

The impact of upper motor neuron involvement on clinical features, disease progression and prognosis in amyotrophic lateral sclerosis.

Journal: Frontiers in neurology

Status: data only, 1 dataset cited

[33351] doi:10.3389/fnhum.2023.1221944 [paper, repository]

Neural representations for multi-context visuomotor adaptation and the impact of common representation on multi-task performance: a multivariate decoding approach.

Journal: Frontiers in human neuroscience

Authors' code: YJ-0000/Multi-context_Representation_during_VisuomotorAdaptation (MIT)

Status: code verified, 41 files readable, 1 match

[33352] doi:10.3389/fnhum.2023.1231513 [paper, repository]

Fractal dimension of the cortical gray matter outweighs other brain MRI features as a predictor of transition to dementia in patients with mild cognitive impairment and leukoaraiosis.

Journal: Frontiers in human neuroscience

Authors' code: Zenodo 7852212 (other-open)

Status: code verified

[33353] doi:10.3389/fninf.2023.1266713 [paper, repository]

oFVSD: a Python package of optimized forward variable selection decoder for high-dimensional neuroimaging data.

Journal: Frontiers in neuroinformatics

Authors' code: tungtokyo1108/FVS_decoder (MIT)

Status: code verified, 7 files readable, 7 matches

[33354] doi:10.3390/biom13101445 [paper, repository]

A Structural Model for the Core Nup358-BicD2 Interface.

Journal: Biomolecules

Authors' code: deepmind/alphafold (Apache-2.0), sokrypton/colabfold (MIT)

Status: code verified, 175 files readable, 2 matches

[33355] doi:10.3390/biomedicines11102633 [paper, data]

Machine Learning Algorithms Applied to Predict Autism Spectrum Disorder Based on Gut Microbiome Composition.

Journal: Biomedicines

Status: data only, 2 datasets cited

[33356] doi:10.7554/elife.81535 [paper, repository]

Optogenetic induction of appetitive and aversive taste memories in &lt;i&gt;Drosophila&lt;/i&gt;.

Journal: eLife

Authors' code: rcwchan/STROBE-fpga (GPL-3.0), rcwchan/STROBE_software (GPL-2.0)

Status: code verified, 26 files readable

[33357] doi:10.7554/elife.86076 [paper, repository]

Long-timescale anti-directional rotation in &lt;i&gt;Drosophila&lt;/i&gt; optomotor behavior.

Journal: eLife

Authors' code: Zenodo 19424913 (CC-BY-4.0), ClandininLab/flystim (MIT)

Status: code verified, 48 files readable

[33358] doi:10.7554/elife.87048 [paper, repository]

Different rules for binocular combination of luminance flicker in cortical and subcortical pathways.

Journal: eLife

Authors' code: bakerdh/PupillometryEEG (GPL-3.0), OSF tbema (no license)

Status: code verified, 20 files readable, 16 matches

[33359] doi:10.7717/peerj-cs.1561 [paper, repository]

Automatic sleep staging by a hybrid model based on deep 1D-ResNet-SE and LSTM with single-channel raw EEG signals.

Journal: PeerJ. Computer science

Authors' code: sleeptight.isr.uc.pt (no license), weiming1122/1D-ResNet-SE-LSTM (no license)

Status: code verified, 8 files readable, 6 matches

Monday, 25 September 2023 (28 papers, 17 on this page)

[33360] doi:10.1002/brb3.3264 [paper, repository]

The neural correlates of texture perception: A systematic review and activation likelihood estimation meta-analysis of functional magnetic resonance imaging studies.

Journal: Brain and behavior

Authors' code: OSF kz7mg (no license)

Status: empty repository

[33361] doi:10.1002/hipo.23577 [paper, repository]

Variational log-Gaussian point-process methods for grid cells.

Journal: Hippocampus

Authors' code: michaelerule/lgcpspatial (GPL-3.0)

Status: code verified, 101 files readable, 30 matches

[33362] doi:10.1007/s11357-023-00941-z [paper, repository]

Sex differences in biological aging and the association with clinical measures in older adults.

Journal: GeroScience

Authors' code: james-cole/brainageR (LGPL-3.0)

Status: code verified, 9 files readable, 1 match

[33363] doi:10.1016/j.isci.2023.108037 [paper]

Developing a human iPSC-derived three-dimensional myelin spheroid platform for modeling myelin diseases.

Journal: iScience

Status: code on request

[33364] doi:10.1016/j.isci.2023.108050 [paper]

Pre- and postsynaptic N-methyl-D-aspartate receptors are required for sequential printing of fear memory engrams.

Journal: iScience

Status: code on request

[33365] doi:10.1016/j.neuroimage.2023.120391 [paper, repository]

A representation of abstract linguistic categories in the visual system underlies successful lipreading.

Journal: NeuroImage

Authors' code: mickcrosse/mTRF-Toolbox (BSD-3-Clause)

Status: code verified, 78 files readable, 10 matches

[33366] doi:10.1016/j.patter.2023.100847 [paper, repository]

MANGEM: A web app for multimodal analysis of neuronal gene expression, electrophysiology, and morphology.

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

Authors' code: daifengwanglab/mangem (MIT), Zenodo 8048263 (MIT), rholson1/mangem (MIT)

Status: code verified, 75 files readable, 17 matches

[33367] doi:10.1038/s41368-023-00246-z [paper, data]

Transcriptional profiling of dental sensory and proprioceptive trigeminal neurons using single-cell RNA sequencing.

Journal: International journal of oral science

Status: data only, 1 dataset cited

[33368] doi:10.1038/s41380-023-02247-0 [paper, data]

Smoking, tobacco dependence, and neurometabolites in the dorsal anterior cingulate cortex.

Journal: Molecular psychiatry

Status: data only, 1 dataset cited

[33369] doi:10.1038/s41467-023-41566-2 [paper, repository]

On the visual analytic intelligence of neural networks.

Journal: Nature communications

Authors' code: IBM/visual-oddity (Apache-2.0)

Status: code verified, 8 files readable

[33370] doi:10.1038/s41593-023-01435-z [paper, data]

IL-12 sensing in neurons induces neuroprotective CNS tissue adaptation and attenuates neuroinflammation in mice.

Journal: Nature neuroscience

Status: code on request, 4 datasets cited

[33371] doi:10.1073/pnas.2303523120 [paper, repository]

Distinct context- and content-dependent population codes in superior colliculus during sensation and action.

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

Authors' code: ecayar/Gap_Task_Project_GandhiLab (no license)

Status: code verified, 9 files readable, 1 match

[33372] doi:10.1152/physiolgenomics.00016.2023 [paper, data]

Subdiaphragmatic vagal nerve stimulation attenuates the development of hypertension and alters nucleus of the solitary tract transcriptional networks in the spontaneously hypertensive rat.

Journal: Physiological genomics

Status: data only, 1 dataset cited

[33373] doi:10.1161/strokeaha.123.043897 [paper, data]

Prediction of Stroke Outcome in Mice Based on Noninvasive MRI and Behavioral Testing.

Journal: Stroke

Status: data only, 2 datasets cited

[33374] doi:10.1162/imag_a_00012 [paper]

The impact of head orientation with respect to B&lt;sub&gt;0&lt;/sub&gt; on diffusion tensor MRI measures.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: code on request

[33375] doi:10.1186/s12915-023-01696-x [paper, repository]

An intelligent workflow for sub-nanoscale 3D reconstruction of intact synapses from serial section electron tomography.

Journal: BMC biology

Authors' code: VictorCSheng/SSET (no license), Zenodo 8275073 (other-open)

Status: code verified, 31 files readable, 2 matches

[33376] doi:10.1186/s12964-023-01288-w [paper, data]

Defective quality control autophagy in Hyperhomocysteinemia promotes ER stress and consequent neuronal apoptosis through proteotoxicity.

Journal: Cell communication and signaling : CCS

Status: data only, 1 dataset cited

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